Query 028382
Match_columns 210
No_of_seqs 152 out of 197
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 10:38:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028382.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028382hhsearch_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 2.2E-40 4.9E-45 244.1 5.5 72 66-137 1-72 (72)
2 PF00643 zf-B_box: B-box zinc 96.6 0.00044 9.6E-09 44.6 -0.3 38 24-65 5-42 (42)
3 cd00021 BBOX B-Box-type zinc f 96.0 0.0044 9.5E-08 38.8 1.7 37 24-64 2-38 (39)
4 smart00336 BBOX B-Box-type zin 95.0 0.018 3.9E-07 36.4 2.0 36 24-63 5-40 (42)
5 PRK01343 zinc-binding protein; 89.0 0.11 2.3E-06 37.3 -0.2 29 114-142 9-38 (57)
6 PF03884 DUF329: Domain of unk 88.2 0.06 1.3E-06 38.5 -2.0 29 114-142 2-35 (57)
7 PF12855 Ecl1: Life-span regul 87.6 0.11 2.5E-06 35.1 -0.8 28 114-141 6-36 (43)
8 COG3024 Uncharacterized protei 87.0 0.18 4E-06 37.0 -0.1 29 114-142 7-40 (65)
9 PRK00418 DNA gyrase inhibitor; 86.9 0.16 3.4E-06 37.0 -0.5 29 114-142 6-39 (62)
10 PF10013 DUF2256: Uncharacteri 79.1 0.56 1.2E-05 31.8 -0.2 23 114-136 8-39 (42)
11 PF02207 zf-UBR: Putative zinc 78.6 0.98 2.1E-05 32.6 0.9 34 35-68 11-48 (71)
12 PF09889 DUF2116: Uncharacteri 70.2 1.2 2.5E-05 32.1 -0.5 25 114-138 3-27 (59)
13 PF13240 zinc_ribbon_2: zinc-r 65.4 2.7 6E-05 24.6 0.5 16 117-132 2-17 (23)
14 COG4338 Uncharacterized protei 60.3 0.73 1.6E-05 32.5 -3.0 24 113-136 11-43 (54)
15 KOG2177 Predicted E3 ubiquitin 56.9 6.4 0.00014 32.0 1.5 39 24-67 88-127 (386)
16 cd02340 ZZ_NBR1_like Zinc fing 55.9 7.4 0.00016 25.8 1.4 28 38-65 15-43 (43)
17 smart00396 ZnF_UBR1 Putative z 55.1 13 0.00028 27.0 2.7 31 32-62 8-42 (71)
18 PF13248 zf-ribbon_3: zinc-rib 54.1 6.5 0.00014 23.3 0.8 19 114-132 2-20 (26)
19 PF06467 zf-FCS: MYM-type Zinc 48.7 4.6 0.0001 25.8 -0.5 25 112-136 4-40 (43)
20 COG4068 Uncharacterized protei 41.1 7.7 0.00017 28.4 -0.3 23 114-136 8-30 (64)
21 PRK05707 DNA polymerase III su 38.9 23 0.0005 32.6 2.3 93 9-102 4-113 (328)
22 KOG4367 Predicted Zn-finger pr 36.5 9.6 0.00021 37.8 -0.6 35 23-61 224-259 (699)
23 KOG4582 Uncharacterized conser 35.8 24 0.00052 32.0 1.9 57 8-67 132-199 (278)
24 PF04438 zf-HIT: HIT zinc fing 33.8 12 0.00026 23.3 -0.3 22 115-136 3-29 (30)
25 TIGR00412 redox_disulf_2 small 32.2 65 0.0014 22.8 3.3 32 73-105 33-66 (76)
26 PF04570 DUF581: Protein of un 28.7 17 0.00036 26.1 -0.3 28 113-140 15-51 (58)
27 cd02341 ZZ_ZZZ3 Zinc finger, Z 26.2 35 0.00076 23.3 1.0 28 38-65 16-48 (48)
28 PF12773 DZR: Double zinc ribb 21.2 40 0.00086 22.1 0.5 12 114-125 12-23 (50)
29 smart00746 TRASH metallochaper 21.1 49 0.0011 18.2 0.8 10 128-137 24-33 (39)
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=2.2e-40 Score=244.09 Aligned_cols=72 Identities=69% Similarity=1.204 Sum_probs=71.1
Q ss_pred EeccccceeeechhhhhhcccceeEEEECCcEEEEeecCCCCCCCCCCcccccccccccCCCCeeeeeccee
Q 028382 66 RRSSYHDVVRVGEIQNIMDISGVQTYVINSARVVFLNERPQPRSGKGVAHICEICGRSLLDPFRFCSLGCKL 137 (210)
Q Consensus 66 RRssY~dVVrv~dIqkl~D~S~IQtYvINsakVVfLn~RPq~r~~kg~~~~C~~C~R~L~d~~~FCSl~CKv 137 (210)
|||||||||||+|||||||||+||||+|||+||||||+|||+++.+++++.|++|+|+|+|+|+||||+|||
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 799999999999999999999999999999999999999999999999999999999999999999999996
No 2
>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=96.61 E-value=0.00044 Score=44.64 Aligned_cols=38 Identities=34% Similarity=0.884 Sum_probs=29.9
Q ss_pred hccccCCCCCCCCceecccCCCccCcCcccCCCCCCCceEEE
Q 028382 24 VCRTHGDAARSECNMYCLDCNDQAFCFYCRSSKHKDHQVIQI 65 (210)
Q Consensus 24 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~~~~H~~HrvlQI 65 (210)
.|..|.. .+.++||.+|.. .+|..|....|++|.++.|
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 5888865 238899999985 9999997667999988754
No 3
>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=95.96 E-value=0.0044 Score=38.79 Aligned_cols=37 Identities=24% Similarity=0.671 Sum_probs=28.4
Q ss_pred hccccCCCCCCCCceecccCCCccCcCcccCCCCCCCceEE
Q 028382 24 VCRTHGDAARSECNMYCLDCNDQAFCFYCRSSKHKDHQVIQ 64 (210)
Q Consensus 24 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~~~~H~~HrvlQ 64 (210)
.|+.|.. +.-.+||.+|.. .+|..|....|++|.++-
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 235899999985 899999666699997764
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=94.97 E-value=0.018 Score=36.39 Aligned_cols=36 Identities=31% Similarity=0.937 Sum_probs=27.9
Q ss_pred hccccCCCCCCCCceecccCCCccCcCcccCCCCCCCceE
Q 028382 24 VCRTHGDAARSECNMYCLDCNDQAFCFYCRSSKHKDHQVI 63 (210)
Q Consensus 24 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~~~~H~~Hrvl 63 (210)
.|..|.. ..-.+||.+|.. .+|..|....|++|+++
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 235899999985 99999965679999775
No 5
>PRK01343 zinc-binding protein; Provisional
Probab=89.01 E-value=0.11 Score=37.29 Aligned_cols=29 Identities=28% Similarity=0.637 Sum_probs=23.4
Q ss_pred cccccccccccCCCC-eeeeecceeCeeec
Q 028382 114 AHICEICGRSLLDPF-RFCSLGCKLAGIKR 142 (210)
Q Consensus 114 ~~~C~~C~R~L~d~~-~FCSl~CKv~~~~~ 142 (210)
...|-+|++.....+ -|||-.||..++.+
T Consensus 9 ~~~CP~C~k~~~~~~rPFCS~RC~~iDLg~ 38 (57)
T PRK01343 9 TRPCPECGKPSTREAYPFCSERCRDIDLNR 38 (57)
T ss_pred CCcCCCCCCcCcCCCCcccCHHHhhhhHHH
Confidence 468999999987665 59999999866543
No 6
>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=88.19 E-value=0.06 Score=38.46 Aligned_cols=29 Identities=48% Similarity=1.000 Sum_probs=18.2
Q ss_pred cccccccccccCC----CCe-eeeecceeCeeec
Q 028382 114 AHICEICGRSLLD----PFR-FCSLGCKLAGIKR 142 (210)
Q Consensus 114 ~~~C~~C~R~L~d----~~~-FCSl~CKv~~~~~ 142 (210)
+..|-+|++...- +|+ |||-.||+..+.+
T Consensus 2 ~v~CP~C~k~~~~~~~n~~rPFCS~RCk~iDLg~ 35 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPFRPFCSERCKLIDLGR 35 (57)
T ss_dssp EEE-TTT--EEE-SSSSS--SSSSHHHHHHHHS-
T ss_pred cccCCCCCCeecccCCCCcCCcccHhhcccCHHH
Confidence 4579999999875 676 9999999877654
No 7
>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=87.57 E-value=0.11 Score=35.06 Aligned_cols=28 Identities=25% Similarity=0.656 Sum_probs=23.6
Q ss_pred ccccccccccc---CCCCeeeeecceeCeee
Q 028382 114 AHICEICGRSL---LDPFRFCSLGCKLAGIK 141 (210)
Q Consensus 114 ~~~C~~C~R~L---~d~~~FCSl~CKv~~~~ 141 (210)
.+.|.+|+|.+ .+...|||-.|++.+..
T Consensus 6 ~~yC~~Cdk~~~~~~~~~lYCSe~Cr~~D~~ 36 (43)
T PF12855_consen 6 NDYCIVCDKQIDPPDDGSLYCSEECRLKDQE 36 (43)
T ss_pred hhHHHHhhccccCCCCCccccCHHHHhHhhh
Confidence 46799999999 66789999999986653
No 8
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.04 E-value=0.18 Score=37.02 Aligned_cols=29 Identities=41% Similarity=0.953 Sum_probs=23.3
Q ss_pred cccccccccccCC----CCe-eeeecceeCeeec
Q 028382 114 AHICEICGRSLLD----PFR-FCSLGCKLAGIKR 142 (210)
Q Consensus 114 ~~~C~~C~R~L~d----~~~-FCSl~CKv~~~~~ 142 (210)
+..|-+||+...- +|| |||-.||+-.+.+
T Consensus 7 ~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDLg~ 40 (65)
T COG3024 7 TVPCPTCGKPVVWGEESPFRPFCSKRCKLIDLGE 40 (65)
T ss_pred cccCCCCCCcccccccCCcCcchhHhhhhcchhh
Confidence 4579999998864 665 9999999877654
No 9
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=86.86 E-value=0.16 Score=37.01 Aligned_cols=29 Identities=38% Similarity=0.944 Sum_probs=22.6
Q ss_pred cccccccccccC----CCCe-eeeecceeCeeec
Q 028382 114 AHICEICGRSLL----DPFR-FCSLGCKLAGIKR 142 (210)
Q Consensus 114 ~~~C~~C~R~L~----d~~~-FCSl~CKv~~~~~ 142 (210)
...|-+|++... .+|+ |||-.||+..+.+
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~IDLg~ 39 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQLIDLGE 39 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHHhhhHHH
Confidence 567999999874 3565 9999999876644
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=79.15 E-value=0.56 Score=31.81 Aligned_cols=23 Identities=39% Similarity=1.139 Sum_probs=19.9
Q ss_pred cccccccccccC---------CCCeeeeecce
Q 028382 114 AHICEICGRSLL---------DPFRFCSLGCK 136 (210)
Q Consensus 114 ~~~C~~C~R~L~---------d~~~FCSl~CK 136 (210)
..+|.+|+|.+. |...|||-.|.
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 568999999995 56899999997
No 11
>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=78.58 E-value=0.98 Score=32.61 Aligned_cols=34 Identities=32% Similarity=0.616 Sum_probs=25.7
Q ss_pred CCceecccCCC---ccCcCcc-cCCCCCCCceEEEEec
Q 028382 35 ECNMYCLDCND---QAFCFYC-RSSKHKDHQVIQIRRS 68 (210)
Q Consensus 35 E~N~FCldC~~---~~~C~~C-~~~~H~~HrvlQIRRs 68 (210)
+--..|++|.. .++|..| ....|.+|+++.++-.
T Consensus 11 q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~ 48 (71)
T PF02207_consen 11 QIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSS 48 (71)
T ss_dssp -EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--
T ss_pred CEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeC
Confidence 55578999976 3799999 8889999998887654
No 12
>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=70.19 E-value=1.2 Score=32.08 Aligned_cols=25 Identities=28% Similarity=0.755 Sum_probs=21.9
Q ss_pred cccccccccccCCCCeeeeecceeC
Q 028382 114 AHICEICGRSLLDPFRFCSLGCKLA 138 (210)
Q Consensus 114 ~~~C~~C~R~L~d~~~FCSl~CKv~ 138 (210)
..+|..||..+..+-.|||-.|+=.
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~~ 27 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCREE 27 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHHH
Confidence 4689999999998889999999943
No 13
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=65.40 E-value=2.7 Score=24.61 Aligned_cols=16 Identities=38% Similarity=1.024 Sum_probs=14.2
Q ss_pred ccccccccCCCCeeee
Q 028382 117 CEICGRSLLDPFRFCS 132 (210)
Q Consensus 117 C~~C~R~L~d~~~FCS 132 (210)
|..||..+.+...||+
T Consensus 2 Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCP 17 (23)
T ss_pred CcccCCCCCCcCcchh
Confidence 7889999999889986
No 14
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.31 E-value=0.73 Score=32.49 Aligned_cols=24 Identities=33% Similarity=0.948 Sum_probs=20.8
Q ss_pred CcccccccccccC---------CCCeeeeecce
Q 028382 113 VAHICEICGRSLL---------DPFRFCSLGCK 136 (210)
Q Consensus 113 ~~~~C~~C~R~L~---------d~~~FCSl~CK 136 (210)
...+|++|+|.+. |...|||-.|+
T Consensus 11 p~KICpvCqRPFsWRkKW~~cWDeVKyCSeRCr 43 (54)
T COG4338 11 PDKICPVCQRPFSWRKKWARCWDEVKYCSERCR 43 (54)
T ss_pred chhhhhhhcCchHHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999984 56899999999
No 15
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=56.91 E-value=6.4 Score=31.95 Aligned_cols=39 Identities=28% Similarity=0.876 Sum_probs=30.8
Q ss_pred hccccCCCCCCCCceecccCCCccCcCccc-CCCCCCCceEEEEe
Q 028382 24 VCRTHGDAARSECNMYCLDCNDQAFCFYCR-SSKHKDHQVIQIRR 67 (210)
Q Consensus 24 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~-~~~H~~HrvlQIRR 67 (210)
.|..|... ..+||..|.. .+|..|. ...|.+|.++.+..
T Consensus 88 ~c~~~~~~----~~~~c~~~~~-~~c~~c~~~~~h~~h~~~~~~~ 127 (386)
T KOG2177|consen 88 LCEKHGEE----LKLFCEEDEK-LLCVLCRESGEHRGHPVLPLEE 127 (386)
T ss_pred hhhhcCCc----ceEEeccccc-ccCCCCCCcccccCCccccHHH
Confidence 57777542 6799999985 8999996 67899998887643
No 16
>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=55.86 E-value=7.4 Score=25.82 Aligned_cols=28 Identities=32% Similarity=0.783 Sum_probs=20.1
Q ss_pred eecccCCCccCcCccc-CCCCCCCceEEE
Q 028382 38 MYCLDCNDQAFCFYCR-SSKHKDHQVIQI 65 (210)
Q Consensus 38 ~FCldC~~~~~C~~C~-~~~H~~HrvlQI 65 (210)
.-|+.|..--||..|. ...|..|+.++|
T Consensus 15 y~C~~C~d~dLC~~C~~~~~H~~H~f~~~ 43 (43)
T cd02340 15 YKCLVCPDYDLCESCEAKGVHPEHAMLKI 43 (43)
T ss_pred EECCCCCCccchHHhhCcCCCCCCCEEeC
Confidence 5688887667999993 335777877754
No 17
>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=55.10 E-value=13 Score=27.00 Aligned_cols=31 Identities=26% Similarity=0.499 Sum_probs=23.7
Q ss_pred CCCCCceecccCCCc---cCcCcccC-CCCCCCce
Q 028382 32 ARSECNMYCLDCNDQ---AFCFYCRS-SKHKDHQV 62 (210)
Q Consensus 32 ~knE~N~FCldC~~~---~~C~~C~~-~~H~~Hrv 62 (210)
.++|.-..|++|... .+|..|.. ..|.+|++
T Consensus 8 ~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~ 42 (71)
T smart00396 8 TGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDY 42 (71)
T ss_pred CCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCE
Confidence 345666889999754 68999966 78999974
No 18
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=54.13 E-value=6.5 Score=23.32 Aligned_cols=19 Identities=26% Similarity=0.742 Sum_probs=15.6
Q ss_pred cccccccccccCCCCeeee
Q 028382 114 AHICEICGRSLLDPFRFCS 132 (210)
Q Consensus 114 ~~~C~~C~R~L~d~~~FCS 132 (210)
...|..|+..+.+..+||+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~ 20 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCP 20 (26)
T ss_pred cCCCcccCCcCCcccccCh
Confidence 3578899998888889986
No 19
>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=48.66 E-value=4.6 Score=25.76 Aligned_cols=25 Identities=24% Similarity=0.571 Sum_probs=15.0
Q ss_pred CCcccccccccccCC------------CCeeeeecce
Q 028382 112 GVAHICEICGRSLLD------------PFRFCSLGCK 136 (210)
Q Consensus 112 g~~~~C~~C~R~L~d------------~~~FCSl~CK 136 (210)
.....|..|++.+.. ...|||..|.
T Consensus 4 ~~~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~ 40 (43)
T PF06467_consen 4 LKMKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCL 40 (43)
T ss_dssp -SCEE-TTT--EEECCC----EE-TTTTSCCSSHHHH
T ss_pred CcCCcCcccCCcccCCCccccccccCcccChhCHHHH
Confidence 346789999887742 1379999885
No 20
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=41.06 E-value=7.7 Score=28.37 Aligned_cols=23 Identities=26% Similarity=0.717 Sum_probs=21.1
Q ss_pred cccccccccccCCCCeeeeecce
Q 028382 114 AHICEICGRSLLDPFRFCSLGCK 136 (210)
Q Consensus 114 ~~~C~~C~R~L~d~~~FCSl~CK 136 (210)
..+|.+|+..+...-+|||-.|.
T Consensus 8 H~HC~VCg~aIp~de~~CSe~C~ 30 (64)
T COG4068 8 HRHCVVCGKAIPPDEQVCSEECG 30 (64)
T ss_pred CccccccCCcCCCccchHHHHHH
Confidence 46899999999988899999997
No 21
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=38.93 E-value=23 Score=32.57 Aligned_cols=93 Identities=11% Similarity=0.270 Sum_probs=50.5
Q ss_pred CCccHHHHhcchhhhhccccCC---CCCC----------CCceecccCCCc---cCcCcccCCCCCCCc-eEEEEecccc
Q 028382 9 VPPWLEPMLRTAFFTVCRTHGD---AARS----------ECNMYCLDCNDQ---AFCFYCRSSKHKDHQ-VIQIRRSSYH 71 (210)
Q Consensus 9 ~P~WL~~LL~~~FF~~C~~H~~---~~kn----------E~N~FCldC~~~---~~C~~C~~~~H~~Hr-vlQIRRssY~ 71 (210)
.-|||...++.-+-..--.|.- ...+ -+-++|.+=... .-|+.|.+-....|+ +..|..-.=.
T Consensus 4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~ 83 (328)
T PRK05707 4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEAD 83 (328)
T ss_pred CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCC
Confidence 4799999998766554445532 1111 113455431111 247777544444453 4444332113
Q ss_pred ceeeechhhhhhcccceeEEEECCcEEEEee
Q 028382 72 DVVRVGEIQNIMDISGVQTYVINSARVVFLN 102 (210)
Q Consensus 72 dVVrv~dIqkl~D~S~IQtYvINsakVVfLn 102 (210)
..|+|++|.++++--..=++ .++.|||.|.
T Consensus 84 ~~i~id~iR~l~~~~~~~~~-~~~~kv~iI~ 113 (328)
T PRK05707 84 KTIKVDQVRELVSFVVQTAQ-LGGRKVVLIE 113 (328)
T ss_pred CCCCHHHHHHHHHHHhhccc-cCCCeEEEEC
Confidence 56899999988654443232 3678888884
No 22
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=36.47 E-value=9.6 Score=37.79 Aligned_cols=35 Identities=31% Similarity=0.872 Sum_probs=25.7
Q ss_pred hhccccCCCCCCCCceecccCCCccCcCcccC-CCCCCCc
Q 028382 23 TVCRTHGDAARSECNMYCLDCNDQAFCFYCRS-SKHKDHQ 61 (210)
Q Consensus 23 ~~C~~H~~~~knE~N~FCldC~~~~~C~~C~~-~~H~~Hr 61 (210)
..|..|.... -.|||+.|.. ++|..|+. ..|..|.
T Consensus 224 ~~ct~h~~e~---~smyc~~ck~-pvc~~clee~khs~he 259 (699)
T KOG4367|consen 224 STCTDHELEN---HSMYCVQCKM-PVCYQCLEEGKHSSHE 259 (699)
T ss_pred hhccCCCCCC---ceEEEEecCC-hHHHHHHHhhcccchh
Confidence 4688887633 6799999985 99999942 2466663
No 23
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=35.78 E-value=24 Score=31.98 Aligned_cols=57 Identities=19% Similarity=0.423 Sum_probs=35.7
Q ss_pred CCCccHHHHhcc-hhh-----hhccc---cCCCCCCCCceecccCCCccCcCcccCC--CCCCCceEEEEe
Q 028382 8 LVPPWLEPMLRT-AFF-----TVCRT---HGDAARSECNMYCLDCNDQAFCFYCRSS--KHKDHQVIQIRR 67 (210)
Q Consensus 8 ~~P~WL~~LL~~-~FF-----~~C~~---H~~~~knE~N~FCldC~~~~~C~~C~~~--~H~~HrvlQIRR 67 (210)
..+.||++-+.+ -++ ..|.. |.-.. --.-|..|...-||..|-.. +|..|..|||.+
T Consensus 132 ~~~~~~~~~~~~~H~~~~~~~v~CD~C~~~~IvG---~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR~~t 199 (278)
T KOG4582|consen 132 SLVITLNPVVGEMHPNISKLSVPCDNCGKPGIVG---ARYKCTVCPDYDLCERCEAGNEHHAAHAMLRLHT 199 (278)
T ss_pred hhhhhcCCCccccCCCcccccccCCCccCCcccc---ceeeecCCCccchhHHhhcCCCCCcccceeeccc
Confidence 346666665543 334 34443 33211 22579999877899999433 678899999766
No 24
>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=33.81 E-value=12 Score=23.26 Aligned_cols=22 Identities=36% Similarity=0.969 Sum_probs=13.0
Q ss_pred ccccccccccC-----CCCeeeeecce
Q 028382 115 HICEICGRSLL-----DPFRFCSLGCK 136 (210)
Q Consensus 115 ~~C~~C~R~L~-----d~~~FCSl~CK 136 (210)
..|.+|+..-. -..+||||.|.
T Consensus 3 ~~C~vC~~~~kY~Cp~C~~~~CSl~C~ 29 (30)
T PF04438_consen 3 KLCSVCGNPAKYRCPRCGARYCSLACY 29 (30)
T ss_dssp EEETSSSSEESEE-TTT--EESSHHHH
T ss_pred CCCccCcCCCEEECCCcCCceeCcEeE
Confidence 35777776221 13579999984
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=32.23 E-value=65 Score=22.81 Aligned_cols=32 Identities=13% Similarity=0.352 Sum_probs=22.7
Q ss_pred eeeechhhhh--hcccceeEEEECCcEEEEeecCC
Q 028382 73 VVRVGEIQNI--MDISGVQTYVINSARVVFLNERP 105 (210)
Q Consensus 73 VVrv~dIqkl--~D~S~IQtYvINsakVVfLn~RP 105 (210)
+++++|++.. +++.+|-|.++||..+ +....|
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 5666665554 7999999999988666 554434
No 26
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=28.71 E-value=17 Score=26.08 Aligned_cols=28 Identities=32% Similarity=0.751 Sum_probs=21.1
Q ss_pred CcccccccccccC---CC--C----eeeeecceeCee
Q 028382 113 VAHICEICGRSLL---DP--F----RFCSLGCKLAGI 140 (210)
Q Consensus 113 ~~~~C~~C~R~L~---d~--~----~FCSl~CKv~~~ 140 (210)
.-..|-.|.|.|. |- | -|||..|.-..|
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 3578999999998 32 3 399999985544
No 27
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=26.23 E-value=35 Score=23.27 Aligned_cols=28 Identities=32% Similarity=0.805 Sum_probs=18.9
Q ss_pred eecccCC--CccCcCcccCC--CC-CCCceEEE
Q 028382 38 MYCLDCN--DQAFCFYCRSS--KH-KDHQVIQI 65 (210)
Q Consensus 38 ~FCldC~--~~~~C~~C~~~--~H-~~HrvlQI 65 (210)
.-|++|. .--+|..|... .| .+|+++.|
T Consensus 16 ~~C~~C~~~d~DlC~~C~~~~~~H~~~H~~~~i 48 (48)
T cd02341 16 YHCSECDDGDFDLCQDCVVKGESHQEDHWLVKI 48 (48)
T ss_pred EECCCCCCCCCccCHHHHhCcCCCCCCCceeeC
Confidence 5688887 55799999432 35 56777654
No 28
>PF12773 DZR: Double zinc ribbon
Probab=21.16 E-value=40 Score=22.07 Aligned_cols=12 Identities=42% Similarity=0.910 Sum_probs=6.1
Q ss_pred cccccccccccC
Q 028382 114 AHICEICGRSLL 125 (210)
Q Consensus 114 ~~~C~~C~R~L~ 125 (210)
...|..||..|.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 344555555554
No 29
>smart00746 TRASH metallochaperone-like domain.
Probab=21.08 E-value=49 Score=18.21 Aligned_cols=10 Identities=50% Similarity=0.999 Sum_probs=7.5
Q ss_pred Ceeeeeccee
Q 028382 128 FRFCSLGCKL 137 (210)
Q Consensus 128 ~~FCSl~CKv 137 (210)
+.|||..|..
T Consensus 24 ~~FCs~~c~~ 33 (39)
T smart00746 24 FYFCSSKCLS 33 (39)
T ss_pred EEEeCHHHHH
Confidence 5788888863
Done!