Query 026438
Match_columns 238
No_of_seqs 187 out of 548
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 08:01:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026438.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026438hhsearch_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 97.5 5.6E-05 1.2E-09 48.4 2.3 39 3-47 1-39 (39)
2 cd00021 BBOX B-Box-type zinc f 97.2 0.00031 6.6E-09 44.9 2.5 38 56-99 2-39 (39)
3 smart00336 BBOX B-Box-type zin 96.9 0.00073 1.6E-08 43.7 2.4 39 3-47 4-42 (42)
4 PF00643 zf-B_box: B-box zinc 96.9 0.00078 1.7E-08 44.2 2.3 39 3-47 4-42 (42)
5 PF00643 zf-B_box: B-box zinc 96.6 0.00091 2E-08 43.9 1.0 40 54-99 3-42 (42)
6 smart00336 BBOX B-Box-type zin 96.3 0.0035 7.6E-08 40.5 2.6 39 55-99 4-42 (42)
7 KOG4367 Predicted Zn-finger pr 96.1 0.0016 3.5E-08 63.7 0.4 81 3-83 163-252 (699)
8 PF13248 zf-ribbon_3: zinc-rib 73.0 2.4 5.3E-05 25.4 1.5 25 1-31 1-25 (26)
9 PF14776 UNC-79: Cation-channe 70.6 3.3 7.1E-05 41.6 2.6 66 22-88 227-304 (525)
10 KOG0129 Predicted RNA-binding 70.1 1.5 3.3E-05 43.8 0.2 56 41-99 442-504 (520)
11 KOG2807 RNA polymerase II tran 68.4 2.1 4.5E-05 41.0 0.7 80 7-86 267-365 (378)
12 PRK14559 putative protein seri 59.0 5.5 0.00012 41.0 1.7 24 1-31 1-24 (645)
13 PF12773 DZR: Double zinc ribb 58.5 11 0.00023 25.3 2.6 15 19-33 9-23 (50)
14 KOG4367 Predicted Zn-finger pr 56.6 3.9 8.4E-05 40.8 0.2 52 54-105 162-215 (699)
15 PF09416 UPF1_Zn_bind: RNA hel 54.6 8.6 0.00019 32.9 2.0 78 4-81 2-94 (152)
16 cd02342 ZZ_UBA_plant Zinc fing 52.1 12 0.00025 25.8 1.9 30 3-32 1-34 (43)
17 TIGR00622 ssl1 transcription f 41.8 17 0.00037 29.6 1.7 62 25-86 18-101 (112)
18 PF04438 zf-HIT: HIT zinc fing 40.3 11 0.00023 23.6 0.3 25 1-26 1-25 (30)
19 PF07975 C1_4: TFIIH C1-like d 38.7 17 0.00037 25.6 1.1 23 13-35 20-42 (51)
20 KOG4582 Uncharacterized conser 38.5 22 0.00047 32.8 2.1 38 3-40 153-196 (278)
21 COG5151 SSL1 RNA polymerase II 37.3 7.3 0.00016 37.3 -1.2 80 7-86 299-408 (421)
22 KOG1428 Inhibitor of type V ad 37.1 8.2 0.00018 43.9 -1.0 59 52-112 3320-3384(3738)
23 PF07649 C1_3: C1-like domain; 35.8 14 0.0003 22.5 0.3 26 4-34 2-27 (30)
24 PF13240 zinc_ribbon_2: zinc-r 34.6 26 0.00057 20.6 1.3 21 57-83 2-22 (23)
25 PRK00415 rps27e 30S ribosomal 33.5 21 0.00044 26.1 0.9 31 1-32 10-40 (59)
26 PF08274 PhnA_Zn_Ribbon: PhnA 31.2 25 0.00053 22.2 0.8 25 54-81 2-26 (30)
27 KOG0129 Predicted RNA-binding 30.9 18 0.0004 36.4 0.3 42 3-47 456-504 (520)
28 cd02335 ZZ_ADA2 Zinc finger, Z 30.2 59 0.0013 22.1 2.7 29 56-84 2-34 (49)
29 KOG3576 Ovo and related transc 29.9 9.5 0.00021 34.7 -1.6 57 3-63 118-182 (267)
30 PF10235 Cript: Microtubule-as 29.4 35 0.00075 26.8 1.6 29 34-65 27-55 (90)
31 KOG2462 C2H2-type Zn-finger pr 28.6 25 0.00053 32.9 0.7 43 3-46 131-184 (279)
32 PF03107 C1_2: C1 domain; Int 25.9 30 0.00065 21.2 0.6 26 4-34 2-27 (30)
33 TIGR02098 MJ0042_CXXC MJ0042 f 23.4 63 0.0014 20.3 1.7 10 1-10 1-10 (38)
34 KOG1428 Inhibitor of type V ad 22.2 32 0.00069 39.6 0.3 44 3-48 3323-3368(3738)
35 PF04216 FdhE: Protein involve 22.2 61 0.0013 29.5 2.1 12 4-15 174-185 (290)
36 PF01667 Ribosomal_S27e: Ribos 20.1 35 0.00076 24.5 0.0 30 1-31 6-35 (55)
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=97.54 E-value=5.6e-05 Score=48.38 Aligned_cols=39 Identities=38% Similarity=0.811 Sum_probs=34.1
Q ss_pred ccccccCCCCcEEEcccccccchhhhchhcccCccccccccccee
Q 026438 3 IQCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (238)
Q Consensus 3 ~~Cd~C~~apA~vyC~aD~A~LC~~CD~~vHsaN~La~kH~RvpL 47 (238)
..|+.++++++.+||..|+..+|..|+...|. .|.|++|
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 36899998899999999999999999988774 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=97.18 E-value=0.00031 Score=44.92 Aligned_cols=38 Identities=42% Similarity=0.831 Sum_probs=33.1
Q ss_pred CccccccCceEEEeccccccccccCCCCCcCCCCCCCCCcceee
Q 026438 56 PCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (238)
Q Consensus 56 ~Cd~C~~~pA~v~C~~D~a~LC~~CD~~iH~an~ls~~HqR~~l 99 (238)
.|+.|+.+++.+||.+|...+|..|+...| ++|+++++
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H------~~H~~~~i 39 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLSVH------SGHRRVPL 39 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChhhc------CCCCEeeC
Confidence 499999989999999999999999997776 37888764
No 3
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.90 E-value=0.00073 Score=43.74 Aligned_cols=39 Identities=36% Similarity=0.642 Sum_probs=33.4
Q ss_pred ccccccCCCCcEEEcccccccchhhhchhcccCccccccccccee
Q 026438 3 IQCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (238)
Q Consensus 3 ~~Cd~C~~apA~vyC~aD~A~LC~~CD~~vHsaN~La~kH~RvpL 47 (238)
..|..++..++.+||..|++.+|..|....| +.|.+++|
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 5799998889999999999999999998766 57777664
No 4
>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=96.87 E-value=0.00078 Score=44.21 Aligned_cols=39 Identities=23% Similarity=0.575 Sum_probs=33.5
Q ss_pred ccccccCCCCcEEEcccccccchhhhchhcccCccccccccccee
Q 026438 3 IQCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (238)
Q Consensus 3 ~~Cd~C~~apA~vyC~aD~A~LC~~CD~~vHsaN~La~kH~RvpL 47 (238)
..|..+.+.++.+||..+...+|..|....|.. |..++|
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~~------H~~~~i 42 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEPLCSECTVSGHKG------HKIVPI 42 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEEEEHHHHHTSTTT------SEEEEC
T ss_pred ccCccCCccceEEEecCCCCccCccCCCCCCCC------CEEeEC
Confidence 579999998899999999999999999998864 777764
No 5
>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=96.57 E-value=0.00091 Score=43.88 Aligned_cols=40 Identities=23% Similarity=0.494 Sum_probs=33.1
Q ss_pred CCCccccccCceEEEeccccccccccCCCCCcCCCCCCCCCcceee
Q 026438 54 LPPCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (238)
Q Consensus 54 ~p~Cd~C~~~pA~v~C~~D~a~LC~~CD~~iH~an~ls~~HqR~~l 99 (238)
...|+.|++..+.+||.++...+|..|....|. +|..++|
T Consensus 3 ~~~C~~H~~~~~~~~C~~C~~~~C~~C~~~~H~------~H~~~~i 42 (42)
T PF00643_consen 3 EPKCPEHPEEPLSLFCEDCNEPLCSECTVSGHK------GHKIVPI 42 (42)
T ss_dssp SSB-SSTTTSBEEEEETTTTEEEEHHHHHTSTT------TSEEEEC
T ss_pred CccCccCCccceEEEecCCCCccCccCCCCCCC------CCEEeEC
Confidence 346999999999999999999999999988884 3877654
No 6
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.30 E-value=0.0035 Score=40.47 Aligned_cols=39 Identities=41% Similarity=0.782 Sum_probs=32.7
Q ss_pred CCccccccCceEEEeccccccccccCCCCCcCCCCCCCCCcceee
Q 026438 55 PPCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (238)
Q Consensus 55 p~Cd~C~~~pA~v~C~~D~a~LC~~CD~~iH~an~ls~~HqR~~l 99 (238)
..|+.|+..++.+||..|...+|..|....| ++|.+.++
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 3599999899999999999999999997766 56777653
No 7
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=96.12 E-value=0.0016 Score=63.70 Aligned_cols=81 Identities=27% Similarity=0.576 Sum_probs=68.0
Q ss_pred ccccccCCCC--cEEEcccccccchhhhchhcccCcccccccccceeccc-------cCCCCCccccccCceEEEecccc
Q 026438 3 IQCDVCEKAP--ATVICCADEAALCAKCDVEVHAANKLASKHQRLLLQCL-------SNKLPPCDICQEKAAFIFCVEDR 73 (238)
Q Consensus 3 ~~Cd~C~~ap--A~vyC~aD~A~LC~~CD~~vHsaN~La~kH~RvpL~~~-------~~~~p~Cd~C~~~pA~v~C~~D~ 73 (238)
..|..|++++ |+|+|..+..+.|.-|..+.|-+...+.||.-+|-.+- +.+...|..|.-+.-..||..+.
T Consensus 163 ~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs~~~s~r~~~~ct~h~~e~~smyc~~ck 242 (699)
T KOG4367|consen 163 LKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVSRRLSPRKVSTCTDHELENHSMYCVQCK 242 (699)
T ss_pred hhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCceeeccchhhhhhccCCCCCCceEEEEecC
Confidence 3699999976 99999999999999999999998888889987665432 23466799999999889999999
Q ss_pred ccccccCCCC
Q 026438 74 ALFCKDCDEP 83 (238)
Q Consensus 74 a~LC~~CD~~ 83 (238)
...|-.|-..
T Consensus 243 ~pvc~~clee 252 (699)
T KOG4367|consen 243 MPVCYQCLEE 252 (699)
T ss_pred ChHHHHHHHh
Confidence 8888888754
No 8
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=72.96 E-value=2.4 Score=25.43 Aligned_cols=25 Identities=24% Similarity=0.706 Sum_probs=18.3
Q ss_pred CCccccccCCCCcEEEcccccccchhhhchh
Q 026438 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (238)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~~CD~~ 31 (238)
|.+.|-.|+... .+++.+|..|..+
T Consensus 1 m~~~Cp~Cg~~~------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 1 MEMFCPNCGAEI------DPDAKFCPNCGAK 25 (26)
T ss_pred CcCCCcccCCcC------CcccccChhhCCC
Confidence 788899999732 5567888888754
No 9
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=70.60 E-value=3.3 Score=41.65 Aligned_cols=66 Identities=21% Similarity=0.393 Sum_probs=42.0
Q ss_pred ccchhhhchhcccCcccccc-cccceeccccCC--CCCccccccCceEEEecc---------ccccccccCCCCCcCCC
Q 026438 22 AALCAKCDVEVHAANKLASK-HQRLLLQCLSNK--LPPCDICQEKAAFIFCVE---------DRALFCKDCDEPIHSPG 88 (238)
Q Consensus 22 A~LC~~CD~~vHsaN~La~k-H~RvpL~~~~~~--~p~Cd~C~~~pA~v~C~~---------D~a~LC~~CD~~iH~an 88 (238)
.+||.+|...+|+.-+.... +.-.|+.+.+.. -..|..- ++.|.+.|.. --..||..|+...|+.-
T Consensus 227 LylC~~Ca~~i~~e~~~~~~~~il~P~~~vS~~CenK~C~S~-~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~~~H~n~ 304 (525)
T PF14776_consen 227 LYLCSECAEEIHREHPDQMFVDILQPMQQVSMTCENKNCRSS-DKSAVVTCFSTECTSYNGNRPIRLCQQCHSNRHNNR 304 (525)
T ss_pred eeeHHHHHHHHhcccchhhhhhhhccccccccccCCCCCcCC-CCCeEEEEechhhccccCCCcchhHHHHhhhhcccc
Confidence 57999999999986544322 334454443321 2234433 4568888853 24689999999999653
No 10
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=70.06 E-value=1.5 Score=43.81 Aligned_cols=56 Identities=21% Similarity=0.354 Sum_probs=41.4
Q ss_pred ccccceeccccCCCCCcccccc-----CceEEEec--cccccccccCCCCCcCCCCCCCCCcceee
Q 026438 41 KHQRLLLQCLSNKLPPCDICQE-----KAAFIFCV--EDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (238)
Q Consensus 41 kH~RvpL~~~~~~~p~Cd~C~~-----~pA~v~C~--~D~a~LC~~CD~~iH~an~ls~~HqR~~l 99 (238)
-++||-+.+.--.-..|+.|+. +.|-+||. .|..++|+.|-..+|+- .+++.+.|+
T Consensus 442 ~~KRVEIkPYv~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPl 504 (520)
T KOG0129|consen 442 IDKRVEIKPYVMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPL 504 (520)
T ss_pred cceeeeecceeccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCce
Confidence 3558877555445667999999 88999995 57789999999999963 344445454
No 11
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=68.40 E-value=2.1 Score=40.98 Aligned_cols=80 Identities=25% Similarity=0.497 Sum_probs=55.2
Q ss_pred ccCC--CCcEEEcccccccc------hhhhchhcccCccccc-ccccceecc---ccC----CCCCccccccCc---eEE
Q 026438 7 VCEK--APATVICCADEAAL------CAKCDVEVHAANKLAS-KHQRLLLQC---LSN----KLPPCDICQEKA---AFI 67 (238)
Q Consensus 7 ~C~~--apA~vyC~aD~A~L------C~~CD~~vHsaN~La~-kH~RvpL~~---~~~----~~p~Cd~C~~~p---A~v 67 (238)
+|.+ .-+.++|..+.|.. |.-|+...=++-.|++ =|.-.||.+ ++. .+..|-.|+... ..+
T Consensus 267 ~CH~~~~~~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y 346 (378)
T KOG2807|consen 267 ACHSELSGGGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRY 346 (378)
T ss_pred eeccccccCceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcE
Confidence 4554 34788899888876 4577766555544554 566677754 222 244599994443 456
Q ss_pred EeccccccccccCCCCCcC
Q 026438 68 FCVEDRALFCKDCDEPIHS 86 (238)
Q Consensus 68 ~C~~D~a~LC~~CD~~iH~ 86 (238)
.|..+...||.+||.-+|.
T Consensus 347 ~C~~Ck~~FCldCDv~iHe 365 (378)
T KOG2807|consen 347 RCESCKNVFCLDCDVFIHE 365 (378)
T ss_pred EchhccceeeccchHHHHh
Confidence 7999999999999998885
No 12
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=58.99 E-value=5.5 Score=41.01 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=14.8
Q ss_pred CCccccccCCCCcEEEcccccccchhhhchh
Q 026438 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (238)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~~CD~~ 31 (238)
|. .|-.|+.. ..+.+.+|..|...
T Consensus 1 M~-~Cp~Cg~~------n~~~akFC~~CG~~ 24 (645)
T PRK14559 1 ML-ICPQCQFE------NPNNNRFCQKCGTS 24 (645)
T ss_pred CC-cCCCCCCc------CCCCCccccccCCC
Confidence 64 69999875 23455666666543
No 13
>PF12773 DZR: Double zinc ribbon
Probab=58.52 E-value=11 Score=25.25 Aligned_cols=15 Identities=27% Similarity=0.798 Sum_probs=9.5
Q ss_pred cccccchhhhchhcc
Q 026438 19 ADEAALCAKCDVEVH 33 (238)
Q Consensus 19 aD~A~LC~~CD~~vH 33 (238)
.+++.+|..|...+-
T Consensus 9 ~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLP 23 (50)
T ss_pred CccccCChhhcCChh
Confidence 455777777775544
No 14
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=56.61 E-value=3.9 Score=40.80 Aligned_cols=52 Identities=23% Similarity=0.532 Sum_probs=42.5
Q ss_pred CCCccccccCc--eEEEeccccccccccCCCCCcCCCCCCCCCcceeeccceee
Q 026438 54 LPPCDICQEKA--AFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLATGIRVA 105 (238)
Q Consensus 54 ~p~Cd~C~~~p--A~v~C~~D~a~LC~~CD~~iH~an~ls~~HqR~~l~~~rv~ 105 (238)
.-.|..|...+ |.|+|..+..++|.-|....|-+-...++|..++...-||.
T Consensus 162 a~kcqlce~a~k~a~v~ceqcdv~yc~pc~~~~hp~rgplakh~l~~~~~grvs 215 (699)
T KOG4367|consen 162 ALKCQLCEKAPKEATVMCEQCDVFYCDPCRLRCHPPRGPLAKHRLVPPAQGRVS 215 (699)
T ss_pred hhhhhhhcCChhhhhhhHhhCceEEechHHhccCCCCCchhhcccCCcccCcee
Confidence 34588887765 88999999999999999999987766778988887755654
No 15
>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=54.65 E-value=8.6 Score=32.90 Aligned_cols=78 Identities=24% Similarity=0.546 Sum_probs=38.8
Q ss_pred cccccC--CCCcEEEcccccccchhhhch--hcccCccc-ccccccceecccc---CCCCCccccccCceEEE----ecc
Q 026438 4 QCDVCE--KAPATVICCADEAALCAKCDV--EVHAANKL-ASKHQRLLLQCLS---NKLPPCDICQEKAAFIF----CVE 71 (238)
Q Consensus 4 ~Cd~C~--~apA~vyC~aD~A~LC~~CD~--~vHsaN~L-a~kH~RvpL~~~~---~~~p~Cd~C~~~pA~v~----C~~ 71 (238)
.|.+|+ ....++.|..+.-.+|..=+. .-|--|.| .+||.=|-|-+-. -....|-.|+.+..+.. ...
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 588999 566888899999999985443 23333434 4588877774322 23556999998875543 344
Q ss_pred cc--cccccc-CC
Q 026438 72 DR--ALFCKD-CD 81 (238)
Q Consensus 72 D~--a~LC~~-CD 81 (238)
|. ..||+. |.
T Consensus 82 d~vvvllCR~pC~ 94 (152)
T PF09416_consen 82 DSVVVLLCRQPCA 94 (152)
T ss_dssp SCEEEEEETTTTT
T ss_pred CCeEEEEeCCchh
Confidence 43 578876 64
No 16
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=52.06 E-value=12 Score=25.76 Aligned_cols=30 Identities=33% Similarity=0.588 Sum_probs=21.8
Q ss_pred ccccccCCCC---cEEEccccccc-chhhhchhc
Q 026438 3 IQCDVCEKAP---ATVICCADEAA-LCAKCDVEV 32 (238)
Q Consensus 3 ~~Cd~C~~ap---A~vyC~aD~A~-LC~~CD~~v 32 (238)
+.||.|+..| ..+.|..+.-+ ||..|-.+.
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 5799999866 45568876655 899986544
No 17
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.76 E-value=17 Score=29.63 Aligned_cols=62 Identities=27% Similarity=0.523 Sum_probs=41.0
Q ss_pred hhhhchhcccCccccc-ccccceeccc---c----CCCCCccccccCc--------------eEEEeccccccccccCCC
Q 026438 25 CAKCDVEVHAANKLAS-KHQRLLLQCL---S----NKLPPCDICQEKA--------------AFIFCVEDRALFCKDCDE 82 (238)
Q Consensus 25 C~~CD~~vHsaN~La~-kH~RvpL~~~---~----~~~p~Cd~C~~~p--------------A~v~C~~D~a~LC~~CD~ 82 (238)
|.-|+..+=++.-|+| =|.=+||... + .....|-.|+..- ..+.|..+...||.+||.
T Consensus 18 CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~ 97 (112)
T TIGR00622 18 CPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDV 97 (112)
T ss_pred CCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccccccch
Confidence 6677766655555655 3555666422 1 1133599998742 235699999999999999
Q ss_pred CCcC
Q 026438 83 PIHS 86 (238)
Q Consensus 83 ~iH~ 86 (238)
-+|.
T Consensus 98 fiHe 101 (112)
T TIGR00622 98 FVHE 101 (112)
T ss_pred hhhh
Confidence 9985
No 18
>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=40.32 E-value=11 Score=23.64 Aligned_cols=25 Identities=32% Similarity=0.644 Sum_probs=17.1
Q ss_pred CCccccccCCCCcEEEcccccccchh
Q 026438 1 MKIQCDVCEKAPATVICCADEAALCA 26 (238)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~ 26 (238)
+..+|.+|+. .+...|......+|.
T Consensus 1 ~~~~C~vC~~-~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 1 PRKLCSVCGN-PAKYRCPRCGARYCS 25 (30)
T ss_dssp --EEETSSSS-EESEE-TTT--EESS
T ss_pred CcCCCccCcC-CCEEECCCcCCceeC
Confidence 3568999998 888889998888875
No 19
>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=38.67 E-value=17 Score=25.63 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=15.3
Q ss_pred cEEEcccccccchhhhchhcccC
Q 026438 13 ATVICCADEAALCAKCDVEVHAA 35 (238)
Q Consensus 13 A~vyC~aD~A~LC~~CD~~vHsa 35 (238)
..+.|..+...+|.+||.-||..
T Consensus 20 ~~y~C~~C~~~FC~dCD~fiHE~ 42 (51)
T PF07975_consen 20 SRYRCPKCKNHFCIDCDVFIHET 42 (51)
T ss_dssp EEE--TTTT--B-HHHHHTTTTT
T ss_pred CeEECCCCCCccccCcChhhhcc
Confidence 34669999999999999999974
No 20
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=38.46 E-value=22 Score=32.85 Aligned_cols=38 Identities=32% Similarity=0.683 Sum_probs=27.8
Q ss_pred ccccccCCCC---cEEEcccccc-cchhhhchhc--ccCccccc
Q 026438 3 IQCDVCEKAP---ATVICCADEA-ALCAKCDVEV--HAANKLAS 40 (238)
Q Consensus 3 ~~Cd~C~~ap---A~vyC~aD~A-~LC~~CD~~v--HsaN~La~ 40 (238)
+.||.|...+ ..+-|.-+.. -||.+|.+.. |.+-++++
T Consensus 153 v~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~~~h~~H~~lR 196 (278)
T KOG4582|consen 153 VPCDNCGKPGIVGARYKCTVCPDYDLCERCEAGNEHHAAHAMLR 196 (278)
T ss_pred ccCCCccCCccccceeeecCCCccchhHHhhcCCCCCcccceee
Confidence 6899999844 6777998865 4999999984 44444444
No 21
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=37.30 E-value=7.3 Score=37.34 Aligned_cols=80 Identities=26% Similarity=0.509 Sum_probs=53.2
Q ss_pred ccCCC--CcEEEcccccccc------hhhhchhcccCcccc-cccccceecccc---C----CCCCccccccC-------
Q 026438 7 VCEKA--PATVICCADEAAL------CAKCDVEVHAANKLA-SKHQRLLLQCLS---N----KLPPCDICQEK------- 63 (238)
Q Consensus 7 ~C~~a--pA~vyC~aD~A~L------C~~CD~~vHsaN~La-~kH~RvpL~~~~---~----~~p~Cd~C~~~------- 63 (238)
+|... .+.++|..+.+.. |.-|+...=....|+ +-|.-.||.... . +..-|-.||..
T Consensus 299 aCHs~~~~gGy~CP~CktkVCsLPi~CP~Csl~LilsthLarSyhhL~PLk~f~E~p~~~~~ks~~Cf~CQ~~fp~~~~~ 378 (421)
T COG5151 299 ACHSEVKGGGYECPVCKTKVCSLPISCPICSLQLILSTHLARSYHHLYPLKPFVEKPEGTNPKSTHCFVCQGPFPKPPVS 378 (421)
T ss_pred eeeeeeccCceeCCcccceeecCCccCcchhHHHHHHHHHHHHHHhhccCcccccccCCCCCCCccceeccCCCCCCCCC
Confidence 45553 4778888888775 567886543333343 357777775422 1 24558888872
Q ss_pred -------ceEEEeccccccccccCCCCCcC
Q 026438 64 -------AAFIFCVEDRALFCKDCDEPIHS 86 (238)
Q Consensus 64 -------pA~v~C~~D~a~LC~~CD~~iH~ 86 (238)
...+.|..+...||.+||.-+|.
T Consensus 379 ~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 379 PFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred cccccccccceechhhhhhhhhhhHHHHHH
Confidence 23456999999999999988875
No 22
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=37.09 E-value=8.2 Score=43.89 Aligned_cols=59 Identities=32% Similarity=0.638 Sum_probs=44.6
Q ss_pred CCCCCcccccc--CceEEEeccccccccccCCCCCcCCCCCCCCCcceeec----cceeeccCCCCc
Q 026438 52 NKLPPCDICQE--KAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLAT----GIRVALSSSCSK 112 (238)
Q Consensus 52 ~~~p~Cd~C~~--~pA~v~C~~D~a~LC~~CD~~iH~an~ls~~HqR~~l~----~~rv~~~s~c~~ 112 (238)
.+.|.|+.|-+ ..|.++|..+. .||.+||.-.|..- -..+|+|.-+. .|.|.+..||.-
T Consensus 3320 kQ~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHr-rtktH~~q~f~eeeea~kvdlHeGC~R 3384 (3738)
T KOG1428|consen 3320 KQMPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHR-RTKTHQRQVFKEEEEAIKVDLHEGCGR 3384 (3738)
T ss_pred hcCCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHh-hccchhhhhhhhhhhhcccchhhcchH
Confidence 34788999855 45889999888 89999997766432 24689996553 478889999964
No 23
>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=35.81 E-value=14 Score=22.54 Aligned_cols=26 Identities=31% Similarity=0.740 Sum_probs=8.3
Q ss_pred cccccCCCCcEEEcccccccchhhhchhccc
Q 026438 4 QCDVCEKAPATVICCADEAALCAKCDVEVHA 34 (238)
Q Consensus 4 ~Cd~C~~apA~vyC~aD~A~LC~~CD~~vHs 34 (238)
.|+.|++.... +..+.|..||-.+|.
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 58888875532 234567888877774
No 24
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=34.64 E-value=26 Score=20.57 Aligned_cols=21 Identities=43% Similarity=1.053 Sum_probs=13.8
Q ss_pred ccccccCceEEEeccccccccccCCCC
Q 026438 57 CDICQEKAAFIFCVEDRALFCKDCDEP 83 (238)
Q Consensus 57 Cd~C~~~pA~v~C~~D~a~LC~~CD~~ 83 (238)
|..|+.+. .+.+.+|..|-.+
T Consensus 2 Cp~CG~~~------~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEI------EDDAKFCPNCGTP 22 (23)
T ss_pred CcccCCCC------CCcCcchhhhCCc
Confidence 66676664 4567778777654
No 25
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=33.52 E-value=21 Score=26.08 Aligned_cols=31 Identities=23% Similarity=0.564 Sum_probs=25.9
Q ss_pred CCccccccCCCCcEEEcccccccchhhhchhc
Q 026438 1 MKIQCDVCEKAPATVICCADEAALCAKCDVEV 32 (238)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~~CD~~v 32 (238)
|++.|..|+ +.-++|=++.....|..|...+
T Consensus 10 ~~VkCp~C~-n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 10 LKVKCPDCG-NEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEEECCCCC-CeEEEEecCCcEEECcccCCCc
Confidence 678899999 5778888899999999998544
No 26
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=31.18 E-value=25 Score=22.22 Aligned_cols=25 Identities=28% Similarity=0.925 Sum_probs=12.3
Q ss_pred CCCccccccCceEEEeccccccccccCC
Q 026438 54 LPPCDICQEKAAFIFCVEDRALFCKDCD 81 (238)
Q Consensus 54 ~p~Cd~C~~~pA~v~C~~D~a~LC~~CD 81 (238)
+|.|+.|++.-.. .+...+.|..|.
T Consensus 2 ~p~Cp~C~se~~y---~D~~~~vCp~C~ 26 (30)
T PF08274_consen 2 LPKCPLCGSEYTY---EDGELLVCPECG 26 (30)
T ss_dssp S---TTT-----E---E-SSSEEETTTT
T ss_pred CCCCCCCCCccee---ccCCEEeCCccc
Confidence 5679999998765 466778888885
No 27
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=30.95 E-value=18 Score=36.40 Aligned_cols=42 Identities=21% Similarity=0.425 Sum_probs=33.4
Q ss_pred ccccccCC-----CCcEEEccc--ccccchhhhchhcccCccccccccccee
Q 026438 3 IQCDVCEK-----APATVICCA--DEAALCAKCDVEVHAANKLASKHQRLLL 47 (238)
Q Consensus 3 ~~Cd~C~~-----apA~vyC~a--D~A~LC~~CD~~vHsaN~La~kH~RvpL 47 (238)
..||.|+. ..|.+||.+ |--++|..|=..+|+.- .++.=.||
T Consensus 456 q~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~~---~r~~HkPl 504 (520)
T KOG0129|consen 456 QLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSGP---GREHHKPL 504 (520)
T ss_pred cchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcCC---chhcCCce
Confidence 46999998 889999995 56899999999999863 45544555
No 28
>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=30.18 E-value=59 Score=22.05 Aligned_cols=29 Identities=28% Similarity=0.525 Sum_probs=19.1
Q ss_pred CccccccCceE---EEeccc-cccccccCCCCC
Q 026438 56 PCDICQEKAAF---IFCVED-RALFCKDCDEPI 84 (238)
Q Consensus 56 ~Cd~C~~~pA~---v~C~~D-~a~LC~~CD~~i 84 (238)
.|+.|...... +.|..+ .--||..|-...
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g 34 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAG 34 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCc
Confidence 47777766544 557666 457888887544
No 29
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=29.95 E-value=9.5 Score=34.68 Aligned_cols=57 Identities=23% Similarity=0.557 Sum_probs=40.2
Q ss_pred ccccccCCC-------CcEEEcccc-cccchhhhchhcccCcccccccccceeccccCCCCCccccccC
Q 026438 3 IQCDVCEKA-------PATVICCAD-EAALCAKCDVEVHAANKLASKHQRLLLQCLSNKLPPCDICQEK 63 (238)
Q Consensus 3 ~~Cd~C~~a-------pA~vyC~aD-~A~LC~~CD~~vHsaN~La~kH~RvpL~~~~~~~p~Cd~C~~~ 63 (238)
..|++|++. .--+-|.+| .-.||..|..-.|-+-. +.||.|..- +...-.|..|..+
T Consensus 118 ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfndtfd-lkrh~rtht---gvrpykc~~c~ka 182 (267)
T KOG3576|consen 118 FTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFNDTFD-LKRHTRTHT---GVRPYKCSLCEKA 182 (267)
T ss_pred eeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccchhh-hhhhhcccc---CccccchhhhhHH
Confidence 468888875 234678888 68899999999887644 589999753 2223357777554
No 30
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=29.38 E-value=35 Score=26.83 Aligned_cols=29 Identities=31% Similarity=0.473 Sum_probs=20.7
Q ss_pred cCcccccccccceeccccCCCCCccccccCce
Q 026438 34 AANKLASKHQRLLLQCLSNKLPPCDICQEKAA 65 (238)
Q Consensus 34 saN~La~kH~RvpL~~~~~~~p~Cd~C~~~pA 65 (238)
.-|+|+++-.|-|+. ..+..|.+|.....
T Consensus 27 ~eNKlLs~~~~nPy~---~~~~~C~~CK~~v~ 55 (90)
T PF10235_consen 27 GENKLLSKKKKNPYA---PYSSKCKICKTKVH 55 (90)
T ss_pred cceeeecccccCccc---ccCccccccccccc
Confidence 468888887775553 34667999988863
No 31
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=28.56 E-value=25 Score=32.93 Aligned_cols=43 Identities=23% Similarity=0.293 Sum_probs=28.7
Q ss_pred ccccccCCCCcEEE---------ccccc--ccchhhhchhcccCcccccccccce
Q 026438 3 IQCDVCEKAPATVI---------CCADE--AALCAKCDVEVHAANKLASKHQRLL 46 (238)
Q Consensus 3 ~~Cd~C~~apA~vy---------C~aD~--A~LC~~CD~~vHsaN~La~kH~Rvp 46 (238)
..|+.|++.-|+.- |..|+ |+-|..||..-=+- ..+++|.|+-
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSm-pALkMHirTH 184 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSM-PALKMHIRTH 184 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeeeh-HHHhhHhhcc
Confidence 46888998766654 77775 78899999553332 2356666654
No 32
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=25.85 E-value=30 Score=21.22 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=17.9
Q ss_pred cccccCCCCcEEEcccccccchhhhchhccc
Q 026438 4 QCDVCEKAPATVICCADEAALCAKCDVEVHA 34 (238)
Q Consensus 4 ~Cd~C~~apA~vyC~aD~A~LC~~CD~~vHs 34 (238)
.|++|++.....+ .+-|..|+..+|.
T Consensus 2 ~C~~C~~~~~~~~-----~Y~C~~c~f~lh~ 27 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-----FYHCSECCFTLHV 27 (30)
T ss_pred CCCCCCCCcCCCE-----eEEeCCCCCeEcC
Confidence 5889988665543 5667777766664
No 33
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=23.36 E-value=63 Score=20.34 Aligned_cols=10 Identities=50% Similarity=1.168 Sum_probs=7.6
Q ss_pred CCccccccCC
Q 026438 1 MKIQCDVCEK 10 (238)
Q Consensus 1 M~~~Cd~C~~ 10 (238)
|++.|..|+.
T Consensus 1 M~~~CP~C~~ 10 (38)
T TIGR02098 1 MRIQCPNCKT 10 (38)
T ss_pred CEEECCCCCC
Confidence 7777888875
No 34
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=22.24 E-value=32 Score=39.61 Aligned_cols=44 Identities=27% Similarity=0.570 Sum_probs=31.7
Q ss_pred ccccccCC--CCcEEEcccccccchhhhchhcccCcccccccccceec
Q 026438 3 IQCDVCEK--APATVICCADEAALCAKCDVEVHAANKLASKHQRLLLQ 48 (238)
Q Consensus 3 ~~Cd~C~~--apA~vyC~aD~A~LC~~CD~~vHsaN~La~kH~RvpL~ 48 (238)
++||+=.. ..|.++|..+. +||..||+-.|-.. -.+.|+|--+.
T Consensus 3323 PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHr-rtktH~~q~f~ 3368 (3738)
T KOG1428|consen 3323 PMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHR-RTKTHQRQVFK 3368 (3738)
T ss_pred CcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHh-hccchhhhhhh
Confidence 46766433 56888998888 99999998776532 24788886664
No 35
>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=22.17 E-value=61 Score=29.55 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=4.0
Q ss_pred cccccCCCCcEE
Q 026438 4 QCDVCEKAPATV 15 (238)
Q Consensus 4 ~Cd~C~~apA~v 15 (238)
.|-+|+..|..-
T Consensus 174 ~CPvCGs~P~~s 185 (290)
T PF04216_consen 174 YCPVCGSPPVLS 185 (290)
T ss_dssp S-TTT---EEEE
T ss_pred cCCCCCCcCceE
Confidence 466666655333
No 36
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=20.10 E-value=35 Score=24.48 Aligned_cols=30 Identities=27% Similarity=0.547 Sum_probs=18.8
Q ss_pred CCccccccCCCCcEEEcccccccchhhhchh
Q 026438 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (238)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~~CD~~ 31 (238)
|++.|..|+ +.-++|=++-...+|..|...
T Consensus 6 m~VkCp~C~-~~q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 6 MDVKCPGCY-NIQTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp EEEE-TTT--SEEEEETT-SS-EE-SSSTSE
T ss_pred EEEECCCCC-CeeEEEecCCeEEEcccCCCE
Confidence 678899998 466778778888888888643
Done!