Query 026840
Match_columns 232
No_of_seqs 142 out of 230
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 13:27:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026840.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026840hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3454 U1 snRNP-specific prot 100.0 3.4E-29 7.3E-34 212.3 3.9 141 3-151 1-161 (165)
2 PF06220 zf-U1: U1 zinc finger 99.6 4.4E-16 9.6E-21 103.9 1.8 37 3-39 1-38 (38)
3 COG5136 U1 snRNP-specific prot 99.1 1.4E-11 3.1E-16 106.0 -0.3 42 3-44 1-44 (188)
4 KOG1813 Predicted E3 ubiquitin 98.7 1.4E-09 3E-14 100.5 -0.7 46 25-83 169-214 (313)
5 COG5152 Uncharacterized conser 98.7 3.5E-09 7.7E-14 94.5 0.8 34 50-83 136-169 (259)
6 smart00451 ZnF_U1 U1-like zinc 98.2 4.6E-07 1E-11 56.9 0.3 35 3-38 1-35 (35)
7 PF00642 zf-CCCH: Zinc finger 98.1 4.9E-07 1.1E-11 55.9 -0.0 25 54-78 2-26 (27)
8 smart00356 ZnF_C3H1 zinc finge 97.7 1.7E-05 3.7E-10 47.2 1.7 22 56-78 5-26 (27)
9 PF12171 zf-C2H2_jaz: Zinc-fin 97.4 8E-05 1.7E-09 45.3 1.3 27 5-32 1-27 (27)
10 KOG1677 CCCH-type Zn-finger pr 96.9 0.0014 3E-08 58.9 4.9 35 49-83 171-205 (332)
11 KOG0150 Spliceosomal protein F 96.9 0.00032 6.8E-09 66.0 0.5 38 3-40 8-45 (336)
12 KOG2185 Predicted RNA-processi 95.2 0.0069 1.5E-07 59.2 0.7 32 51-83 136-167 (486)
13 PF12874 zf-met: Zinc-finger o 94.8 0.0065 1.4E-07 35.6 -0.3 25 6-31 1-25 (25)
14 PF14608 zf-CCCH_2: Zinc finge 93.4 0.046 1E-06 31.6 1.3 19 57-78 1-19 (19)
15 KOG4727 U1-like Zn-finger prot 93.3 0.028 6.1E-07 49.6 0.5 36 3-39 73-108 (193)
16 KOG1039 Predicted E3 ubiquitin 92.2 0.071 1.5E-06 50.6 1.6 25 56-81 9-33 (344)
17 KOG1677 CCCH-type Zn-finger pr 91.2 0.11 2.5E-06 46.7 1.7 35 49-83 126-161 (332)
18 PF13465 zf-H2C2_2: Zinc-finge 86.8 0.3 6.5E-06 29.6 0.8 15 2-16 11-25 (26)
19 KOG2494 C3H1-type Zn-finger pr 80.0 0.57 1.2E-05 44.7 0.1 26 54-80 36-62 (331)
20 KOG2333 Uncharacterized conser 79.3 0.65 1.4E-05 46.9 0.2 29 55-83 76-106 (614)
21 KOG3408 U1-like Zn-finger-cont 78.6 0.89 1.9E-05 38.3 0.8 36 2-38 54-89 (129)
22 PF08026 Antimicrobial_5: Bee 70.1 3.3 7.1E-05 28.4 1.7 19 138-156 4-22 (39)
23 PF13894 zf-C2H2_4: C2H2-type 68.1 2.4 5.1E-05 23.3 0.6 19 6-25 1-19 (24)
24 COG5063 CTH1 CCCH-type Zn-fing 64.3 4 8.6E-05 39.2 1.7 29 55-83 274-302 (351)
25 PF06212 GRIM-19: GRIM-19 prot 62.4 4 8.6E-05 34.1 1.2 11 141-151 10-20 (130)
26 COG0633 Fdx Ferredoxin [Energy 61.9 3.9 8.5E-05 31.9 1.0 17 193-209 38-56 (102)
27 PF00096 zf-C2H2: Zinc finger, 61.3 3.5 7.6E-05 23.3 0.5 12 6-17 1-12 (23)
28 KOG1763 Uncharacterized conser 60.8 2.8 6.1E-05 40.0 0.0 29 53-82 90-118 (343)
29 PF08394 Arc_trans_TRASH: Arch 60.3 2.9 6.4E-05 28.3 0.0 19 8-26 1-19 (37)
30 PF04988 AKAP95: A-kinase anch 53.9 5.3 0.00011 35.0 0.6 40 6-45 92-131 (165)
31 PHA02768 hypothetical protein; 52.6 5.6 0.00012 29.0 0.4 17 1-17 1-17 (55)
32 KOG1040 Polyadenylation factor 49.1 7.2 0.00016 37.1 0.7 26 52-78 74-99 (325)
33 KOG2384 Major histocompatibili 47.7 5.4 0.00012 36.3 -0.3 28 4-33 83-110 (223)
34 KOG2202 U2 snRNP splicing fact 47.2 4.9 0.00011 37.4 -0.7 39 45-83 5-43 (260)
35 COG5063 CTH1 CCCH-type Zn-fing 46.7 13 0.00028 35.8 2.0 28 53-80 312-339 (351)
36 COG5252 Uncharacterized conser 46.5 9.7 0.00021 35.7 1.1 75 35-140 116-213 (299)
37 PF12756 zf-C2H2_2: C2H2 type 46.0 4.6 0.0001 29.0 -0.9 30 5-35 50-79 (100)
38 PF01799 Fer2_2: [2Fe-2S] bind 40.3 8.3 0.00018 29.2 -0.3 10 190-199 21-30 (75)
39 PF13912 zf-C2H2_6: C2H2-type 39.7 12 0.00027 21.8 0.5 14 5-18 1-14 (27)
40 KOG3300 NADH:ubiquinone oxidor 38.2 16 0.00035 31.4 1.1 13 140-152 13-25 (146)
41 PF02748 PyrI_C: Aspartate car 38.1 12 0.00026 26.7 0.2 12 4-15 34-45 (52)
42 KOG0717 Molecular chaperone (D 38.1 12 0.00027 37.6 0.4 37 6-43 293-329 (508)
43 COG5188 PRP9 Splicing factor 3 35.9 10 0.00022 37.3 -0.4 33 4-37 237-269 (470)
44 PF03194 LUC7: LUC7 N_terminus 35.3 13 0.00028 33.8 0.0 28 6-33 191-220 (254)
45 smart00355 ZnF_C2H2 zinc finge 33.2 20 0.00044 19.4 0.6 20 6-26 1-20 (26)
46 PF13900 GVQW: Putative bindin 31.9 30 0.00065 24.8 1.5 18 126-144 3-20 (48)
47 smart00586 ZnF_DBF Zinc finger 31.8 8.7 0.00019 27.4 -1.3 13 194-206 4-16 (49)
48 PF07975 C1_4: TFIIH C1-like d 30.7 14 0.0003 26.6 -0.4 18 4-21 28-45 (51)
49 PF02162 XYPPX: XYPPX repeat ( 30.3 31 0.00067 19.5 1.0 9 142-150 3-11 (15)
50 KOG2482 Predicted C2H2-type Zn 30.2 12 0.00027 36.6 -0.9 37 5-42 195-233 (423)
51 KOG1492 C3H1-type Zn-finger pr 29.3 24 0.00053 33.1 0.8 27 54-80 287-313 (377)
52 COG5112 UFD2 U1-like Zn-finger 29.3 23 0.0005 29.6 0.6 35 3-38 53-87 (126)
53 KOG1595 CCCH-type Zn-finger pr 29.2 36 0.00079 34.6 2.1 29 53-82 234-262 (528)
54 PF04959 ARS2: Arsenite-resist 28.8 12 0.00025 33.7 -1.3 46 4-49 76-126 (214)
55 CHL00134 petF ferredoxin; Vali 27.8 27 0.00058 27.0 0.7 16 194-209 41-58 (99)
56 KOG3792 Transcription factor N 25.8 24 0.00051 37.4 0.1 31 3-34 357-387 (816)
57 KOG0854 Alkyl hydroperoxide re 25.5 26 0.00057 31.8 0.3 21 145-165 22-42 (224)
58 COG2080 CoxS Aerobic-type carb 23.9 22 0.00049 30.8 -0.4 8 192-199 97-104 (156)
59 TIGR02008 fdx_plant ferredoxin 23.8 33 0.00071 26.2 0.5 15 196-210 43-57 (97)
60 PRK09908 xanthine dehydrogenas 22.6 24 0.00052 30.5 -0.4 9 191-199 99-107 (159)
61 PF07535 zf-DBF: DBF zinc fing 22.3 25 0.00055 24.9 -0.3 14 194-207 4-17 (49)
62 PF10589 NADH_4Fe-4S: NADH-ubi 22.1 14 0.00031 25.3 -1.6 10 194-203 15-24 (46)
63 KOG2202 U2 snRNP splicing fact 21.6 42 0.0009 31.4 0.8 25 54-79 151-175 (260)
64 KOG0227 Splicing factor 3a, su 21.0 53 0.0011 30.0 1.3 35 3-38 51-85 (222)
65 TIGR03198 pucE xanthine dehydr 20.8 27 0.00059 29.7 -0.5 9 191-199 94-102 (151)
66 KOG1040 Polyadenylation factor 20.7 98 0.0021 29.6 3.1 26 54-79 104-129 (325)
No 1
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=99.95 E-value=3.4e-29 Score=212.31 Aligned_cols=141 Identities=21% Similarity=0.264 Sum_probs=118.2
Q ss_pred CCccccccccccc-cCChhhhhccCCCCcchHHHHHhhhccc-cCCCCCCCCcCccccccccccccCCCCCCceeccCCC
Q 026840 3 LGKYYCDYCDKQF-QDTYFARKRHLQGIQHLRAKALWYDSLN-ETNQTYPDGFPKGVCSRFVKTGFCPFGDSCKYLHPKN 80 (232)
Q Consensus 3 mkkYYCDYCdk~f-~Ds~~~RK~Hl~G~kH~Raka~yY~qFk-DPetIL~EE~~K~pCk~f~~TG~C~FGdsCkFsH~~~ 80 (232)
|+||||||||++| ||+++|||.|+.|++|++|+++||++|. +++++|.+|..+..|+.+ |+|.+..+|+|+|+.+
T Consensus 1 MpRYyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~YY~k~~eeqAq~liD~~~~~~~~~~---g~~~~~~~~~~~~~~~ 77 (165)
T KOG3454|consen 1 MPRYYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDYYQKWMEEQAQKLIDETILRFIGKK---GQKVPFSNARFSAPPE 77 (165)
T ss_pred CCcchhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccc---ccCCccccccccCCcc
Confidence 8999999999999 9999999999999999999999999885 888999999988888775 4899999999999987
Q ss_pred CcCCcc---------------CCcCcccccccccccccccccccccccCCCCCCCCCccccccCcc---CCCCCCCCCCC
Q 026840 81 NPAQNT---------------GNQGLRATGFTDINARSSSVDQRIYLAGGSSFPGDMMRDSMGMSW---GNLPPSLKPPP 142 (232)
Q Consensus 81 ~~~qel---------------~~~~Lp~G~~edwl~~sl~~~~~~~l~~~~s~~~~~~~~~~~~~w---~~LPPSL~pPP 142 (232)
..++.+ +.-.+|++.|++|++. ++++....+...+......+++.| ..+|||+++|+
T Consensus 78 ~~~~~~~pp~~~~~~~~~~~~~~P~mP~~~l~~p~~~-----~~p~~~~~p~~~i~~~~~~~~~~~~~~~~rpps~~~p~ 152 (165)
T KOG3454|consen 78 PVKASIPPPPEMEAPARPGPLGMPMMPPGPLMNPMGF-----RPPPPKMSPEPIIMMGVRGPPGTIPPVRPRPPSMRAPK 152 (165)
T ss_pred cccccCCCCcccCCCCCCCCcCCccCCCCCCCCcccc-----CCCCCCCCCCCccccccCCCCCCCCccCCCCccccCCC
Confidence 766554 3356788899999987 555555444444444455678889 99999999999
Q ss_pred CCCCCCCCc
Q 026840 143 EGGYPLLPL 151 (232)
Q Consensus 143 ~gG~p~lp~ 151 (232)
.|||++++.
T Consensus 153 ~~~~~~~~~ 161 (165)
T KOG3454|consen 153 PGGWPLQPR 161 (165)
T ss_pred CCCCCCCCC
Confidence 999999874
No 2
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=99.58 E-value=4.4e-16 Score=103.93 Aligned_cols=37 Identities=38% Similarity=0.826 Sum_probs=25.5
Q ss_pred CCccccccccccc-cCChhhhhccCCCCcchHHHHHhh
Q 026840 3 LGKYYCDYCDKQF-QDTYFARKRHLQGIQHLRAKALWY 39 (232)
Q Consensus 3 mkkYYCDYCdk~f-~Ds~~~RK~Hl~G~kH~Raka~yY 39 (232)
||||||||||++| +|++++||.|++|.+|++|+++||
T Consensus 1 m~ryyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~y 38 (38)
T PF06220_consen 1 MPRYYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRYY 38 (38)
T ss_dssp --S-B-TTT--B-S--SHHHHHHHT--THHHHHHHHHT
T ss_pred CcCeecccccceecCCChHHHHHhhccHHHHHHHHHhC
Confidence 8999999999999 999999999999999999999997
No 3
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=99.09 E-value=1.4e-11 Score=106.04 Aligned_cols=42 Identities=29% Similarity=0.664 Sum_probs=38.7
Q ss_pred CCccccccccccc-cCChhhhhccCCCCcchHHHHHhhh-cccc
Q 026840 3 LGKYYCDYCDKQF-QDTYFARKRHLQGIQHLRAKALWYD-SLNE 44 (232)
Q Consensus 3 mkkYYCDYCdk~f-~Ds~~~RK~Hl~G~kH~Raka~yY~-qFkD 44 (232)
|+|||||||+++| ||++++||.|+.|.+|.+++++||- .++|
T Consensus 1 MpRY~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~dYY~~~a~d 44 (188)
T COG5136 1 MPRYFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKDYYMEMAED 44 (188)
T ss_pred CcchHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHHHHHHHHHH
Confidence 8999999999999 9999999999999999999999994 4443
No 4
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=98.74 E-value=1.4e-09 Score=100.48 Aligned_cols=46 Identities=30% Similarity=0.748 Sum_probs=41.4
Q ss_pred cCCCCcchHHHHHhhhccccCCCCCCCCcCccccccccccccCCCCCCceeccCCCCcC
Q 026840 25 HLQGIQHLRAKALWYDSLNETNQTYPDGFPKGVCSRFVKTGFCPFGDSCKYLHPKNNPA 83 (232)
Q Consensus 25 Hl~G~kH~Raka~yY~qFkDPetIL~EE~~K~pCk~f~~TG~C~FGdsCkFsH~~~~~~ 83 (232)
+++...|+|+..+|. +++++|++|.+||||+|||+|+|+|++++++
T Consensus 169 pira~~~~r~~~~~d-------------~qpDicKdykeTgycg~gdSckFlh~r~DyK 214 (313)
T KOG1813|consen 169 PIRAAMHTRAGERID-------------YQPDICKDYKETGYCGYGDSCKFLHDRSDYK 214 (313)
T ss_pred ccchhhhhcccceee-------------cCchhhhhhHhhCcccccchhhhhhhhhhcc
Confidence 777777777777775 7899999999999999999999999999996
No 5
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=98.70 E-value=3.5e-09 Score=94.47 Aligned_cols=34 Identities=35% Similarity=0.826 Sum_probs=31.6
Q ss_pred CCCcCccccccccccccCCCCCCceeccCCCCcC
Q 026840 50 PDGFPKGVCSRFVKTGFCPFGDSCKYLHPKNNPA 83 (232)
Q Consensus 50 ~EE~~K~pCk~f~~TG~C~FGdsCkFsH~~~~~~ 83 (232)
..+++|++|++|.+||||+|||+|||+|+|+|++
T Consensus 136 viD~qpdVCKdyk~TGYCGYGDsCKflH~R~D~K 169 (259)
T COG5152 136 VIDTQPDVCKDYKETGYCGYGDSCKFLHDRSDFK 169 (259)
T ss_pred eeecCcccccchhhcccccCCchhhhhhhhhhhh
Confidence 3468999999999999999999999999999987
No 6
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=98.16 E-value=4.6e-07 Score=56.88 Aligned_cols=35 Identities=29% Similarity=0.647 Sum_probs=30.2
Q ss_pred CCccccccccccccCChhhhhccCCCCcchHHHHHh
Q 026840 3 LGKYYCDYCDKQFQDTYFARKRHLQGIQHLRAKALW 38 (232)
Q Consensus 3 mkkYYCDYCdk~f~Ds~~~RK~Hl~G~kH~Raka~y 38 (232)
+++||||+|+++|.++.+- +.|+.|.+|.++.+.+
T Consensus 1 ~~~~~C~~C~~~~~~~~~~-~~H~~gk~H~~~~~~~ 35 (35)
T smart00451 1 TGGFYCKLCNVTFTDEISV-EAHLKGKKHKKNVKKR 35 (35)
T ss_pred CcCeEccccCCccCCHHHH-HHHHChHHHHHHHHcC
Confidence 4689999999999976666 9999999999987653
No 7
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 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 C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=98.13 E-value=4.9e-07 Score=55.92 Aligned_cols=25 Identities=44% Similarity=1.152 Sum_probs=20.3
Q ss_pred CccccccccccccCCCCCCceeccC
Q 026840 54 PKGVCSRFVKTGFCPFGDSCKYLHP 78 (232)
Q Consensus 54 ~K~pCk~f~~TG~C~FGdsCkFsH~ 78 (232)
...+|+.|.++|.|.||++|+|+|.
T Consensus 2 k~~~C~~f~~~g~C~~G~~C~f~H~ 26 (27)
T PF00642_consen 2 KTKLCRFFMRTGTCPFGDKCRFAHG 26 (27)
T ss_dssp TSSB-HHHHHTS--TTGGGSSSBSS
T ss_pred ccccChhhccCCccCCCCCcCccCC
Confidence 4579999999999999999999997
No 8
>smart00356 ZnF_C3H1 zinc finger.
Probab=97.73 E-value=1.7e-05 Score=47.22 Aligned_cols=22 Identities=55% Similarity=1.491 Sum_probs=20.6
Q ss_pred cccccccccccCCCCCCceeccC
Q 026840 56 GVCSRFVKTGFCPFGDSCKYLHP 78 (232)
Q Consensus 56 ~pCk~f~~TG~C~FGdsCkFsH~ 78 (232)
.+|+.| ++|.|.+|++|+|+|.
T Consensus 5 ~~C~~~-~~g~C~~g~~C~~~H~ 26 (27)
T smart00356 5 ELCKFF-KRGYCPYGDRCKFAHP 26 (27)
T ss_pred CcCcCc-cCCCCCCCCCcCCCCc
Confidence 489999 7999999999999997
No 9
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=97.37 E-value=8e-05 Score=45.31 Aligned_cols=27 Identities=37% Similarity=0.794 Sum_probs=23.3
Q ss_pred ccccccccccccCChhhhhccCCCCcch
Q 026840 5 KYYCDYCDKQFQDTYFARKRHLQGIQHL 32 (232)
Q Consensus 5 kYYCDYCdk~f~Ds~~~RK~Hl~G~kH~ 32 (232)
+|||+.||+.|.| ..+-+.|++|.+|+
T Consensus 1 q~~C~~C~k~f~~-~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 1 QFYCDACDKYFSS-ENQLKQHMKSKKHK 27 (27)
T ss_dssp -CBBTTTTBBBSS-HHHHHCCTTSHHHH
T ss_pred CCCcccCCCCcCC-HHHHHHHHccCCCC
Confidence 5999999999988 67779999998885
No 10
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=96.89 E-value=0.0014 Score=58.91 Aligned_cols=35 Identities=29% Similarity=0.889 Sum_probs=29.9
Q ss_pred CCCCcCccccccccccccCCCCCCceeccCCCCcC
Q 026840 49 YPDGFPKGVCSRFVKTGFCPFGDSCKYLHPKNNPA 83 (232)
Q Consensus 49 L~EE~~K~pCk~f~~TG~C~FGdsCkFsH~~~~~~ 83 (232)
+...+.-++|..|.+||+|.||+.|+|-|...+..
T Consensus 171 ~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~~~ 205 (332)
T KOG1677|consen 171 NPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPEDR 205 (332)
T ss_pred CCCCCCCcCCCccccCCCCCCCCcCeecCCCcccc
Confidence 34456778999999999999999999999977554
No 11
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=96.85 E-value=0.00032 Score=65.96 Aligned_cols=38 Identities=26% Similarity=0.406 Sum_probs=34.4
Q ss_pred CCccccccccccccCChhhhhccCCCCcchHHHHHhhh
Q 026840 3 LGKYYCDYCDKQFQDTYFARKRHLQGIQHLRAKALWYD 40 (232)
Q Consensus 3 mkkYYCDYCdk~f~Ds~~~RK~Hl~G~kH~Raka~yY~ 40 (232)
-+|+|||||.+.|+|++..+.-|-+|.+|+.+++--..
T Consensus 8 ~~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~Krit 45 (336)
T KOG0150|consen 8 QPKKFCDYCKIWIKDNPASVRFHERGKRHKENVAKRIT 45 (336)
T ss_pred ccchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHHHHH
Confidence 37999999999999999999999999999998876553
No 12
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=95.18 E-value=0.0069 Score=59.17 Aligned_cols=32 Identities=28% Similarity=0.691 Sum_probs=25.8
Q ss_pred CCcCccccccccccccCCCCCCceeccCCCCcC
Q 026840 51 DGFPKGVCSRFVKTGFCPFGDSCKYLHPKNNPA 83 (232)
Q Consensus 51 EE~~K~pCk~f~~TG~C~FGdsCkFsH~~~~~~ 83 (232)
.-..-+||+.|++ |.|+|+.+|||||--.-.+
T Consensus 136 Th~sMkpC~ffLe-g~CRF~enCRfSHG~~V~l 167 (486)
T KOG2185|consen 136 THESMKPCKFFLE-GRCRFGENCRFSHGLDVPL 167 (486)
T ss_pred cchhhccchHhhc-cccccCcccccccCcccch
Confidence 3346689999996 9999999999999754443
No 13
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=94.84 E-value=0.0065 Score=35.62 Aligned_cols=25 Identities=36% Similarity=0.903 Sum_probs=22.0
Q ss_pred cccccccccccCChhhhhccCCCCcc
Q 026840 6 YYCDYCDKQFQDTYFARKRHLQGIQH 31 (232)
Q Consensus 6 YYCDYCdk~f~Ds~~~RK~Hl~G~kH 31 (232)
|+|+-|++.|.+ ...-+.|++|.+|
T Consensus 1 ~~C~~C~~~f~s-~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSS-ENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESS-HHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCC-HHHHHHHHCcCCC
Confidence 799999999987 6777889999877
No 14
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=93.39 E-value=0.046 Score=31.63 Aligned_cols=19 Identities=37% Similarity=0.852 Sum_probs=15.7
Q ss_pred ccccccccccCCCCCCceeccC
Q 026840 57 VCSRFVKTGFCPFGDSCKYLHP 78 (232)
Q Consensus 57 pCk~f~~TG~C~FGdsCkFsH~ 78 (232)
+||.+.+ |..+++|.|+|+
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 5886653 999999999995
No 15
>KOG4727 consensus U1-like Zn-finger protein [General function prediction only]
Probab=93.31 E-value=0.028 Score=49.62 Aligned_cols=36 Identities=33% Similarity=0.615 Sum_probs=29.5
Q ss_pred CCccccccccccccCChhhhhccCCCCcchHHHHHhh
Q 026840 3 LGKYYCDYCDKQFQDTYFARKRHLQGIQHLRAKALWY 39 (232)
Q Consensus 3 mkkYYCDYCdk~f~Ds~~~RK~Hl~G~kH~Raka~yY 39 (232)
+.=||||-||+.++|+.+ =--|++|.+|+|+--.=+
T Consensus 73 ~~GyyCdVCdcvvKDSin-flDHiNgKkHqrnlgmsm 108 (193)
T KOG4727|consen 73 KGGYYCDVCDCVVKDSIN-FLDHINGKKHQRNLGMSM 108 (193)
T ss_pred cCceeeeecceeehhhHH-HHHHhccHHHHHHHhhhh
Confidence 346999999999999765 467999999999866544
No 16
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.19 E-value=0.071 Score=50.60 Aligned_cols=25 Identities=36% Similarity=0.891 Sum_probs=23.2
Q ss_pred cccccccccccCCCCCCceeccCCCC
Q 026840 56 GVCSRFVKTGFCPFGDSCKYLHPKNN 81 (232)
Q Consensus 56 ~pCk~f~~TG~C~FGdsCkFsH~~~~ 81 (232)
.+|+.|.+ |+|+||+.|||+|..++
T Consensus 9 tic~~~~~-g~c~~g~~cr~~h~~~~ 33 (344)
T KOG1039|consen 9 TICKYYQK-GNCKFGDLCRLSHSLPD 33 (344)
T ss_pred hhhhhccc-ccccccceeeeeccCch
Confidence 89999985 99999999999999885
No 17
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=91.20 E-value=0.11 Score=46.68 Aligned_cols=35 Identities=26% Similarity=0.781 Sum_probs=29.1
Q ss_pred CCCCcCccccccccccccCCC-CCCceeccCCCCcC
Q 026840 49 YPDGFPKGVCSRFVKTGFCPF-GDSCKYLHPKNNPA 83 (232)
Q Consensus 49 L~EE~~K~pCk~f~~TG~C~F-GdsCkFsH~~~~~~ 83 (232)
..+-+.-..|+.|.++|.|.| |++|||.|..++..
T Consensus 126 ~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r 161 (332)
T KOG1677|consen 126 KPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELR 161 (332)
T ss_pred CcccccCCcceeeecCccccccCchhhhcCCccccc
Confidence 344456789999999999999 99999998876654
No 18
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=86.83 E-value=0.3 Score=29.63 Aligned_cols=15 Identities=40% Similarity=0.897 Sum_probs=13.1
Q ss_pred CCCcccccccccccc
Q 026840 2 PLGKYYCDYCDKQFQ 16 (232)
Q Consensus 2 ~mkkYYCDYCdk~f~ 16 (232)
+.++|-|++|++.|.
T Consensus 11 ~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 11 GEKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSSEEESSSSEEES
T ss_pred CCCCCCCCCCcCeeC
Confidence 578999999999983
No 19
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=80.05 E-value=0.57 Score=44.67 Aligned_cols=26 Identities=38% Similarity=0.950 Sum_probs=22.8
Q ss_pred CccccccccccccCCCCCC-ceeccCCC
Q 026840 54 PKGVCSRFVKTGFCPFGDS-CKYLHPKN 80 (232)
Q Consensus 54 ~K~pCk~f~~TG~C~FGds-CkFsH~~~ 80 (232)
.-.+||+|++ |.|.=||. |||-|+..
T Consensus 36 ~~eVCReF~r-n~C~R~d~~CkfaHP~~ 62 (331)
T KOG2494|consen 36 TLEVCREFLR-NTCSRGDRECKFAHPPK 62 (331)
T ss_pred HHHHHHHHHh-ccccCCCccccccCCCC
Confidence 3479999996 99999999 99999965
No 20
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=79.31 E-value=0.65 Score=46.93 Aligned_cols=29 Identities=24% Similarity=0.777 Sum_probs=22.6
Q ss_pred cccccccccc--ccCCCCCCceeccCCCCcC
Q 026840 55 KGVCSRFVKT--GFCPFGDSCKYLHPKNNPA 83 (232)
Q Consensus 55 K~pCk~f~~T--G~C~FGdsCkFsH~~~~~~ 83 (232)
-..|-...++ ..|.|||+|||.|+-+.++
T Consensus 76 n~LCPsli~g~~~~C~f~d~Crf~HDi~ayL 106 (614)
T KOG2333|consen 76 NRLCPSLIQGDISKCSFGDNCRFVHDIEAYL 106 (614)
T ss_pred hccChHhhcCCCccCcccccccccccHHHHH
Confidence 4678888877 5788888888888877665
No 21
>KOG3408 consensus U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification]
Probab=78.59 E-value=0.89 Score=38.28 Aligned_cols=36 Identities=31% Similarity=0.435 Sum_probs=31.1
Q ss_pred CCCccccccccccccCChhhhhccCCCCcchHHHHHh
Q 026840 2 PLGKYYCDYCDKQFQDTYFARKRHLQGIQHLRAKALW 38 (232)
Q Consensus 2 ~mkkYYCDYCdk~f~Ds~~~RK~Hl~G~kH~Raka~y 38 (232)
++.-|||=-|+++|-| ..+.+.|.++..|+|-++.-
T Consensus 54 G~GqfyCi~CaRyFi~-~~~l~~H~ktK~HKrRvK~l 89 (129)
T KOG3408|consen 54 GGGQFYCIECARYFID-AKALKTHFKTKVHKRRVKEL 89 (129)
T ss_pred CCceeehhhhhhhhcc-hHHHHHHHhccHHHHHHHhc
Confidence 4678999999999977 67999999999999866653
No 22
>PF08026 Antimicrobial_5: Bee antimicrobial peptide; InterPro: IPR012524 This entry represents antimicrobial peptides produced by bees. These peptides have strong antimicrobial and some anti-fungal activity and has homology to abaecin which is the largest proline-rich antimicrobial peptide isolated from European bumblebee Bombus pascuorum [].; GO: 0042381 hemolymph coagulation, 0005576 extracellular region
Probab=70.12 E-value=3.3 Score=28.42 Aligned_cols=19 Identities=37% Similarity=0.990 Sum_probs=16.4
Q ss_pred CCCCCCCCCCCCCcccccC
Q 026840 138 LKPPPEGGYPLLPLWIGDS 156 (232)
Q Consensus 138 L~pPP~gG~p~lp~~~~~~ 156 (232)
+++||+|||.++|-.-|..
T Consensus 4 ~~~P~pG~~kpFPTFPGqG 22 (39)
T PF08026_consen 4 VNPPPPGGWKPFPTFPGQG 22 (39)
T ss_pred ccCCCCCCcccCCcCCCCC
Confidence 3899999999999887765
No 23
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=68.10 E-value=2.4 Score=23.33 Aligned_cols=19 Identities=26% Similarity=0.712 Sum_probs=11.8
Q ss_pred cccccccccccCChhhhhcc
Q 026840 6 YYCDYCDKQFQDTYFARKRH 25 (232)
Q Consensus 6 YYCDYCdk~f~Ds~~~RK~H 25 (232)
|-|++|++.|.+ ....+.|
T Consensus 1 ~~C~~C~~~~~~-~~~l~~H 19 (24)
T PF13894_consen 1 FQCPICGKSFRS-KSELRQH 19 (24)
T ss_dssp EE-SSTS-EESS-HHHHHHH
T ss_pred CCCcCCCCcCCc-HHHHHHH
Confidence 679999999966 4444444
No 24
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=64.33 E-value=4 Score=39.21 Aligned_cols=29 Identities=28% Similarity=0.809 Sum_probs=25.4
Q ss_pred ccccccccccccCCCCCCceeccCCCCcC
Q 026840 55 KGVCSRFVKTGFCPFGDSCKYLHPKNNPA 83 (232)
Q Consensus 55 K~pCk~f~~TG~C~FGdsCkFsH~~~~~~ 83 (232)
-+||..+...|+|.||..|.|-|-....+
T Consensus 274 TePcinwe~sGyc~yg~Rc~F~hgd~~~i 302 (351)
T COG5063 274 TEPCINWEKSGYCPYGLRCCFKHGDDSDI 302 (351)
T ss_pred cCCccchhhcccCccccccccccCChhhc
Confidence 47899999999999999999999866665
No 25
>PF06212 GRIM-19: GRIM-19 protein; InterPro: IPR009346 This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-beta and RA. A bovine homologue of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localisation and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity [].
Probab=62.40 E-value=4 Score=34.06 Aligned_cols=11 Identities=55% Similarity=1.289 Sum_probs=9.2
Q ss_pred CCCCCCCCCCc
Q 026840 141 PPEGGYPLLPL 151 (232)
Q Consensus 141 PP~gG~p~lp~ 151 (232)
||+||||+..+
T Consensus 10 PP~GGY~pv~y 20 (130)
T PF06212_consen 10 PPPGGYPPVQY 20 (130)
T ss_pred CCCCCCCCCcc
Confidence 57899998876
No 26
>COG0633 Fdx Ferredoxin [Energy production and conversion]
Probab=61.88 E-value=3.9 Score=31.90 Aligned_cols=17 Identities=53% Similarity=1.126 Sum_probs=14.2
Q ss_pred Eee--ceeeeEeeEeecCc
Q 026840 193 VQC--GYCVTCRVKICSGI 209 (232)
Q Consensus 193 ~~~--~~~~~~~~~~~~~~ 209 (232)
.+| |+|.||+|++-.|.
T Consensus 38 ~~C~~g~C~TC~v~v~~G~ 56 (102)
T COG0633 38 YACRGGACGTCRVKVLEGF 56 (102)
T ss_pred ecCCCCccCccEEEEecCc
Confidence 456 58999999999993
No 27
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=61.26 E-value=3.5 Score=23.32 Aligned_cols=12 Identities=42% Similarity=1.068 Sum_probs=10.6
Q ss_pred cccccccccccC
Q 026840 6 YYCDYCDKQFQD 17 (232)
Q Consensus 6 YYCDYCdk~f~D 17 (232)
|-|++|++.|.+
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 679999999965
No 28
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=60.79 E-value=2.8 Score=40.02 Aligned_cols=29 Identities=34% Similarity=0.621 Sum_probs=23.2
Q ss_pred cCccccccccccccCCCCCCceeccCCCCc
Q 026840 53 FPKGVCSRFVKTGFCPFGDSCKYLHPKNNP 82 (232)
Q Consensus 53 ~~K~pCk~f~~TG~C~FGdsCkFsH~~~~~ 82 (232)
..--+|-.|.+ |+|.=|+-|+|||+....
T Consensus 90 PKSvvCafFk~-g~C~KG~kCKFsHdl~~~ 118 (343)
T KOG1763|consen 90 PKSVVCAFFKQ-GTCTKGDKCKFSHDLAVE 118 (343)
T ss_pred chHHHHHHHhc-cCCCCCCcccccchHHHh
Confidence 34457888885 999999999999996544
No 29
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=60.35 E-value=2.9 Score=28.30 Aligned_cols=19 Identities=26% Similarity=0.520 Sum_probs=16.8
Q ss_pred cccccccccCChhhhhccC
Q 026840 8 CDYCDKQFQDTYFARKRHL 26 (232)
Q Consensus 8 CDYCdk~f~Ds~~~RK~Hl 26 (232)
||||++.+.+.|.+.|.++
T Consensus 1 Cd~CG~~I~~eP~~~k~~~ 19 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGN 19 (37)
T ss_pred CCccCCcccCCEEEEEECC
Confidence 9999999999998888754
No 30
>PF04988 AKAP95: A-kinase anchoring protein 95 (AKAP95); InterPro: IPR007071 A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=53.94 E-value=5.3 Score=35.00 Aligned_cols=40 Identities=15% Similarity=0.276 Sum_probs=37.1
Q ss_pred cccccccccccCChhhhhccCCCCcchHHHHHhhhccccC
Q 026840 6 YYCDYCDKQFQDTYFARKRHLQGIQHLRAKALWYDSLNET 45 (232)
Q Consensus 6 YYCDYCdk~f~Ds~~~RK~Hl~G~kH~Raka~yY~qFkDP 45 (232)
..|-=||.++....+.-.+|+....|.+|++.+.+|+++.
T Consensus 92 ~hCsACd~~IP~~~~~vQ~Hl~S~~H~~Nrr~~~eq~Kr~ 131 (165)
T PF04988_consen 92 AHCSACDVFIPMQHSSVQKHLKSQDHNKNRRAMMEQSKRS 131 (165)
T ss_pred hhhhHhhhhccCcHHHHHHHhccHHHHhhHHHHHHHHHHH
Confidence 4799999999999999999999999999999999988764
No 31
>PHA02768 hypothetical protein; Provisional
Probab=52.58 E-value=5.6 Score=29.00 Aligned_cols=17 Identities=29% Similarity=0.645 Sum_probs=14.5
Q ss_pred CCCCccccccccccccC
Q 026840 1 MPLGKYYCDYCDKQFQD 17 (232)
Q Consensus 1 m~mkkYYCDYCdk~f~D 17 (232)
|..--|.|+.|++.|..
T Consensus 1 ~~~~~y~C~~CGK~Fs~ 17 (55)
T PHA02768 1 MALLGYECPICGEIYIK 17 (55)
T ss_pred CcccccCcchhCCeecc
Confidence 67778999999999954
No 32
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=49.11 E-value=7.2 Score=37.06 Aligned_cols=26 Identities=38% Similarity=0.950 Sum_probs=22.9
Q ss_pred CcCccccccccccccCCCCCCceeccC
Q 026840 52 GFPKGVCSRFVKTGFCPFGDSCKYLHP 78 (232)
Q Consensus 52 E~~K~pCk~f~~TG~C~FGdsCkFsH~ 78 (232)
-..+.+||+|++ |-|+-||.|-|+|.
T Consensus 74 ~~~~~vcK~~l~-glC~kgD~C~Flhe 99 (325)
T KOG1040|consen 74 SRGKVVCKHWLR-GLCKKGDQCEFLHE 99 (325)
T ss_pred cCCceeehhhhh-hhhhccCcCcchhh
Confidence 567889999996 99999999999996
No 33
>KOG2384 consensus Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only]
Probab=47.73 E-value=5.4 Score=36.30 Aligned_cols=28 Identities=25% Similarity=0.630 Sum_probs=19.8
Q ss_pred CccccccccccccCChhhhhccCCCCcchH
Q 026840 4 GKYYCDYCDKQFQDTYFARKRHLQGIQHLR 33 (232)
Q Consensus 4 kkYYCDYCdk~f~Ds~~~RK~Hl~G~kH~R 33 (232)
--+||+-||.++++++.. .|...+.|+-
T Consensus 83 ~lfyCE~Cd~~ip~~~~s--nH~tSttHll 110 (223)
T KOG2384|consen 83 ALFYCEVCDIYIPNSKKS--NHFTSTTHLL 110 (223)
T ss_pred ccchhhhhhhhccCCCCc--cchhhHHHHh
Confidence 368999999999886643 3555555553
No 34
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=47.18 E-value=4.9 Score=37.38 Aligned_cols=39 Identities=31% Similarity=0.496 Sum_probs=33.8
Q ss_pred CCCCCCCCcCccccccccccccCCCCCCceeccCCCCcC
Q 026840 45 TNQTYPDGFPKGVCSRFVKTGFCPFGDSCKYLHPKNNPA 83 (232)
Q Consensus 45 PetIL~EE~~K~pCk~f~~TG~C~FGdsCkFsH~~~~~~ 83 (232)
.+.|..+|..|--|..|.++|-|.+|+.|.=.|-.+...
T Consensus 5 lasifgtekdKv~c~fy~k~gacR~gdrcsR~h~kpt~s 43 (260)
T KOG2202|consen 5 LASIFGTEKDKVNCSFYFKIGACRHGDRCSRLHEKPTFS 43 (260)
T ss_pred HHHHhcccccccccchHHhhcccccccHHHHhhcccccc
Confidence 356777788999999999999999999998889877665
No 35
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=46.72 E-value=13 Score=35.83 Aligned_cols=28 Identities=25% Similarity=0.364 Sum_probs=25.5
Q ss_pred cCccccccccccccCCCCCCceeccCCC
Q 026840 53 FPKGVCSRFVKTGFCPFGDSCKYLHPKN 80 (232)
Q Consensus 53 ~~K~pCk~f~~TG~C~FGdsCkFsH~~~ 80 (232)
+..++|+.++.+|.|..|..|+++|+..
T Consensus 312 y~~~~crt~~~~g~~p~g~~~c~~~dkk 339 (351)
T COG5063 312 YLDGPCRTRAKGGAFPSGGAVCKSFDKK 339 (351)
T ss_pred ccccccccccccCccCCCCchhhccccc
Confidence 5689999999999999999999999943
No 36
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=46.48 E-value=9.7 Score=35.72 Aligned_cols=75 Identities=27% Similarity=0.460 Sum_probs=0.0
Q ss_pred HHHhhhccccCCCCCCCC-----cCcccccccccc---------ccCCCC-CCceeccCCCCcCCccCCcCccccccccc
Q 026840 35 KALWYDSLNETNQTYPDG-----FPKGVCSRFVKT---------GFCPFG-DSCKYLHPKNNPAQNTGNQGLRATGFTDI 99 (232)
Q Consensus 35 ka~yY~qFkDPetIL~EE-----~~K~pCk~f~~T---------G~C~FG-dsCkFsH~~~~~~qel~~~~Lp~G~~edw 99 (232)
+.+-|+-.+|.++-++-+ ....+|+.|++. =+|.+| +.|-|.|..++.-
T Consensus 116 K~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkYgw~W~CPng~~~C~y~H~Lp~Gy---------------- 179 (299)
T COG5252 116 KPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKYGWGWTCPNGNMRCSYIHKLPDGY---------------- 179 (299)
T ss_pred ccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCccceeeCCCCCceeeeeeccCccc----------------
Q ss_pred ccccccccccccccCCCCCCCCCccccccCcc--------CCCCCCCCC
Q 026840 100 NARSSSVDQRIYLAGGSSFPGDMMRDSMGMSW--------GNLPPSLKP 140 (232)
Q Consensus 100 l~~sl~~~~~~~l~~~~s~~~~~~~~~~~~~w--------~~LPPSL~p 140 (232)
-|+... .-.+++.-.++ +.|||+|-|
T Consensus 180 ---VLsrdk------------~Kd~tq~eislEefIE~eR~~L~~~LTP 213 (299)
T COG5252 180 ---VLSRDK------------IKDSTQVEISLEEFIELERQSLPEKLTP 213 (299)
T ss_pred ---eecccc------------ccccccccccHHHHHHHHhccCCCcCCc
No 37
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=45.98 E-value=4.6 Score=29.04 Aligned_cols=30 Identities=27% Similarity=0.677 Sum_probs=23.0
Q ss_pred ccccccccccccCChhhhhccCCCCcchHHH
Q 026840 5 KYYCDYCDKQFQDTYFARKRHLQGIQHLRAK 35 (232)
Q Consensus 5 kYYCDYCdk~f~Ds~~~RK~Hl~G~kH~Rak 35 (232)
.+.|.+|++.|.+ ...-+.|++...|....
T Consensus 50 ~~~C~~C~~~f~s-~~~l~~Hm~~~~H~~~~ 79 (100)
T PF12756_consen 50 SFRCPYCNKTFRS-REALQEHMRSKHHKKRN 79 (100)
T ss_dssp SEEBSSSS-EESS-HHHHHHHHHHTTTTC-S
T ss_pred CCCCCccCCCCcC-HHHHHHHHcCccCCCcc
Confidence 4999999999874 77888898888887643
No 38
>PF01799 Fer2_2: [2Fe-2S] binding domain; InterPro: IPR002888 The [2Fe-2S] binding domain is found in a range of enzymes including dehydrogenases, oxidases and oxidoreductases. The aldehyde oxido-reductase (Mop) from the sulphate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas is a homodimer of 907 amino acid residues subunits and is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different [2Fe-2S] centres. It is folded into four domains of which the first two bind the iron sulphur centres and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands [].; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 2E3T_A 1WYG_A 3AN1_B 2E1Q_C 2CKJ_A 3B9J_I 3NVY_J 1FO4_B 3NRZ_J 3AM9_A ....
Probab=40.28 E-value=8.3 Score=29.19 Aligned_cols=10 Identities=50% Similarity=1.301 Sum_probs=6.3
Q ss_pred eeEEeeceee
Q 026840 190 ISVVQCGYCV 199 (232)
Q Consensus 190 ~~~~~~~~~~ 199 (232)
-.++|||||.
T Consensus 21 ~~a~QCGfCt 30 (75)
T PF01799_consen 21 HGAVQCGFCT 30 (75)
T ss_dssp TT--SSSSSH
T ss_pred hCCCcCCcch
Confidence 4578999995
No 39
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=39.72 E-value=12 Score=21.82 Aligned_cols=14 Identities=36% Similarity=0.869 Sum_probs=11.4
Q ss_pred ccccccccccccCC
Q 026840 5 KYYCDYCDKQFQDT 18 (232)
Q Consensus 5 kYYCDYCdk~f~Ds 18 (232)
.|.|+.|++.|.+-
T Consensus 1 ~~~C~~C~~~F~~~ 14 (27)
T PF13912_consen 1 PFECDECGKTFSSL 14 (27)
T ss_dssp SEEETTTTEEESSH
T ss_pred CCCCCccCCccCCh
Confidence 37899999999553
No 40
>KOG3300 consensus NADH:ubiquinone oxidoreductase, B16.6 subunit/cell death-regulatory protein [Energy production and conversion; Cell cycle control, cell division, chromosome partitioning]
Probab=38.19 E-value=16 Score=31.41 Aligned_cols=13 Identities=38% Similarity=0.759 Sum_probs=10.7
Q ss_pred CCCCCCCCCCCcc
Q 026840 140 PPPEGGYPLLPLW 152 (232)
Q Consensus 140 pPP~gG~p~lp~~ 152 (232)
=||+|||.+.+|=
T Consensus 13 mPPpGGy~~i~y~ 25 (146)
T KOG3300|consen 13 MPPPGGYAPIRYA 25 (146)
T ss_pred CCCCCCcCccccc
Confidence 3689999999874
No 41
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=38.11 E-value=12 Score=26.69 Aligned_cols=12 Identities=33% Similarity=0.905 Sum_probs=8.8
Q ss_pred Cccccccccccc
Q 026840 4 GKYYCDYCDKQF 15 (232)
Q Consensus 4 kkYYCDYCdk~f 15 (232)
.+|-|.|||+.+
T Consensus 34 ~~~rC~YCe~~~ 45 (52)
T PF02748_consen 34 IKLRCHYCERII 45 (52)
T ss_dssp CEEEETTT--EE
T ss_pred CEEEeeCCCCEe
Confidence 578999999998
No 42
>KOG0717 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=38.06 E-value=12 Score=37.65 Aligned_cols=37 Identities=24% Similarity=0.401 Sum_probs=32.4
Q ss_pred cccccccccccCChhhhhccCCCCcchHHHHHhhhccc
Q 026840 6 YYCDYCDKQFQDTYFARKRHLQGIQHLRAKALWYDSLN 43 (232)
Q Consensus 6 YYCDYCdk~f~Ds~~~RK~Hl~G~kH~Raka~yY~qFk 43 (232)
+||--|+|+|.. ...+|-|-+..+|.++++.-=++.+
T Consensus 293 lyC~vCnKsFKs-eKq~kNHEnSKKHkenv~eLrqemE 329 (508)
T KOG0717|consen 293 LYCVVCNKSFKS-EKQLKNHENSKKHKENVAELRQEME 329 (508)
T ss_pred eEEeeccccccc-hHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 899999999976 7899999999999999988765543
No 43
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=35.94 E-value=10 Score=37.33 Aligned_cols=33 Identities=27% Similarity=0.486 Sum_probs=26.3
Q ss_pred CccccccccccccCChhhhhccCCCCcchHHHHH
Q 026840 4 GKYYCDYCDKQFQDTYFARKRHLQGIQHLRAKAL 37 (232)
Q Consensus 4 kkYYCDYCdk~f~Ds~~~RK~Hl~G~kH~Raka~ 37 (232)
+++||..|.+.|.. ..+=.-|+.|..|.++.+.
T Consensus 237 ~~~YC~~C~r~f~~-~~VFe~Hl~gK~H~k~~~~ 269 (470)
T COG5188 237 PKVYCVKCGREFSR-SKVFEYHLEGKRHCKEGQG 269 (470)
T ss_pred cceeeHhhhhHhhh-hHHHHHHHhhhhhhhhhhh
Confidence 68999999999955 3456678899999887654
No 44
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=35.25 E-value=13 Score=33.79 Aligned_cols=28 Identities=29% Similarity=0.451 Sum_probs=25.7
Q ss_pred cccccccccc--cCChhhhhccCCCCcchH
Q 026840 6 YYCDYCDKQF--QDTYFARKRHLQGIQHLR 33 (232)
Q Consensus 6 YYCDYCdk~f--~Ds~~~RK~Hl~G~kH~R 33 (232)
--||-|..+| .|+..-..-|..|.+|+.
T Consensus 191 ~VCeVCGA~Ls~~D~d~RladH~~GK~HlG 220 (254)
T PF03194_consen 191 EVCEVCGAFLSVGDNDRRLADHFGGKQHLG 220 (254)
T ss_pred cchhhhhhHHhccchHHHHHHHhccchhhh
Confidence 4699999999 899999999999999986
No 45
>smart00355 ZnF_C2H2 zinc finger.
Probab=33.23 E-value=20 Score=19.41 Aligned_cols=20 Identities=40% Similarity=0.735 Sum_probs=13.3
Q ss_pred cccccccccccCChhhhhccC
Q 026840 6 YYCDYCDKQFQDTYFARKRHL 26 (232)
Q Consensus 6 YYCDYCdk~f~Ds~~~RK~Hl 26 (232)
|-|+.|++.|.+ .+....|.
T Consensus 1 ~~C~~C~~~f~~-~~~l~~H~ 20 (26)
T smart00355 1 YRCPECGKVFKS-KSALKEHM 20 (26)
T ss_pred CCCCCCcchhCC-HHHHHHHH
Confidence 679999999954 33334444
No 46
>PF13900 GVQW: Putative binding domain
Probab=31.93 E-value=30 Score=24.83 Aligned_cols=18 Identities=50% Similarity=1.182 Sum_probs=13.0
Q ss_pred cccCccCCCCCCCCCCCCC
Q 026840 126 SMGMSWGNLPPSLKPPPEG 144 (232)
Q Consensus 126 ~~~~~w~~LPPSL~pPP~g 144 (232)
+-++-|.|| -||+|||+|
T Consensus 3 qAgvqw~~l-~SLQp~ppg 20 (48)
T PF13900_consen 3 QAGVQWHDL-SSLQPPPPG 20 (48)
T ss_pred ccccccccc-CcCCccccc
Confidence 346778887 488888875
No 47
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=31.81 E-value=8.7 Score=27.42 Aligned_cols=13 Identities=46% Similarity=0.935 Sum_probs=11.2
Q ss_pred eeceeeeEeeEee
Q 026840 194 QCGYCVTCRVKIC 206 (232)
Q Consensus 194 ~~~~~~~~~~~~~ 206 (232)
++|||--||+|.=
T Consensus 4 k~GYCE~Cr~kfd 16 (49)
T smart00586 4 KPGYCENCREKYD 16 (49)
T ss_pred CCcccccHhHHHh
Confidence 6899999999854
No 48
>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=30.73 E-value=14 Score=26.57 Aligned_cols=18 Identities=22% Similarity=0.490 Sum_probs=10.7
Q ss_pred CccccccccccccCChhh
Q 026840 4 GKYYCDYCDKQFQDTYFA 21 (232)
Q Consensus 4 kkYYCDYCdk~f~Ds~~~ 21 (232)
+.+||--||.+.|+++.+
T Consensus 28 ~~~FC~dCD~fiHE~LH~ 45 (51)
T PF07975_consen 28 KNHFCIDCDVFIHETLHN 45 (51)
T ss_dssp T--B-HHHHHTTTTTS-S
T ss_pred CCccccCcChhhhccccC
Confidence 456778888888887653
No 49
>PF02162 XYPPX: XYPPX repeat (two copies); InterPro: IPR006031 This repeat is found in a wide variety of proteins and generally consists of the motif XYPPX where X can be any amino acid. The family includes annexin VII ANX7_DICDI, the carboxy tail of certain rhodopsins OPSD_LOLSU. This family also includes plaque matrix proteins, however this motif is embedded in a ten residue repeat in FP1_MYTED. The molecular function of this repeat is unknown. It is also not clear is all the members of this family share a common evolutionary ancestor due to its short length and biased amino acid composition.
Probab=30.27 E-value=31 Score=19.55 Aligned_cols=9 Identities=44% Similarity=0.837 Sum_probs=4.9
Q ss_pred CCCCCCCCC
Q 026840 142 PEGGYPLLP 150 (232)
Q Consensus 142 P~gG~p~lp 150 (232)
|+.|||++.
T Consensus 3 ppqG~pPQ~ 11 (15)
T PF02162_consen 3 PPQGYPPQG 11 (15)
T ss_pred CCcCCCCCC
Confidence 445666554
No 50
>KOG2482 consensus Predicted C2H2-type Zn-finger protein [Transcription]
Probab=30.16 E-value=12 Score=36.59 Aligned_cols=37 Identities=35% Similarity=0.632 Sum_probs=29.9
Q ss_pred ccccccccccccCChhhhhccCCCCcchH--HHHHhhhcc
Q 026840 5 KYYCDYCDKQFQDTYFARKRHLQGIQHLR--AKALWYDSL 42 (232)
Q Consensus 5 kYYCDYCdk~f~Ds~~~RK~Hl~G~kH~R--aka~yY~qF 42 (232)
+.-|=||.|-|.| ...=|.|++.++|.| .+.+.|+.|
T Consensus 195 r~~CLyCekifrd-kntLkeHMrkK~HrrinPknreYDkf 233 (423)
T KOG2482|consen 195 RLRCLYCEKIFRD-KNTLKEHMRKKRHRRINPKNREYDKF 233 (423)
T ss_pred hheeeeeccccCC-cHHHHHHHHhccCcccCCCccccceE
Confidence 6789999999988 456688999999988 455667766
No 51
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=29.34 E-value=24 Score=33.15 Aligned_cols=27 Identities=41% Similarity=0.824 Sum_probs=23.9
Q ss_pred CccccccccccccCCCCCCceeccCCC
Q 026840 54 PKGVCSRFVKTGFCPFGDSCKYLHPKN 80 (232)
Q Consensus 54 ~K~pCk~f~~TG~C~FGdsCkFsH~~~ 80 (232)
+-.+|..|.+-|+|..|.+||-.|..+
T Consensus 287 napicfefakygfcelgtscknqhilq 313 (377)
T KOG1492|consen 287 NAPICFEFAKYGFCELGTSCKNQHILQ 313 (377)
T ss_pred CCceeeeehhcceeccccccccceeee
Confidence 457899999999999999999999843
No 52
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=29.33 E-value=23 Score=29.64 Aligned_cols=35 Identities=34% Similarity=0.456 Sum_probs=28.7
Q ss_pred CCccccccccccccCChhhhhccCCCCcchHHHHHh
Q 026840 3 LGKYYCDYCDKQFQDTYFARKRHLQGIQHLRAKALW 38 (232)
Q Consensus 3 mkkYYCDYCdk~f~Ds~~~RK~Hl~G~kH~Raka~y 38 (232)
..-+||=-|+++|- +..+=+.|.+|.-|.|-.+.-
T Consensus 53 lGqhYCieCaryf~-t~~aL~~HkkgkvHkRR~Kel 87 (126)
T COG5112 53 LGQHYCIECARYFI-TEKALMEHKKGKVHKRRAKEL 87 (126)
T ss_pred CceeeeehhHHHHH-HHHHHHHHhccchhHHHHHHH
Confidence 45789999999994 356778999999999876654
No 53
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=29.20 E-value=36 Score=34.62 Aligned_cols=29 Identities=38% Similarity=0.747 Sum_probs=25.0
Q ss_pred cCccccccccccccCCCCCCceeccCCCCc
Q 026840 53 FPKGVCSRFVKTGFCPFGDSCKYLHPKNNP 82 (232)
Q Consensus 53 ~~K~pCk~f~~TG~C~FGdsCkFsH~~~~~ 82 (232)
|.-.||=.|.+ |-|.=||+|-|-|-+-+.
T Consensus 234 Ys~tpCPefrk-G~C~rGD~CEyaHgvfEc 262 (528)
T KOG1595|consen 234 YSSTPCPEFRK-GSCERGDSCEYAHGVFEC 262 (528)
T ss_pred ccCccCccccc-CCCCCCCccccccceehh
Confidence 56789999996 999999999999987554
No 54
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=28.84 E-value=12 Score=33.66 Aligned_cols=46 Identities=20% Similarity=0.567 Sum_probs=27.5
Q ss_pred CccccccccccccCChhhhh----ccCCCCcchHHHHHhhhcc-ccCCCCC
Q 026840 4 GKYYCDYCDKQFQDTYFARK----RHLQGIQHLRAKALWYDSL-NETNQTY 49 (232)
Q Consensus 4 kkYYCDYCdk~f~Ds~~~RK----~Hl~G~kH~Raka~yY~qF-kDPetIL 49 (232)
-||-|..|.|-|+..-.+|| +|-.-+..++....||..| .||+.+.
T Consensus 76 ~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ve~~~~ev~~fnnY~~Dp~rp~ 126 (214)
T PF04959_consen 76 DKWRCPLCGKLFKGPEFVRKHIFNKHPEKVEEVKKEVEYFNNYLLDPKRPQ 126 (214)
T ss_dssp EEEEE-SSS-EESSHHHHHHHHHHH-HHHHHHHHHHHHHHHHH--------
T ss_pred CEECCCCCCcccCChHHHHHHHhhcCHHHHHHHHHHHHHHHHHhcCcccCC
Confidence 48999999999988777765 6666666666777787766 5665543
No 55
>CHL00134 petF ferredoxin; Validated
Probab=27.82 E-value=27 Score=27.00 Aligned_cols=16 Identities=44% Similarity=1.014 Sum_probs=14.1
Q ss_pred ee--ceeeeEeeEeecCc
Q 026840 194 QC--GYCVTCRVKICSGI 209 (232)
Q Consensus 194 ~~--~~~~~~~~~~~~~~ 209 (232)
.| |.|-+|++++-+|-
T Consensus 41 ~C~~G~Cg~C~v~v~~G~ 58 (99)
T CHL00134 41 SCRAGACSTCAGKVTEGT 58 (99)
T ss_pred CCCCccCCCCEEEEEeCc
Confidence 56 89999999999993
No 56
>KOG3792 consensus Transcription factor NFAT, subunit NF90 [General function prediction only]
Probab=25.77 E-value=24 Score=37.44 Aligned_cols=31 Identities=35% Similarity=0.661 Sum_probs=27.9
Q ss_pred CCccccccccccccCChhhhhccCCCCcchHH
Q 026840 3 LGKYYCDYCDKQFQDTYFARKRHLQGIQHLRA 34 (232)
Q Consensus 3 mkkYYCDYCdk~f~Ds~~~RK~Hl~G~kH~Ra 34 (232)
+++|-|--||+.|.| +++--.|++|+.|---
T Consensus 357 ~~~f~cKlcdckf~d-~nak~mhl~grRhrLQ 387 (816)
T KOG3792|consen 357 LLRFHCKLCDCKFND-PNAKEMHLKGRRHRLQ 387 (816)
T ss_pred hHhhhhhhhcCCCCC-cchHHhhhhcccccce
Confidence 579999999999998 8899999999999753
No 57
>KOG0854 consensus Alkyl hydroperoxide reductase, thiol specific antioxidant and related enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=25.50 E-value=26 Score=31.82 Aligned_cols=21 Identities=43% Similarity=0.597 Sum_probs=16.3
Q ss_pred CCCCCCcccccCCccccccce
Q 026840 145 GYPLLPLWIGDSSAVSFSHPI 165 (232)
Q Consensus 145 G~p~lp~~~~~~~~~~~~~~~ 165 (232)
|==-+--|.|||-+|-||||-
T Consensus 22 g~i~fhd~~gdSW~vLFSHPa 42 (224)
T KOG0854|consen 22 GKIKFHDYLGDSWGVLFSHPA 42 (224)
T ss_pred cceehhhhcccceEEEecCcc
Confidence 333455699999999999984
No 58
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=23.94 E-value=22 Score=30.77 Aligned_cols=8 Identities=63% Similarity=1.676 Sum_probs=6.0
Q ss_pred EEeeceee
Q 026840 192 VVQCGYCV 199 (232)
Q Consensus 192 ~~~~~~~~ 199 (232)
++|||||.
T Consensus 97 ~~QCGyCt 104 (156)
T COG2080 97 AFQCGYCT 104 (156)
T ss_pred CCcCCCCc
Confidence 56888885
No 59
>TIGR02008 fdx_plant ferredoxin [2Fe-2S]. This model represents single domain 2Fe-2S (also called plant type) ferredoxins. In general, these occur as a single domain proteins or with a chloroplast transit peptide. Species tend to be photosynthetic, but several forms may occur in one species and individually may not be associated with photocynthesis. Halobacterial forms differ somewhat in architecture; they score between trusted and noise cutoffs. Sequences scoring below the noise cutoff tend to be ferredoxin-related domains of larger proteins.
Probab=23.76 E-value=33 Score=26.21 Aligned_cols=15 Identities=40% Similarity=0.702 Sum_probs=13.2
Q ss_pred ceeeeEeeEeecCcc
Q 026840 196 GYCVTCRVKICSGID 210 (232)
Q Consensus 196 ~~~~~~~~~~~~~~~ 210 (232)
|.|-+|++++-+|-.
T Consensus 43 G~Cg~C~v~v~~G~~ 57 (97)
T TIGR02008 43 GACSTCAGKVEEGTV 57 (97)
T ss_pred ccCCCCceEEEeCcE
Confidence 789999999999954
No 60
>PRK09908 xanthine dehydrogenase subunit XdhC; Provisional
Probab=22.56 E-value=24 Score=30.46 Aligned_cols=9 Identities=56% Similarity=1.527 Sum_probs=7.1
Q ss_pred eEEeeceee
Q 026840 191 SVVQCGYCV 199 (232)
Q Consensus 191 ~~~~~~~~~ 199 (232)
.++|||||.
T Consensus 99 ~a~QCGyCt 107 (159)
T PRK09908 99 GAVQCGFCT 107 (159)
T ss_pred CCCcCCCCC
Confidence 357999995
No 61
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=22.29 E-value=25 Score=24.94 Aligned_cols=14 Identities=50% Similarity=1.006 Sum_probs=11.4
Q ss_pred eeceeeeEeeEeec
Q 026840 194 QCGYCVTCRVKICS 207 (232)
Q Consensus 194 ~~~~~~~~~~~~~~ 207 (232)
+.|||--|++|.=.
T Consensus 4 k~GYCE~C~~ky~~ 17 (49)
T PF07535_consen 4 KPGYCENCRVKYDD 17 (49)
T ss_pred CCccCccccchhhh
Confidence 47999999998643
No 62
>PF10589 NADH_4Fe-4S: NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; InterPro: IPR019575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the F subunit of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2. This entry represents the iron-sulphur binding domain of the F subunit.; GO: 0055114 oxidation-reduction process; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1.
Probab=22.07 E-value=14 Score=25.33 Aligned_cols=10 Identities=50% Similarity=1.401 Sum_probs=5.5
Q ss_pred eeceeeeEee
Q 026840 194 QCGYCVTCRV 203 (232)
Q Consensus 194 ~~~~~~~~~~ 203 (232)
.||-|+.||+
T Consensus 15 SCGkC~PCR~ 24 (46)
T PF10589_consen 15 SCGKCTPCRE 24 (46)
T ss_dssp --S--HHHHC
T ss_pred CCCCCCCcHh
Confidence 5999999997
No 63
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=21.60 E-value=42 Score=31.42 Aligned_cols=25 Identities=32% Similarity=0.903 Sum_probs=21.4
Q ss_pred CccccccccccccCCCCCCceeccCC
Q 026840 54 PKGVCSRFVKTGFCPFGDSCKYLHPK 79 (232)
Q Consensus 54 ~K~pCk~f~~TG~C~FGdsCkFsH~~ 79 (232)
.--+|..|..| .|..|..|.|.|..
T Consensus 151 rea~C~~~e~~-~C~rG~~CnFmH~k 175 (260)
T KOG2202|consen 151 REAICGQFERT-ECSRGGACNFMHVK 175 (260)
T ss_pred hhhhhcccccc-cCCCCCcCcchhhh
Confidence 44578888865 99999999999996
No 64
>KOG0227 consensus Splicing factor 3a, subunit 2 [RNA processing and modification]
Probab=20.99 E-value=53 Score=29.99 Aligned_cols=35 Identities=31% Similarity=0.447 Sum_probs=29.3
Q ss_pred CCccccccccccccCChhhhhccCCCCcchHHHHHh
Q 026840 3 LGKYYCDYCDKQFQDTYFARKRHLQGIQHLRAKALW 38 (232)
Q Consensus 3 mkkYYCDYCdk~f~Ds~~~RK~Hl~G~kH~Raka~y 38 (232)
..+|-|--|. ++|.+-.+=-.|.+|.+|+.|.++=
T Consensus 51 ~G~yeCkLCl-T~H~ne~Syl~HtqGKKHq~Nlarr 85 (222)
T KOG0227|consen 51 LGKYECKLCL-TLHNNEGSYLAHTQGKKHQTNLARR 85 (222)
T ss_pred Ccceeehhhh-hhhcchhhhhhhhccchhhHHHHHH
Confidence 3589999996 5788888999999999999966654
No 65
>TIGR03198 pucE xanthine dehydrogenase E subunit. This gene has been characterized in B. subtilis as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component.
Probab=20.84 E-value=27 Score=29.70 Aligned_cols=9 Identities=56% Similarity=1.379 Sum_probs=7.0
Q ss_pred eEEeeceee
Q 026840 191 SVVQCGYCV 199 (232)
Q Consensus 191 ~~~~~~~~~ 199 (232)
.++|||||.
T Consensus 94 ~a~QCGfCt 102 (151)
T TIGR03198 94 GGFQCGYCT 102 (151)
T ss_pred CCCcCCCCC
Confidence 357999995
No 66
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=20.67 E-value=98 Score=29.58 Aligned_cols=26 Identities=35% Similarity=0.662 Sum_probs=18.2
Q ss_pred CccccccccccccCCCCCCceeccCC
Q 026840 54 PKGVCSRFVKTGFCPFGDSCKYLHPK 79 (232)
Q Consensus 54 ~K~pCk~f~~TG~C~FGdsCkFsH~~ 79 (232)
....|..|-..|.|.=|+.|-|.|-.
T Consensus 104 k~rec~ff~~~g~c~~~~~c~y~h~d 129 (325)
T KOG1040|consen 104 KMRECKFFSLFGECTNGKDCPYLHGD 129 (325)
T ss_pred ccccccccccccccccccCCcccCCC
Confidence 34477777777777777777777765
Done!