Query 026124
Match_columns 243
No_of_seqs 176 out of 550
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 04:04:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026124.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026124hhsearch_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 97.6 4.5E-05 9.8E-10 49.0 2.4 39 3-47 1-39 (39)
2 cd00021 BBOX B-Box-type zinc f 97.2 0.00025 5.5E-09 45.5 2.6 38 56-99 2-39 (39)
3 PF00643 zf-B_box: B-box zinc 97.0 0.00056 1.2E-08 45.1 2.7 39 3-47 4-42 (42)
4 smart00336 BBOX B-Box-type zin 97.0 0.0006 1.3E-08 44.3 2.5 39 3-47 4-42 (42)
5 PF00643 zf-B_box: B-box zinc 96.6 0.00087 1.9E-08 44.1 0.9 40 54-99 3-42 (42)
6 smart00336 BBOX B-Box-type zin 96.4 0.0032 6.8E-08 40.8 2.7 39 55-99 4-42 (42)
7 KOG4367 Predicted Zn-finger pr 95.3 0.0049 1.1E-07 60.7 0.0 82 3-84 163-253 (699)
8 PF13248 zf-ribbon_3: zinc-rib 72.0 2.7 5.8E-05 25.4 1.5 25 1-31 1-25 (26)
9 KOG2807 RNA polymerase II tran 67.3 1.9 4.1E-05 41.5 0.2 76 11-86 273-365 (378)
10 KOG0129 Predicted RNA-binding 64.1 2.1 4.6E-05 43.0 -0.1 47 41-87 442-495 (520)
11 PF12773 DZR: Double zinc ribb 61.7 9.4 0.0002 25.7 2.8 16 18-33 8-23 (50)
12 PF14776 UNC-79: Cation-channe 60.5 6.8 0.00015 39.6 2.6 66 22-88 227-304 (525)
13 PRK14559 putative protein seri 58.5 5.7 0.00012 41.1 1.7 25 1-32 1-25 (645)
14 PF09416 UPF1_Zn_bind: RNA hel 54.2 9.1 0.0002 32.9 2.0 78 4-81 2-94 (152)
15 KOG4367 Predicted Zn-finger pr 51.1 5.4 0.00012 40.0 0.2 52 54-105 162-215 (699)
16 PRK00415 rps27e 30S ribosomal 41.0 14 0.00031 27.0 1.1 31 1-32 10-40 (59)
17 cd02342 ZZ_UBA_plant Zinc fing 40.2 23 0.0005 24.4 1.9 30 3-32 1-34 (43)
18 PF07649 C1_3: C1-like domain; 39.7 11 0.00024 23.2 0.3 26 4-34 2-27 (30)
19 PF07975 C1_4: TFIIH C1-like d 39.3 18 0.00038 25.7 1.3 23 13-35 20-42 (51)
20 TIGR00622 ssl1 transcription f 39.3 20 0.00044 29.3 1.8 62 25-86 18-101 (112)
21 PF04438 zf-HIT: HIT zinc fing 39.1 12 0.00027 23.5 0.4 25 1-26 1-25 (30)
22 KOG3576 Ovo and related transc 37.7 5.1 0.00011 36.6 -2.1 57 3-63 118-182 (267)
23 KOG0129 Predicted RNA-binding 37.0 14 0.0003 37.4 0.6 42 3-47 456-504 (520)
24 KOG1428 Inhibitor of type V ad 33.5 11 0.00023 43.3 -0.9 58 53-112 3321-3384(3738)
25 KOG1428 Inhibitor of type V ad 32.1 20 0.00042 41.4 0.8 45 3-49 3323-3369(3738)
26 KOG4582 Uncharacterized conser 31.2 32 0.00069 31.9 2.0 38 3-40 153-196 (278)
27 PF03107 C1_2: C1 domain; Int 31.0 22 0.00047 22.0 0.6 26 4-34 2-27 (30)
28 COG5151 SSL1 RNA polymerase II 29.5 12 0.00026 36.1 -1.1 80 7-86 299-408 (421)
29 PF13240 zinc_ribbon_2: zinc-r 29.1 38 0.00082 20.0 1.4 21 57-83 2-22 (23)
30 KOG2462 C2H2-type Zn-finger pr 27.1 26 0.00057 32.9 0.6 56 3-64 131-197 (279)
31 PF10235 Cript: Microtubule-as 26.0 45 0.00098 26.4 1.7 47 34-83 27-78 (90)
32 cd02335 ZZ_ADA2 Zinc finger, Z 25.3 86 0.0019 21.4 2.8 29 56-84 2-34 (49)
33 PF01667 Ribosomal_S27e: Ribos 24.4 25 0.00054 25.4 -0.0 30 1-31 6-35 (55)
34 KOG0329 ATP-dependent RNA heli 24.0 34 0.00073 32.7 0.8 26 204-236 218-243 (387)
35 PLN00209 ribosomal protein S27 23.4 39 0.00085 26.6 0.9 30 1-31 35-64 (86)
36 PTZ00083 40S ribosomal protein 22.7 41 0.0009 26.4 0.9 30 1-31 34-63 (85)
37 PF00569 ZZ: Zinc finger, ZZ t 22.5 60 0.0013 21.8 1.6 30 2-31 4-37 (46)
38 PF08274 PhnA_Zn_Ribbon: PhnA 22.3 46 0.001 21.1 0.9 25 54-81 2-26 (30)
39 PF04216 FdhE: Protein involve 21.8 59 0.0013 29.8 1.9 12 4-15 174-185 (290)
40 PF11781 RRN7: RNA polymerase 21.5 56 0.0012 21.4 1.2 24 4-30 10-33 (36)
41 PRK14714 DNA polymerase II lar 21.3 54 0.0012 36.8 1.7 25 57-84 695-719 (1337)
42 KOG1280 Uncharacterized conser 20.4 44 0.00095 32.6 0.8 37 38-84 2-42 (381)
43 TIGR02098 MJ0042_CXXC MJ0042 f 20.4 76 0.0017 20.1 1.7 10 1-10 1-10 (38)
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=97.60 E-value=4.5e-05 Score=49.01 Aligned_cols=39 Identities=41% Similarity=0.820 Sum_probs=34.0
Q ss_pred ccccccCCCCeEEEecccccccchhhchhcccCcccccCccccee
Q 026124 3 IQCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (243)
Q Consensus 3 ~~Cd~C~~apA~vyC~aD~A~LC~~CD~~vHsaN~La~rH~RvpL 47 (243)
..|+.++++++.+||..|++.+|..|+...| +.|.|++|
T Consensus 1 ~~C~~H~~~~~~~fC~~~~~~iC~~C~~~~H------~~H~~~~i 39 (39)
T cd00021 1 RLCDEHGEEPLSLFCETDRALLCVDCDLSVH------SGHRRVPL 39 (39)
T ss_pred CCCCccCCcceEEEeCccChhhhhhcChhhc------CCCCEeeC
Confidence 3689999889999999999999999998777 37888875
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=97.23 E-value=0.00025 Score=45.47 Aligned_cols=38 Identities=42% Similarity=0.831 Sum_probs=33.3
Q ss_pred CCcccccCCeeEEeccCcccccccCCCCccCCCCCCCCCcceee
Q 026124 56 PCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (243)
Q Consensus 56 ~Cd~C~~~pA~v~C~~D~a~LC~~CD~~iHsan~ls~~HqR~~l 99 (243)
.|+.|+.+++.+||.+|...+|..|+...| ++|+++++
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 47888764
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=97.03 E-value=0.00056 Score=45.09 Aligned_cols=39 Identities=23% Similarity=0.575 Sum_probs=33.6
Q ss_pred ccccccCCCCeEEEecccccccchhhchhcccCcccccCccccee
Q 026124 3 IQCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (243)
Q Consensus 3 ~~Cd~C~~apA~vyC~aD~A~LC~~CD~~vHsaN~La~rH~RvpL 47 (243)
..|+.+++.++.+||..++..+|..|....|.. |..++|
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 579999998899999999999999999988854 877764
No 4
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.98 E-value=0.0006 Score=44.31 Aligned_cols=39 Identities=36% Similarity=0.642 Sum_probs=33.5
Q ss_pred ccccccCCCCeEEEecccccccchhhchhcccCcccccCccccee
Q 026124 3 IQCDVCEKAPATVICCADEAALCAKCDVEVHAANKLASKHQRLLL 47 (243)
Q Consensus 3 ~~Cd~C~~apA~vyC~aD~A~LC~~CD~~vHsaN~La~rH~RvpL 47 (243)
..|..+++.++.+||..|++.+|..|....| +.|.+++|
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 5799999889999999999999999997766 67777664
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=96.56 E-value=0.00087 Score=44.15 Aligned_cols=40 Identities=23% Similarity=0.494 Sum_probs=33.1
Q ss_pred CCCCcccccCCeeEEeccCcccccccCCCCccCCCCCCCCCcceee
Q 026124 54 LPPCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (243)
Q Consensus 54 ~p~Cd~C~~~pA~v~C~~D~a~LC~~CD~~iHsan~ls~~HqR~~l 99 (243)
...|+.|++..+.+||.++...+|..|....|. +|+.++|
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 346999999999999999999999999988874 3877654
No 6
>smart00336 BBOX B-Box-type zinc finger.
Probab=96.38 E-value=0.0032 Score=40.85 Aligned_cols=39 Identities=41% Similarity=0.782 Sum_probs=32.9
Q ss_pred CCCcccccCCeeEEeccCcccccccCCCCccCCCCCCCCCcceee
Q 026124 55 PPCDICQEKAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLA 99 (243)
Q Consensus 55 p~Cd~C~~~pA~v~C~~D~a~LC~~CD~~iHsan~ls~~HqR~~l 99 (243)
..|+.|+..++.+||..|...+|..|....| ++|.+.++
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=95.26 E-value=0.0049 Score=60.73 Aligned_cols=82 Identities=26% Similarity=0.518 Sum_probs=68.5
Q ss_pred ccccccCCC--CeEEEecccccccchhhchhcccCcccccCcccceeccc-------cCCCCCCcccccCCeeEEeccCc
Q 026124 3 IQCDVCEKA--PATVICCADEAALCAKCDVEVHAANKLASKHQRLLLQCL-------SNKLPPCDICQEKAAFIFCVEDR 73 (243)
Q Consensus 3 ~~Cd~C~~a--pA~vyC~aD~A~LC~~CD~~vHsaN~La~rH~RvpL~~~-------~~~~p~Cd~C~~~pA~v~C~~D~ 73 (243)
..|..|+++ .|+|+|..+..+.|.-|..+.|-+...+.||.-+|-++. +.+...|..|+-+.-..||..+.
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 369999985 589999999999999999999998888889987775543 23466799999998889999999
Q ss_pred ccccccCCCCc
Q 026124 74 ALFCKDCDEPI 84 (243)
Q Consensus 74 a~LC~~CD~~i 84 (243)
...|-.|-...
T Consensus 243 ~pvc~~clee~ 253 (699)
T KOG4367|consen 243 MPVCYQCLEEG 253 (699)
T ss_pred ChHHHHHHHhh
Confidence 98998887654
No 8
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=72.04 E-value=2.7 Score=25.40 Aligned_cols=25 Identities=24% Similarity=0.706 Sum_probs=18.4
Q ss_pred CCccccccCCCCeEEEecccccccchhhchh
Q 026124 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (243)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~~CD~~ 31 (243)
|...|-.|+... .+++.+|..|..+
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 5667888888754
No 9
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=67.27 E-value=1.9 Score=41.48 Aligned_cols=76 Identities=25% Similarity=0.460 Sum_probs=52.4
Q ss_pred CCeEEEeccccccc------chhhchhcccCccccc-Ccccceecccc---C----CCCCCcccccCC---eeEEeccCc
Q 026124 11 APATVICCADEAAL------CAKCDVEVHAANKLAS-KHQRLLLQCLS---N----KLPPCDICQEKA---AFIFCVEDR 73 (243)
Q Consensus 11 apA~vyC~aD~A~L------C~~CD~~vHsaN~La~-rH~RvpL~~~~---~----~~p~Cd~C~~~p---A~v~C~~D~ 73 (243)
..+.++|..+.|.. |.-|+...=++--|++ =|.-.||.+.. . ++..|-.|+... ..+.|..+.
T Consensus 273 ~~~Gy~CP~CkakvCsLP~eCpiC~ltLVss~hLARSyhhL~PL~~F~Eip~~~~~~~~~Cf~C~~~~~~~~~y~C~~Ck 352 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVCSLPIECPICSLTLVSSPHLARSYHHLFPLKPFVEIPETEYNGSRFCFACQGELLSSGRYRCESCK 352 (378)
T ss_pred ccCceeCCcccCeeecCCccCCccceeEecchHHHHHHHhhcCCcchhhccccccCCCcceeeeccccCCCCcEEchhcc
Confidence 45668888888876 4567766555444554 56667775542 1 244599995433 456799999
Q ss_pred ccccccCCCCccC
Q 026124 74 ALFCKDCDEPIHS 86 (243)
Q Consensus 74 a~LC~~CD~~iHs 86 (243)
..||.+||.-+|.
T Consensus 353 ~~FCldCDv~iHe 365 (378)
T KOG2807|consen 353 NVFCLDCDVFIHE 365 (378)
T ss_pred ceeeccchHHHHh
Confidence 9999999998884
No 10
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=64.08 E-value=2.1 Score=42.98 Aligned_cols=47 Identities=26% Similarity=0.445 Sum_probs=37.6
Q ss_pred CcccceeccccCCCCCCccccc-----CCeeEEec--cCcccccccCCCCccCC
Q 026124 41 KHQRLLLQCLSNKLPPCDICQE-----KAAFIFCV--EDRALFCKDCDEPIHSP 87 (243)
Q Consensus 41 rH~RvpL~~~~~~~p~Cd~C~~-----~pA~v~C~--~D~a~LC~~CD~~iHsa 87 (243)
-++||-+.+.--.-..|+.|+. +.|-+||. .|..++|..|-..+|+-
T Consensus 442 ~~KRVEIkPYv~eDq~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~ 495 (520)
T KOG0129|consen 442 IDKRVEIKPYVMEDQLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG 495 (520)
T ss_pred cceeeeecceeccccchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC
Confidence 3458877655545677999999 88999995 57889999999999963
No 11
>PF12773 DZR: Double zinc ribbon
Probab=61.73 E-value=9.4 Score=25.68 Aligned_cols=16 Identities=25% Similarity=0.711 Sum_probs=10.1
Q ss_pred cccccccchhhchhcc
Q 026124 18 CADEAALCAKCDVEVH 33 (243)
Q Consensus 18 ~aD~A~LC~~CD~~vH 33 (243)
..+++.+|..|...+-
T Consensus 8 ~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 8 NPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCccccCChhhcCChh
Confidence 3456777777775544
No 12
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=60.46 E-value=6.8 Score=39.64 Aligned_cols=66 Identities=21% Similarity=0.397 Sum_probs=42.2
Q ss_pred cccchhhchhcccCcccccC-cccceeccccCC--CCCCcccccCCeeEEec---------cCcccccccCCCCccCCC
Q 026124 22 AALCAKCDVEVHAANKLASK-HQRLLLQCLSNK--LPPCDICQEKAAFIFCV---------EDRALFCKDCDEPIHSPG 88 (243)
Q Consensus 22 A~LC~~CD~~vHsaN~La~r-H~RvpL~~~~~~--~p~Cd~C~~~pA~v~C~---------~D~a~LC~~CD~~iHsan 88 (243)
.+||.+|...+|+.-+.... +.-.|+.+.+.. ...|..- ++.|.+.|. +--..||..|....|+.-
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 57999999999986544332 344455444321 2234432 566888874 224689999999998644
No 13
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=58.50 E-value=5.7 Score=41.09 Aligned_cols=25 Identities=24% Similarity=0.671 Sum_probs=15.9
Q ss_pred CCccccccCCCCeEEEecccccccchhhchhc
Q 026124 1 MKIQCDVCEKAPATVICCADEAALCAKCDVEV 32 (243)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~~CD~~v 32 (243)
|+ .|-.|+.. ..+.+.+|..|...+
T Consensus 1 M~-~Cp~Cg~~------n~~~akFC~~CG~~l 25 (645)
T PRK14559 1 ML-ICPQCQFE------NPNNNRFCQKCGTSL 25 (645)
T ss_pred CC-cCCCCCCc------CCCCCccccccCCCC
Confidence 53 69999875 245566677775443
No 14
>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=54.25 E-value=9.1 Score=32.93 Aligned_cols=78 Identities=24% Similarity=0.533 Sum_probs=38.6
Q ss_pred cccccC--CCCeEEEecccccccchhhch--hcccCccc-ccCcccceeccccC---CCCCCcccccCCeeEE----ecc
Q 026124 4 QCDVCE--KAPATVICCADEAALCAKCDV--EVHAANKL-ASKHQRLLLQCLSN---KLPPCDICQEKAAFIF----CVE 71 (243)
Q Consensus 4 ~Cd~C~--~apA~vyC~aD~A~LC~~CD~--~vHsaN~L-a~rH~RvpL~~~~~---~~p~Cd~C~~~pA~v~----C~~ 71 (243)
.|.+|+ ....++.|..+.-.+|..=+. .-|--|-| .+||.-|-|-+-.. ....|..|+.+..+.. ...
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 567778899999999985443 22333333 35888777744322 3556999998885443 444
Q ss_pred Cc--cccccc-CC
Q 026124 72 DR--ALFCKD-CD 81 (243)
Q Consensus 72 D~--a~LC~~-CD 81 (243)
|. ..||+. |.
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 577866 64
No 15
>KOG4367 consensus Predicted Zn-finger protein [Function unknown]
Probab=51.09 E-value=5.4 Score=40.00 Aligned_cols=52 Identities=23% Similarity=0.532 Sum_probs=42.7
Q ss_pred CCCCcccccCC--eeEEeccCcccccccCCCCccCCCCCCCCCcceeeccceee
Q 026124 54 LPPCDICQEKA--AFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLATGIRVA 105 (243)
Q Consensus 54 ~p~Cd~C~~~p--A~v~C~~D~a~LC~~CD~~iHsan~ls~~HqR~~l~g~rV~ 105 (243)
...|..|...+ |.|+|..+..++|.-|....|-+-...++|..++...=||.
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 44588887766 88999999999999999999987776788988887754655
No 16
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=41.01 E-value=14 Score=27.04 Aligned_cols=31 Identities=23% Similarity=0.564 Sum_probs=26.4
Q ss_pred CCccccccCCCCeEEEecccccccchhhchhc
Q 026124 1 MKIQCDVCEKAPATVICCADEAALCAKCDVEV 32 (243)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~~CD~~v 32 (243)
|++.|..|+ +.-++|=++..+..|..|...+
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 678999999 4788999999999999998544
No 17
>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=40.15 E-value=23 Score=24.45 Aligned_cols=30 Identities=33% Similarity=0.576 Sum_probs=21.5
Q ss_pred ccccccCCCCe---EEEecccccc-cchhhchhc
Q 026124 3 IQCDVCEKAPA---TVICCADEAA-LCAKCDVEV 32 (243)
Q Consensus 3 ~~Cd~C~~apA---~vyC~aD~A~-LC~~CD~~v 32 (243)
+.||.|+..|= .+.|..+.-+ ||..|-.+.
T Consensus 1 I~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~~ 34 (43)
T cd02342 1 IQCDGCGVLPITGPRYKSKVKEDYDLCTICFSRM 34 (43)
T ss_pred CCCCCCCCCcccccceEeCCCCCCccHHHHhhhh
Confidence 57999998553 4668877655 899996554
No 18
>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=39.73 E-value=11 Score=23.16 Aligned_cols=26 Identities=31% Similarity=0.740 Sum_probs=8.5
Q ss_pred cccccCCCCeEEEecccccccchhhchhccc
Q 026124 4 QCDVCEKAPATVICCADEAALCAKCDVEVHA 34 (243)
Q Consensus 4 ~Cd~C~~apA~vyC~aD~A~LC~~CD~~vHs 34 (243)
.|+.|++.... +..+.|..||-.+|.
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 58889875442 234567888877774
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=39.30 E-value=18 Score=25.72 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=15.4
Q ss_pred eEEEecccccccchhhchhcccC
Q 026124 13 ATVICCADEAALCAKCDVEVHAA 35 (243)
Q Consensus 13 A~vyC~aD~A~LC~~CD~~vHsa 35 (243)
..+.|..+...+|.+||.-||..
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 45669999999999999999974
No 20
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=39.28 E-value=20 Score=29.33 Aligned_cols=62 Identities=27% Similarity=0.522 Sum_probs=40.0
Q ss_pred chhhchhcccCccccc-Ccccceecccc-------CCCCCCcccccCC--------------eeEEeccCcccccccCCC
Q 026124 25 CAKCDVEVHAANKLAS-KHQRLLLQCLS-------NKLPPCDICQEKA--------------AFIFCVEDRALFCKDCDE 82 (243)
Q Consensus 25 C~~CD~~vHsaN~La~-rH~RvpL~~~~-------~~~p~Cd~C~~~p--------------A~v~C~~D~a~LC~~CD~ 82 (243)
|.-|+..+=++.-|+| =|.-.||.... .....|-.|+..- ..+.|..+...||.+||.
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 5667665544444554 35555554321 1133599998732 235699999999999999
Q ss_pred CccC
Q 026124 83 PIHS 86 (243)
Q Consensus 83 ~iHs 86 (243)
-+|.
T Consensus 98 fiHe 101 (112)
T TIGR00622 98 FVHE 101 (112)
T ss_pred hhhh
Confidence 9885
No 21
>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=39.15 E-value=12 Score=23.51 Aligned_cols=25 Identities=32% Similarity=0.644 Sum_probs=17.1
Q ss_pred CCccccccCCCCeEEEecccccccch
Q 026124 1 MKIQCDVCEKAPATVICCADEAALCA 26 (243)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~ 26 (243)
+..+|.+|+. .+...|....+.+|.
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 3567999998 888889998888875
No 22
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=37.72 E-value=5.1 Score=36.58 Aligned_cols=57 Identities=23% Similarity=0.557 Sum_probs=40.6
Q ss_pred ccccccCCC-------CeEEEeccc-ccccchhhchhcccCcccccCcccceeccccCCCCCCcccccC
Q 026124 3 IQCDVCEKA-------PATVICCAD-EAALCAKCDVEVHAANKLASKHQRLLLQCLSNKLPPCDICQEK 63 (243)
Q Consensus 3 ~~Cd~C~~a-------pA~vyC~aD-~A~LC~~CD~~vHsaN~La~rH~RvpL~~~~~~~p~Cd~C~~~ 63 (243)
..|++|++. .--+-|.+| ..+||.-|....|-+-. +.||.|..- +.....|..|..+
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 58899999999987654 589999753 2334457777554
No 23
>KOG0129 consensus Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis]
Probab=36.95 E-value=14 Score=37.36 Aligned_cols=42 Identities=21% Similarity=0.434 Sum_probs=33.4
Q ss_pred ccccccCC-----CCeEEEecc--cccccchhhchhcccCcccccCccccee
Q 026124 3 IQCDVCEK-----APATVICCA--DEAALCAKCDVEVHAANKLASKHQRLLL 47 (243)
Q Consensus 3 ~~Cd~C~~-----apA~vyC~a--D~A~LC~~CD~~vHsaN~La~rH~RvpL 47 (243)
..||.|+. ..|.+||++ |--++|..|=+.+|+. ..++.-.||
T Consensus 456 q~CdeC~g~~c~~q~aPfFC~n~~C~QYYCe~CWa~~HS~---~~r~~HkPl 504 (520)
T KOG0129|consen 456 QLCDECGGRRCGGQFAPFFCRNATCFQYYCESCWAKIHSG---PGREHHKPL 504 (520)
T ss_pred cchhhhcCeeccCccCCcccCCccHHhhhchHHHHHhhcC---CchhcCCce
Confidence 46999998 889999995 5689999999999985 244444565
No 24
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=33.52 E-value=11 Score=43.29 Aligned_cols=58 Identities=33% Similarity=0.645 Sum_probs=44.0
Q ss_pred CCCCCccccc--CCeeEEeccCcccccccCCCCccCCCCCCCCCcceeec----cceeeccCCCCc
Q 026124 53 KLPPCDICQE--KAAFIFCVEDRALFCKDCDEPIHSPGSLSANHQRFLAT----GIRVALSSSCSK 112 (243)
Q Consensus 53 ~~p~Cd~C~~--~pA~v~C~~D~a~LC~~CD~~iHsan~ls~~HqR~~l~----g~rV~~~s~C~~ 112 (243)
+.|.|+.|.+ ..|.++|..+. .||.+||.-.|..- ..++|+|.-+. .|.|-+..||.-
T Consensus 3321 Q~PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHr-rtktH~~q~f~eeeea~kvdlHeGC~R 3384 (3738)
T KOG1428|consen 3321 QMPMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHR-RTKTHQRQVFKEEEEAIKVDLHEGCGR 3384 (3738)
T ss_pred cCCcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHh-hccchhhhhhhhhhhhcccchhhcchH
Confidence 4788999865 45889999888 89999997765432 34789996554 477888899954
No 25
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=32.06 E-value=20 Score=41.35 Aligned_cols=45 Identities=27% Similarity=0.535 Sum_probs=33.5
Q ss_pred ccccccCC--CCeEEEecccccccchhhchhcccCcccccCcccceecc
Q 026124 3 IQCDVCEK--APATVICCADEAALCAKCDVEVHAANKLASKHQRLLLQC 49 (243)
Q Consensus 3 ~~Cd~C~~--apA~vyC~aD~A~LC~~CD~~vHsaN~La~rH~RvpL~~ 49 (243)
++||.-.. ..|.++|..+. +||.+||+-.|-.. -.+.|+|--+.+
T Consensus 3323 PmCdNHDDG~TaA~ilC~~C~-nLCtdC~~~lHLHr-rtktH~~q~f~e 3369 (3738)
T KOG1428|consen 3323 PMCDNHDDGETAAIILCNVCG-NLCTDCDRFLHLHR-RTKTHQRQVFKE 3369 (3738)
T ss_pred CcccCCCCCceeEEEehhhhh-hhHHHHHHHHHHHh-hccchhhhhhhh
Confidence 46776544 57889999888 99999998877533 357899876644
No 26
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=31.25 E-value=32 Score=31.89 Aligned_cols=38 Identities=32% Similarity=0.666 Sum_probs=27.8
Q ss_pred ccccccCCC---CeEEEecccccc-cchhhchhc--ccCccccc
Q 026124 3 IQCDVCEKA---PATVICCADEAA-LCAKCDVEV--HAANKLAS 40 (243)
Q Consensus 3 ~~Cd~C~~a---pA~vyC~aD~A~-LC~~CD~~v--HsaN~La~ 40 (243)
+.||.|... ...+-|..+..+ ||.+|.+.. |.+-++++
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 689999983 456779988654 999999884 44444444
No 27
>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=30.99 E-value=22 Score=22.00 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=18.4
Q ss_pred cccccCCCCeEEEecccccccchhhchhccc
Q 026124 4 QCDVCEKAPATVICCADEAALCAKCDVEVHA 34 (243)
Q Consensus 4 ~Cd~C~~apA~vyC~aD~A~LC~~CD~~vHs 34 (243)
.|++|++.....+ .+-|..|+..+|.
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 5899988665553 6777777777764
No 28
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=29.51 E-value=12 Score=36.08 Aligned_cols=80 Identities=26% Similarity=0.508 Sum_probs=52.3
Q ss_pred ccCC--CCeEEEeccccccc------chhhchhcccCcccc-cCcccceeccccC-------CCCCCcccccC-------
Q 026124 7 VCEK--APATVICCADEAAL------CAKCDVEVHAANKLA-SKHQRLLLQCLSN-------KLPPCDICQEK------- 63 (243)
Q Consensus 7 ~C~~--apA~vyC~aD~A~L------C~~CD~~vHsaN~La-~rH~RvpL~~~~~-------~~p~Cd~C~~~------- 63 (243)
+|.. ..+.++|..+.+.. |.-|+...=...-|+ +-|.-.||....- +...|-.|+..
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 4544 34567888887765 567876543322233 4677778765421 34558888872
Q ss_pred -------CeeEEeccCcccccccCCCCccC
Q 026124 64 -------AAFIFCVEDRALFCKDCDEPIHS 86 (243)
Q Consensus 64 -------pA~v~C~~D~a~LC~~CD~~iHs 86 (243)
...+.|..+...||.+||.-+|.
T Consensus 379 ~~~~~~ss~rY~Ce~CK~~FC~dCdvfiHe 408 (421)
T COG5151 379 PFDESTSSGRYQCELCKSTFCSDCDVFIHE 408 (421)
T ss_pred cccccccccceechhhhhhhhhhhHHHHHH
Confidence 23456999999999999988874
No 29
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=29.13 E-value=38 Score=20.02 Aligned_cols=21 Identities=43% Similarity=1.053 Sum_probs=13.6
Q ss_pred CcccccCCeeEEeccCcccccccCCCC
Q 026124 57 CDICQEKAAFIFCVEDRALFCKDCDEP 83 (243)
Q Consensus 57 Cd~C~~~pA~v~C~~D~a~LC~~CD~~ 83 (243)
|..|+.+. .+.+.+|..|..+
T Consensus 2 Cp~CG~~~------~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEI------EDDAKFCPNCGTP 22 (23)
T ss_pred CcccCCCC------CCcCcchhhhCCc
Confidence 66666664 4567778777644
No 30
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=27.07 E-value=26 Score=32.93 Aligned_cols=56 Identities=23% Similarity=0.306 Sum_probs=34.5
Q ss_pred ccccccCCCCeEEE---------ecccc--cccchhhchhcccCcccccCcccceeccccCCCCCCcccccCC
Q 026124 3 IQCDVCEKAPATVI---------CCADE--AALCAKCDVEVHAANKLASKHQRLLLQCLSNKLPPCDICQEKA 64 (243)
Q Consensus 3 ~~Cd~C~~apA~vy---------C~aD~--A~LC~~CD~~vHsaN~La~rH~RvpL~~~~~~~p~Cd~C~~~p 64 (243)
..|+.|++.-|+.- |..|+ |+-|..||+.-=+ =..+++|.|.--.+ -.|.+|+.+-
T Consensus 131 ~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvS-mpALkMHirTH~l~-----c~C~iCGKaF 197 (279)
T KOG2462|consen 131 YKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVS-MPALKMHIRTHTLP-----CECGICGKAF 197 (279)
T ss_pred eeccccccccccccccchhhcccccccccccccCCCCCceeee-hHHHhhHhhccCCC-----cccccccccc
Confidence 46888888766654 77775 7889999954333 23456777654211 1366666543
No 31
>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=25.99 E-value=45 Score=26.36 Aligned_cols=47 Identities=26% Similarity=0.465 Sum_probs=28.6
Q ss_pred cCcccccCcccceeccccCCCCCCcccccCCee---EEeccCc--ccccccCCCC
Q 026124 34 AANKLASKHQRLLLQCLSNKLPPCDICQEKAAF---IFCVEDR--ALFCKDCDEP 83 (243)
Q Consensus 34 saN~La~rH~RvpL~~~~~~~p~Cd~C~~~pA~---v~C~~D~--a~LC~~CD~~ 83 (243)
+-|+|+++-.|-|+ ...+..|.+|...... .||..+. ..+|.-|...
T Consensus 27 ~eNKlLs~~~~nPy---~~~~~~C~~CK~~v~q~g~~YCq~CAYkkGiCamCGKk 78 (90)
T PF10235_consen 27 GENKLLSKKKKNPY---APYSSKCKICKTKVHQPGAKYCQTCAYKKGICAMCGKK 78 (90)
T ss_pred cceeeecccccCcc---cccCccccccccccccCCCccChhhhcccCcccccCCe
Confidence 46888887777554 3346679999887633 4454442 3455555433
No 32
>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=25.31 E-value=86 Score=21.37 Aligned_cols=29 Identities=28% Similarity=0.525 Sum_probs=19.0
Q ss_pred CCcccccCCee---EEeccC-cccccccCCCCc
Q 026124 56 PCDICQEKAAF---IFCVED-RALFCKDCDEPI 84 (243)
Q Consensus 56 ~Cd~C~~~pA~---v~C~~D-~a~LC~~CD~~i 84 (243)
.|+.|...... +.|..+ .--||.+|-...
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 47777766644 556666 457888887544
No 33
>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=24.36 E-value=25 Score=25.39 Aligned_cols=30 Identities=27% Similarity=0.560 Sum_probs=19.6
Q ss_pred CCccccccCCCCeEEEecccccccchhhchh
Q 026124 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (243)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~~CD~~ 31 (243)
|++.|..|++ .-++|=.+-...+|..|...
T Consensus 6 m~VkCp~C~~-~q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 6 MDVKCPGCYN-IQTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp EEEE-TTT-S-EEEEETT-SS-EE-SSSTSE
T ss_pred EEEECCCCCC-eeEEEecCCeEEEcccCCCE
Confidence 6788999994 67778888888888888743
No 34
>KOG0329 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=24.04 E-value=34 Score=32.65 Aligned_cols=26 Identities=42% Similarity=0.629 Sum_probs=21.2
Q ss_pred cchhhhhhhhhhhhhhhhhHhHHHHHHhhcCCC
Q 026124 204 SQMMMMSISLSQILVKHKEIISTVIHRLMNYPY 236 (243)
Q Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 236 (243)
-+-||+++.+|+= |..|||+.||+|.
T Consensus 218 KQvmmfsatlske-------iRpvC~kFmQdPm 243 (387)
T KOG0329|consen 218 KQVMMFSATLSKE-------IRPVCHKFMQDPM 243 (387)
T ss_pred ceeeeeeeecchh-------hHHHHHhhhcCch
Confidence 4678888887753 6789999999985
No 35
>PLN00209 ribosomal protein S27; Provisional
Probab=23.41 E-value=39 Score=26.59 Aligned_cols=30 Identities=23% Similarity=0.635 Sum_probs=24.9
Q ss_pred CCccccccCCCCeEEEecccccccchhhchh
Q 026124 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (243)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~~CD~~ 31 (243)
|++.|..|++ .-+||=.+-....|..|...
T Consensus 35 m~VkCp~C~n-~q~VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 35 MDVKCQGCFN-ITTVFSHSQTVVVCGSCQTV 64 (86)
T ss_pred EEEECCCCCC-eeEEEecCceEEEccccCCE
Confidence 6788999994 77888888899999999743
No 36
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=22.75 E-value=41 Score=26.39 Aligned_cols=30 Identities=30% Similarity=0.720 Sum_probs=24.9
Q ss_pred CCccccccCCCCeEEEecccccccchhhchh
Q 026124 1 MKIQCDVCEKAPATVICCADEAALCAKCDVE 31 (243)
Q Consensus 1 M~~~Cd~C~~apA~vyC~aD~A~LC~~CD~~ 31 (243)
|++.|-.|++ .-+||=.+-...+|..|...
T Consensus 34 m~VkCp~C~n-~q~VFShA~t~V~C~~Cg~~ 63 (85)
T PTZ00083 34 MDVKCPGCSQ-ITTVFSHAQTVVLCGGCSSQ 63 (85)
T ss_pred EEEECCCCCC-eeEEEecCceEEEccccCCE
Confidence 6788999994 77888889999999999743
No 37
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=22.53 E-value=60 Score=21.85 Aligned_cols=30 Identities=23% Similarity=0.486 Sum_probs=20.3
Q ss_pred CccccccCCC---CeEEEecccc-cccchhhchh
Q 026124 2 KIQCDVCEKA---PATVICCADE-AALCAKCDVE 31 (243)
Q Consensus 2 ~~~Cd~C~~a---pA~vyC~aD~-A~LC~~CD~~ 31 (243)
...|+.|+.. ...+.|..+. --||..|=.+
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~ 37 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSK 37 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhC
Confidence 5789999983 4557788774 7799999765
No 38
>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=22.33 E-value=46 Score=21.14 Aligned_cols=25 Identities=28% Similarity=0.925 Sum_probs=12.1
Q ss_pred CCCCcccccCCeeEEeccCcccccccCC
Q 026124 54 LPPCDICQEKAAFIFCVEDRALFCKDCD 81 (243)
Q Consensus 54 ~p~Cd~C~~~pA~v~C~~D~a~LC~~CD 81 (243)
++.|+.|++.-.. .+...+.|..|.
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 4679999988755 566678888885
No 39
>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=21.80 E-value=59 Score=29.79 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=4.1
Q ss_pred cccccCCCCeEE
Q 026124 4 QCDVCEKAPATV 15 (243)
Q Consensus 4 ~Cd~C~~apA~v 15 (243)
.|-+|+..|..-
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 466666554443
No 40
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=21.48 E-value=56 Score=21.36 Aligned_cols=24 Identities=25% Similarity=0.623 Sum_probs=19.9
Q ss_pred cccccCCCCeEEEecccccccchhhch
Q 026124 4 QCDVCEKAPATVICCADEAALCAKCDV 30 (243)
Q Consensus 4 ~Cd~C~~apA~vyC~aD~A~LC~~CD~ 30 (243)
.|+.|+.. +|=..|.-+.|.+|..
T Consensus 10 ~C~~C~~~---~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR---WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe---EeEccCCEEEhhhCce
Confidence 49999864 8888999999999874
No 41
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.29 E-value=54 Score=36.84 Aligned_cols=25 Identities=24% Similarity=0.534 Sum_probs=12.1
Q ss_pred CcccccCCeeEEeccCcccccccCCCCc
Q 026124 57 CDICQEKAAFIFCVEDRALFCKDCDEPI 84 (243)
Q Consensus 57 Cd~C~~~pA~v~C~~D~a~LC~~CD~~i 84 (243)
|..|+..... ....+..|..|+.+.
T Consensus 695 CPsCGaev~~---des~a~~CP~CGtpl 719 (1337)
T PRK14714 695 CPDCGAEVPP---DESGRVECPRCDVEL 719 (1337)
T ss_pred CccCCCccCC---CccccccCCCCCCcc
Confidence 6666664311 111145677776554
No 42
>KOG1280 consensus Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only]
Probab=20.45 E-value=44 Score=32.59 Aligned_cols=37 Identities=27% Similarity=0.353 Sum_probs=26.8
Q ss_pred cccCcccceeccccCCCCCCcccccCCeeEEeccCc----ccccccCCCCc
Q 026124 38 LASKHQRLLLQCLSNKLPPCDICQEKAAFIFCVEDR----ALFCKDCDEPI 84 (243)
Q Consensus 38 La~rH~RvpL~~~~~~~p~Cd~C~~~pA~v~C~~D~----a~LC~~CD~~i 84 (243)
++++|++|- |+.|+...-.++|..|. --||.+|-.+.
T Consensus 2 ~~~rHe~v~----------CdgC~k~~~t~rrYkCL~C~DyDlC~sCyen~ 42 (381)
T KOG1280|consen 2 LTSRHEGVS----------CDGCGKTAFTFRRYKCLRCSDYDLCFSCYENG 42 (381)
T ss_pred CCCCcCCce----------eccccccceeeeeeEeeeecchhHHHHHhhcC
Confidence 578999996 99999988777654432 24777776544
No 43
>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=20.43 E-value=76 Score=20.06 Aligned_cols=10 Identities=50% Similarity=1.168 Sum_probs=7.5
Q ss_pred CCccccccCC
Q 026124 1 MKIQCDVCEK 10 (243)
Q Consensus 1 M~~~Cd~C~~ 10 (243)
|++.|..|+.
T Consensus 1 M~~~CP~C~~ 10 (38)
T TIGR02098 1 MRIQCPNCKT 10 (38)
T ss_pred CEEECCCCCC
Confidence 6777877775
Done!