Query 026591
Match_columns 236
No_of_seqs 129 out of 190
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 10:00:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026591.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026591hhsearch_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 4.6E-38 1E-42 235.6 5.3 71 62-132 1-72 (72)
2 PF00643 zf-B_box: B-box zinc 96.6 0.00065 1.4E-08 44.6 0.5 37 22-61 5-42 (42)
3 cd00021 BBOX B-Box-type zinc f 94.9 0.019 4.1E-07 36.5 1.9 36 22-60 2-38 (39)
4 smart00336 BBOX B-Box-type zin 94.1 0.04 8.7E-07 35.4 2.2 35 22-59 5-40 (42)
5 PF12855 Ecl1: Life-span regul 86.6 0.14 3.1E-06 35.2 -0.8 28 109-136 6-36 (43)
6 PF03884 DUF329: Domain of unk 75.3 0.56 1.2E-05 34.1 -1.1 27 110-136 3-34 (57)
7 PRK00418 DNA gyrase inhibitor; 74.0 1.4 3E-05 32.7 0.7 28 109-136 6-38 (62)
8 COG3024 Uncharacterized protei 73.2 1 2.3E-05 33.7 -0.1 29 109-137 7-40 (65)
9 PRK01343 zinc-binding protein; 63.1 2.9 6.4E-05 30.5 0.5 28 109-136 9-37 (57)
10 PF10013 DUF2256: Uncharacteri 61.8 2.7 5.8E-05 29.1 0.0 23 109-131 8-39 (42)
11 PF09889 DUF2116: Uncharacteri 60.9 2.7 5.8E-05 30.8 -0.1 31 110-140 4-34 (59)
12 PF13240 zinc_ribbon_2: zinc-r 59.4 4.5 9.8E-05 24.1 0.7 17 111-127 1-17 (23)
13 PF02207 zf-UBR: Putative zinc 52.9 7.4 0.00016 28.5 1.1 32 32-63 10-47 (71)
14 PF01412 ArfGap: Putative GTPa 50.2 2.4 5.3E-05 33.8 -2.0 49 32-81 10-72 (116)
15 KOG2177 Predicted E3 ubiquitin 50.0 9.2 0.0002 31.6 1.4 38 22-63 88-127 (386)
16 KOG4367 Predicted Zn-finger pr 46.3 6.8 0.00015 39.4 0.1 35 20-57 223-259 (699)
17 PF13248 zf-ribbon_3: zinc-rib 45.5 12 0.00025 22.7 1.0 18 110-127 3-20 (26)
18 cd02340 ZZ_NBR1_like Zinc fing 38.1 15 0.00033 24.8 0.8 27 35-61 14-43 (43)
19 PF06467 zf-FCS: MYM-type Zinc 35.5 9.3 0.0002 24.8 -0.6 23 109-131 6-40 (43)
20 COG4068 Uncharacterized protei 34.0 13 0.00028 27.7 -0.1 23 109-131 8-30 (64)
21 COG4338 Uncharacterized protei 32.6 4 8.6E-05 29.3 -2.9 24 108-131 11-43 (54)
22 KOG0703 Predicted GTPase-activ 31.2 14 0.0003 34.8 -0.4 49 34-83 24-86 (287)
23 smart00105 ArfGap Putative GTP 29.3 8.7 0.00019 30.5 -1.8 42 34-76 2-57 (112)
24 smart00396 ZnF_UBR1 Putative z 26.9 61 0.0013 24.0 2.5 29 30-58 8-42 (71)
25 PF04438 zf-HIT: HIT zinc fing 22.7 26 0.00057 22.1 -0.2 20 111-131 4-29 (30)
26 PF12156 ATPase-cat_bd: Putati 22.4 14 0.00031 28.4 -1.7 36 111-146 2-48 (88)
27 PLN00209 ribosomal protein S27 21.6 91 0.002 24.7 2.6 58 53-132 21-85 (86)
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=4.6e-38 Score=235.57 Aligned_cols=71 Identities=63% Similarity=1.165 Sum_probs=69.9
Q ss_pred EeccccceeeecccccccccCCccceEECCceEEEeecCCCCCC-CCCCCcccccccccCCCceeeeeeccc
Q 026591 62 RRYVYQDVIRLDDAAKLVDCDYVQPYINNGAKVIFLNQRPQSRT-RSSGNICSTCDRSLQDSYLFCCLSCKI 132 (236)
Q Consensus 62 RR~sY~dVVRv~DIqkl~D~S~IQtY~INsakVVFLn~RPq~r~-kg~~~~C~~C~R~L~d~~~FCSL~CKv 132 (236)
|||+||||||++||||+||||+||||+||++||||||+|||+++ |+.++.|++|+|+|+|+|+||||+|||
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 79999999999999999999999999999999999999999999 999999999999999999999999997
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=0.00065 Score=44.64 Aligned_cols=37 Identities=32% Similarity=0.815 Sum_probs=29.8
Q ss_pred cCccCCCCCCCCCceeecccccccCCccccC-CCCCceeEE
Q 026591 22 GCIIHEEERKNEKNIYCLDCCTSLCPHCLSL-HGSHRLLQI 61 (236)
Q Consensus 22 ~C~~H~~~~knE~N~FCldC~~s~C~~C~~~-H~~HrvlQI 61 (236)
.|..|.. .+.++||.+|...+|..|... |.+|.++.|
T Consensus 5 ~C~~H~~---~~~~~~C~~C~~~~C~~C~~~~H~~H~~~~i 42 (42)
T PF00643_consen 5 KCPEHPE---EPLSLFCEDCNEPLCSECTVSGHKGHKIVPI 42 (42)
T ss_dssp B-SSTTT---SBEEEEETTTTEEEEHHHHHTSTTTSEEEEC
T ss_pred cCccCCc---cceEEEecCCCCccCccCCCCCCCCCEEeEC
Confidence 5888874 347999999999999999865 999987754
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=94.87 E-value=0.019 Score=36.48 Aligned_cols=36 Identities=28% Similarity=0.524 Sum_probs=28.0
Q ss_pred cCccCCCCCCCCCceeecccccccCCcccc-CCCCCceeE
Q 026591 22 GCIIHEEERKNEKNIYCLDCCTSLCPHCLS-LHGSHRLLQ 60 (236)
Q Consensus 22 ~C~~H~~~~knE~N~FCldC~~s~C~~C~~-~H~~HrvlQ 60 (236)
.|+.|.. +.-.+||.+|...+|..|.. .|++|.++.
T Consensus 2 ~C~~H~~---~~~~~fC~~~~~~iC~~C~~~~H~~H~~~~ 38 (39)
T cd00021 2 LCDEHGE---EPLSLFCETDRALLCVDCDLSVHSGHRRVP 38 (39)
T ss_pred CCCccCC---cceEEEeCccChhhhhhcChhhcCCCCEee
Confidence 4777753 23589999999999999964 588887654
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=94.13 E-value=0.04 Score=35.42 Aligned_cols=35 Identities=26% Similarity=0.712 Sum_probs=27.8
Q ss_pred cCccCCCCCCCCCceeecccccccCCccccC-CCCCcee
Q 026591 22 GCIIHEEERKNEKNIYCLDCCTSLCPHCLSL-HGSHRLL 59 (236)
Q Consensus 22 ~C~~H~~~~knE~N~FCldC~~s~C~~C~~~-H~~Hrvl 59 (236)
.|+.|.. ..-.+||-+|...+|..|... |++|+++
T Consensus 5 ~C~~h~~---~~~~~~C~~c~~~iC~~C~~~~H~~H~~~ 40 (42)
T smart00336 5 KCDSHGD---EPAEFFCEECGALLCRTCDEAEHRGHTVV 40 (42)
T ss_pred cCCCCCC---CceEEECCCCCcccccccChhhcCCCcee
Confidence 4777764 235899999999999999754 8889765
No 5
>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=86.56 E-value=0.14 Score=35.20 Aligned_cols=28 Identities=25% Similarity=0.787 Sum_probs=23.8
Q ss_pred CCccccccccc---CCCceeeeeecccceEE
Q 026591 109 GNICSTCDRSL---QDSYLFCCLSCKIDYLI 136 (236)
Q Consensus 109 ~~~C~~C~R~L---~d~~~FCSL~CKv~~v~ 136 (236)
.+.|.+|+|.+ .+...|||-.|++....
T Consensus 6 ~~yC~~Cdk~~~~~~~~~lYCSe~Cr~~D~~ 36 (43)
T PF12855_consen 6 NDYCIVCDKQIDPPDDGSLYCSEECRLKDQE 36 (43)
T ss_pred hhHHHHhhccccCCCCCccccCHHHHhHhhh
Confidence 35799999999 67899999999997644
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=75.29 E-value=0.56 Score=34.14 Aligned_cols=27 Identities=26% Similarity=0.609 Sum_probs=17.0
Q ss_pred CcccccccccCC----Cce-eeeeecccceEE
Q 026591 110 NICSTCDRSLQD----SYL-FCCLSCKIDYLI 136 (236)
Q Consensus 110 ~~C~~C~R~L~d----~~~-FCSL~CKv~~v~ 136 (236)
..|-+|++...- +|+ |||-.||+-.+.
T Consensus 3 v~CP~C~k~~~~~~~n~~rPFCS~RCk~iDLg 34 (57)
T PF03884_consen 3 VKCPICGKPVEWSPENPFRPFCSERCKLIDLG 34 (57)
T ss_dssp EE-TTT--EEE-SSSSS--SSSSHHHHHHHHS
T ss_pred ccCCCCCCeecccCCCCcCCcccHhhcccCHH
Confidence 468999998885 665 999999987543
No 7
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=74.03 E-value=1.4 Score=32.66 Aligned_cols=28 Identities=25% Similarity=0.657 Sum_probs=21.5
Q ss_pred CCcccccccccC----CCc-eeeeeecccceEE
Q 026591 109 GNICSTCDRSLQ----DSY-LFCCLSCKIDYLI 136 (236)
Q Consensus 109 ~~~C~~C~R~L~----d~~-~FCSL~CKv~~v~ 136 (236)
...|-+|++... .+| -|||-.||+-.+.
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~IDLg 38 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQLIDLG 38 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHHhhhHH
Confidence 457999999874 356 5999999987543
No 8
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=73.23 E-value=1 Score=33.70 Aligned_cols=29 Identities=28% Similarity=0.559 Sum_probs=22.5
Q ss_pred CCcccccccccCC----Cc-eeeeeecccceEEe
Q 026591 109 GNICSTCDRSLQD----SY-LFCCLSCKIDYLIR 137 (236)
Q Consensus 109 ~~~C~~C~R~L~d----~~-~FCSL~CKv~~v~~ 137 (236)
+..|-+|++...= +| -|||-.||+-.+.+
T Consensus 7 ~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDLg~ 40 (65)
T COG3024 7 TVPCPTCGKPVVWGEESPFRPFCSKRCKLIDLGE 40 (65)
T ss_pred cccCCCCCCcccccccCCcCcchhHhhhhcchhh
Confidence 4579999998874 55 59999999976543
No 9
>PRK01343 zinc-binding protein; Provisional
Probab=63.14 E-value=2.9 Score=30.52 Aligned_cols=28 Identities=21% Similarity=0.442 Sum_probs=22.3
Q ss_pred CCcccccccccCCCc-eeeeeecccceEE
Q 026591 109 GNICSTCDRSLQDSY-LFCCLSCKIDYLI 136 (236)
Q Consensus 109 ~~~C~~C~R~L~d~~-~FCSL~CKv~~v~ 136 (236)
...|-+|++....++ -|||-.||.-.+.
T Consensus 9 ~~~CP~C~k~~~~~~rPFCS~RC~~iDLg 37 (57)
T PRK01343 9 TRPCPECGKPSTREAYPFCSERCRDIDLN 37 (57)
T ss_pred CCcCCCCCCcCcCCCCcccCHHHhhhhHH
Confidence 468999999877654 7999999986533
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=61.80 E-value=2.7 Score=29.09 Aligned_cols=23 Identities=30% Similarity=0.930 Sum_probs=19.7
Q ss_pred CCcccccccccC---------CCceeeeeecc
Q 026591 109 GNICSTCDRSLQ---------DSYLFCCLSCK 131 (236)
Q Consensus 109 ~~~C~~C~R~L~---------d~~~FCSL~CK 131 (236)
..+|.+|+|... |.-.|||-.|.
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 458999999988 46899999996
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=60.95 E-value=2.7 Score=30.78 Aligned_cols=31 Identities=23% Similarity=0.644 Sum_probs=26.3
Q ss_pred CcccccccccCCCceeeeeecccceEEeccC
Q 026591 110 NICSTCDRSLQDSYLFCCLSCKIDYLIRIEG 140 (236)
Q Consensus 110 ~~C~~C~R~L~d~~~FCSL~CKv~~v~~~~~ 140 (236)
.+|..||..+..+-.|||-.|+-+...++.+
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCREEYRKRQKR 34 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHHHHHHHHHH
Confidence 5899999999999999999999887665543
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=59.38 E-value=4.5 Score=24.13 Aligned_cols=17 Identities=29% Similarity=0.856 Sum_probs=14.6
Q ss_pred cccccccccCCCceeee
Q 026591 111 ICSTCDRSLQDSYLFCC 127 (236)
Q Consensus 111 ~C~~C~R~L~d~~~FCS 127 (236)
.|..|+..+.+...||+
T Consensus 1 ~Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCP 17 (23)
T ss_pred CCcccCCCCCCcCcchh
Confidence 37889999999999986
No 13
>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=52.91 E-value=7.4 Score=28.54 Aligned_cols=32 Identities=28% Similarity=0.693 Sum_probs=24.3
Q ss_pred CCCceeeccccc----ccCCcc-cc-CCCCCceeEEEe
Q 026591 32 NEKNIYCLDCCT----SLCPHC-LS-LHGSHRLLQIRR 63 (236)
Q Consensus 32 nE~N~FCldC~~----s~C~~C-~~-~H~~HrvlQIRR 63 (236)
++--..|++|.. .+|..| .. .|.+|++..++-
T Consensus 10 ~q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~ 47 (71)
T PF02207_consen 10 GQIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRS 47 (71)
T ss_dssp T-EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE-
T ss_pred CCEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEe
Confidence 466788999985 599999 54 599999887754
No 14
>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=50.18 E-value=2.4 Score=33.79 Aligned_cols=49 Identities=20% Similarity=0.470 Sum_probs=29.7
Q ss_pred CCCceeeccccc------------ccCCccccCCCC--CceeEEEeccccceeeeccccccccc
Q 026591 32 NEKNIYCLDCCT------------SLCPHCLSLHGS--HRLLQIRRYVYQDVIRLDDAAKLVDC 81 (236)
Q Consensus 32 nE~N~FCldC~~------------s~C~~C~~~H~~--HrvlQIRR~sY~dVVRv~DIqkl~D~ 81 (236)
...|..|.||.+ -+|..|...|+. .++-+| |+.-.|-+..+||+.+...
T Consensus 10 ~~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR~lg~~is~V-kSi~~d~w~~~ev~~~~~~ 72 (116)
T PF01412_consen 10 KPGNKVCADCGAPNPTWASLNYGIFLCLECAGIHRSLGVHISRV-KSITMDNWSPEEVQRMREG 72 (116)
T ss_dssp STTCTB-TTT-SBS--EEETTTTEEE-HHHHHHHHHHTTTT--E-EETTTS---HHHHHHHHHS
T ss_pred CcCcCcCCCCCCCCCCEEEeecChhhhHHHHHHHHHhcccchhc-cccccCCCCHHHHHHHHHH
Confidence 346999999963 189999888874 345555 7777888888888776544
No 15
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.97 E-value=9.2 Score=31.62 Aligned_cols=38 Identities=29% Similarity=0.552 Sum_probs=30.3
Q ss_pred cCccCCCCCCCCCceeecccccccCCccc--cCCCCCceeEEEe
Q 026591 22 GCIIHEEERKNEKNIYCLDCCTSLCPHCL--SLHGSHRLLQIRR 63 (236)
Q Consensus 22 ~C~~H~~~~knE~N~FCldC~~s~C~~C~--~~H~~HrvlQIRR 63 (236)
.|..|... ..+||..|...+|..|. ..|..|+++.+..
T Consensus 88 ~c~~~~~~----~~~~c~~~~~~~c~~c~~~~~h~~h~~~~~~~ 127 (386)
T KOG2177|consen 88 LCEKHGEE----LKLFCEEDEKLLCVLCRESGEHRGHPVLPLEE 127 (386)
T ss_pred hhhhcCCc----ceEEecccccccCCCCCCcccccCCccccHHH
Confidence 56766543 68999999999999996 4699998877753
No 16
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=46.29 E-value=6.8 Score=39.43 Aligned_cols=35 Identities=37% Similarity=0.877 Sum_probs=27.8
Q ss_pred cccCccCCCCCCCCCceeecccccccCCccccC--CCCCc
Q 026591 20 FNGCIIHEEERKNEKNIYCLDCCTSLCPHCLSL--HGSHR 57 (236)
Q Consensus 20 F~~C~~H~~~~knE~N~FCldC~~s~C~~C~~~--H~~Hr 57 (236)
-..|..|+.. ...|||+.|.-.+|..|+.+ |..|.
T Consensus 223 ~~~ct~h~~e---~~smyc~~ck~pvc~~clee~khs~he 259 (699)
T KOG4367|consen 223 VSTCTDHELE---NHSMYCVQCKMPVCYQCLEEGKHSSHE 259 (699)
T ss_pred hhhccCCCCC---CceEEEEecCChHHHHHHHhhcccchh
Confidence 3468888753 25799999999999999975 77774
No 17
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=45.47 E-value=12 Score=22.67 Aligned_cols=18 Identities=22% Similarity=0.685 Sum_probs=15.3
Q ss_pred CcccccccccCCCceeee
Q 026591 110 NICSTCDRSLQDSYLFCC 127 (236)
Q Consensus 110 ~~C~~C~R~L~d~~~FCS 127 (236)
..|..|+..+.+.++||+
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~ 20 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCP 20 (26)
T ss_pred CCCcccCCcCCcccccCh
Confidence 478899998888899996
No 18
>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=38.13 E-value=15 Score=24.77 Aligned_cols=27 Identities=37% Similarity=0.835 Sum_probs=19.5
Q ss_pred ceeeccccc-ccCCcccc--CCCCCceeEE
Q 026591 35 NIYCLDCCT-SLCPHCLS--LHGSHRLLQI 61 (236)
Q Consensus 35 N~FCldC~~-s~C~~C~~--~H~~HrvlQI 61 (236)
-.-|+.|.. .+|..|.. .|..|+.++|
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 356788865 79999954 4878887754
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=35.47 E-value=9.3 Score=24.76 Aligned_cols=23 Identities=30% Similarity=0.745 Sum_probs=14.0
Q ss_pred CCcccccccccCC-C-----------ceeeeeecc
Q 026591 109 GNICSTCDRSLQD-S-----------YLFCCLSCK 131 (236)
Q Consensus 109 ~~~C~~C~R~L~d-~-----------~~FCSL~CK 131 (236)
...|..|++.+.. + ..|||..|.
T Consensus 6 ~~~C~~C~~~~~~~~~~~~~~~~g~~~~FCS~~C~ 40 (43)
T PF06467_consen 6 MKTCSYCKKYIPNKPTMIEVQYDGKMKQFCSQSCL 40 (43)
T ss_dssp CEE-TTT--EEECCC----EE-TTTTSCCSSHHHH
T ss_pred CCcCcccCCcccCCCccccccccCcccChhCHHHH
Confidence 4678888877743 2 379999885
No 20
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=34.05 E-value=13 Score=27.71 Aligned_cols=23 Identities=17% Similarity=0.583 Sum_probs=21.1
Q ss_pred CCcccccccccCCCceeeeeecc
Q 026591 109 GNICSTCDRSLQDSYLFCCLSCK 131 (236)
Q Consensus 109 ~~~C~~C~R~L~d~~~FCSL~CK 131 (236)
..+|..|+..+...-+|||-.|.
T Consensus 8 H~HC~VCg~aIp~de~~CSe~C~ 30 (64)
T COG4068 8 HRHCVVCGKAIPPDEQVCSEECG 30 (64)
T ss_pred CccccccCCcCCCccchHHHHHH
Confidence 35899999999999999999998
No 21
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.65 E-value=4 Score=29.35 Aligned_cols=24 Identities=29% Similarity=0.923 Sum_probs=20.5
Q ss_pred CCCcccccccccC---------CCceeeeeecc
Q 026591 108 SGNICSTCDRSLQ---------DSYLFCCLSCK 131 (236)
Q Consensus 108 ~~~~C~~C~R~L~---------d~~~FCSL~CK 131 (236)
...+|+.|+|... |...|||-.|+
T Consensus 11 p~KICpvCqRPFsWRkKW~~cWDeVKyCSeRCr 43 (54)
T COG4338 11 PDKICPVCQRPFSWRKKWARCWDEVKYCSERCR 43 (54)
T ss_pred chhhhhhhcCchHHHHHHHHHHHHHHHHHHHHH
Confidence 4579999999887 46789999998
No 22
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=31.20 E-value=14 Score=34.79 Aligned_cols=49 Identities=20% Similarity=0.445 Sum_probs=37.2
Q ss_pred Cceeecccccc------------cCCccccCCCC--CceeEEEeccccceeeecccccccccCC
Q 026591 34 KNIYCLDCCTS------------LCPHCLSLHGS--HRLLQIRRYVYQDVIRLDDAAKLVDCDY 83 (236)
Q Consensus 34 ~N~FCldC~~s------------~C~~C~~~H~~--HrvlQIRR~sY~dVVRv~DIqkl~D~S~ 83 (236)
-|.+|.||.+. +|-.|..-|+. -+|-+| +++-.|-+.-++|+.++.+-+
T Consensus 24 ~N~~CADC~a~~P~WaSwnlGvFiC~~C~giHR~lg~hiSkV-kSv~LD~W~~eqv~~m~~~GN 86 (287)
T KOG0703|consen 24 DNKVCADCGAKGPRWASWNLGVFICLRCAGIHRSLGVHISKV-KSVTLDEWTDEQVDFMISMGN 86 (287)
T ss_pred ccCcccccCCCCCCeEEeecCeEEEeecccccccccchhhee-eeeeccccCHHHHHHHHHHcc
Confidence 39999999531 89999999985 467777 677788888788877765543
No 23
>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=29.30 E-value=8.7 Score=30.47 Aligned_cols=42 Identities=26% Similarity=0.548 Sum_probs=27.3
Q ss_pred Cceeecccccc------------cCCccccCCCCC--ceeEEEeccccceeeecccc
Q 026591 34 KNIYCLDCCTS------------LCPHCLSLHGSH--RLLQIRRYVYQDVIRLDDAA 76 (236)
Q Consensus 34 ~N~FCldC~~s------------~C~~C~~~H~~H--rvlQIRR~sY~dVVRv~DIq 76 (236)
-|..|.||... +|..|..-|+.. ++-.| |+.-.|.+..++|+
T Consensus 2 ~N~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR~lg~his~V-kSl~md~w~~~~i~ 57 (112)
T smart00105 2 GNKKCFDCGAPNPTWASVNLGVFLCIECSGIHRSLGVHISKV-RSLTLDTWTEEELR 57 (112)
T ss_pred CCCcccCCCCCCCCcEEeccceeEhHHhHHHHHhcCCCcCee-eecccCCCCHHHHH
Confidence 38899999641 799998888863 33334 45555655555553
No 24
>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=26.92 E-value=61 Score=23.95 Aligned_cols=29 Identities=28% Similarity=0.591 Sum_probs=22.5
Q ss_pred CCCCCceeeccccc----ccCCcccc--CCCCCce
Q 026591 30 RKNEKNIYCLDCCT----SLCPHCLS--LHGSHRL 58 (236)
Q Consensus 30 ~knE~N~FCldC~~----s~C~~C~~--~H~~Hrv 58 (236)
.++|--..|++|.. .+|..|.. .|.+|++
T Consensus 8 ~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~ 42 (71)
T smart00396 8 TGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDY 42 (71)
T ss_pred CCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCE
Confidence 45667788999974 58999966 5999983
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=22.70 E-value=26 Score=22.13 Aligned_cols=20 Identities=30% Similarity=0.893 Sum_probs=12.1
Q ss_pred cccccccccCC------Cceeeeeecc
Q 026591 111 ICSTCDRSLQD------SYLFCCLSCK 131 (236)
Q Consensus 111 ~C~~C~R~L~d------~~~FCSL~CK 131 (236)
.|.+|+. ... ..+||||.|.
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 5666766 221 3579999884
No 26
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=22.39 E-value=14 Score=28.37 Aligned_cols=36 Identities=28% Similarity=0.780 Sum_probs=26.9
Q ss_pred cccccccccCC-----------CceeeeeecccceEEeccCCccccc
Q 026591 111 ICSTCDRSLQD-----------SYLFCCLSCKIDYLIRIEGGLSKFF 146 (236)
Q Consensus 111 ~C~~C~R~L~d-----------~~~FCSL~CKv~~v~~~~~dls~~l 146 (236)
.|.+|+-.+.+ .-.||+-+|+-.+-+-++.+|.++-
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~i~~~gL~~yY 48 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQLIHENGLESYY 48 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHHHHHcchHHHH
Confidence 58889888841 2589999999876665667777654
No 27
>PLN00209 ribosomal protein S27; Provisional
Probab=21.61 E-value=91 Score=24.66 Aligned_cols=58 Identities=24% Similarity=0.387 Sum_probs=35.7
Q ss_pred CCCCceeEEEeccccceeeecccccccccCCccceEECCceEEEeecCCCCCCCCCCCcccccccccCCC-------cee
Q 026591 53 HGSHRLLQIRRYVYQDVIRLDDAAKLVDCDYVQPYINNGAKVIFLNQRPQSRTRSSGNICSTCDRSLQDS-------YLF 125 (236)
Q Consensus 53 H~~HrvlQIRR~sY~dVVRv~DIqkl~D~S~IQtY~INsakVVFLn~RPq~r~kg~~~~C~~C~R~L~d~-------~~F 125 (236)
|...+++|-=++-+.|| |--||..||+-.-....+ ..|..|+..|..| ..=
T Consensus 21 hK~k~Lv~~PnS~Fm~V-------kCp~C~n~q~VFShA~t~---------------V~C~~Cg~~L~~PTGGKa~l~~g 78 (86)
T PLN00209 21 HKLKRLVQSPNSFFMDV-------KCQGCFNITTVFSHSQTV---------------VVCGSCQTVLCQPTGGKARLTEG 78 (86)
T ss_pred hhceeeecCCCCEEEEE-------ECCCCCCeeEEEecCceE---------------EEccccCCEeeccCCCCeEecCC
Confidence 55566777655555554 356788887644443333 3788999999764 234
Q ss_pred eeeeccc
Q 026591 126 CCLSCKI 132 (236)
Q Consensus 126 CSL~CKv 132 (236)
||+..|+
T Consensus 79 c~fr~k~ 85 (86)
T PLN00209 79 CSFRKKG 85 (86)
T ss_pred ceEEecC
Confidence 6665554
Done!