Query 028583
Match_columns 207
No_of_seqs 152 out of 198
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 13:47:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028583.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028583hhsearch_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 1.5E-40 3.3E-45 244.3 6.2 72 60-133 1-72 (72)
2 PF00643 zf-B_box: B-box zinc 96.7 0.00044 9.6E-09 44.5 0.2 38 18-59 5-42 (42)
3 cd00021 BBOX B-Box-type zinc f 95.9 0.006 1.3E-07 38.1 2.2 37 18-58 2-38 (39)
4 smart00336 BBOX B-Box-type zin 94.9 0.023 5E-07 35.8 2.5 36 18-57 5-40 (42)
5 PF03884 DUF329: Domain of unk 89.2 0.039 8.5E-07 39.3 -2.3 29 110-138 2-35 (57)
6 PRK01343 zinc-binding protein; 89.0 0.12 2.6E-06 36.9 -0.0 29 110-138 9-38 (57)
7 COG3024 Uncharacterized protei 87.2 0.17 3.7E-06 37.0 -0.1 30 110-139 7-41 (65)
8 PF12855 Ecl1: Life-span regul 87.0 0.13 2.8E-06 34.7 -0.8 30 109-138 5-37 (43)
9 PRK00418 DNA gyrase inhibitor; 86.5 0.19 4.1E-06 36.5 -0.3 29 110-138 6-39 (62)
10 PF10013 DUF2256: Uncharacteri 77.2 0.72 1.6E-05 31.2 -0.1 23 110-132 8-39 (42)
11 PF02207 zf-UBR: Putative zinc 75.7 1.5 3.2E-05 31.6 1.2 35 28-62 10-48 (71)
12 PF09889 DUF2116: Uncharacteri 70.0 1.2 2.6E-05 31.9 -0.4 25 110-134 3-27 (59)
13 PF13240 zinc_ribbon_2: zinc-r 65.9 2.7 5.9E-05 24.5 0.6 16 113-128 2-17 (23)
14 smart00396 ZnF_UBR1 Putative z 60.8 9.6 0.00021 27.6 2.8 31 26-56 8-42 (71)
15 PF13248 zf-ribbon_3: zinc-rib 58.7 5.1 0.00011 23.7 0.9 19 110-128 2-20 (26)
16 KOG2177 Predicted E3 ubiquitin 54.4 7.7 0.00017 31.4 1.6 39 18-61 88-127 (386)
17 PRK05707 DNA polymerase III su 53.5 11 0.00024 34.5 2.7 95 1-96 2-113 (328)
18 COG4338 Uncharacterized protei 53.1 1.4 3E-05 31.0 -2.6 24 109-132 11-43 (54)
19 cd02340 ZZ_NBR1_like Zinc fing 51.4 9.4 0.0002 25.2 1.4 28 32-59 15-43 (43)
20 PF06467 zf-FCS: MYM-type Zinc 49.5 4.6 9.9E-05 25.7 -0.4 24 109-132 5-40 (43)
21 KOG4367 Predicted Zn-finger pr 42.1 7.7 0.00017 38.3 -0.3 35 17-55 224-259 (699)
22 COG4068 Uncharacterized protei 41.5 8.1 0.00017 28.2 -0.2 23 110-132 8-30 (64)
23 TIGR00412 redox_disulf_2 small 34.1 60 0.0013 22.9 3.4 32 67-99 33-66 (76)
24 KOG4582 Uncharacterized conser 33.6 29 0.00062 31.4 2.0 48 32-102 168-217 (278)
25 PF04438 zf-HIT: HIT zinc fing 32.1 13 0.00028 23.0 -0.3 20 112-132 4-29 (30)
26 PF04570 DUF581: Protein of un 29.6 15 0.00034 26.2 -0.3 29 109-137 15-52 (58)
27 PF08002 DUF1697: Protein of u 26.3 47 0.001 26.8 1.9 30 65-95 16-48 (137)
28 KOG0704 ADP-ribosylation facto 24.8 1.1E+02 0.0024 29.4 4.3 62 1-75 1-74 (386)
29 PF12773 DZR: Double zinc ribb 21.9 38 0.00083 22.1 0.5 12 110-121 12-23 (50)
30 PF05379 Peptidase_C23: Carlav 21.3 1.1E+02 0.0024 23.2 3.0 30 68-97 43-72 (89)
31 cd02341 ZZ_ZZZ3 Zinc finger, Z 20.5 52 0.0011 22.3 1.0 28 32-59 16-48 (48)
32 PRK07993 DNA polymerase III su 20.4 64 0.0014 29.7 1.8 52 42-96 61-115 (334)
33 PF06906 DUF1272: Protein of u 20.4 70 0.0015 23.0 1.6 23 111-133 6-31 (57)
34 PRK08699 DNA polymerase III su 20.2 66 0.0014 29.5 1.8 30 66-96 91-120 (325)
35 smart00105 ArfGap Putative GTP 20.0 32 0.0007 26.6 -0.2 45 30-76 2-59 (112)
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=1.5e-40 Score=244.31 Aligned_cols=72 Identities=67% Similarity=1.139 Sum_probs=70.5
Q ss_pred EeccccceeehhhHHhhhcccceeeEEECCeEEEEeeCCCCCCCCCCCCCCccccccccccCCCCeeeeeccee
Q 028583 60 RRSSYHDVVRVAEIQKALDISEVQTYVINSARVLFLNERPQPKGPVGKGVSHLCEICGRSLLDPFRFCSLGCKL 133 (207)
Q Consensus 60 RRssYhdVVRv~diqkllDiS~IQtYviNsakVVfLn~RPq~r~~~~k~~~~~C~~C~R~L~d~~rFCSl~CKv 133 (207)
|||||||||||+|||||||||+||||+|||+||||||+|||+++ ++++++.|++|+|+|+|+|+||||+|||
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 RRYSYHDVVRVSDIQKLLDCSGIQTYVINSAKVVFLNPRPQSRP--SKGSGNICETCHRSLQDPYRFCSLSCKV 72 (72)
T ss_pred CcccccceEEHHHhHhhccccccEEEEeCCceEEEEccCCcCCC--CCCCCCccCCCCCCCCCCCeEEeeeEEC
Confidence 79999999999999999999999999999999999999999998 8889999999999999999999999996
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=96.70 E-value=0.00044 Score=44.54 Aligned_cols=38 Identities=34% Similarity=0.879 Sum_probs=29.9
Q ss_pred CCcCCCCCCCCCCceeeccCCCCccCCcccCCCCCCCCeeEE
Q 028583 18 ICPRHNDSPRNECNMYCLDCMSGAFCFYCRSSRHKDHPVIQI 59 (207)
Q Consensus 18 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~~~~H~~HrvlQI 59 (207)
.|..|.. .+.++||.+|.. .+|..|....|++|.++.|
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 5888864 238899999985 9999997666999988764
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=95.91 E-value=0.006 Score=38.05 Aligned_cols=37 Identities=22% Similarity=0.602 Sum_probs=28.4
Q ss_pred CCcCCCCCCCCCCceeeccCCCCccCCcccCCCCCCCCeeE
Q 028583 18 ICPRHNDSPRNECNMYCLDCMSGAFCFYCRSSRHKDHPVIQ 58 (207)
Q Consensus 18 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~~~~H~~HrvlQ 58 (207)
.|+.|.. +.-.+||.+|.. .+|..|....|++|.++-
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 4777743 235799999985 999999666699997764
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=94.94 E-value=0.023 Score=35.82 Aligned_cols=36 Identities=28% Similarity=0.834 Sum_probs=28.0
Q ss_pred CCcCCCCCCCCCCceeeccCCCCccCCcccCCCCCCCCee
Q 028583 18 ICPRHNDSPRNECNMYCLDCMSGAFCFYCRSSRHKDHPVI 57 (207)
Q Consensus 18 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~~~~H~~Hrvl 57 (207)
.|..|.. ..-.+||.+|.. .+|..|....|++|.++
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 4777754 235799999995 99999965679999775
No 5
>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=89.25 E-value=0.039 Score=39.28 Aligned_cols=29 Identities=45% Similarity=0.966 Sum_probs=18.0
Q ss_pred CccccccccccCC----CCe-eeeecceecceec
Q 028583 110 SHLCEICGRSLLD----PFR-FCSLGCKLEGIKK 138 (207)
Q Consensus 110 ~~~C~~C~R~L~d----~~r-FCSl~CKv~~~~~ 138 (207)
+..|-+|++...- +|+ |||-.||+..+.+
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 4579999998875 676 9999999876655
No 6
>PRK01343 zinc-binding protein; Provisional
Probab=89.03 E-value=0.12 Score=36.93 Aligned_cols=29 Identities=24% Similarity=0.606 Sum_probs=23.2
Q ss_pred CccccccccccCCCC-eeeeecceecceec
Q 028583 110 SHLCEICGRSLLDPF-RFCSLGCKLEGIKK 138 (207)
Q Consensus 110 ~~~C~~C~R~L~d~~-rFCSl~CKv~~~~~ 138 (207)
...|-+|++.....| -|||-.|+..++.+
T Consensus 9 ~~~CP~C~k~~~~~~rPFCS~RC~~iDLg~ 38 (57)
T PRK01343 9 TRPCPECGKPSTREAYPFCSERCRDIDLNR 38 (57)
T ss_pred CCcCCCCCCcCcCCCCcccCHHHhhhhHHH
Confidence 457999999987665 59999999766554
No 7
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.20 E-value=0.17 Score=37.02 Aligned_cols=30 Identities=40% Similarity=0.883 Sum_probs=23.4
Q ss_pred CccccccccccCC----CCe-eeeecceecceecc
Q 028583 110 SHLCEICGRSLLD----PFR-FCSLGCKLEGIKKN 139 (207)
Q Consensus 110 ~~~C~~C~R~L~d----~~r-FCSl~CKv~~~~~~ 139 (207)
+..|-+|++...- +|| |||-.||+..+.+=
T Consensus 7 ~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDLg~W 41 (65)
T COG3024 7 TVPCPTCGKPVVWGEESPFRPFCSKRCKLIDLGEW 41 (65)
T ss_pred cccCCCCCCcccccccCCcCcchhHhhhhcchhhh
Confidence 4469999998864 665 99999998776653
No 8
>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=87.00 E-value=0.13 Score=34.66 Aligned_cols=30 Identities=27% Similarity=0.688 Sum_probs=24.4
Q ss_pred CCcccccccccc---CCCCeeeeecceecceec
Q 028583 109 VSHLCEICGRSL---LDPFRFCSLGCKLEGIKK 138 (207)
Q Consensus 109 ~~~~C~~C~R~L---~d~~rFCSl~CKv~~~~~ 138 (207)
..+.|.+|+|-+ .+...|||-.|++.....
T Consensus 5 F~~yC~~Cdk~~~~~~~~~lYCSe~Cr~~D~~~ 37 (43)
T PF12855_consen 5 FNDYCIVCDKQIDPPDDGSLYCSEECRLKDQEK 37 (43)
T ss_pred hhhHHHHhhccccCCCCCccccCHHHHhHhhhc
Confidence 356799999999 667899999999865443
No 9
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=86.49 E-value=0.19 Score=36.47 Aligned_cols=29 Identities=38% Similarity=0.890 Sum_probs=22.4
Q ss_pred CccccccccccC---C-CCe-eeeecceecceec
Q 028583 110 SHLCEICGRSLL---D-PFR-FCSLGCKLEGIKK 138 (207)
Q Consensus 110 ~~~C~~C~R~L~---d-~~r-FCSl~CKv~~~~~ 138 (207)
...|-+|++... + +|+ |||-.||+..+.+
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~IDLg~ 39 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQLIDLGE 39 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHHhhhHHH
Confidence 457999999874 3 575 9999999866554
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=77.20 E-value=0.72 Score=31.16 Aligned_cols=23 Identities=39% Similarity=1.138 Sum_probs=19.8
Q ss_pred CccccccccccC---------CCCeeeeecce
Q 028583 110 SHLCEICGRSLL---------DPFRFCSLGCK 132 (207)
Q Consensus 110 ~~~C~~C~R~L~---------d~~rFCSl~CK 132 (207)
..+|.+|+|.+. |...|||-.|.
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 467999999995 56899999996
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=75.65 E-value=1.5 Score=31.56 Aligned_cols=35 Identities=31% Similarity=0.583 Sum_probs=26.4
Q ss_pred CCCceeeccCCC---CccCCcc-cCCCCCCCCeeEEEec
Q 028583 28 NECNMYCLDCMS---GAFCFYC-RSSRHKDHPVIQIRRS 62 (207)
Q Consensus 28 nE~N~FCldC~~---~~~C~~C-~~~~H~~HrvlQIRRs 62 (207)
++--..|++|.. .++|..| ....|.+|+++.++-.
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 356678999976 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=70.05 E-value=1.2 Score=31.87 Aligned_cols=25 Identities=32% Similarity=0.814 Sum_probs=21.7
Q ss_pred CccccccccccCCCCeeeeecceec
Q 028583 110 SHLCEICGRSLLDPFRFCSLGCKLE 134 (207)
Q Consensus 110 ~~~C~~C~R~L~d~~rFCSl~CKv~ 134 (207)
..+|..||..+..+-.|||-.|+=.
T Consensus 3 HkHC~~CG~~Ip~~~~fCS~~C~~~ 27 (59)
T PF09889_consen 3 HKHCPVCGKPIPPDESFCSPKCREE 27 (59)
T ss_pred CCcCCcCCCcCCcchhhhCHHHHHH
Confidence 3579999999998899999999943
No 13
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=65.89 E-value=2.7 Score=24.54 Aligned_cols=16 Identities=38% Similarity=1.024 Sum_probs=14.1
Q ss_pred ccccccccCCCCeeee
Q 028583 113 CEICGRSLLDPFRFCS 128 (207)
Q Consensus 113 C~~C~R~L~d~~rFCS 128 (207)
|..|+..|.|...||+
T Consensus 2 Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCP 17 (23)
T ss_pred CcccCCCCCCcCcchh
Confidence 7889999999889986
No 14
>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=60.77 E-value=9.6 Score=27.64 Aligned_cols=31 Identities=26% Similarity=0.452 Sum_probs=24.1
Q ss_pred CCCCCceeeccCCCC---ccCCcccC-CCCCCCCe
Q 028583 26 PRNECNMYCLDCMSG---AFCFYCRS-SRHKDHPV 56 (207)
Q Consensus 26 ~knE~N~FCldC~~~---~~C~~C~~-~~H~~Hrv 56 (207)
.++|--..|++|... .+|..|.. ..|.+|++
T Consensus 8 ~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~ 42 (71)
T smart00396 8 TGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDY 42 (71)
T ss_pred CCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCE
Confidence 356777889999754 68999976 78999983
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=58.74 E-value=5.1 Score=23.69 Aligned_cols=19 Identities=26% Similarity=0.763 Sum_probs=15.7
Q ss_pred CccccccccccCCCCeeee
Q 028583 110 SHLCEICGRSLLDPFRFCS 128 (207)
Q Consensus 110 ~~~C~~C~R~L~d~~rFCS 128 (207)
...|..|+..+.+..+||+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~ 20 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCP 20 (26)
T ss_pred cCCCcccCCcCCcccccCh
Confidence 3578999998888889996
No 16
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=54.36 E-value=7.7 Score=31.44 Aligned_cols=39 Identities=28% Similarity=0.879 Sum_probs=30.7
Q ss_pred CCcCCCCCCCCCCceeeccCCCCccCCccc-CCCCCCCCeeEEEe
Q 028583 18 ICPRHNDSPRNECNMYCLDCMSGAFCFYCR-SSRHKDHPVIQIRR 61 (207)
Q Consensus 18 ~C~~H~~~~knE~N~FCldC~~~~~C~~C~-~~~H~~HrvlQIRR 61 (207)
.|..|... ..+||..|.. .+|..|. ...|.+|.++.+..
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 6799999984 8999996 77899998877643
No 17
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=53.46 E-value=11 Score=34.49 Aligned_cols=95 Identities=16% Similarity=0.305 Sum_probs=51.8
Q ss_pred CCcChhHHHhhccccccCCcCCCC---CCCC----------CCceeeccCCCC---ccCCcccCCCCCCCC-eeEEEecc
Q 028583 1 MLVPPWLESLLSTSFFTICPRHND---SPRN----------ECNMYCLDCMSG---AFCFYCRSSRHKDHP-VIQIRRSS 63 (207)
Q Consensus 1 m~~P~WL~~LL~~~FF~~C~~H~~---~~kn----------E~N~FCldC~~~---~~C~~C~~~~H~~Hr-vlQIRRss 63 (207)
|..-|||...++.-+-..--.|.- +..+ -+-++|.+=... .-|+.|..-....|+ +..|..-.
T Consensus 2 ~~~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~ 81 (328)
T PRK05707 2 AEIYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEE 81 (328)
T ss_pred CcCCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccC
Confidence 346799999998766555455532 1111 013455421111 247777544444443 44443321
Q ss_pred ccceeehhhHHhhhcccceeeEEECCeEEEEee
Q 028583 64 YHDVVRVAEIQKALDISEVQTYVINSARVLFLN 96 (207)
Q Consensus 64 YhdVVRv~diqkllDiS~IQtYviNsakVVfLn 96 (207)
=...|+|++|..+++--..=++ .++.|||.|.
T Consensus 82 ~~~~i~id~iR~l~~~~~~~~~-~~~~kv~iI~ 113 (328)
T PRK05707 82 ADKTIKVDQVRELVSFVVQTAQ-LGGRKVVLIE 113 (328)
T ss_pred CCCCCCHHHHHHHHHHHhhccc-cCCCeEEEEC
Confidence 1356999999998754443232 3678888884
No 18
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.07 E-value=1.4 Score=31.01 Aligned_cols=24 Identities=29% Similarity=0.942 Sum_probs=20.9
Q ss_pred CCccccccccccC---------CCCeeeeecce
Q 028583 109 VSHLCEICGRSLL---------DPFRFCSLGCK 132 (207)
Q Consensus 109 ~~~~C~~C~R~L~---------d~~rFCSl~CK 132 (207)
...+|++|+|.+. |...|||-.|+
T Consensus 11 p~KICpvCqRPFsWRkKW~~cWDeVKyCSeRCr 43 (54)
T COG4338 11 PDKICPVCQRPFSWRKKWARCWDEVKYCSERCR 43 (54)
T ss_pred chhhhhhhcCchHHHHHHHHHHHHHHHHHHHHH
Confidence 5778999999984 56899999999
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=51.45 E-value=9.4 Score=25.22 Aligned_cols=28 Identities=29% Similarity=0.690 Sum_probs=20.3
Q ss_pred eeeccCCCCccCCccc-CCCCCCCCeeEE
Q 028583 32 MYCLDCMSGAFCFYCR-SSRHKDHPVIQI 59 (207)
Q Consensus 32 ~FCldC~~~~~C~~C~-~~~H~~HrvlQI 59 (207)
.-|+.|..--||..|. ...|..|+.++|
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 5688887567999993 335777877754
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=49.51 E-value=4.6 Score=25.69 Aligned_cols=24 Identities=29% Similarity=0.775 Sum_probs=14.9
Q ss_pred CCccccccccccCC-C-----------Ceeeeecce
Q 028583 109 VSHLCEICGRSLLD-P-----------FRFCSLGCK 132 (207)
Q Consensus 109 ~~~~C~~C~R~L~d-~-----------~rFCSl~CK 132 (207)
....|..|++.+.. + ..|||..|.
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 45689999987743 1 379999885
No 21
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=42.12 E-value=7.7 Score=38.28 Aligned_cols=35 Identities=29% Similarity=0.847 Sum_probs=25.4
Q ss_pred cCCcCCCCCCCCCCceeeccCCCCccCCcccC-CCCCCCC
Q 028583 17 TICPRHNDSPRNECNMYCLDCMSGAFCFYCRS-SRHKDHP 55 (207)
Q Consensus 17 ~~C~~H~~~~knE~N~FCldC~~~~~C~~C~~-~~H~~Hr 55 (207)
..|..|.... -.|||+.|.. ++|..|+. ..|..|.
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 4688887532 5699999986 99999942 2466663
No 22
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=41.55 E-value=8.1 Score=28.15 Aligned_cols=23 Identities=26% Similarity=0.730 Sum_probs=21.0
Q ss_pred CccccccccccCCCCeeeeecce
Q 028583 110 SHLCEICGRSLLDPFRFCSLGCK 132 (207)
Q Consensus 110 ~~~C~~C~R~L~d~~rFCSl~CK 132 (207)
..+|.+|+..+...-+|||-.|.
T Consensus 8 H~HC~VCg~aIp~de~~CSe~C~ 30 (64)
T COG4068 8 HRHCVVCGKAIPPDEQVCSEECG 30 (64)
T ss_pred CccccccCCcCCCccchHHHHHH
Confidence 46899999999998999999997
No 23
>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=34.07 E-value=60 Score=22.93 Aligned_cols=32 Identities=9% Similarity=0.313 Sum_probs=22.4
Q ss_pred eeehhhHHhh--hcccceeeEEECCeEEEEeeCCC
Q 028583 67 VVRVAEIQKA--LDISEVQTYVINSARVLFLNERP 99 (207)
Q Consensus 67 VVRv~diqkl--lDiS~IQtYviNsakVVfLn~RP 99 (207)
+++++|++.. +++.+|-|.++||..+ +....|
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 7999999999988766 554433
No 24
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=33.62 E-value=29 Score=31.42 Aligned_cols=48 Identities=19% Similarity=0.459 Sum_probs=34.9
Q ss_pred eeeccCCCCccCCcccCC--CCCCCCeeEEEeccccceeehhhHHhhhcccceeeEEECCeEEEEeeCCCCCC
Q 028583 32 MYCLDCMSGAFCFYCRSS--RHKDHPVIQIRRSSYHDVVRVAEIQKALDISEVQTYVINSARVLFLNERPQPK 102 (207)
Q Consensus 32 ~FCldC~~~~~C~~C~~~--~H~~HrvlQIRRssYhdVVRv~diqkllDiS~IQtYviNsakVVfLn~RPq~r 102 (207)
.-|+.|...-||..|-.. .|..|..|||.+ +.....+.++++.++-+.
T Consensus 168 yKC~~C~dYDLCe~Ce~~~~~h~~H~~lR~~t-----------------------~~t~~~~~~~~~~p~~~~ 217 (278)
T KOG4582|consen 168 YKCTVCPDYDLCERCEAGNEHHAAHAMLRLHT-----------------------NETPFSGYVMLSSPPNPV 217 (278)
T ss_pred eeecCCCccchhHHhhcCCCCCcccceeeccc-----------------------ccCCCCcceeccCCCCcc
Confidence 679999877899999433 678899999765 555566677776655444
No 25
>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=32.13 E-value=13 Score=22.97 Aligned_cols=20 Identities=45% Similarity=1.127 Sum_probs=12.2
Q ss_pred cccccccccCC------CCeeeeecce
Q 028583 112 LCEICGRSLLD------PFRFCSLGCK 132 (207)
Q Consensus 112 ~C~~C~R~L~d------~~rFCSl~CK 132 (207)
.|.+|+. ... ..+||||.|.
T Consensus 4 ~C~vC~~-~~kY~Cp~C~~~~CSl~C~ 29 (30)
T PF04438_consen 4 LCSVCGN-PAKYRCPRCGARYCSLACY 29 (30)
T ss_dssp EETSSSS-EESEE-TTT--EESSHHHH
T ss_pred CCccCcC-CCEEECCCcCCceeCcEeE
Confidence 4667776 221 3579999984
No 26
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=29.61 E-value=15 Score=26.16 Aligned_cols=29 Identities=34% Similarity=0.785 Sum_probs=21.4
Q ss_pred CCccccccccccC---CC--Ce----eeeecceeccee
Q 028583 109 VSHLCEICGRSLL---DP--FR----FCSLGCKLEGIK 137 (207)
Q Consensus 109 ~~~~C~~C~R~L~---d~--~r----FCSl~CKv~~~~ 137 (207)
.-..|-.|.|.|. |- |+ |||..|.-..|.
T Consensus 15 FL~~C~~C~k~L~~~~DiymYrGd~aFCS~ECR~~qi~ 52 (58)
T PF04570_consen 15 FLSFCYLCKKKLDPGKDIYMYRGDKAFCSEECRSQQIL 52 (58)
T ss_pred HHHHHHccCCCCCCCCCeeeeccccccccHHHHHHHHH
Confidence 4567999999998 32 33 999999854443
No 27
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=26.33 E-value=47 Score=26.76 Aligned_cols=30 Identities=33% Similarity=0.681 Sum_probs=20.7
Q ss_pred cceeehhhHHhh---hcccceeeEEECCeEEEEe
Q 028583 65 HDVVRVAEIQKA---LDISEVQTYVINSARVLFL 95 (207)
Q Consensus 65 hdVVRv~diqkl---lDiS~IQtYviNsakVVfL 95 (207)
++-|+..|+..+ +-..+|+||+ +|.-|||-
T Consensus 16 ~nki~MaeLr~~l~~~Gf~~V~Tyi-~SGNvvf~ 48 (137)
T PF08002_consen 16 KNKIKMAELREALEDLGFTNVRTYI-QSGNVVFE 48 (137)
T ss_dssp BS---HHHHHHHHHHCT-EEEEEET-TTTEEEEE
T ss_pred CCcccHHHHHHHHHHcCCCCceEEE-eeCCEEEe
Confidence 455777888776 6788999995 78888887
No 28
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=24.76 E-value=1.1e+02 Score=29.38 Aligned_cols=62 Identities=27% Similarity=0.433 Sum_probs=43.2
Q ss_pred CCcChhHHHhhccccccCCcCCCCCCCCCCceeeccCCCC-----------ccCCcccCCCCCC-CCeeEEEecccccee
Q 028583 1 MLVPPWLESLLSTSFFTICPRHNDSPRNECNMYCLDCMSG-----------AFCFYCRSSRHKD-HPVIQIRRSSYHDVV 68 (207)
Q Consensus 1 m~~P~WL~~LL~~~FF~~C~~H~~~~knE~N~FCldC~~~-----------~~C~~C~~~~H~~-HrvlQIRRssYhdVV 68 (207)
|.-|.=++.|++-+ +-.-|-+|+||... -+|-.| ..-|++ .-.|=..|++=.|--
T Consensus 1 masprtrr~L~~lk------------p~deNk~CfeC~a~NPQWvSvsyGIfICLEC-SG~HRgLGVhiSFVRSVTMD~w 67 (386)
T KOG0704|consen 1 MASPRTRRVLLELK------------PQDENKKCFECGAPNPQWVSVSYGIFICLEC-SGKHRGLGVHISFVRSVTMDKW 67 (386)
T ss_pred CCChHHHHHHHhcC------------ccccCCceeecCCCCCCeEeecccEEEEEec-CCcccccceeeEEEEeeecccc
Confidence 55666777777632 22468899999652 379999 888887 345677788888877
Q ss_pred ehhhHHh
Q 028583 69 RVAEIQK 75 (207)
Q Consensus 69 Rv~diqk 75 (207)
+-.||.|
T Consensus 68 keiel~k 74 (386)
T KOG0704|consen 68 KEIELKK 74 (386)
T ss_pred cHHHHHH
Confidence 6666644
No 29
>PF12773 DZR: Double zinc ribbon
Probab=21.88 E-value=38 Score=22.08 Aligned_cols=12 Identities=33% Similarity=0.902 Sum_probs=6.0
Q ss_pred CccccccccccC
Q 028583 110 SHLCEICGRSLL 121 (207)
Q Consensus 110 ~~~C~~C~R~L~ 121 (207)
...|..|+..|.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 344555555554
No 30
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=21.32 E-value=1.1e+02 Score=23.20 Aligned_cols=30 Identities=13% Similarity=0.327 Sum_probs=25.4
Q ss_pred eehhhHHhhhcccceeeEEECCeEEEEeeC
Q 028583 68 VRVAEIQKALDISEVQTYVINSARVLFLNE 97 (207)
Q Consensus 68 VRv~diqkllDiS~IQtYviNsakVVfLn~ 97 (207)
|-+.+++.++.+-+|+.++.-+.+.+-||+
T Consensus 43 l~l~~le~~f~~F~I~A~v~~~g~~~~lN~ 72 (89)
T PF05379_consen 43 LDLEDLEELFELFDICAHVNFGGETFVLNE 72 (89)
T ss_pred cCHHHHHHHHHHcCeEEEEEECCEEEEECC
Confidence 678899999999999999986667777774
No 31
>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=20.53 E-value=52 Score=22.34 Aligned_cols=28 Identities=29% Similarity=0.631 Sum_probs=18.9
Q ss_pred eeeccCC--CCccCCcccCC--CC-CCCCeeEE
Q 028583 32 MYCLDCM--SGAFCFYCRSS--RH-KDHPVIQI 59 (207)
Q Consensus 32 ~FCldC~--~~~~C~~C~~~--~H-~~HrvlQI 59 (207)
.-|++|. .--+|..|... .| .+|+++.|
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 32
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=20.44 E-value=64 Score=29.65 Aligned_cols=52 Identities=15% Similarity=0.282 Sum_probs=31.7
Q ss_pred cCCcccC---CCCCCCCeeEEEeccccceeehhhHHhhhcccceeeEEECCeEEEEee
Q 028583 42 FCFYCRS---SRHKDHPVIQIRRSSYHDVVRVAEIQKALDISEVQTYVINSARVLFLN 96 (207)
Q Consensus 42 ~C~~C~~---~~H~~HrvlQIRRssYhdVVRv~diqkllDiS~IQtYviNsakVVfLn 96 (207)
.|+.|.. ..|+| +..|..-.....|+|++|..+.+--..-+|. ++.|||+|.
T Consensus 61 ~C~sC~~~~~g~HPD--~~~i~p~~~~~~I~idqiR~l~~~~~~~~~~-g~~kV~iI~ 115 (334)
T PRK07993 61 HCRGCQLMQAGTHPD--YYTLTPEKGKSSLGVDAVREVTEKLYEHARL-GGAKVVWLP 115 (334)
T ss_pred CCHHHHHHHcCCCCC--EEEEecccccccCCHHHHHHHHHHHhhcccc-CCceEEEEc
Confidence 5888854 34555 3333222223569999999987654444432 678888885
No 33
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=20.43 E-value=70 Score=22.97 Aligned_cols=23 Identities=30% Similarity=0.746 Sum_probs=18.9
Q ss_pred ccccccccccCC-C--Ceeeeeccee
Q 028583 111 HLCEICGRSLLD-P--FRFCSLGCKL 133 (207)
Q Consensus 111 ~~C~~C~R~L~d-~--~rFCSl~CKv 133 (207)
..||.|++.|.- + .+-||..|-+
T Consensus 6 pnCE~C~~dLp~~s~~A~ICSfECTF 31 (57)
T PF06906_consen 6 PNCECCDKDLPPDSPEAYICSFECTF 31 (57)
T ss_pred CCccccCCCCCCCCCcceEEeEeCcc
Confidence 469999999974 3 6889999975
No 34
>PRK08699 DNA polymerase III subunit delta'; Validated
Probab=20.20 E-value=66 Score=29.47 Aligned_cols=30 Identities=10% Similarity=0.288 Sum_probs=22.2
Q ss_pred ceeehhhHHhhhcccceeeEEECCeEEEEee
Q 028583 66 DVVRVAEIQKALDISEVQTYVINSARVLFLN 96 (207)
Q Consensus 66 dVVRv~diqkllDiS~IQtYviNsakVVfLn 96 (207)
..|+|++|..+.+....=+|. ++.|||++.
T Consensus 91 ~~I~id~iR~l~~~~~~~p~~-~~~kV~iiE 120 (325)
T PRK08699 91 LQIKIDAVREIIDNVYLTSVR-GGLRVILIH 120 (325)
T ss_pred CCcCHHHHHHHHHHHhhCccc-CCceEEEEe
Confidence 368999999987766553443 788899884
No 35
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=20.04 E-value=32 Score=26.63 Aligned_cols=45 Identities=27% Similarity=0.429 Sum_probs=29.3
Q ss_pred CceeeccCCCC-----------ccCCcccCCCCCCC--CeeEEEeccccceeehhhHHhh
Q 028583 30 CNMYCLDCMSG-----------AFCFYCRSSRHKDH--PVIQIRRSSYHDVVRVAEIQKA 76 (207)
Q Consensus 30 ~N~FCldC~~~-----------~~C~~C~~~~H~~H--rvlQIRRssYhdVVRv~diqkl 76 (207)
-|..|.||... -+|..| ...|+.. ++-. .|+.-.|...-+||+.+
T Consensus 2 ~N~~CaDC~~~~p~w~s~~~GifvC~~C-sgiHR~lg~his~-VkSl~md~w~~~~i~~~ 59 (112)
T smart00105 2 GNKKCFDCGAPNPTWASVNLGVFLCIEC-SGIHRSLGVHISK-VRSLTLDTWTEEELRLL 59 (112)
T ss_pred CCCcccCCCCCCCCcEEeccceeEhHHh-HHHHHhcCCCcCe-eeecccCCCCHHHHHHH
Confidence 47889999642 368888 7777763 2323 45666677777777544
Done!