Query 022701
Match_columns 293
No_of_seqs 162 out of 538
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:31:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022701.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022701hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00021 BBOX B-Box-type zinc f 97.4 8.7E-05 1.9E-09 49.0 2.3 38 47-90 2-39 (39)
2 cd00021 BBOX B-Box-type zinc f 97.3 0.00015 3.2E-09 47.9 2.4 39 3-47 1-39 (39)
3 PF00643 zf-B_box: B-box zinc 97.1 0.00018 3.9E-09 48.8 1.1 41 44-90 2-42 (42)
4 smart00336 BBOX B-Box-type zin 97.1 0.00052 1.1E-08 45.9 2.8 41 44-90 2-42 (42)
5 smart00336 BBOX B-Box-type zin 96.5 0.0025 5.3E-08 42.6 2.6 39 3-47 4-42 (42)
6 PF00643 zf-B_box: B-box zinc 96.4 0.0023 5.1E-08 43.3 2.0 40 2-47 3-42 (42)
7 KOG4367 Predicted Zn-finger pr 94.6 0.0089 1.9E-07 60.6 -0.2 74 4-77 164-255 (699)
8 KOG4367 Predicted Zn-finger pr 70.0 1.7 3.6E-05 44.7 0.4 46 46-91 163-210 (699)
9 PF13248 zf-ribbon_3: zinc-rib 56.8 8.5 0.00019 24.0 1.7 25 1-31 1-25 (26)
10 cd02341 ZZ_ZZZ3 Zinc finger, Z 53.8 11 0.00024 27.0 2.1 40 48-90 3-48 (48)
11 PF04438 zf-HIT: HIT zinc fing 52.7 7.5 0.00016 25.4 1.0 24 45-69 2-25 (30)
12 cd02335 ZZ_ADA2 Zinc finger, Z 50.0 19 0.00042 25.5 2.9 31 47-77 2-36 (49)
13 PF12773 DZR: Double zinc ribb 49.2 17 0.00037 25.2 2.5 30 19-54 9-38 (50)
14 PRK14873 primosome assembly pr 46.6 13 0.00028 39.7 2.2 46 13-63 382-428 (665)
15 PRK14559 putative protein seri 44.9 20 0.00043 38.3 3.2 47 3-72 2-48 (645)
16 COG1198 PriA Primosomal protei 33.7 30 0.00064 37.6 2.5 46 13-63 434-481 (730)
17 cd02249 ZZ Zinc finger, ZZ typ 32.7 44 0.00096 23.1 2.4 30 47-76 2-34 (46)
18 PF09416 UPF1_Zn_bind: RNA hel 32.4 43 0.00094 29.7 2.9 69 4-72 2-94 (152)
19 KOG2807 RNA polymerase II tran 32.0 21 0.00045 35.6 0.9 66 12-77 274-365 (378)
20 TIGR00595 priA primosomal prot 31.2 32 0.00068 35.3 2.1 45 13-62 212-258 (505)
21 cd02334 ZZ_dystrophin Zinc fin 29.4 57 0.0012 23.5 2.6 31 47-77 2-36 (49)
22 PF03660 PHF5: PHF5-like prote 27.4 13 0.00029 31.1 -1.1 50 22-71 20-76 (106)
23 KOG1601 GATA-4/5/6 transcripti 27.3 88 0.0019 27.0 3.9 87 5-92 8-100 (340)
24 PF07649 C1_3: C1-like domain; 24.9 25 0.00055 22.2 0.1 26 4-34 2-27 (30)
25 KOG1705 Uncharacterized conser 24.3 60 0.0013 27.0 2.2 54 10-63 4-61 (110)
26 PF07975 C1_4: TFIIH C1-like d 21.3 30 0.00065 25.4 -0.1 22 56-77 20-41 (51)
27 PRK04023 DNA polymerase II lar 21.1 68 0.0015 36.4 2.4 57 21-93 625-686 (1121)
28 PF04216 FdhE: Protein involve 20.7 78 0.0017 29.9 2.5 61 3-72 173-245 (290)
No 1
>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=97.45 E-value=8.7e-05 Score=49.02 Aligned_cols=38 Identities=32% Similarity=0.768 Sum_probs=33.4
Q ss_pred cccccCCCCceeeccccccccccCCccCccCCCCCCCCCcceec
Q 022701 47 LCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (293)
Q Consensus 47 LCd~C~~~PA~v~C~~d~a~LC~~CD~~~H~An~~as~HqR~pl 90 (293)
+|+.+..+++.+||..|...+|..|+..+|. .|.++||
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i 39 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL 39 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence 6888888899999999999999999988763 7888775
No 2
>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=97.34 E-value=0.00015 Score=47.91 Aligned_cols=39 Identities=38% Similarity=0.809 Sum_probs=34.0
Q ss_pred CCCCccCCCCeEEEecCCccccccccCcccccccchhcccccccc
Q 022701 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (293)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpL 47 (293)
.+|+.++.+++.+||..|.+.+|..|+...|. .|.++++
T Consensus 1 ~~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H~------~H~~~~i 39 (39)
T cd00021 1 RLCDEHGEEPLSLFCETDRALLCVDCDLSVHS------GHRRVPL 39 (39)
T ss_pred CCCCccCCcceEEEeCccChhhhhhcChhhcC------CCCEeeC
Confidence 36999999899999999999999999988875 5887764
No 3
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=97.14 E-value=0.00018 Score=48.84 Aligned_cols=41 Identities=27% Similarity=0.525 Sum_probs=34.8
Q ss_pred ccccccccCCCCceeeccccccccccCCccCccCCCCCCCCCcceec
Q 022701 44 RTLLCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (293)
Q Consensus 44 RvpLCd~C~~~PA~v~C~~d~a~LC~~CD~~~H~An~~as~HqR~pl 90 (293)
+.+.|..|...++.+||..|..++|..|....|.. |+.+||
T Consensus 2 ~~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H~~~~i 42 (42)
T PF00643_consen 2 QEPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------HKIVPI 42 (42)
T ss_dssp SSSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------SEEEEC
T ss_pred cCccCccCCccceEEEecCCCCccCccCCCCCCCC------CEEeEC
Confidence 35689999998899999999999999999998753 888775
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=97.05 E-value=0.00052 Score=45.86 Aligned_cols=41 Identities=29% Similarity=0.545 Sum_probs=34.8
Q ss_pred ccccccccCCCCceeeccccccccccCCccCccCCCCCCCCCcceec
Q 022701 44 RTLLCERCNSQPALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTI 90 (293)
Q Consensus 44 RvpLCd~C~~~PA~v~C~~d~a~LC~~CD~~~H~An~~as~HqR~pl 90 (293)
|..+|+.|...++.+||..|...+|..|....| ..|.+.||
T Consensus 2 ~~~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 2 RPPKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred cCCcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 567899999999999999999999999997755 57777664
No 5
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.45 E-value=0.0025 Score=42.56 Aligned_cols=39 Identities=36% Similarity=0.718 Sum_probs=33.0
Q ss_pred CCCCccCCCCeEEEecCCccccccccCcccccccchhcccccccc
Q 022701 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (293)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpL 47 (293)
..|..++..++.+||..|.+.+|..|....| +.|.+.+|
T Consensus 4 ~~C~~h~~~~~~~~C~~c~~~iC~~C~~~~H------~~H~~~~l 42 (42)
T smart00336 4 PKCDSHGDEPAEFFCEECGALLCRTCDEAEH------RGHTVVLL 42 (42)
T ss_pred CcCCCCCCCceEEECCCCCcccccccChhhc------CCCceecC
Confidence 5799999889999999999999999998866 35766553
No 6
>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=96.35 E-value=0.0023 Score=43.30 Aligned_cols=40 Identities=18% Similarity=0.337 Sum_probs=33.9
Q ss_pred CCCCCccCCCCeEEEecCCccccccccCcccccccchhcccccccc
Q 022701 2 GYMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL 47 (293)
Q Consensus 2 ~~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpL 47 (293)
...|..|...++.+||..+...+|..|....|.. |..++|
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------HKIVPI 42 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------SEEEEC
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCCC------CEEeEC
Confidence 4679999999999999999999999999999864 766654
No 7
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=94.57 E-value=0.0089 Score=60.58 Aligned_cols=74 Identities=18% Similarity=0.428 Sum_probs=59.7
Q ss_pred CCCccCCC--CeEEEecCCccccccccCcccccccchhcccccccc----------------ccccCCCCceeecccccc
Q 022701 4 MCDFCGDQ--RSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLL----------------CERCNSQPALVRCAEERV 65 (293)
Q Consensus 4 ~Cd~C~~a--~A~vyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpL----------------Cd~C~~~PA~v~C~~d~a 65 (293)
.|.+|+++ .|.|+|+.+..+.|.-|..+.|-+..-..+|.-++- |.-++...-..||..|++
T Consensus 164 kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~ck~ 243 (699)
T KOG4367|consen 164 KCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQCKM 243 (699)
T ss_pred hhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEecCC
Confidence 58999987 589999999999999999999988665566654432 555555557799999999
Q ss_pred ccccCCccCccC
Q 022701 66 SLCQNCDWIGHG 77 (293)
Q Consensus 66 ~LC~~CD~~~H~ 77 (293)
+.|-.|-..+.+
T Consensus 244 pvc~~clee~kh 255 (699)
T KOG4367|consen 244 PVCYQCLEEGKH 255 (699)
T ss_pred hHHHHHHHhhcc
Confidence 999999987643
No 8
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=69.99 E-value=1.7 Score=44.73 Aligned_cols=46 Identities=26% Similarity=0.504 Sum_probs=40.1
Q ss_pred ccccccCCCC--ceeeccccccccccCCccCccCCCCCCCCCcceecc
Q 022701 46 LLCERCNSQP--ALVRCAEERVSLCQNCDWIGHGTSTSASSHKRQTIN 91 (293)
Q Consensus 46 pLCd~C~~~P--A~v~C~~d~a~LC~~CD~~~H~An~~as~HqR~pln 91 (293)
.-|..|+..| |.++|..|.++.|.-|....|-+-.+.++|..+|-+
T Consensus 163 ~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~ 210 (699)
T KOG4367|consen 163 LKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPA 210 (699)
T ss_pred hhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcc
Confidence 3488998887 889999999999999999999887788899887765
No 9
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=56.81 E-value=8.5 Score=23.96 Aligned_cols=25 Identities=28% Similarity=0.703 Sum_probs=18.8
Q ss_pred CCCCCCccCCCCeEEEecCCccccccccCcc
Q 022701 1 MGYMCDFCGDQRSIVYCRSDAACLCLSCDRN 31 (293)
Q Consensus 1 M~~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~ 31 (293)
|...|-.|+... .+.+.+|..|.++
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCC
Confidence 778899998742 5668888888765
No 10
>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=53.81 E-value=11 Score=27.04 Aligned_cols=40 Identities=30% Similarity=0.662 Sum_probs=27.0
Q ss_pred ccccCCCCc---eeeccccc---cccccCCccCccCCCCCCCCCcceec
Q 022701 48 CERCNSQPA---LVRCAEER---VSLCQNCDWIGHGTSTSASSHKRQTI 90 (293)
Q Consensus 48 Cd~C~~~PA---~v~C~~d~---a~LC~~CD~~~H~An~~as~HqR~pl 90 (293)
|+.|+..|- .+.|..|. --||+.|-..+- .-...|..++|
T Consensus 3 Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~~---~H~~~H~~~~i 48 (48)
T cd02341 3 CDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKGE---SHQEDHWLVKI 48 (48)
T ss_pred CCCCCCCccccceEECCCCCCCCCccCHHHHhCcC---CCCCCCceeeC
Confidence 888888773 46788877 889999987762 11245655543
No 11
>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=52.75 E-value=7.5 Score=25.37 Aligned_cols=24 Identities=33% Similarity=0.771 Sum_probs=17.6
Q ss_pred cccccccCCCCceeecccccccccc
Q 022701 45 TLLCERCNSQPALVRCAEERVSLCQ 69 (293)
Q Consensus 45 vpLCd~C~~~PA~v~C~~d~a~LC~ 69 (293)
..+|.+|+. ++.+.|..|.+..|.
T Consensus 2 ~~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 2 RKLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp -EEETSSSS-EESEE-TTT--EESS
T ss_pred cCCCccCcC-CCEEECCCcCCceeC
Confidence 358999999 999999999998874
No 12
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=49.99 E-value=19 Score=25.46 Aligned_cols=31 Identities=29% Similarity=0.654 Sum_probs=24.4
Q ss_pred cccccCCCCce---eecccc-ccccccCCccCccC
Q 022701 47 LCERCNSQPAL---VRCAEE-RVSLCQNCDWIGHG 77 (293)
Q Consensus 47 LCd~C~~~PA~---v~C~~d-~a~LC~~CD~~~H~ 77 (293)
.|+.|...+.. +.|..| .--||..|-..+..
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g~~ 36 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAGAE 36 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCcCC
Confidence 48888887754 779988 78899999887643
No 13
>PF12773 DZR: Double zinc ribbon
Probab=49.23 E-value=17 Score=25.15 Aligned_cols=30 Identities=20% Similarity=0.582 Sum_probs=19.9
Q ss_pred CCccccccccCcccccccchhccccccccccccCCC
Q 022701 19 SDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQ 54 (293)
Q Consensus 19 aD~A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~~~ 54 (293)
.+.+..|..|...+- ........|..|+..
T Consensus 9 ~~~~~fC~~CG~~l~------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP------PPDQSKKICPNCGAE 38 (50)
T ss_pred CccccCChhhcCChh------hccCCCCCCcCCcCC
Confidence 456888888887766 233445567777765
No 14
>PRK14873 primosome assembly protein PriA; Provisional
Probab=46.62 E-value=13 Score=39.70 Aligned_cols=46 Identities=20% Similarity=0.380 Sum_probs=31.1
Q ss_pred eEEEecCCc-cccccccCcccccccchhccccccccccccCCCCceeecccc
Q 022701 13 SIVYCRSDA-ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEE 63 (293)
Q Consensus 13 A~vyC~aD~-A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~~~PA~v~C~~d 63 (293)
..++|+.+. ..-|..||...-. ++..+.+.|..|+.......|..|
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~L~~-----h~~~~~l~Ch~CG~~~~p~~Cp~C 428 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGPLGL-----PSAGGTPRCRWCGRAAPDWRCPRC 428 (665)
T ss_pred CeeEhhhCcCeeECCCCCCceeE-----ecCCCeeECCCCcCCCcCccCCCC
Confidence 567898885 5669999966543 134457889999976544445543
No 15
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=44.91 E-value=20 Score=38.31 Aligned_cols=47 Identities=19% Similarity=0.610 Sum_probs=30.5
Q ss_pred CCCCccCCCCeEEEecCCccccccccCcccccccchhccccccccccccCCCCceeeccccccccccCCc
Q 022701 3 YMCDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEERVSLCQNCD 72 (293)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~~~PA~v~C~~d~a~LC~~CD 72 (293)
..|-.|+.. -.+.|++|..|...+-. ..|..|+..-. -.+.+|..|.
T Consensus 2 ~~Cp~Cg~~------n~~~akFC~~CG~~l~~-----------~~Cp~CG~~~~------~~~~fC~~CG 48 (645)
T PRK14559 2 LICPQCQFE------NPNNNRFCQKCGTSLTH-----------KPCPQCGTEVP------VDEAHCPNCG 48 (645)
T ss_pred CcCCCCCCc------CCCCCccccccCCCCCC-----------CcCCCCCCCCC------cccccccccC
Confidence 368888887 35678889999876521 24888887632 2344555554
No 16
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=33.73 E-value=30 Score=37.61 Aligned_cols=46 Identities=28% Similarity=0.638 Sum_probs=32.6
Q ss_pred eEEEecCCcc-ccccccCcccccccchhccccccccccccCCC-Cceeecccc
Q 022701 13 SIVYCRSDAA-CLCLSCDRNVHLANALSKRHSRTLLCERCNSQ-PALVRCAEE 63 (293)
Q Consensus 13 A~vyC~aD~A-~LC~~CD~~vHsAN~La~RH~RvpLCd~C~~~-PA~v~C~~d 63 (293)
..+.|+.+.- .=|..||...-. +++.+...|..|+.+ +-...|..|
T Consensus 434 ~~l~C~~Cg~v~~Cp~Cd~~lt~-----H~~~~~L~CH~Cg~~~~~p~~Cp~C 481 (730)
T COG1198 434 PLLLCRDCGYIAECPNCDSPLTL-----HKATGQLRCHYCGYQEPIPQSCPEC 481 (730)
T ss_pred ceeecccCCCcccCCCCCcceEE-----ecCCCeeEeCCCCCCCCCCCCCCCC
Confidence 4688888864 449999976543 356688899999987 444555543
No 17
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=32.72 E-value=44 Score=23.13 Aligned_cols=30 Identities=23% Similarity=0.540 Sum_probs=22.3
Q ss_pred cccccCCC--Cceeeccccc-cccccCCccCcc
Q 022701 47 LCERCNSQ--PALVRCAEER-VSLCQNCDWIGH 76 (293)
Q Consensus 47 LCd~C~~~--PA~v~C~~d~-a~LC~~CD~~~H 76 (293)
.|+.|... ...++|..|. --||..|-...+
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~~ 34 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKGK 34 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcCc
Confidence 47778772 1457788886 889999987764
No 18
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=32.37 E-value=43 Score=29.73 Aligned_cols=69 Identities=28% Similarity=0.698 Sum_probs=35.1
Q ss_pred CCCccC--CCCeEEEecCCccccccccCc--ccccccchhc-cccccc------------cccccCCCCce----eeccc
Q 022701 4 MCDFCG--DQRSIVYCRSDAACLCLSCDR--NVHLANALSK-RHSRTL------------LCERCNSQPAL----VRCAE 62 (293)
Q Consensus 4 ~Cd~C~--~a~A~vyC~aD~A~LC~~CD~--~vHsAN~La~-RH~Rvp------------LCd~C~~~PA~----v~C~~ 62 (293)
.|.+|| ...++|.|......+|-.=+. .-|--+-|++ ||..+. -|-.|+..... +-...
T Consensus 2 aC~YCG~~~p~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lgdt~leCy~Cg~~NvF~LGFipak~ 81 (152)
T PF09416_consen 2 ACAYCGIHDPSCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLGDTVLECYNCGSRNVFLLGFIPAKS 81 (152)
T ss_dssp S-TTT----CCCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-S-B---TTT----TTTEEEEEETT
T ss_pred CccccCCCCcccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCCCcEEEEEecCCCceeeEEEEEecc
Confidence 699999 778999999999999985443 2233333333 555533 28888877643 23344
Q ss_pred cc--cccccC-Cc
Q 022701 63 ER--VSLCQN-CD 72 (293)
Q Consensus 63 d~--a~LC~~-CD 72 (293)
+. +.||+. |-
T Consensus 82 d~vvvllCR~pC~ 94 (152)
T PF09416_consen 82 DSVVVLLCRQPCA 94 (152)
T ss_dssp SCEEEEEETTTTT
T ss_pred CCeEEEEeCCchh
Confidence 44 567866 75
No 19
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=31.98 E-value=21 Score=35.63 Aligned_cols=66 Identities=23% Similarity=0.469 Sum_probs=44.5
Q ss_pred CeEEEecCCcccc------ccccCcccccccchhc-ccccccc----------------ccccCCC---Cceeecccccc
Q 022701 12 RSIVYCRSDAACL------CLSCDRNVHLANALSK-RHSRTLL----------------CERCNSQ---PALVRCAEERV 65 (293)
Q Consensus 12 ~A~vyC~aD~A~L------C~~CD~~vHsAN~La~-RH~RvpL----------------Cd~C~~~---PA~v~C~~d~a 65 (293)
.+.++|..+.|+. |.-|+..+=++.-|++ -|.-.|| |-.|+.. .-.++|..|+-
T Consensus 274 ~~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck~ 353 (378)
T KOG2807|consen 274 GGGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCKN 353 (378)
T ss_pred cCceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhccc
Confidence 4667777777775 4567766655544544 1222222 7788433 24588999999
Q ss_pred ccccCCccCccC
Q 022701 66 SLCQNCDWIGHG 77 (293)
Q Consensus 66 ~LC~~CD~~~H~ 77 (293)
.+|..||.-.|.
T Consensus 354 ~FCldCDv~iHe 365 (378)
T KOG2807|consen 354 VFCLDCDVFIHE 365 (378)
T ss_pred eeeccchHHHHh
Confidence 999999998886
No 20
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.23 E-value=32 Score=35.33 Aligned_cols=45 Identities=24% Similarity=0.553 Sum_probs=30.2
Q ss_pred eEEEecCCc-cccccccCcccccccchhccccccccccccCCCCc-eeeccc
Q 022701 13 SIVYCRSDA-ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPA-LVRCAE 62 (293)
Q Consensus 13 A~vyC~aD~-A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~~~PA-~v~C~~ 62 (293)
..++|+.+. ..-|..||...-. +++.+.+.|..|+.... ...|..
T Consensus 212 ~~~~C~~Cg~~~~C~~C~~~l~~-----h~~~~~l~Ch~Cg~~~~~~~~Cp~ 258 (505)
T TIGR00595 212 KNLLCRSCGYILCCPNCDVSLTY-----HKKEGKLRCHYCGYQEPIPKTCPQ 258 (505)
T ss_pred CeeEhhhCcCccCCCCCCCceEE-----ecCCCeEEcCCCcCcCCCCCCCCC
Confidence 467888885 5569999966543 24566778999987654 334443
No 21
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=29.35 E-value=57 Score=23.51 Aligned_cols=31 Identities=32% Similarity=0.733 Sum_probs=23.5
Q ss_pred cccccCCCCc---eeecccc-ccccccCCccCccC
Q 022701 47 LCERCNSQPA---LVRCAEE-RVSLCQNCDWIGHG 77 (293)
Q Consensus 47 LCd~C~~~PA---~v~C~~d-~a~LC~~CD~~~H~ 77 (293)
.|+.|+..|. .+.|..| .--||+.|-+.++.
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g~~ 36 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSGRT 36 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCCCc
Confidence 4888988763 4668877 56799999988754
No 22
>PF03660 PHF5: PHF5-like protein; InterPro: IPR005345 Phf5 is a member of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger proteins. At least one example, from Mus musculus (Mouse), may act as a chromatin-associated protein []. The Schizosaccharomyces pombe (Fission yeast) ini1 gene is essential, required for splicing []. It is localised in the nucleus, but not detected in the nucleolus and can be complemented by human ini1 []. The proteins of this family contain five CXXC motifs.; PDB: 2K0A_A.
Probab=27.42 E-value=13 Score=31.12 Aligned_cols=50 Identities=20% Similarity=0.551 Sum_probs=18.9
Q ss_pred cccccccCcccccccchhccccccccccccCCCCceeeccccc-------cccccCC
Q 022701 22 ACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEER-------VSLCQNC 71 (293)
Q Consensus 22 A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~~~PA~v~C~~d~-------a~LC~~C 71 (293)
+.||..||-+--.-...++-...+.+|+.|..-.-.-+|..|. |..|..|
T Consensus 20 G~lC~kCdGkCpiCDS~Vrp~~~VrICdeCs~G~~~~rCIiCg~~~g~sdAYYC~eC 76 (106)
T PF03660_consen 20 GRLCEKCDGKCPICDSYVRPCTKVRICDECSFGSLQGRCIICGSGPGVSDAYYCWEC 76 (106)
T ss_dssp -EE-GGGTT--TTT-------EE-EEEHHHHTSSTTSB-TTTSSSB--EE-EE-HHH
T ss_pred hhhhhhcCCcccccCCccCCcceEEECCcCCCCCcCceEEEecCCCCcccceehhhh
Confidence 4455555554443333344456677777665554444444443 5556666
No 23
>KOG1601 consensus GATA-4/5/6 transcription factors [Transcription]
Probab=27.26 E-value=88 Score=27.03 Aligned_cols=87 Identities=18% Similarity=0.099 Sum_probs=56.5
Q ss_pred CCccCCCCeEEEecCCccccccccCcccccccchhccccccccccccCCCCce--eecccccccc----ccCCccCccCC
Q 022701 5 CDFCGDQRSIVYCRSDAACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPAL--VRCAEERVSL----CQNCDWIGHGT 78 (293)
Q Consensus 5 Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~~~PA~--v~C~~d~a~L----C~~CD~~~H~A 78 (293)
|+.+....... |..|...+|..++.+++..+.+...|.++.++..+...++. +.+......+ +..+....+..
T Consensus 8 ~~~~~~~~~~~-~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (340)
T KOG1601|consen 8 LDSCRFDDLLN-LNADDSLLDISVDARLSASNSLAFPHEPTRLSSSPESFVAATSFSIDLSVPSLDMPGLEGFSLFVSEN 86 (340)
T ss_pred ccccCcccccc-cccccccCCcccccccccccccccccccccccchhhhhhccccccccccccccccccccccccccccc
Confidence 55565555555 99999999999999999998766788888888877622222 2333333333 45566556655
Q ss_pred CCCCCCCcceeccC
Q 022701 79 STSASSHKRQTINC 92 (293)
Q Consensus 79 n~~as~HqR~pln~ 92 (293)
++...+|..+++..
T Consensus 87 ~~~~~~~~~~~~~~ 100 (340)
T KOG1601|consen 87 NPNSLRHPPVPSMP 100 (340)
T ss_pred cCCCCCCCCccccc
Confidence 55556666544443
No 24
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=24.93 E-value=25 Score=22.25 Aligned_cols=26 Identities=31% Similarity=0.584 Sum_probs=8.6
Q ss_pred CCCccCCCCeEEEecCCccccccccCccccc
Q 022701 4 MCDFCGDQRSIVYCRSDAACLCLSCDRNVHL 34 (293)
Q Consensus 4 ~Cd~C~~a~A~vyC~aD~A~LC~~CD~~vHs 34 (293)
.|+.|+..... +..+-|..||..+|.
T Consensus 2 ~C~~C~~~~~~-----~~~Y~C~~Cdf~lH~ 27 (30)
T PF07649_consen 2 RCDACGKPIDG-----GWFYRCSECDFDLHE 27 (30)
T ss_dssp --TTTS----S-------EEE-TTT-----H
T ss_pred cCCcCCCcCCC-----CceEECccCCCccCh
Confidence 58888886432 234568889988884
No 25
>KOG1705 consensus Uncharacterized conserved protein, contains CXXC motifs [Function unknown]
Probab=24.33 E-value=60 Score=27.01 Aligned_cols=54 Identities=20% Similarity=0.527 Sum_probs=31.9
Q ss_pred CCCeEEEecCC----ccccccccCcccccccchhccccccccccccCCCCceeecccc
Q 022701 10 DQRSIVYCRSD----AACLCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVRCAEE 63 (293)
Q Consensus 10 ~a~A~vyC~aD----~A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~~~PA~v~C~~d 63 (293)
..|-.|.|+-- -..||..||.+----...++--.-+.+|+.|.-..-.-+|..|
T Consensus 4 HhpDLi~CrkQPGi~~G~LCEkCDgkC~ICDS~VRP~tlVRiC~eC~~Gs~q~~ciic 61 (110)
T KOG1705|consen 4 HHPDLIMCRKQPGIAIGRLCEKCDGKCVICDSYVRPCTLVRICDECNYGSYQGRCVIC 61 (110)
T ss_pred cCCcEEEEecCCCchhhhhHHhcCCcccccccccccceeeeeehhcCCccccCceEEe
Confidence 35667788754 3678999997654322212222226788888766655455444
No 26
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=21.28 E-value=30 Score=25.39 Aligned_cols=22 Identities=27% Similarity=0.635 Sum_probs=14.9
Q ss_pred ceeeccccccccccCCccCccC
Q 022701 56 ALVRCAEERVSLCQNCDWIGHG 77 (293)
Q Consensus 56 A~v~C~~d~a~LC~~CD~~~H~ 77 (293)
..++|..|+..+|..||.-+|.
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE 41 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHE 41 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTT
T ss_pred CeEECCCCCCccccCcChhhhc
Confidence 5678999999999999998885
No 27
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.14 E-value=68 Score=36.42 Aligned_cols=57 Identities=18% Similarity=0.511 Sum_probs=0.0
Q ss_pred ccccccccCcccccccchhccccccccccccCCCC-ceeecccccccc----ccCCccCccCCCCCCCCCcceeccCC
Q 022701 21 AACLCLSCDRNVHLANALSKRHSRTLLCERCNSQP-ALVRCAEERVSL----CQNCDWIGHGTSTSASSHKRQTINCY 93 (293)
Q Consensus 21 ~A~LC~~CD~~vHsAN~La~RH~RvpLCd~C~~~P-A~v~C~~d~a~L----C~~CD~~~H~An~~as~HqR~pln~y 93 (293)
..+.|..|+...... .|..|+..+ ...||..|.... |.+|.... .....+.++|..+
T Consensus 625 g~RfCpsCG~~t~~f-----------rCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El-----~~~s~~~i~l~~~ 686 (1121)
T PRK04023 625 GRRKCPSCGKETFYR-----------RCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREP-----TPYSKRKIDLKEL 686 (1121)
T ss_pred cCccCCCCCCcCCcc-----------cCCCCCCCCCcceeCccccCcCCCCcCCCCCCCC-----CccceEEecHHHH
No 28
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=20.75 E-value=78 Score=29.87 Aligned_cols=61 Identities=21% Similarity=0.520 Sum_probs=28.6
Q ss_pred CCCCccCCCCeEEEecCCc----cc-cccccCcccccccchhccccccccccccCCCCceee--c-----cccccccccC
Q 022701 3 YMCDFCGDQRSIVYCRSDA----AC-LCLSCDRNVHLANALSKRHSRTLLCERCNSQPALVR--C-----AEERVSLCQN 70 (293)
Q Consensus 3 ~~Cd~C~~a~A~vyC~aD~----A~-LC~~CD~~vHsAN~La~RH~RvpLCd~C~~~PA~v~--C-----~~d~a~LC~~ 70 (293)
..|-+||+.|..=+=+.+. -+ .|.-|+..-|. .| .-|..|+.....-+ = ..-++-.|..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~--------~R-~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~ 243 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRF--------VR-IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCES 243 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE----------T-TS-TTT---SS-EEE--------SEEEEEETT
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeee--------cC-CCCcCCCCCCCcceeeEecCCCCcEEEEECCc
Confidence 4799999997776666653 22 38888854442 23 36999987764311 1 1347788999
Q ss_pred Cc
Q 022701 71 CD 72 (293)
Q Consensus 71 CD 72 (293)
|.
T Consensus 244 C~ 245 (290)
T PF04216_consen 244 CG 245 (290)
T ss_dssp TT
T ss_pred cc
Confidence 96
Done!