Query 029339
Match_columns 195
No_of_seqs 150 out of 194
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 11:20:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029339.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029339hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04640 PLATZ: PLATZ transcri 100.0 1.2E-41 2.7E-46 248.7 5.5 72 51-122 1-72 (72)
2 PF03884 DUF329: Domain of unk 97.0 0.0001 2.2E-09 52.2 -1.0 41 99-139 2-47 (57)
3 PF00643 zf-B_box: B-box zinc 96.9 0.0002 4.2E-09 45.8 -0.3 38 9-50 5-42 (42)
4 PRK01343 zinc-binding protein; 96.8 0.00035 7.5E-09 49.6 0.4 40 99-138 9-49 (57)
5 PRK00418 DNA gyrase inhibitor; 96.7 0.00058 1.3E-08 49.2 0.7 40 99-138 6-50 (62)
6 COG3024 Uncharacterized protei 96.5 0.00083 1.8E-08 48.8 0.6 38 99-136 7-49 (65)
7 cd00021 BBOX B-Box-type zinc f 96.1 0.0035 7.7E-08 38.8 1.8 37 9-49 2-38 (39)
8 smart00336 BBOX B-Box-type zin 95.4 0.012 2.6E-07 36.8 2.1 36 9-48 5-40 (42)
9 PF12855 Ecl1: Life-span regul 90.2 0.066 1.4E-06 35.9 -0.6 29 99-127 6-37 (43)
10 PF10013 DUF2256: Uncharacteri 83.5 0.38 8.1E-06 32.4 0.1 23 99-121 8-39 (42)
11 PF09889 DUF2116: Uncharacteri 77.5 0.68 1.5E-05 33.0 -0.2 28 99-126 3-30 (59)
12 PF02207 zf-UBR: Putative zinc 77.4 1.2 2.5E-05 31.9 1.0 35 19-53 10-48 (71)
13 COG4338 Uncharacterized protei 73.8 0.29 6.3E-06 34.3 -2.8 24 98-121 11-43 (54)
14 PF13240 zinc_ribbon_2: zinc-r 67.6 2.6 5.7E-05 24.5 0.8 17 101-117 1-17 (23)
15 smart00396 ZnF_UBR1 Putative z 63.6 8 0.00017 27.8 2.8 31 17-47 8-42 (71)
16 PF13248 zf-ribbon_3: zinc-rib 60.7 4.6 0.0001 23.8 0.9 19 99-117 2-20 (26)
17 KOG2177 Predicted E3 ubiquitin 60.0 5.4 0.00012 31.8 1.5 40 9-53 88-128 (386)
18 COG4068 Uncharacterized protei 57.3 3.5 7.5E-05 30.0 -0.0 23 99-121 8-30 (64)
19 cd02340 ZZ_NBR1_like Zinc fing 56.6 7.3 0.00016 25.6 1.4 29 22-50 14-43 (43)
20 PF06467 zf-FCS: MYM-type Zinc 53.1 4 8.7E-05 25.7 -0.2 24 98-121 5-40 (43)
21 KOG4582 Uncharacterized conser 46.4 21 0.00047 31.9 3.2 67 23-112 168-237 (278)
22 KOG4367 Predicted Zn-finger pr 42.9 6.6 0.00014 38.6 -0.6 35 8-46 224-259 (699)
23 PF08002 DUF1697: Protein of u 39.3 17 0.00038 29.0 1.4 30 56-86 16-48 (137)
24 PF04570 DUF581: Protein of un 32.6 14 0.00031 26.2 -0.0 28 98-125 15-51 (58)
25 TIGR00412 redox_disulf_2 small 28.4 84 0.0018 22.0 3.3 32 58-90 33-66 (76)
26 PF04438 zf-HIT: HIT zinc fing 27.1 19 0.00041 22.1 -0.2 21 101-121 4-29 (30)
27 PF12773 DZR: Double zinc ribb 26.0 32 0.0007 22.3 0.8 11 100-110 13-23 (50)
28 smart00746 TRASH metallochaper 24.1 43 0.00093 18.2 1.0 10 113-122 24-33 (39)
29 PTZ00083 40S ribosomal protein 23.3 67 0.0015 24.7 2.1 49 41-112 19-67 (85)
30 PLN00209 ribosomal protein S27 23.2 67 0.0015 24.7 2.1 49 41-112 20-68 (86)
31 cd02337 ZZ_CBP Zinc finger, ZZ 22.7 28 0.00061 22.7 -0.0 30 21-50 12-41 (41)
32 PF04945 YHS: YHS domain; Int 21.2 24 0.00051 23.0 -0.6 10 113-122 25-34 (47)
33 PF01412 ArfGap: Putative GTPa 20.7 19 0.0004 27.8 -1.4 52 18-71 9-73 (116)
No 1
>PF04640 PLATZ: PLATZ transcription factor; InterPro: IPR006734 This family includes a conserved region in several uncharacterised plant proteins.
Probab=100.00 E-value=1.2e-41 Score=248.66 Aligned_cols=72 Identities=69% Similarity=1.204 Sum_probs=71.1
Q ss_pred EeecccceeeechhhhhhcccceeEEEECCceEEEecCCCCCCCCCCCCccccccccccCCCCeeeccccee
Q 029339 51 RRSSYHDVVRVGEIQNIMDISGVQTYVINSARVVFLNERPQPRSGKGVAHICEICGRSLLDPFRFCSLGCKL 122 (195)
Q Consensus 51 RRssYhdVVrv~diqkllDiS~IQtYvINsakVVFLn~RPq~~~~~~~~~~C~~C~R~L~d~~rFCSl~CKv 122 (195)
|||||||||||+|||||||||+||||+||++||||||+|||+++++++++.|++|+|+|+|+|+||||+|||
T Consensus 1 Rr~sY~dVVrv~di~kl~D~s~IQtY~iNs~kVVfLn~Rpq~~~~~~~~~~C~~C~R~L~d~~~fCSl~CKv 72 (72)
T PF04640_consen 1 RRYSYHDVVRVSDIQKLLDCSGIQTYVINSAKVVFLNPRPQSRPSKGSGNICETCHRSLQDPYRFCSLSCKV 72 (72)
T ss_pred CcccccceEEHHHhHhhccccccEEEEeCCceEEEEccCCcCCCCCCCCCccCCCCCCCCCCCeEEeeeEEC
Confidence 899999999999999999999999999999999999999999999999999999999999999999999996
No 2
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=97.01 E-value=0.0001 Score=52.18 Aligned_cols=41 Identities=37% Similarity=0.727 Sum_probs=26.0
Q ss_pred CccccccccccCC----CCe-eecccceecccccCCCcccccccch
Q 029339 99 AHICEICGRSLLD----PFR-FCSLGCKLAGIKRDGNASFTLEIKN 139 (195)
Q Consensus 99 ~~~C~~C~R~L~d----~~r-FCSl~CKv~~~~~~~~~~~~l~~~~ 139 (195)
+..|.+|++...- +|+ |||-+||+.++.++.+-.+.|....
T Consensus 2 ~v~CP~C~k~~~~~~~n~~rPFCS~RCk~iDLg~W~~e~Y~Ip~~~ 47 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPFRPFCSERCKLIDLGRWANEEYRIPGEP 47 (57)
T ss_dssp EEE-TTT--EEE-SSSSS--SSSSHHHHHHHHS-SSSSS----SSS
T ss_pred cccCCCCCCeecccCCCCcCCcccHhhcccCHHHHhcCCcccCCCC
Confidence 4579999998865 677 9999999999999998888887655
No 3
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=96.91 E-value=0.0002 Score=45.81 Aligned_cols=38 Identities=34% Similarity=0.884 Sum_probs=30.0
Q ss_pred cccccCCCCCCCCceecccCCCCcCCcccCCCCCCCCceeEE
Q 029339 9 VCRTHGDAARSECNMYCLDCNDQAFCFYCRSSKHKDHQVIQI 50 (195)
Q Consensus 9 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~~~~H~~HrvlQI 50 (195)
.|..|.+ .+.++||.+|.. .+|..|....|++|.++.|
T Consensus 5 ~C~~H~~---~~~~~~C~~C~~-~~C~~C~~~~H~~H~~~~i 42 (42)
T PF00643_consen 5 KCPEHPE---EPLSLFCEDCNE-PLCSECTVSGHKGHKIVPI 42 (42)
T ss_dssp B-SSTTT---SBEEEEETTTTE-EEEHHHHHTSTTTSEEEEC
T ss_pred cCccCCc---cceEEEecCCCC-ccCccCCCCCCCCCEEeEC
Confidence 5888875 338899999985 9999996666999988754
No 4
>PRK01343 zinc-binding protein; Provisional
Probab=96.83 E-value=0.00035 Score=49.59 Aligned_cols=40 Identities=23% Similarity=0.426 Sum_probs=34.4
Q ss_pred CccccccccccCCCCe-eecccceecccccCCCcccccccc
Q 029339 99 AHICEICGRSLLDPFR-FCSLGCKLAGIKRDGNASFTLEIK 138 (195)
Q Consensus 99 ~~~C~~C~R~L~d~~r-FCSl~CKv~~~~~~~~~~~~l~~~ 138 (195)
...|.+|++....+|+ |||-+|+..++.+|.+-.+.|...
T Consensus 9 ~~~CP~C~k~~~~~~rPFCS~RC~~iDLg~W~~e~Y~Ip~~ 49 (57)
T PRK01343 9 TRPCPECGKPSTREAYPFCSERCRDIDLNRWLSGSYVIPGA 49 (57)
T ss_pred CCcCCCCCCcCcCCCCcccCHHHhhhhHHHHhCCCcccCCC
Confidence 5689999999877765 999999999999998888877653
No 5
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=96.68 E-value=0.00058 Score=49.17 Aligned_cols=40 Identities=28% Similarity=0.621 Sum_probs=33.8
Q ss_pred CccccccccccC----CCCe-eecccceecccccCCCcccccccc
Q 029339 99 AHICEICGRSLL----DPFR-FCSLGCKLAGIKRDGNASFTLEIK 138 (195)
Q Consensus 99 ~~~C~~C~R~L~----d~~r-FCSl~CKv~~~~~~~~~~~~l~~~ 138 (195)
...|.+|++... .+|| |||-+||+.+++++.+-.+.|...
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~IDLg~W~~e~y~Ip~~ 50 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQLIDLGEWAAEEKRIPSS 50 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHHhhhHHHHHcCCcccCCC
Confidence 568999999874 3686 999999999999998888888654
No 6
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=96.52 E-value=0.00083 Score=48.82 Aligned_cols=38 Identities=32% Similarity=0.756 Sum_probs=32.9
Q ss_pred CccccccccccCC----CCe-eecccceecccccCCCcccccc
Q 029339 99 AHICEICGRSLLD----PFR-FCSLGCKLAGIKRDGNASFTLE 136 (195)
Q Consensus 99 ~~~C~~C~R~L~d----~~r-FCSl~CKv~~~~~~~~~~~~l~ 136 (195)
+..|.+|++...- +|| |||-+||+.+++++.+-.+.+.
T Consensus 7 ~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDLg~Wa~eey~Ip 49 (65)
T COG3024 7 TVPCPTCGKPVVWGEESPFRPFCSKRCKLIDLGEWAAEEYAIP 49 (65)
T ss_pred cccCCCCCCcccccccCCcCcchhHhhhhcchhhhhccCcccC
Confidence 5679999998854 677 9999999999999988777777
No 7
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=96.11 E-value=0.0035 Score=38.76 Aligned_cols=37 Identities=24% Similarity=0.671 Sum_probs=28.6
Q ss_pred cccccCCCCCCCCceecccCCCCcCCcccCCCCCCCCceeE
Q 029339 9 VCRTHGDAARSECNMYCLDCNDQAFCFYCRSSKHKDHQVIQ 49 (195)
Q Consensus 9 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~~~~H~~HrvlQ 49 (195)
.|+.|.. +.-.+||.+|.. .+|..|....|++|.++-
T Consensus 2 ~C~~H~~---~~~~~fC~~~~~-~iC~~C~~~~H~~H~~~~ 38 (39)
T cd00021 2 LCDEHGE---EPLSLFCETDRA-LLCVDCDLSVHSGHRRVP 38 (39)
T ss_pred CCCccCC---cceEEEeCccCh-hhhhhcChhhcCCCCEee
Confidence 4777753 245799999985 899999666699997764
No 8
>smart00336 BBOX B-Box-type zinc finger.
Probab=95.39 E-value=0.012 Score=36.78 Aligned_cols=36 Identities=31% Similarity=0.937 Sum_probs=28.1
Q ss_pred cccccCCCCCCCCceecccCCCCcCCcccCCCCCCCCcee
Q 029339 9 VCRTHGDAARSECNMYCLDCNDQAFCFYCRSSKHKDHQVI 48 (195)
Q Consensus 9 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~~~~H~~Hrvl 48 (195)
.|+.|.. ..-.+||.+|.. .+|..|....|++|.++
T Consensus 5 ~C~~h~~---~~~~~~C~~c~~-~iC~~C~~~~H~~H~~~ 40 (42)
T smart00336 5 KCDSHGD---EPAEFFCEECGA-LLCRTCDEAEHRGHTVV 40 (42)
T ss_pred cCCCCCC---CceEEECCCCCc-ccccccChhhcCCCcee
Confidence 4777764 335799999985 89999965679999775
No 9
>PF12855 Ecl1: Life-span regulatory factor; InterPro: IPR024368 The fungal proteins in this entry are involved in the regulation of chronological life-span [, ]. Overexpression of these proteins has been shown to extend the chronological life-span of wild-type strains. The mechanism by which this happens is not known, but microarray data suggests that they may function as pleiptropic stress regulators.
Probab=90.20 E-value=0.066 Score=35.94 Aligned_cols=29 Identities=24% Similarity=0.665 Sum_probs=24.3
Q ss_pred Ccccccccccc---CCCCeeecccceeccccc
Q 029339 99 AHICEICGRSL---LDPFRFCSLGCKLAGIKR 127 (195)
Q Consensus 99 ~~~C~~C~R~L---~d~~rFCSl~CKv~~~~~ 127 (195)
.+.|.+|+|-+ .+...|||..|++.+...
T Consensus 6 ~~yC~~Cdk~~~~~~~~~lYCSe~Cr~~D~~~ 37 (43)
T PF12855_consen 6 NDYCIVCDKQIDPPDDGSLYCSEECRLKDQEK 37 (43)
T ss_pred hhHHHHhhccccCCCCCccccCHHHHhHhhhc
Confidence 46899999999 667889999999877644
No 10
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=83.49 E-value=0.38 Score=32.43 Aligned_cols=23 Identities=39% Similarity=1.139 Sum_probs=19.9
Q ss_pred CccccccccccC---------CCCeeecccce
Q 029339 99 AHICEICGRSLL---------DPFRFCSLGCK 121 (195)
Q Consensus 99 ~~~C~~C~R~L~---------d~~rFCSl~CK 121 (195)
...|.+|+|... |...|||-+|.
T Consensus 8 ~K~C~~C~rpf~WRKKW~~~Wd~VkYCS~rCR 39 (42)
T PF10013_consen 8 SKICPVCGRPFTWRKKWARCWDEVKYCSDRCR 39 (42)
T ss_pred CCcCcccCCcchHHHHHHHhchhhccHHHHhc
Confidence 569999999984 56899999997
No 11
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=77.47 E-value=0.68 Score=32.99 Aligned_cols=28 Identities=29% Similarity=0.636 Sum_probs=23.2
Q ss_pred CccccccccccCCCCeeecccceecccc
Q 029339 99 AHICEICGRSLLDPFRFCSLGCKLAGIK 126 (195)
Q Consensus 99 ~~~C~~C~R~L~d~~rFCSl~CKv~~~~ 126 (195)
..+|..||.++...-.|||-.|+-...+
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~~~~k 30 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCREEYRK 30 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHHHHHH
Confidence 3589999999998889999999954443
No 12
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=77.36 E-value=1.2 Score=31.89 Aligned_cols=35 Identities=31% Similarity=0.602 Sum_probs=26.5
Q ss_pred CCCceecccCCC---CcCCccc-CCCCCCCCceeEEEee
Q 029339 19 SECNMYCLDCND---QAFCFYC-RSSKHKDHQVIQIRRS 53 (195)
Q Consensus 19 nE~N~FCldC~~---~~~C~~C-~~~~H~~HrvlQIRRs 53 (195)
++--..|++|.. .++|..| ....|.+|++..++-.
T Consensus 10 ~q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~ 48 (71)
T PF02207_consen 10 GQIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSS 48 (71)
T ss_dssp T-EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--
T ss_pred CCEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeC
Confidence 366678999976 3799999 8889999998877654
No 13
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.78 E-value=0.29 Score=34.26 Aligned_cols=24 Identities=33% Similarity=0.948 Sum_probs=20.8
Q ss_pred CCccccccccccC---------CCCeeecccce
Q 029339 98 VAHICEICGRSLL---------DPFRFCSLGCK 121 (195)
Q Consensus 98 ~~~~C~~C~R~L~---------d~~rFCSl~CK 121 (195)
.+.+|++|+|... |...|||..|+
T Consensus 11 p~KICpvCqRPFsWRkKW~~cWDeVKyCSeRCr 43 (54)
T COG4338 11 PDKICPVCQRPFSWRKKWARCWDEVKYCSERCR 43 (54)
T ss_pred chhhhhhhcCchHHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999984 56789999999
No 14
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=67.55 E-value=2.6 Score=24.50 Aligned_cols=17 Identities=35% Similarity=0.950 Sum_probs=14.7
Q ss_pred cccccccccCCCCeeec
Q 029339 101 ICEICGRSLLDPFRFCS 117 (195)
Q Consensus 101 ~C~~C~R~L~d~~rFCS 117 (195)
.|..|+..|.+...||+
T Consensus 1 ~Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCP 17 (23)
T ss_pred CCcccCCCCCCcCcchh
Confidence 38899999999888986
No 15
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=63.64 E-value=8 Score=27.84 Aligned_cols=31 Identities=26% Similarity=0.499 Sum_probs=24.4
Q ss_pred CCCCCceecccCCCC---cCCcccCC-CCCCCCce
Q 029339 17 ARSECNMYCLDCNDQ---AFCFYCRS-SKHKDHQV 47 (195)
Q Consensus 17 ~knE~N~FCldC~~~---~~C~~C~~-~~H~~Hrv 47 (195)
.++|--..|++|... .+|..|.. ..|.+|++
T Consensus 8 ~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~ 42 (71)
T smart00396 8 TGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDY 42 (71)
T ss_pred CCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCE
Confidence 456777899999754 68899966 78999984
No 16
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=60.72 E-value=4.6 Score=23.77 Aligned_cols=19 Identities=26% Similarity=0.742 Sum_probs=15.9
Q ss_pred CccccccccccCCCCeeec
Q 029339 99 AHICEICGRSLLDPFRFCS 117 (195)
Q Consensus 99 ~~~C~~C~R~L~d~~rFCS 117 (195)
...|..|+..+.+..+||+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~ 20 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCP 20 (26)
T ss_pred cCCCcccCCcCCcccccCh
Confidence 3579999998888899996
No 17
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.03 E-value=5.4 Score=31.82 Aligned_cols=40 Identities=28% Similarity=0.863 Sum_probs=31.2
Q ss_pred cccccCCCCCCCCceecccCCCCcCCcccC-CCCCCCCceeEEEee
Q 029339 9 VCRTHGDAARSECNMYCLDCNDQAFCFYCR-SSKHKDHQVIQIRRS 53 (195)
Q Consensus 9 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~-~~~H~~HrvlQIRRs 53 (195)
.|..|... ..+||..|.. .+|..|. ...|.+|.++.+...
T Consensus 88 ~c~~~~~~----~~~~c~~~~~-~~c~~c~~~~~h~~h~~~~~~~~ 128 (386)
T KOG2177|consen 88 LCEKHGEE----LKLFCEEDEK-LLCVLCRESGEHRGHPVLPLEEA 128 (386)
T ss_pred hhhhcCCc----ceEEeccccc-ccCCCCCCcccccCCccccHHHH
Confidence 56777652 6799999985 8999996 778999988876543
No 18
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=57.26 E-value=3.5 Score=29.95 Aligned_cols=23 Identities=26% Similarity=0.717 Sum_probs=21.2
Q ss_pred CccccccccccCCCCeeecccce
Q 029339 99 AHICEICGRSLLDPFRFCSLGCK 121 (195)
Q Consensus 99 ~~~C~~C~R~L~d~~rFCSl~CK 121 (195)
..+|.+|+..+...-+|||..|.
T Consensus 8 H~HC~VCg~aIp~de~~CSe~C~ 30 (64)
T COG4068 8 HRHCVVCGKAIPPDEQVCSEECG 30 (64)
T ss_pred CccccccCCcCCCccchHHHHHH
Confidence 46899999999999999999997
No 19
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=56.63 E-value=7.3 Score=25.63 Aligned_cols=29 Identities=31% Similarity=0.760 Sum_probs=20.9
Q ss_pred ceecccCCCCcCCcccC-CCCCCCCceeEE
Q 029339 22 NMYCLDCNDQAFCFYCR-SSKHKDHQVIQI 50 (195)
Q Consensus 22 N~FCldC~~~~~C~~C~-~~~H~~HrvlQI 50 (195)
-.-|+.|.+--+|..|. ...|..|..++|
T Consensus 14 ry~C~~C~d~dLC~~C~~~~~H~~H~f~~~ 43 (43)
T cd02340 14 RYKCLVCPDYDLCESCEAKGVHPEHAMLKI 43 (43)
T ss_pred eEECCCCCCccchHHhhCcCCCCCCCEEeC
Confidence 36789997667999993 335777877654
No 20
>PF06467 zf-FCS: MYM-type Zinc finger with FCS sequence motif; InterPro: IPR010507 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. MYM-type zinc fingers were identified in MYM family proteins []. Human protein Q14202 from SWISSPROT is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1 []. Q9UBW7 from SWISSPROT is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1 []; in atypical myeloproliferative disorders it is rearranged []. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2L8E_A 2DAS_A.
Probab=53.14 E-value=4 Score=25.74 Aligned_cols=24 Identities=29% Similarity=0.794 Sum_probs=15.0
Q ss_pred CCccccccccccCC-C-----------Ceeecccce
Q 029339 98 VAHICEICGRSLLD-P-----------FRFCSLGCK 121 (195)
Q Consensus 98 ~~~~C~~C~R~L~d-~-----------~rFCSl~CK 121 (195)
....|..|++.+.. + ..|||..|.
T Consensus 5 ~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~ 40 (43)
T PF06467_consen 5 KMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCL 40 (43)
T ss_dssp SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHH
T ss_pred cCCcCcccCCcccCCCccccccccCcccChhCHHHH
Confidence 46789999987732 1 379999985
No 21
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=46.40 E-value=21 Score=31.94 Aligned_cols=67 Identities=18% Similarity=0.258 Sum_probs=42.3
Q ss_pred eecccCCCCcCCcccC-CC-CCCCCceeEEEeecccceeeechhhhhhcccceeEEEECCceEEEecCCCCCCCCC-CCC
Q 029339 23 MYCLDCNDQAFCFYCR-SS-KHKDHQVIQIRRSSYHDVVRVGEIQNIMDISGVQTYVINSARVVFLNERPQPRSGK-GVA 99 (195)
Q Consensus 23 ~FCldC~~~~~C~~C~-~~-~H~~HrvlQIRRssYhdVVrv~diqkllDiS~IQtYvINsakVVFLn~RPq~~~~~-~~~ 99 (195)
+-|+.|.+.-||..|- .. .|..|..|||.+ +.....+.++++.++-+.... -.-
T Consensus 168 yKC~~C~dYDLCe~Ce~~~~~h~~H~~lR~~t-----------------------~~t~~~~~~~~~~p~~~~~~~~~~~ 224 (278)
T KOG4582|consen 168 YKCTVCPDYDLCERCEAGNEHHAAHAMLRLHT-----------------------NETPFSGYVMLSSPPNPVNLNKRPI 224 (278)
T ss_pred eeecCCCccchhHHhhcCCCCCcccceeeccc-----------------------ccCCCCcceeccCCCCccccccccc
Confidence 5799998778999994 33 688899999765 555666677776555543221 122
Q ss_pred ccccccccccCCC
Q 029339 100 HICEICGRSLLDP 112 (195)
Q Consensus 100 ~~C~~C~R~L~d~ 112 (195)
..|..+.+.-.++
T Consensus 225 ~~~~~~~~~~~~~ 237 (278)
T KOG4582|consen 225 FVGHSKVRGNDWY 237 (278)
T ss_pred ccccccccccCCc
Confidence 3445555444443
No 22
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=42.85 E-value=6.6 Score=38.56 Aligned_cols=35 Identities=31% Similarity=0.883 Sum_probs=25.0
Q ss_pred ccccccCCCCCCCCceecccCCCCcCCcccCC-CCCCCCc
Q 029339 8 TVCRTHGDAARSECNMYCLDCNDQAFCFYCRS-SKHKDHQ 46 (195)
Q Consensus 8 ~~C~~H~~~~knE~N~FCldC~~~~~C~~C~~-~~H~~Hr 46 (195)
..|..|... ...|||+.|.. ++|..|+. ..|..|.
T Consensus 224 ~~ct~h~~e---~~smyc~~ck~-pvc~~clee~khs~he 259 (699)
T KOG4367|consen 224 STCTDHELE---NHSMYCVQCKM-PVCYQCLEEGKHSSHE 259 (699)
T ss_pred hhccCCCCC---CceEEEEecCC-hHHHHHHHhhcccchh
Confidence 468888752 25699999986 89999942 2466663
No 23
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=39.33 E-value=17 Score=29.02 Aligned_cols=30 Identities=30% Similarity=0.630 Sum_probs=20.7
Q ss_pred cceeeechhhhh---hcccceeEEEECCceEEEe
Q 029339 56 HDVVRVGEIQNI---MDISGVQTYVINSARVVFL 86 (195)
Q Consensus 56 hdVVrv~diqkl---lDiS~IQtYvINsakVVFL 86 (195)
++-|+..|+..+ +-..+|+|| |||.-|||-
T Consensus 16 ~nki~MaeLr~~l~~~Gf~~V~Ty-i~SGNvvf~ 48 (137)
T PF08002_consen 16 KNKIKMAELREALEDLGFTNVRTY-IQSGNVVFE 48 (137)
T ss_dssp BS---HHHHHHHHHHCT-EEEEEE-TTTTEEEEE
T ss_pred CCcccHHHHHHHHHHcCCCCceEE-EeeCCEEEe
Confidence 345677777775 678899999 688899998
No 24
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=32.60 E-value=14 Score=26.19 Aligned_cols=28 Identities=36% Similarity=0.814 Sum_probs=21.0
Q ss_pred CCccccccccccC---CC--Ce----eecccceeccc
Q 029339 98 VAHICEICGRSLL---DP--FR----FCSLGCKLAGI 125 (195)
Q Consensus 98 ~~~~C~~C~R~L~---d~--~r----FCSl~CKv~~~ 125 (195)
.-..|-.|.|.|. |- |+ |||..|--..|
T Consensus 15 FL~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~qi 51 (58)
T PF04570_consen 15 FLSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQQI 51 (58)
T ss_pred HHHHHHccCCCCCCCCCeeeeccccccccHHHHHHHH
Confidence 3468999999997 32 44 99999985444
No 25
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=28.37 E-value=84 Score=21.97 Aligned_cols=32 Identities=13% Similarity=0.352 Sum_probs=22.3
Q ss_pred eeeechhhhh--hcccceeEEEECCceEEEecCCC
Q 029339 58 VVRVGEIQNI--MDISGVQTYVINSARVVFLNERP 90 (195)
Q Consensus 58 VVrv~diqkl--lDiS~IQtYvINsakVVFLn~RP 90 (195)
+++|+|++.. +++.+|-|.+||+..+ +....|
T Consensus 33 ~~~v~~~~~a~~~~v~~vPti~i~G~~~-~~G~~~ 66 (76)
T TIGR00412 33 FEKVTDMNEILEAGVTATPGVAVDGELV-IMGKIP 66 (76)
T ss_pred EEEeCCHHHHHHcCCCcCCEEEECCEEE-EEeccC
Confidence 4666655554 7899999999988655 555444
No 26
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=27.06 E-value=19 Score=22.15 Aligned_cols=21 Identities=38% Similarity=1.012 Sum_probs=12.0
Q ss_pred cccccccccCC-----CCeeecccce
Q 029339 101 ICEICGRSLLD-----PFRFCSLGCK 121 (195)
Q Consensus 101 ~C~~C~R~L~d-----~~rFCSl~CK 121 (195)
.|.+|+..-.- ..+||||.|.
T Consensus 4 ~C~vC~~~~kY~Cp~C~~~~CSl~C~ 29 (30)
T PF04438_consen 4 LCSVCGNPAKYRCPRCGARYCSLACY 29 (30)
T ss_dssp EETSSSSEESEE-TTT--EESSHHHH
T ss_pred CCccCcCCCEEECCCcCCceeCcEeE
Confidence 56667662210 2569999984
No 27
>PF12773 DZR: Double zinc ribbon
Probab=25.96 E-value=32 Score=22.27 Aligned_cols=11 Identities=36% Similarity=0.921 Sum_probs=5.5
Q ss_pred ccccccccccC
Q 029339 100 HICEICGRSLL 110 (195)
Q Consensus 100 ~~C~~C~R~L~ 110 (195)
..|..|+..|.
T Consensus 13 ~fC~~CG~~l~ 23 (50)
T PF12773_consen 13 KFCPHCGTPLP 23 (50)
T ss_pred cCChhhcCChh
Confidence 44555555554
No 28
>smart00746 TRASH metallochaperone-like domain.
Probab=24.14 E-value=43 Score=18.22 Aligned_cols=10 Identities=50% Similarity=0.999 Sum_probs=7.5
Q ss_pred Ceeeccccee
Q 029339 113 FRFCSLGCKL 122 (195)
Q Consensus 113 ~rFCSl~CKv 122 (195)
+.|||..|..
T Consensus 24 ~~FCs~~c~~ 33 (39)
T smart00746 24 FYFCSSKCLS 33 (39)
T ss_pred EEEeCHHHHH
Confidence 5788888864
No 29
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=23.30 E-value=67 Score=24.65 Aligned_cols=49 Identities=33% Similarity=0.482 Sum_probs=36.1
Q ss_pred CCCCCceeEEEeecccceeeechhhhhhcccceeEEEECCceEEEecCCCCCCCCCCCCccccccccccCCC
Q 029339 41 KHKDHQVIQIRRSSYHDVVRVGEIQNIMDISGVQTYVINSARVVFLNERPQPRSGKGVAHICEICGRSLLDP 112 (195)
Q Consensus 41 ~H~~HrvlQIRRssYhdVVrv~diqkllDiS~IQtYvINsakVVFLn~RPq~~~~~~~~~~C~~C~R~L~d~ 112 (195)
-|+..+++|-=+|-+.|| |..||..||+ ||=+ +| ....|..|+..|..|
T Consensus 19 khK~k~Lv~~PnS~Fm~V-------kCp~C~n~q~--------VFSh--A~------t~V~C~~Cg~~L~~P 67 (85)
T PTZ00083 19 KHKLKRLVQGPNSYFMDV-------KCPGCSQITT--------VFSH--AQ------TVVLCGGCSSQLCQP 67 (85)
T ss_pred hhhceeEecCCCCeEEEE-------ECCCCCCeeE--------EEec--Cc------eEEEccccCCEeecc
Confidence 477788888888877777 5788888886 5543 22 245799999999764
No 30
>PLN00209 ribosomal protein S27; Provisional
Probab=23.18 E-value=67 Score=24.70 Aligned_cols=49 Identities=31% Similarity=0.483 Sum_probs=35.9
Q ss_pred CCCCCceeEEEeecccceeeechhhhhhcccceeEEEECCceEEEecCCCCCCCCCCCCccccccccccCCC
Q 029339 41 KHKDHQVIQIRRSSYHDVVRVGEIQNIMDISGVQTYVINSARVVFLNERPQPRSGKGVAHICEICGRSLLDP 112 (195)
Q Consensus 41 ~H~~HrvlQIRRssYhdVVrv~diqkllDiS~IQtYvINsakVVFLn~RPq~~~~~~~~~~C~~C~R~L~d~ 112 (195)
-|+..+++|-=+|-+.|| |.-||..||+ ||=+ +| ....|..|+..|..|
T Consensus 20 khK~k~Lv~~PnS~Fm~V-------kCp~C~n~q~--------VFSh--A~------t~V~C~~Cg~~L~~P 68 (86)
T PLN00209 20 KHKLKRLVQSPNSFFMDV-------KCQGCFNITT--------VFSH--SQ------TVVVCGSCQTVLCQP 68 (86)
T ss_pred hhhceeeecCCCCEEEEE-------ECCCCCCeeE--------EEec--Cc------eEEEccccCCEeecc
Confidence 477778888878777776 5778888886 5543 22 245799999999765
No 31
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=22.73 E-value=28 Score=22.71 Aligned_cols=30 Identities=23% Similarity=0.652 Sum_probs=21.7
Q ss_pred CceecccCCCCcCCcccCCCCCCCCceeEE
Q 029339 21 CNMYCLDCNDQAFCFYCRSSKHKDHQVIQI 50 (195)
Q Consensus 21 ~N~FCldC~~~~~C~~C~~~~H~~HrvlQI 50 (195)
.-.-|..|..--+|..|.......|.+.||
T Consensus 12 ~r~~C~~C~dfDLC~~C~~~~~H~H~~~~~ 41 (41)
T cd02337 12 TRWHCTVCEDYDLCITCYNTKNHPHKMEKL 41 (41)
T ss_pred CceECCCCcchhhHHHHhCCCCCCcccccC
Confidence 447799998767999995444447777764
No 32
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=21.24 E-value=24 Score=22.98 Aligned_cols=10 Identities=60% Similarity=1.321 Sum_probs=8.8
Q ss_pred Ceeeccccee
Q 029339 113 FRFCSLGCKL 122 (195)
Q Consensus 113 ~rFCSl~CKv 122 (195)
|.|||-+|+-
T Consensus 25 Y~FCS~~C~~ 34 (47)
T PF04945_consen 25 YYFCSEGCKE 34 (47)
T ss_dssp EEESSHHHHH
T ss_pred EEEcCHHHHH
Confidence 7899999983
No 33
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=20.72 E-value=19 Score=27.83 Aligned_cols=52 Identities=21% Similarity=0.448 Sum_probs=30.6
Q ss_pred CCCCceecccCCCC-----------cCCcccCCCCCCC--CceeEEEeecccceeeechhhhhhccc
Q 029339 18 RSECNMYCLDCNDQ-----------AFCFYCRSSKHKD--HQVIQIRRSSYHDVVRVGEIQNIMDIS 71 (195)
Q Consensus 18 knE~N~FCldC~~~-----------~~C~~C~~~~H~~--HrvlQIRRssYhdVVrv~diqkllDiS 71 (195)
+..-|..|.||... -+|..| ...|+. .++-+| |+.-.|-....||+.+..+.
T Consensus 9 ~~~~N~~CaDCg~~~p~w~s~~~GiflC~~C-ag~HR~lg~~is~V-kSi~~d~w~~~ev~~~~~~G 73 (116)
T PF01412_consen 9 KKPGNKVCADCGAPNPTWASLNYGIFLCLEC-AGIHRSLGVHISRV-KSITMDNWSPEEVQRMREGG 73 (116)
T ss_dssp CSTTCTB-TTT-SBS--EEETTTTEEE-HHH-HHHHHHHTTTT--E-EETTTS---HHHHHHHHHSH
T ss_pred cCcCcCcCCCCCCCCCCEEEeecChhhhHHH-HHHHHHhcccchhc-cccccCCCCHHHHHHHHHHC
Confidence 34678999999542 478888 666764 234444 77788888888888876553
Done!