Query 031802
Match_columns 153
No_of_seqs 113 out of 172
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:33:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031802.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031802hhsearch_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 2.8E-42 6.1E-47 242.1 5.4 72 66-137 1-72 (72)
2 PF00643 zf-B_box: B-box zinc 96.8 0.00038 8.2E-09 42.7 0.4 37 25-65 5-42 (42)
3 cd00021 BBOX B-Box-type zinc f 95.7 0.0084 1.8E-07 35.6 2.1 36 25-64 2-38 (39)
4 smart00336 BBOX B-Box-type zin 94.8 0.029 6.2E-07 33.7 2.4 35 25-63 5-40 (42)
5 PF12855 Ecl1: Life-span regul 88.2 0.098 2.1E-06 33.5 -0.8 29 114-142 6-37 (43)
6 PRK01343 zinc-binding protein; 85.4 0.37 8E-06 32.7 0.8 27 114-140 9-36 (57)
7 PRK00418 DNA gyrase inhibitor; 84.8 0.49 1.1E-05 32.6 1.1 26 114-139 6-36 (62)
8 PF03884 DUF329: Domain of unk 82.2 0.21 4.5E-06 33.9 -1.5 26 115-140 3-33 (57)
9 COG3024 Uncharacterized protei 81.8 0.46 1E-05 33.1 0.1 27 114-140 7-38 (65)
10 PF10013 DUF2256: Uncharacteri 76.1 0.91 2E-05 29.2 0.1 22 115-136 9-39 (42)
11 PF13240 zinc_ribbon_2: zinc-r 70.1 2.1 4.6E-05 23.7 0.7 16 117-132 2-17 (23)
12 PF09889 DUF2116: Uncharacteri 69.9 1.4 3.1E-05 30.0 -0.1 30 115-144 4-33 (59)
13 PF06467 zf-FCS: MYM-type Zinc 66.7 1.4 3.1E-05 26.6 -0.5 24 113-136 5-40 (43)
14 PF02207 zf-UBR: Putative zinc 63.5 3.5 7.5E-05 28.1 0.9 35 34-68 9-48 (71)
15 PF13248 zf-ribbon_3: zinc-rib 57.6 5.6 0.00012 22.3 0.9 18 115-132 3-20 (26)
16 KOG4367 Predicted Zn-finger pr 57.5 3.6 7.8E-05 38.6 0.1 35 23-61 223-259 (699)
17 cd02340 ZZ_NBR1_like Zinc fing 53.8 7.9 0.00017 24.3 1.2 27 39-65 15-43 (43)
18 COG4338 Uncharacterized protei 45.8 1.7 3.7E-05 29.0 -2.8 24 114-137 12-44 (54)
19 KOG2177 Predicted E3 ubiquitin 38.4 17 0.00038 27.9 1.2 38 25-67 88-127 (386)
20 PF04570 DUF581: Protein of un 37.1 12 0.00026 25.4 0.1 29 113-141 15-52 (58)
21 COG4068 Uncharacterized protei 37.0 11 0.00025 26.0 0.0 22 115-136 9-30 (64)
22 smart00396 ZnF_UBR1 Putative z 34.7 51 0.0011 22.6 3.0 31 32-62 7-42 (71)
23 KOG4582 Uncharacterized conser 31.3 46 0.001 28.6 2.8 56 9-67 132-199 (278)
24 PF08459 UvrC_HhH_N: UvrC Heli 31.2 12 0.00025 29.8 -0.8 26 82-107 16-41 (155)
25 TIGR00412 redox_disulf_2 small 30.8 62 0.0014 21.6 2.9 32 73-105 33-66 (76)
26 PF01412 ArfGap: Putative GTPa 29.6 8.2 0.00018 28.6 -1.8 50 35-85 10-72 (116)
27 PF08002 DUF1697: Protein of u 27.5 22 0.00047 27.2 0.2 29 72-101 17-48 (137)
28 PF06906 DUF1272: Protein of u 26.5 49 0.0011 22.5 1.7 22 116-137 7-31 (57)
29 PF01286 XPA_N: XPA protein N- 25.5 29 0.00063 21.2 0.4 23 115-137 4-26 (34)
30 PF12156 ATPase-cat_bd: Putati 25.1 10 0.00023 27.0 -1.9 34 116-149 2-46 (88)
31 PF12773 DZR: Double zinc ribb 24.9 33 0.00071 21.2 0.6 19 114-132 12-33 (50)
32 PF06156 DUF972: Protein of un 21.6 58 0.0012 24.3 1.5 30 13-43 77-107 (107)
33 cd02341 ZZ_ZZZ3 Zinc finger, Z 20.1 65 0.0014 20.7 1.3 27 39-65 16-48 (48)
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=2.8e-42 Score=242.15 Aligned_cols=72 Identities=74% Similarity=1.225 Sum_probs=71.1
Q ss_pred EeccccceeEecccccceeccceeeEEECCeEEEEeeCCCCCCCCCCCCCcccccccccCCCCeeeecccee
Q 031802 66 RRSSYHDVIRVSEIQKVLDISGVQTYVINSARVVFLNERPQPRPGKGVTNTCEVCDRSLLDSFRFCSLGCKV 137 (153)
Q Consensus 66 RR~sY~dVVrv~diqkl~D~S~IQtYviNs~kVVfLn~RPq~r~~kg~~~~C~~C~R~L~d~~~FCSl~CKv 137 (153)
|||||||||||+||||+||||+||||+|||+||||||+|||++++++.++.|++|+|+|+|+++||||+|||
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 899999999999999999999999999999999999999999999999999999999999999999999997
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=96.79 E-value=0.00038 Score=42.70 Aligned_cols=37 Identities=35% Similarity=0.874 Sum_probs=28.9
Q ss_pred cCCCCCCCCCCCCceeccccCCccCCccccc-CCCCCceEEE
Q 031802 25 QCKLHPDSHKSECNMYCLDCMNGAFCSLCLD-YHKDHRAIQI 65 (153)
Q Consensus 25 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~Hr~lQI 65 (153)
.|..|.+ .+.++||.+|.. ++|..|.. .|++|+++.|
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 338899999975 89999985 4999987754
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=95.68 E-value=0.0084 Score=35.56 Aligned_cols=36 Identities=22% Similarity=0.543 Sum_probs=27.2
Q ss_pred cCCCCCCCCCCCCceeccccCCccCCcccc-cCCCCCceEE
Q 031802 25 QCKLHPDSHKSECNMYCLDCMNGAFCSLCL-DYHKDHRAIQ 64 (153)
Q Consensus 25 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl-~~H~~Hr~lQ 64 (153)
.|+.|.. +...+||.+|.. .+|..|. ..|++|.++-
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 236899999975 8999997 4588887654
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=94.77 E-value=0.029 Score=33.66 Aligned_cols=35 Identities=26% Similarity=0.795 Sum_probs=27.0
Q ss_pred cCCCCCCCCCCCCceeccccCCccCCccccc-CCCCCceE
Q 031802 25 QCKLHPDSHKSECNMYCLDCMNGAFCSLCLD-YHKDHRAI 63 (153)
Q Consensus 25 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~-~H~~Hr~l 63 (153)
.|+.|.+ ....+||.+|.. .+|..|.. .|++|+++
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 335899999975 89999985 58899865
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=88.25 E-value=0.098 Score=33.54 Aligned_cols=29 Identities=28% Similarity=0.649 Sum_probs=24.2
Q ss_pred CCccccccccc---CCCCeeeeccceeceeec
Q 031802 114 TNTCEVCDRSL---LDSFRFCSLGCKVTLITT 142 (153)
Q Consensus 114 ~~~C~~C~R~L---~d~~~FCSl~CKv~~~~~ 142 (153)
.+.|.+|+|-. .+...|||-+|++.+..+
T Consensus 6 ~~yC~~Cdk~~~~~~~~~lYCSe~Cr~~D~~~ 37 (43)
T PF12855_consen 6 NDYCIVCDKQIDPPDDGSLYCSEECRLKDQEK 37 (43)
T ss_pred hhHHHHhhccccCCCCCccccCHHHHhHhhhc
Confidence 45799999999 668899999999976554
No 6
>PRK01343 zinc-binding protein; Provisional
Probab=85.41 E-value=0.37 Score=32.75 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=21.4
Q ss_pred CCcccccccccCCCC-eeeeccceecee
Q 031802 114 TNTCEVCDRSLLDSF-RFCSLGCKVTLI 140 (153)
Q Consensus 114 ~~~C~~C~R~L~d~~-~FCSl~CKv~~~ 140 (153)
...|-+|++.....+ -|||-.|+..+.
T Consensus 9 ~~~CP~C~k~~~~~~rPFCS~RC~~iDL 36 (57)
T PRK01343 9 TRPCPECGKPSTREAYPFCSERCRDIDL 36 (57)
T ss_pred CCcCCCCCCcCcCCCCcccCHHHhhhhH
Confidence 357999999887655 699999998543
No 7
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=84.77 E-value=0.49 Score=32.65 Aligned_cols=26 Identities=35% Similarity=0.790 Sum_probs=20.4
Q ss_pred CCcccccccccC---C-CCe-eeeccceece
Q 031802 114 TNTCEVCDRSLL---D-SFR-FCSLGCKVTL 139 (153)
Q Consensus 114 ~~~C~~C~R~L~---d-~~~-FCSl~CKv~~ 139 (153)
+..|-+|++... + +|+ |||-.||+.+
T Consensus 6 ~v~CP~C~k~~~w~~~~~~rPFCS~RCk~ID 36 (62)
T PRK00418 6 TVNCPTCGKPVEWGEISPFRPFCSKRCQLID 36 (62)
T ss_pred cccCCCCCCcccccCCCCcCCcccHHHHhhh
Confidence 457999999874 3 574 9999999854
No 8
>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=82.19 E-value=0.21 Score=33.86 Aligned_cols=26 Identities=35% Similarity=0.823 Sum_probs=16.1
Q ss_pred CcccccccccCC----CCe-eeeccceecee
Q 031802 115 NTCEVCDRSLLD----SFR-FCSLGCKVTLI 140 (153)
Q Consensus 115 ~~C~~C~R~L~d----~~~-FCSl~CKv~~~ 140 (153)
..|-+|++...- +++ |||-.||+.+.
T Consensus 3 v~CP~C~k~~~~~~~n~~rPFCS~RCk~iDL 33 (57)
T PF03884_consen 3 VKCPICGKPVEWSPENPFRPFCSERCKLIDL 33 (57)
T ss_dssp EE-TTT--EEE-SSSSS--SSSSHHHHHHHH
T ss_pred ccCCCCCCeecccCCCCcCCcccHhhcccCH
Confidence 469999998875 676 99999998543
No 9
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.75 E-value=0.46 Score=33.13 Aligned_cols=27 Identities=37% Similarity=0.850 Sum_probs=21.0
Q ss_pred CCcccccccccCC----CCe-eeeccceecee
Q 031802 114 TNTCEVCDRSLLD----SFR-FCSLGCKVTLI 140 (153)
Q Consensus 114 ~~~C~~C~R~L~d----~~~-FCSl~CKv~~~ 140 (153)
+..|-+|++...- +|| |||-.||+-+.
T Consensus 7 ~v~CP~Cgkpv~w~~~s~frPFCSkRCklIDL 38 (65)
T COG3024 7 TVPCPTCGKPVVWGEESPFRPFCSKRCKLIDL 38 (65)
T ss_pred cccCCCCCCcccccccCCcCcchhHhhhhcch
Confidence 3469999998864 665 99999998543
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=76.12 E-value=0.91 Score=29.17 Aligned_cols=22 Identities=36% Similarity=1.025 Sum_probs=19.0
Q ss_pred CcccccccccC---------CCCeeeeccce
Q 031802 115 NTCEVCDRSLL---------DSFRFCSLGCK 136 (153)
Q Consensus 115 ~~C~~C~R~L~---------d~~~FCSl~CK 136 (153)
.+|.+|+|... |..+|||-.|.
T Consensus 9 K~C~~C~rpf~WRKKW~~~Wd~VkYCS~rCR 39 (42)
T PF10013_consen 9 KICPVCGRPFTWRKKWARCWDEVKYCSDRCR 39 (42)
T ss_pred CcCcccCCcchHHHHHHHhchhhccHHHHhc
Confidence 47999999996 46899999996
No 11
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=70.14 E-value=2.1 Score=23.72 Aligned_cols=16 Identities=31% Similarity=0.926 Sum_probs=13.8
Q ss_pred ccccccccCCCCeeee
Q 031802 117 CEVCDRSLLDSFRFCS 132 (153)
Q Consensus 117 C~~C~R~L~d~~~FCS 132 (153)
|..|+..+.+...||+
T Consensus 2 Cp~CG~~~~~~~~fC~ 17 (23)
T PF13240_consen 2 CPNCGAEIEDDAKFCP 17 (23)
T ss_pred CcccCCCCCCcCcchh
Confidence 7789999999888886
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=69.91 E-value=1.4 Score=29.98 Aligned_cols=30 Identities=23% Similarity=0.558 Sum_probs=24.3
Q ss_pred CcccccccccCCCCeeeeccceeceeecCC
Q 031802 115 NTCEVCDRSLLDSFRFCSLGCKVTLITTNF 144 (153)
Q Consensus 115 ~~C~~C~R~L~d~~~FCSl~CKv~~~~~~~ 144 (153)
.+|..||..+..+-.|||-.|+-....+..
T Consensus 4 kHC~~CG~~Ip~~~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 4 KHCPVCGKPIPPDESFCSPKCREEYRKRQK 33 (59)
T ss_pred CcCCcCCCcCCcchhhhCHHHHHHHHHHHH
Confidence 479999999998889999999876544433
No 13
>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=66.69 E-value=1.4 Score=26.64 Aligned_cols=24 Identities=29% Similarity=0.758 Sum_probs=15.0
Q ss_pred CCCcccccccccCC-C-----------Ceeeeccce
Q 031802 113 VTNTCEVCDRSLLD-S-----------FRFCSLGCK 136 (153)
Q Consensus 113 ~~~~C~~C~R~L~d-~-----------~~FCSl~CK 136 (153)
....|..|++.+.. + ..|||.+|.
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 35689999887743 2 389999885
No 14
>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=63.47 E-value=3.5 Score=28.14 Aligned_cols=35 Identities=29% Similarity=0.621 Sum_probs=24.3
Q ss_pred CCCCceeccccCC---ccCCccc-c-cCCCCCceEEEEec
Q 031802 34 KSECNMYCLDCMN---GAFCSLC-L-DYHKDHRAIQIRRS 68 (153)
Q Consensus 34 knE~N~FCldC~~---~~~C~~C-l-~~H~~Hr~lQIRR~ 68 (153)
+++--..|++|.. .++|..| . ..|.+|++..++-.
T Consensus 9 ~~q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~ 48 (71)
T PF02207_consen 9 SGQIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSS 48 (71)
T ss_dssp TT-EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--
T ss_pred CCCEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeC
Confidence 3466788999975 4799999 5 47999998866544
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=57.55 E-value=5.6 Score=22.30 Aligned_cols=18 Identities=22% Similarity=0.621 Sum_probs=14.8
Q ss_pred CcccccccccCCCCeeee
Q 031802 115 NTCEVCDRSLLDSFRFCS 132 (153)
Q Consensus 115 ~~C~~C~R~L~d~~~FCS 132 (153)
..|..|+..+.+..+||+
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~ 20 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCP 20 (26)
T ss_pred CCCcccCCcCCcccccCh
Confidence 468889998887889986
No 16
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=57.50 E-value=3.6 Score=38.64 Aligned_cols=35 Identities=31% Similarity=0.770 Sum_probs=27.3
Q ss_pred cccCCCCCCCCCCCCceeccccCCccCCccccc--CCCCCc
Q 031802 23 FVQCKLHPDSHKSECNMYCLDCMNGAFCSLCLD--YHKDHR 61 (153)
Q Consensus 23 F~~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~--~H~~Hr 61 (153)
-..|..|+... ..|||+.|.- ++|..|+. .|..|.
T Consensus 223 ~~~ct~h~~e~---~smyc~~ck~-pvc~~clee~khs~he 259 (699)
T KOG4367|consen 223 VSTCTDHELEN---HSMYCVQCKM-PVCYQCLEEGKHSSHE 259 (699)
T ss_pred hhhccCCCCCC---ceEEEEecCC-hHHHHHHHhhcccchh
Confidence 45788887643 6799999975 89999995 577775
No 17
>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=53.79 E-value=7.9 Score=24.28 Aligned_cols=27 Identities=30% Similarity=0.707 Sum_probs=20.1
Q ss_pred eeccccCCccCCccccc--CCCCCceEEE
Q 031802 39 MYCLDCMNGAFCSLCLD--YHKDHRAIQI 65 (153)
Q Consensus 39 ~FCldC~~~~~C~~Cl~--~H~~Hr~lQI 65 (153)
.-|+.|.+--+|..|-. .|..|+.++|
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 56888876679999963 5777877653
No 18
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.76 E-value=1.7 Score=29.03 Aligned_cols=24 Identities=33% Similarity=0.929 Sum_probs=20.3
Q ss_pred CCcccccccccC---------CCCeeeecccee
Q 031802 114 TNTCEVCDRSLL---------DSFRFCSLGCKV 137 (153)
Q Consensus 114 ~~~C~~C~R~L~---------d~~~FCSl~CKv 137 (153)
+..|++|+|... |...|||-.|+-
T Consensus 12 ~KICpvCqRPFsWRkKW~~cWDeVKyCSeRCrr 44 (54)
T COG4338 12 DKICPVCQRPFSWRKKWARCWDEVKYCSERCRR 44 (54)
T ss_pred hhhhhhhcCchHHHHHHHHHHHHHHHHHHHHHH
Confidence 568999999985 468999999983
No 19
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.39 E-value=17 Score=27.85 Aligned_cols=38 Identities=21% Similarity=0.638 Sum_probs=29.0
Q ss_pred cCCCCCCCCCCCCceeccccCCccCCcccc--cCCCCCceEEEEe
Q 031802 25 QCKLHPDSHKSECNMYCLDCMNGAFCSLCL--DYHKDHRAIQIRR 67 (153)
Q Consensus 25 ~C~~H~~~~knE~N~FCldC~~~~~C~~Cl--~~H~~Hr~lQIRR 67 (153)
.|..|... ..+||..|.. .+|..|. ..|.+|+++-+..
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 6799999975 8999996 4799999776543
No 20
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=37.09 E-value=12 Score=25.40 Aligned_cols=29 Identities=31% Similarity=0.708 Sum_probs=21.8
Q ss_pred CCCcccccccccCC---C--Ce----eeeccceeceee
Q 031802 113 VTNTCEVCDRSLLD---S--FR----FCSLGCKVTLIT 141 (153)
Q Consensus 113 ~~~~C~~C~R~L~d---~--~~----FCSl~CKv~~~~ 141 (153)
.-..|..|+|.|.. - |+ |||..|.-+.|.
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 34689999999983 2 33 999999766554
No 21
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=36.98 E-value=11 Score=26.04 Aligned_cols=22 Identities=27% Similarity=0.711 Sum_probs=20.3
Q ss_pred CcccccccccCCCCeeeeccce
Q 031802 115 NTCEVCDRSLLDSFRFCSLGCK 136 (153)
Q Consensus 115 ~~C~~C~R~L~d~~~FCSl~CK 136 (153)
.+|.+|+..+...-+|||-.|.
T Consensus 9 ~HC~VCg~aIp~de~~CSe~C~ 30 (64)
T COG4068 9 RHCVVCGKAIPPDEQVCSEECG 30 (64)
T ss_pred ccccccCCcCCCccchHHHHHH
Confidence 5799999999998999999997
No 22
>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=34.72 E-value=51 Score=22.56 Aligned_cols=31 Identities=29% Similarity=0.531 Sum_probs=23.0
Q ss_pred CCCCCCceeccccCCc---cCCcccc--cCCCCCce
Q 031802 32 SHKSECNMYCLDCMNG---AFCSLCL--DYHKDHRA 62 (153)
Q Consensus 32 ~~knE~N~FCldC~~~---~~C~~Cl--~~H~~Hr~ 62 (153)
..++|.-.-|.+|... .+|..|. ..|.+|++
T Consensus 7 ~~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~ 42 (71)
T smart00396 7 FTGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDY 42 (71)
T ss_pred cCCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCE
Confidence 3467777889999632 5888885 46999983
No 23
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=31.33 E-value=46 Score=28.56 Aligned_cols=56 Identities=20% Similarity=0.324 Sum_probs=35.3
Q ss_pred CCCCcHHHHhcc-ccc-----c---cCCCCCCCCCCCCceeccccCCccCCccccc---CCCCCceEEEEe
Q 031802 9 RWPPWLKPLLRE-SFF-----V---QCKLHPDSHKSECNMYCLDCMNGAFCSLCLD---YHKDHRAIQIRR 67 (153)
Q Consensus 9 ~~P~WL~~LL~~-~FF-----~---~C~~H~~~~knE~N~FCldC~~~~~C~~Cl~---~H~~Hr~lQIRR 67 (153)
..+.||++-+++ -++ . .|..|+-.+ --.-|..|.+--+|..|-. .|..|..||+.+
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 345566655542 233 2 455555432 2256999987779999952 566899999887
No 24
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=31.21 E-value=12 Score=29.81 Aligned_cols=26 Identities=35% Similarity=0.424 Sum_probs=22.6
Q ss_pred ceeccceeeEEECCeEEEEeeCCCCC
Q 031802 82 VLDISGVQTYVINSARVVFLNERPQP 107 (153)
Q Consensus 82 l~D~S~IQtYviNs~kVVfLn~RPq~ 107 (153)
.+|+|.+|.--.-++-|||.|.+|.+
T Consensus 16 ~fDiSh~~G~~~Vgs~Vvf~~G~~~k 41 (155)
T PF08459_consen 16 CFDISHIQGSDTVGSMVVFENGKPDK 41 (155)
T ss_dssp EEEEEECTTTCEEEEEEEEETTEE-G
T ss_pred EEECcccCCcccEEEEEEEECCccCh
Confidence 59999999888899999999988864
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=30.81 E-value=62 Score=21.62 Aligned_cols=32 Identities=9% Similarity=0.360 Sum_probs=22.2
Q ss_pred eeEecccccc--eeccceeeEEECCeEEEEeeCCC
Q 031802 73 VIRVSEIQKV--LDISGVQTYVINSARVVFLNERP 105 (153)
Q Consensus 73 VVrv~diqkl--~D~S~IQtYviNs~kVVfLn~RP 105 (153)
+++++|++.. +++.+|-|.++||..+ +....|
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 5666655554 7899999999988655 554334
No 26
>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=29.63 E-value=8.2 Score=28.57 Aligned_cols=50 Identities=22% Similarity=0.363 Sum_probs=27.4
Q ss_pred CCCceeccccCCc-----------cCCcccccCCCC--CceEEEEeccccceeEecccccceec
Q 031802 35 SECNMYCLDCMNG-----------AFCSLCLDYHKD--HRAIQIRRSSYHDVIRVSEIQKVLDI 85 (153)
Q Consensus 35 nE~N~FCldC~~~-----------~~C~~Cl~~H~~--Hr~lQIRR~sY~dVVrv~diqkl~D~ 85 (153)
..-|..|.||... -+|..|...|+. .++-+| |+.-.|-...+||+.+...
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 3467889999531 189999877763 223333 6677777777777776543
No 27
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=27.51 E-value=22 Score=27.21 Aligned_cols=29 Identities=38% Similarity=0.690 Sum_probs=19.5
Q ss_pred ceeEecccccc---eeccceeeEEECCeEEEEe
Q 031802 72 DVIRVSEIQKV---LDISGVQTYVINSARVVFL 101 (153)
Q Consensus 72 dVVrv~diqkl---~D~S~IQtYviNs~kVVfL 101 (153)
+-|+..|+... +-..+|+|| |+|+-|||=
T Consensus 17 nki~MaeLr~~l~~~Gf~~V~Ty-i~SGNvvf~ 48 (137)
T PF08002_consen 17 NKIKMAELREALEDLGFTNVRTY-IQSGNVVFE 48 (137)
T ss_dssp S---HHHHHHHHHHCT-EEEEEE-TTTTEEEEE
T ss_pred CcccHHHHHHHHHHcCCCCceEE-EeeCCEEEe
Confidence 45666666664 677899999 588889997
No 28
>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=26.53 E-value=49 Score=22.55 Aligned_cols=22 Identities=41% Similarity=0.934 Sum_probs=18.3
Q ss_pred cccccccccCC-C--Ceeeecccee
Q 031802 116 TCEVCDRSLLD-S--FRFCSLGCKV 137 (153)
Q Consensus 116 ~C~~C~R~L~d-~--~~FCSl~CKv 137 (153)
.||.|++.|.. + .+-||..|-.
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTF 31 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTF 31 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcc
Confidence 59999999975 3 6899999865
No 29
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=25.46 E-value=29 Score=21.18 Aligned_cols=23 Identities=22% Similarity=0.657 Sum_probs=13.9
Q ss_pred CcccccccccCCCCeeeecccee
Q 031802 115 NTCEVCDRSLLDSFRFCSLGCKV 137 (153)
Q Consensus 115 ~~C~~C~R~L~d~~~FCSl~CKv 137 (153)
..|..|++.++|+|.+=...+.|
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~~V 26 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDLPV 26 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-S-
T ss_pred chHhHhCCHHHHHHHHHhCCccc
Confidence 47999999999998877776665
No 30
>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=25.05 E-value=10 Score=27.04 Aligned_cols=34 Identities=24% Similarity=0.447 Sum_probs=23.1
Q ss_pred cccccccccC---------C--CCeeeeccceeceeecCCCCcCc
Q 031802 116 TCEVCDRSLL---------D--SFRFCSLGCKVTLITTNFNVVPF 149 (153)
Q Consensus 116 ~C~~C~R~L~---------d--~~~FCSl~CKv~~~~~~~~~~~~ 149 (153)
.|.+|+-.+. + .-.||.-||+-..-.-+..+|..
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FCC~GC~~V~~~i~~~gL~~ 46 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFCCPGCQAVYQLIHENGLES 46 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccccHHHHHHHHHHHHcchHH
Confidence 4888998884 1 25799999997654444445544
No 31
>PF12773 DZR: Double zinc ribbon
Probab=24.87 E-value=33 Score=21.23 Aligned_cols=19 Identities=32% Similarity=0.718 Sum_probs=12.2
Q ss_pred CCcccccccccC--C-CCeeee
Q 031802 114 TNTCEVCDRSLL--D-SFRFCS 132 (153)
Q Consensus 114 ~~~C~~C~R~L~--d-~~~FCS 132 (153)
...|..|+..|. + ...+|+
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~ 33 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICP 33 (50)
T ss_pred ccCChhhcCChhhccCCCCCCc
Confidence 567888888877 3 344553
No 32
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=21.63 E-value=58 Score=24.34 Aligned_cols=30 Identities=33% Similarity=0.637 Sum_probs=23.7
Q ss_pred cHHHHhcccccccCCCCCCCCC-CCCceeccc
Q 031802 13 WLKPLLRESFFVQCKLHPDSHK-SECNMYCLD 43 (153)
Q Consensus 13 WL~~LL~~~FF~~C~~H~~~~k-nE~N~FCld 43 (153)
=|..|..+. |=-|..|-+++| +|-.+||++
T Consensus 77 NL~~LY~EG-FHICn~~yG~~R~~edClFCl~ 107 (107)
T PF06156_consen 77 NLARLYQEG-FHICNVHYGSRRNDEDCLFCLS 107 (107)
T ss_pred HHHHHHhcC-eeeCcHHhCCcCCCCCCcccCC
Confidence 467777777 778999988777 677789875
No 33
>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=20.13 E-value=65 Score=20.74 Aligned_cols=27 Identities=30% Similarity=0.701 Sum_probs=18.9
Q ss_pred eeccccC--CccCCccccc---CC-CCCceEEE
Q 031802 39 MYCLDCM--NGAFCSLCLD---YH-KDHRAIQI 65 (153)
Q Consensus 39 ~FCldC~--~~~~C~~Cl~---~H-~~Hr~lQI 65 (153)
.-|++|. +--+|+.|.. .| .+|+.+.|
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 5679999963 35 36777654
Done!