Query psy16544
Match_columns 63
No_of_seqs 106 out of 403
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 23:57:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16544.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16544hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00647 IBR In Between Ring 99.4 2E-13 4.2E-18 73.8 3.8 45 17-61 1-47 (64)
2 PF01485 IBR: IBR domain; Int 99.2 6.2E-13 1.3E-17 71.7 -0.7 43 17-59 1-44 (64)
3 KOG1815|consensus 99.2 2E-11 4.4E-16 87.3 4.3 60 2-61 126-185 (444)
4 KOG1814|consensus 98.3 3.9E-07 8.4E-12 65.9 3.1 56 2-59 242-297 (445)
5 KOG0006|consensus 97.3 0.00022 4.8E-09 51.0 3.0 51 7-60 290-340 (446)
6 KOG1812|consensus 95.9 0.0085 1.8E-07 42.9 3.0 47 2-50 203-249 (384)
7 PF02150 RNA_POL_M_15KD: RNA p 87.7 0.3 6.6E-06 23.9 1.0 24 34-59 1-24 (35)
8 PF11789 zf-Nse: Zinc-finger o 75.5 1.4 3.1E-05 23.6 0.8 25 18-43 33-57 (57)
9 PF01530 zf-C2HC: Zinc finger, 70.9 1.9 4E-05 20.9 0.5 9 36-44 3-11 (31)
10 PF09788 Tmemb_55A: Transmembr 68.2 3.1 6.8E-05 28.8 1.3 17 35-51 124-140 (256)
11 smart00661 RPOL9 RNA polymeras 67.3 3.8 8.2E-05 20.7 1.3 14 34-49 20-33 (52)
12 cd01388 SOX-TCF_HMG-box SOX-TC 65.4 12 0.00025 20.2 3.1 25 13-37 45-72 (72)
13 KOG2906|consensus 65.2 7 0.00015 23.7 2.3 25 34-60 1-26 (105)
14 PRK11867 2-oxoglutarate ferred 64.8 3.1 6.6E-05 28.8 0.8 19 25-46 9-27 (286)
15 cd01389 MATA_HMG-box MATA_HMG- 61.2 21 0.00045 19.4 3.6 28 12-39 44-74 (77)
16 PF11706 zf-CGNR: CGNR zinc fi 60.2 9.1 0.0002 19.6 1.9 25 34-58 2-26 (44)
17 COG1579 Zn-ribbon protein, pos 59.0 10 0.00023 25.9 2.5 37 12-50 173-235 (239)
18 PF13719 zinc_ribbon_5: zinc-r 57.8 7.2 0.00016 18.9 1.2 22 36-59 4-29 (37)
19 KOG3084|consensus 57.1 6.3 0.00014 28.4 1.2 33 21-55 137-169 (345)
20 PF14803 Nudix_N_2: Nudix N-te 55.9 11 0.00023 18.3 1.6 23 35-59 1-26 (34)
21 PRK12544 RNA polymerase sigma 54.1 15 0.00032 23.6 2.6 25 1-25 9-33 (206)
22 COG5516 Conserved protein cont 50.8 11 0.00023 25.2 1.5 27 33-59 147-173 (196)
23 KOG4684|consensus 50.3 10 0.00022 26.2 1.3 18 33-50 137-154 (275)
24 TIGR00319 desulf_FeS4 desulfof 45.4 23 0.00051 16.5 1.9 23 40-62 11-33 (34)
25 cd00974 DSRD Desulforedoxin (D 42.0 29 0.00063 16.2 1.9 23 40-62 8-30 (34)
26 TIGR02098 MJ0042_CXXC MJ0042 f 41.4 18 0.00039 17.1 1.2 21 37-59 5-29 (38)
27 PF07891 DUF1666: Protein of u 39.5 36 0.00077 23.6 2.7 21 14-34 42-64 (247)
28 PF02671 PAH: Paired amphipath 37.6 35 0.00077 16.8 2.0 19 4-22 26-45 (47)
29 PF09297 zf-NADH-PPase: NADH p 36.7 28 0.0006 16.1 1.4 17 34-52 3-19 (32)
30 PF14369 zf-RING_3: zinc-finge 36.4 27 0.00059 16.8 1.3 23 35-59 3-25 (35)
31 TIGR01053 LSD1 zinc finger dom 35.1 43 0.00093 15.8 1.9 22 36-60 3-24 (31)
32 PF13248 zf-ribbon_3: zinc-rib 32.8 15 0.00032 16.4 0.0 8 32-39 14-21 (26)
33 PF13240 zinc_ribbon_2: zinc-r 31.5 16 0.00035 16.0 0.0 11 32-44 11-21 (23)
34 TIGR02177 PorB_KorB 2-oxoacid: 31.2 20 0.00044 24.9 0.5 9 35-45 2-10 (287)
35 PRK00398 rpoP DNA-directed RNA 30.2 53 0.0011 16.2 1.9 11 35-47 22-32 (46)
36 PRK09628 oorB 2-oxoglutarate-a 30.1 29 0.00062 23.9 1.1 9 34-44 16-24 (277)
37 PF10426 zf-RAG1: Recombinatio 30.0 28 0.0006 16.6 0.7 14 35-48 3-16 (30)
38 PF13717 zinc_ribbon_4: zinc-r 30.0 51 0.0011 15.8 1.7 23 36-60 4-30 (36)
39 PF01233 NMT: Myristoyl-CoA:pr 29.9 53 0.0011 21.4 2.2 21 12-32 33-53 (162)
40 PF02748 PyrI_C: Aspartate car 29.7 24 0.00053 18.5 0.5 11 35-45 7-17 (52)
41 PRK11869 2-oxoacid ferredoxin 29.5 20 0.00044 24.8 0.3 11 35-47 9-19 (280)
42 COG2051 RPS27A Ribosomal prote 29.0 61 0.0013 18.2 2.1 23 35-59 20-42 (67)
43 PRK05778 2-oxoglutarate ferred 28.5 23 0.00049 24.8 0.4 13 34-48 18-30 (301)
44 PF10952 DUF2753: Protein of u 28.2 75 0.0016 20.2 2.6 35 11-48 64-98 (140)
45 PF12773 DZR: Double zinc ribb 28.0 18 0.00038 18.1 -0.2 15 31-47 9-23 (50)
46 PF01599 Ribosomal_S27: Riboso 27.2 37 0.00079 17.7 0.9 20 33-52 17-37 (47)
47 PF12564 TypeIII_RM_meth: Type 26.3 73 0.0016 17.2 2.1 19 1-19 1-19 (57)
48 PF12894 Apc4_WD40: Anaphase-p 26.3 40 0.00086 17.2 1.0 9 33-41 16-24 (47)
49 PF02184 HAT: HAT (Half-A-TPR) 26.2 65 0.0014 15.5 1.7 12 23-34 9-20 (32)
50 COG1013 PorB Pyruvate:ferredox 25.6 21 0.00046 24.8 -0.2 12 34-47 15-26 (294)
51 PF11709 Mit_ribos_Mrp51: Mito 25.4 65 0.0014 22.6 2.2 30 1-30 143-173 (312)
52 PF03119 DNA_ligase_ZBD: NAD-d 25.1 81 0.0018 14.3 1.8 20 37-59 2-21 (28)
53 PF13963 Transpos_assoc: Trans 25.1 69 0.0015 17.7 1.9 29 18-48 23-51 (77)
54 PRK11866 2-oxoacid ferredoxin 23.1 31 0.00067 23.8 0.3 11 33-45 6-16 (279)
55 PF09872 DUF2099: Uncharacteri 22.9 33 0.00071 23.9 0.3 10 30-39 22-31 (258)
56 PF06397 Desulfoferrod_N: Desu 22.7 58 0.0012 16.0 1.1 18 41-58 11-28 (36)
57 COG1594 RPB9 DNA-directed RNA 22.5 83 0.0018 18.9 2.0 25 33-59 1-26 (113)
58 PF11823 DUF3343: Protein of u 22.4 50 0.0011 17.8 1.0 35 19-53 12-52 (73)
59 PRK14102 nifW nitrogenase stab 22.1 89 0.0019 18.9 2.1 20 10-29 55-74 (105)
60 COG5220 TFB3 Cdk activating ki 22.0 17 0.00037 25.5 -1.2 34 12-47 31-64 (314)
61 KOG0801|consensus 21.9 64 0.0014 21.5 1.5 24 37-62 141-164 (205)
62 PF14982 UPF0731: UPF0731 fami 21.8 38 0.00083 19.4 0.4 17 31-47 40-56 (79)
63 PF03206 NifW: Nitrogen fixati 21.1 1E+02 0.0023 18.5 2.2 18 12-29 56-73 (105)
64 PF07862 Nif11: Nitrogen fixat 20.5 97 0.0021 15.3 1.8 22 1-22 1-26 (49)
65 PRK10353 3-methyl-adenine DNA 20.2 1.4E+02 0.003 19.7 2.9 18 1-18 71-88 (187)
66 COG5627 MMS21 DNA repair prote 20.1 78 0.0017 22.2 1.7 35 15-50 208-242 (275)
67 cd07357 HN_L-whirlin_R2_like S 20.0 1.1E+02 0.0025 17.7 2.1 20 5-25 60-79 (81)
No 1
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=99.42 E-value=2e-13 Score=73.80 Aligned_cols=45 Identities=29% Similarity=0.565 Sum_probs=40.2
Q ss_pred HHHHHHHHHhHHhhCCCeeEeCCCCCcceEEcc-CCCceeeEe-cCC
Q psy16544 17 EKYEDFMVRRVLSIEPDARWCPTPDCGKVFDGQ-FLVPKHVLR-SLE 61 (63)
Q Consensus 17 ~kY~~~~~~~~V~~~~~~rWCP~p~C~~av~~~-~~~~~~V~c-~~~ 61 (63)
+||++|+++++|+.+++++|||+|+|+.++... ......|.| .|.
T Consensus 1 ~~y~~~~~~~~i~~~~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~ 47 (64)
T smart00647 1 EKYERLLLESYVESNPDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCG 47 (64)
T ss_pred ChHHHHHHHHHHhcCCCccCCCCCCCcceEEecCCCCCCeeECCCCC
Confidence 489999999999999999999999999999997 457788999 553
No 2
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=99.25 E-value=6.2e-13 Score=71.71 Aligned_cols=43 Identities=35% Similarity=0.808 Sum_probs=27.4
Q ss_pred HHHHHHHHHhHHhhCCCeeEeCCCCCcceEEccCCCcee-eEec
Q psy16544 17 EKYEDFMVRRVLSIEPDARWCPTPDCGKVFDGQFLVPKH-VLRS 59 (63)
Q Consensus 17 ~kY~~~~~~~~V~~~~~~rWCP~p~C~~av~~~~~~~~~-V~c~ 59 (63)
+||++|++++||+.+++++|||+|+|+.++......... |+|+
T Consensus 1 eky~~~~~~~~~~~~~~~~~Cp~~~C~~~~~~~~~~~~~~~~C~ 44 (64)
T PF01485_consen 1 EKYQKFLLKRYLESDPNIRWCPNPDCEYIIEKDDGCNSPIVTCP 44 (64)
T ss_dssp HCHHHCCCHS---S---CC--TTSST---ECS-SSTTS--CCTT
T ss_pred ChHHHHHHHHHHHCCCCccCCCCCCCcccEEecCCCCCCeeECC
Confidence 589999999999999999999999999999998887664 8888
No 3
>KOG1815|consensus
Probab=99.19 E-value=2e-11 Score=87.31 Aligned_cols=60 Identities=23% Similarity=0.430 Sum_probs=52.8
Q ss_pred ChhHHhhhcCChHHHHHHHHHHHHhHHhhCCCeeEeCCCCCcceEEccCCCceeeEecCC
Q psy16544 2 KIQYIHSILSDQALFEKYEDFMVRRVLSIEPDARWCPTPDCGKVFDGQFLVPKHVLRSLE 61 (63)
Q Consensus 2 ~~~~I~~ll~d~~~~~kY~~~~~~~~V~~~~~~rWCP~p~C~~av~~~~~~~~~V~c~~~ 61 (63)
.+++|..++++.+..+||+++++++||+.+..++|||+|||++++.........|.|++.
T Consensus 126 ~~~~i~~~~s~~~~~~ky~~~i~~syve~~~~lkwCP~~~C~~av~~~~~~~~~v~C~~g 185 (444)
T KOG1815|consen 126 GEDTVEKLVSDKEDKEKYQRYILRSYVEDNVPLKWCPAPGCGLAVKFGSLESVEVDCGCG 185 (444)
T ss_pred CCceeeeecCCHHHHHHHHHHHHHHHHhcCCccccCCCCCCCceeeccCCCccceeCCCC
Confidence 456777788654589999999999999999999999999999999988888899999874
No 4
>KOG1814|consensus
Probab=98.34 E-value=3.9e-07 Score=65.89 Aligned_cols=56 Identities=21% Similarity=0.406 Sum_probs=48.6
Q ss_pred ChhHHhhhcCChHHHHHHHHHHHHhHHhhCCCeeEeCCCCCcceEEccCCCceeeEec
Q psy16544 2 KIQYIHSILSDQALFEKYEDFMVRRVLSIEPDARWCPTPDCGKVFDGQFLVPKHVLRS 59 (63)
Q Consensus 2 ~~~~I~~ll~d~~~~~kY~~~~~~~~V~~~~~~rWCP~p~C~~av~~~~~~~~~V~c~ 59 (63)
++.+++++|. .++++||+++++++.++.+.++.+||++.|+..+ ...++...++||
T Consensus 242 ~~g~vKelvg-~EL~arYe~l~lqk~l~~msdv~yCPr~~Cq~p~-~~d~~~~l~~Cs 297 (445)
T KOG1814|consen 242 PPGQVKELVG-DELFARYEKLMLQKTLELMSDVVYCPRACCQLPV-KQDPGRALAICS 297 (445)
T ss_pred CchHHHHHHH-HHHHHHHHHHHHHHHHHhhcccccCChhhccCcc-ccCchhhhhhhc
Confidence 4668899996 5799999999999999999999999999999999 455555777776
No 5
>KOG0006|consensus
Probab=97.30 E-value=0.00022 Score=51.03 Aligned_cols=51 Identities=18% Similarity=0.355 Sum_probs=42.8
Q ss_pred hhhcCChHHHHHHHHHHHHhHHhhCCCeeEeCCCCCcceEEccCCCceeeEecC
Q psy16544 7 HSILSDQALFEKYEDFMVRRVLSIEPDARWCPTPDCGKVFDGQFLVPKHVLRSL 60 (63)
Q Consensus 7 ~~ll~d~~~~~kY~~~~~~~~V~~~~~~rWCP~p~C~~av~~~~~~~~~V~c~~ 60 (63)
.++|. ++.+++||+|..+.+|-...- .-||+||||..+..++ +-|.|+|.-
T Consensus 290 F~ilg-~e~Y~rYQr~atEe~vlq~gG-VlCP~pgCG~gll~EP-D~rkvtC~~ 340 (446)
T KOG0006|consen 290 FRILG-EEQYNRYQRYATEECVLQMGG-VLCPRPGCGAGLLPEP-DQRKVTCEG 340 (446)
T ss_pred heecc-hhHHHHHHHhhhhhheeecCC-EecCCCCCCcccccCC-CCCcccCCC
Confidence 45665 678999999999999998774 4899999999999888 458899863
No 6
>KOG1812|consensus
Probab=95.88 E-value=0.0085 Score=42.90 Aligned_cols=47 Identities=19% Similarity=0.433 Sum_probs=40.2
Q ss_pred ChhHHhhhcCChHHHHHHHHHHHHhHHhhCCCeeEeCCCCCcceEEccC
Q psy16544 2 KIQYIHSILSDQALFEKYEDFMVRRVLSIEPDARWCPTPDCGKVFDGQF 50 (63)
Q Consensus 2 ~~~~I~~ll~d~~~~~kY~~~~~~~~V~~~~~~rWCP~p~C~~av~~~~ 50 (63)
+.+....+|. +.+.++|++++.+.++...+.+ +||.|+|...+....
T Consensus 203 ~~~~c~~llt-~kl~e~~e~~~~e~~i~~~~~~-ycp~~~C~~l~~~~e 249 (384)
T KOG1812|consen 203 TLESCRKLLT-PKLREMWEQRLKEEVIPSLDRV-YCPYPRCSSLMSKTE 249 (384)
T ss_pred CHHHHhhhcC-HHHHHHHHHHHHHHhhhhhhcc-cCCCCCchHhhhhhh
Confidence 4566778885 6899999999999999999999 999999998877644
No 7
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=87.69 E-value=0.3 Score=23.88 Aligned_cols=24 Identities=29% Similarity=0.555 Sum_probs=16.3
Q ss_pred eeEeCCCCCcceEEccCCCceeeEec
Q psy16544 34 ARWCPTPDCGKVFDGQFLVPKHVLRS 59 (63)
Q Consensus 34 ~rWCP~p~C~~av~~~~~~~~~V~c~ 59 (63)
|+|||. |++......+....+.|.
T Consensus 1 m~FCp~--C~nlL~p~~~~~~~~~C~ 24 (35)
T PF02150_consen 1 MRFCPE--CGNLLYPKEDKEKRVACR 24 (35)
T ss_dssp --BETT--TTSBEEEEEETTTTEEES
T ss_pred CeeCCC--CCccceEcCCCccCcCCC
Confidence 578986 999988876665555664
No 8
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=75.53 E-value=1.4 Score=23.61 Aligned_cols=25 Identities=16% Similarity=0.563 Sum_probs=15.7
Q ss_pred HHHHHHHHhHHhhCCCeeEeCCCCCc
Q psy16544 18 KYEDFMVRRVLSIEPDARWCPTPDCG 43 (63)
Q Consensus 18 kY~~~~~~~~V~~~~~~rWCP~p~C~ 43 (63)
-|++-.+..|+. +....-||.+||.
T Consensus 33 ~fek~aI~~~i~-~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 33 TFEKEAILQYIQ-RNGSKRCPVAGCN 57 (57)
T ss_dssp EEEHHHHHHHCT-TTS-EE-SCCC-S
T ss_pred eecHHHHHHHHH-hcCCCCCCCCCCC
Confidence 366677777774 4456789999995
No 9
>PF01530 zf-C2HC: Zinc finger, C2HC type; InterPro: IPR002515 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 CysCysHisCys (C2HC) type zinc finger domain found in eukaryotes. Proteins containing these domains include: MYST family histone acetyltransferases [, [] Myelin transcription factor Myt1 [] Suppressor of tumourigenicity protein 18 (ST18) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2CS8_A 1PXE_A 2JX1_A 2JYD_A.
Probab=70.85 E-value=1.9 Score=20.88 Aligned_cols=9 Identities=56% Similarity=1.343 Sum_probs=5.7
Q ss_pred EeCCCCCcc
Q psy16544 36 WCPTPDCGK 44 (63)
Q Consensus 36 WCP~p~C~~ 44 (63)
-||.|+|.-
T Consensus 3 ~CPtpGCdg 11 (31)
T PF01530_consen 3 KCPTPGCDG 11 (31)
T ss_dssp SSSSTT--S
T ss_pred cCCCCCCCc
Confidence 399999974
No 10
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=68.22 E-value=3.1 Score=28.82 Aligned_cols=17 Identities=24% Similarity=0.604 Sum_probs=14.5
Q ss_pred eEeCCCCCcceEEccCC
Q psy16544 35 RWCPTPDCGKVFDGQFL 51 (63)
Q Consensus 35 rWCP~p~C~~av~~~~~ 51 (63)
--||+|+|.++|...+.
T Consensus 124 IaCPRp~CkRiI~L~~~ 140 (256)
T PF09788_consen 124 IACPRPNCKRIINLGPS 140 (256)
T ss_pred ccCCCCCCcceEEeCCc
Confidence 46999999999988665
No 11
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=67.35 E-value=3.8 Score=20.67 Aligned_cols=14 Identities=21% Similarity=0.264 Sum_probs=8.1
Q ss_pred eeEeCCCCCcceEEcc
Q psy16544 34 ARWCPTPDCGKVFDGQ 49 (63)
Q Consensus 34 ~rWCP~p~C~~av~~~ 49 (63)
...||. |++.....
T Consensus 20 ~~vC~~--Cg~~~~~~ 33 (52)
T smart00661 20 RFVCRK--CGYEEPIE 33 (52)
T ss_pred EEECCc--CCCeEECC
Confidence 456764 77665543
No 12
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=65.37 E-value=12 Score=20.20 Aligned_cols=25 Identities=16% Similarity=0.331 Sum_probs=19.3
Q ss_pred hHHHHHHHHH---HHHhHHhhCCCeeEe
Q psy16544 13 QALFEKYEDF---MVRRVLSIEPDARWC 37 (63)
Q Consensus 13 ~~~~~kY~~~---~~~~~V~~~~~~rWC 37 (63)
++....|.+. ....|.+.+|+.+||
T Consensus 45 ~~eK~~y~~~a~~~k~~y~~~~p~y~y~ 72 (72)
T cd01388 45 NEEKQPYYEEAKKLKELHMKLYPDYKWR 72 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCcCCCCC
Confidence 4567777654 567889999999987
No 13
>KOG2906|consensus
Probab=65.24 E-value=7 Score=23.71 Aligned_cols=25 Identities=20% Similarity=0.353 Sum_probs=17.2
Q ss_pred eeEeCCCCCcceEEccCCCc-eeeEecC
Q psy16544 34 ARWCPTPDCGKVFDGQFLVP-KHVLRSL 60 (63)
Q Consensus 34 ~rWCP~p~C~~av~~~~~~~-~~V~c~~ 60 (63)
|.+||. |++..++..++. ....|+-
T Consensus 1 m~FCP~--Cgn~Live~g~~~~rf~C~t 26 (105)
T KOG2906|consen 1 MLFCPT--CGNMLIVESGESCNRFSCRT 26 (105)
T ss_pred CcccCC--CCCEEEEecCCeEeeEEcCC
Confidence 458986 888888877665 5555543
No 14
>PRK11867 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed
Probab=64.79 E-value=3.1 Score=28.75 Aligned_cols=19 Identities=32% Similarity=0.919 Sum_probs=11.4
Q ss_pred HhHHhhCCCeeEeCCCCCcceE
Q psy16544 25 RRVLSIEPDARWCPTPDCGKVF 46 (63)
Q Consensus 25 ~~~V~~~~~~rWCP~p~C~~av 46 (63)
+.|. .+..-+|||+ |+...
T Consensus 9 ~~~~-~~~~~~~CpG--Cg~~~ 27 (286)
T PRK11867 9 KDFR-NDQEPRWCPG--CGDGS 27 (286)
T ss_pred HHhc-CCCCCCcCCC--CCCHH
Confidence 3454 3434469986 98654
No 15
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=61.18 E-value=21 Score=19.39 Aligned_cols=28 Identities=18% Similarity=0.321 Sum_probs=21.4
Q ss_pred ChHHHHHHHHH---HHHhHHhhCCCeeEeCC
Q psy16544 12 DQALFEKYEDF---MVRRVLSIEPDARWCPT 39 (63)
Q Consensus 12 d~~~~~kY~~~---~~~~~V~~~~~~rWCP~ 39 (63)
+++..+.|++. ....|...+|+.+|.|.
T Consensus 44 s~eeK~~y~~~A~~~k~~~~~~~p~Yky~p~ 74 (77)
T cd01389 44 SPEVKAYYKELAEEEKERHAREYPDYKYTPR 74 (77)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCCcccCC
Confidence 35667778654 45678889999999996
No 16
>PF11706 zf-CGNR: CGNR zinc finger; InterPro: IPR021005 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 a C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family. ; PDB: 3H0N_A.
Probab=60.16 E-value=9.1 Score=19.61 Aligned_cols=25 Identities=28% Similarity=0.396 Sum_probs=6.4
Q ss_pred eeEeCCCCCcceEEccCCCceeeEe
Q psy16544 34 ARWCPTPDCGKVFDGQFLVPKHVLR 58 (63)
Q Consensus 34 ~rWCP~p~C~~av~~~~~~~~~V~c 58 (63)
|+=|.+++|+.++.-.+.....-=|
T Consensus 2 lr~C~~~~C~~~F~D~sr~~~RrwC 26 (44)
T PF11706_consen 2 LRRCANPDCRWVFLDTSRNGRRRWC 26 (44)
T ss_dssp EEE--STT---EEE--SSS-----S
T ss_pred ccccCCCCCceEEEeCCCCCCceec
Confidence 3445566666655544433333333
No 17
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=59.03 E-value=10 Score=25.90 Aligned_cols=37 Identities=22% Similarity=0.530 Sum_probs=26.1
Q ss_pred ChHHHHHHHHHHHHh--------------------------HHhhCCCeeEeCCCCCcceEEccC
Q psy16544 12 DQALFEKYEDFMVRR--------------------------VLSIEPDARWCPTPDCGKVFDGQF 50 (63)
Q Consensus 12 d~~~~~kY~~~~~~~--------------------------~V~~~~~~rWCP~p~C~~av~~~~ 50 (63)
+++++..|+++.... -|.....+.+||. ||.++..+.
T Consensus 173 ~~ell~~yeri~~~~kg~gvvpl~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~--CgRILy~~e 235 (239)
T COG1579 173 DPELLSEYERIRKNKKGVGVVPLEGRVCGGCHMKLPSQTLSKVRKKDEIVFCPY--CGRILYYDE 235 (239)
T ss_pred CHHHHHHHHHHHhcCCCceEEeecCCcccCCeeeecHHHHHHHhcCCCCccCCc--cchHHHhhh
Confidence 688999999987766 2344556778875 877766543
No 18
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=57.77 E-value=7.2 Score=18.94 Aligned_cols=22 Identities=23% Similarity=0.262 Sum_probs=16.4
Q ss_pred EeCCCCCcceEEccCC----CceeeEec
Q psy16544 36 WCPTPDCGKVFDGQFL----VPKHVLRS 59 (63)
Q Consensus 36 WCP~p~C~~av~~~~~----~~~~V~c~ 59 (63)
-||. |+.......+ ..+.|.|+
T Consensus 4 ~CP~--C~~~f~v~~~~l~~~~~~vrC~ 29 (37)
T PF13719_consen 4 TCPN--CQTRFRVPDDKLPAGGRKVRCP 29 (37)
T ss_pred ECCC--CCceEEcCHHHcccCCcEEECC
Confidence 4765 9999888653 56788886
No 19
>KOG3084|consensus
Probab=57.12 E-value=6.3 Score=28.40 Aligned_cols=33 Identities=21% Similarity=0.378 Sum_probs=25.8
Q ss_pred HHHHHhHHhhCCCeeEeCCCCCcceEEccCCCcee
Q psy16544 21 DFMVRRVLSIEPDARWCPTPDCGKVFDGQFLVPKH 55 (63)
Q Consensus 21 ~~~~~~~V~~~~~~rWCP~p~C~~av~~~~~~~~~ 55 (63)
-+..+++++-...+|+||+ ||.+-+-..++.+.
T Consensus 137 ~a~ars~l~W~skykFCp~--CG~~tkp~e~g~k~ 169 (345)
T KOG3084|consen 137 TAVARSLLDWVSKYKFCPG--CGSPTKPEEAGTKL 169 (345)
T ss_pred HHHHHHHHHHHHHhccCcc--cCCCcccccCCccc
Confidence 3456778888888999987 99998887776543
No 20
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=55.90 E-value=11 Score=18.31 Aligned_cols=23 Identities=17% Similarity=0.531 Sum_probs=8.6
Q ss_pred eEeCCCCCcceEEc---cCCCceeeEec
Q psy16544 35 RWCPTPDCGKVFDG---QFLVPKHVLRS 59 (63)
Q Consensus 35 rWCP~p~C~~av~~---~~~~~~~V~c~ 59 (63)
|+||. |+..+.. ..++..+-+|+
T Consensus 1 kfC~~--CG~~l~~~ip~gd~r~R~vC~ 26 (34)
T PF14803_consen 1 KFCPQ--CGGPLERRIPEGDDRERLVCP 26 (34)
T ss_dssp -B-TT--T--B-EEE--TT-SS-EEEET
T ss_pred Ccccc--ccChhhhhcCCCCCccceECC
Confidence 46765 7777655 22444555554
No 21
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=54.14 E-value=15 Score=23.64 Aligned_cols=25 Identities=20% Similarity=0.412 Sum_probs=19.6
Q ss_pred CChhHHhhhcCChHHHHHHHHHHHH
Q psy16544 1 MKIQYIHSILSDQALFEKYEDFMVR 25 (63)
Q Consensus 1 ~~~~~I~~ll~d~~~~~kY~~~~~~ 25 (63)
|.-.++..||.||.+++.|++.+++
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~l~~ 33 (206)
T PRK12544 9 MDSSDLGNLLQDPVFLEDLRKQMIK 33 (206)
T ss_pred cchhhHHHHhhhHHHHHHHHHHHHH
Confidence 5567788899998888888877664
No 22
>COG5516 Conserved protein containing a Zn-ribbon-like motif, possibly RNA-binding [General function prediction only]
Probab=50.77 E-value=11 Score=25.17 Aligned_cols=27 Identities=26% Similarity=0.409 Sum_probs=18.7
Q ss_pred CeeEeCCCCCcceEEccCCCceeeEec
Q psy16544 33 DARWCPTPDCGKVFDGQFLVPKHVLRS 59 (63)
Q Consensus 33 ~~rWCP~p~C~~av~~~~~~~~~V~c~ 59 (63)
.+|-||.|||+.-+.-.+-....-=||
T Consensus 147 rlRiC~n~gCtwlFvDrSRnrsRrWCs 173 (196)
T COG5516 147 RLRICPNPGCTWLFVDRSRNRSRRWCS 173 (196)
T ss_pred heeecCCCCceEEEEecchhhccchhh
Confidence 489999999998876555444444444
No 23
>KOG4684|consensus
Probab=50.25 E-value=10 Score=26.25 Aligned_cols=18 Identities=22% Similarity=0.650 Sum_probs=14.6
Q ss_pred CeeEeCCCCCcceEEccC
Q psy16544 33 DARWCPTPDCGKVFDGQF 50 (63)
Q Consensus 33 ~~rWCP~p~C~~av~~~~ 50 (63)
.--=||+|+|.++|-.++
T Consensus 137 qRIACPRpnCkRiInL~p 154 (275)
T KOG4684|consen 137 QRIACPRPNCKRIINLDP 154 (275)
T ss_pred ceeccCCCCcceeeecCC
Confidence 345699999999998765
No 24
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=45.43 E-value=23 Score=16.54 Aligned_cols=23 Identities=17% Similarity=0.273 Sum_probs=16.6
Q ss_pred CCCcceEEccCCCceeeEecCCC
Q psy16544 40 PDCGKVFDGQFLVPKHVLRSLEP 62 (63)
Q Consensus 40 p~C~~av~~~~~~~~~V~c~~~~ 62 (63)
..|+++|.+-......++|.-+|
T Consensus 11 ~~Cgniv~v~~~~~~~l~Ccg~~ 33 (34)
T TIGR00319 11 EVCGNIVEVLHAGGGQLVCCGEP 33 (34)
T ss_pred CCCCcEEEEEECCCcceeccCCc
Confidence 56999998876665667776554
No 25
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=42.05 E-value=29 Score=16.23 Aligned_cols=23 Identities=13% Similarity=0.211 Sum_probs=15.9
Q ss_pred CCCcceEEccCCCceeeEecCCC
Q psy16544 40 PDCGKVFDGQFLVPKHVLRSLEP 62 (63)
Q Consensus 40 p~C~~av~~~~~~~~~V~c~~~~ 62 (63)
..|+++|.+-......++|--+|
T Consensus 8 ~~CGniv~v~~~~~~~l~Ccg~~ 30 (34)
T cd00974 8 EICGNIVEVLNVGGGTLVCCGQP 30 (34)
T ss_pred CCCCcEEEEEECCCcceeecCcc
Confidence 46999998866555567776544
No 26
>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=41.36 E-value=18 Score=17.11 Aligned_cols=21 Identities=24% Similarity=0.311 Sum_probs=11.4
Q ss_pred eCCCCCcceEEccCC----CceeeEec
Q psy16544 37 CPTPDCGKVFDGQFL----VPKHVLRS 59 (63)
Q Consensus 37 CP~p~C~~av~~~~~----~~~~V~c~ 59 (63)
||. |+..+..+.. ....|.|+
T Consensus 5 CP~--C~~~~~v~~~~~~~~~~~v~C~ 29 (38)
T TIGR02098 5 CPN--CKTSFRVVDSQLGANGGKVRCG 29 (38)
T ss_pred CCC--CCCEEEeCHHHcCCCCCEEECC
Confidence 543 7776666532 22356665
No 27
>PF07891 DUF1666: Protein of unknown function (DUF1666); InterPro: IPR012870 These sequences are derived from hypothetical plant proteins of unknown function. The region in question is approximately 250 residues long.
Probab=39.49 E-value=36 Score=23.60 Aligned_cols=21 Identities=19% Similarity=0.502 Sum_probs=16.6
Q ss_pred HHHHHHHHH--HHHhHHhhCCCe
Q psy16544 14 ALFEKYEDF--MVRRVLSIEPDA 34 (63)
Q Consensus 14 ~~~~kY~~~--~~~~~V~~~~~~ 34 (63)
.+...||+| ++++||++.|.-
T Consensus 42 ~VA~eFQqFQVLLQRFiENEPfe 64 (247)
T PF07891_consen 42 HVAGEFQQFQVLLQRFIENEPFE 64 (247)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCC
Confidence 455678887 899999999853
No 28
>PF02671 PAH: Paired amphipathic helix repeat; InterPro: IPR003822 This family contains the paired amphipathic helix (PAH) repeat. The family contains the eukaryotic Sin3 proteins, which have at least three PAH domains (PAH1, PAH2, and PAH3). Sin3 proteins are components of a co-repressor complex that silences transcription, playing important roles in the transition between proliferation and differentiation. Sin3 proteins are recruited to the DNA by various DNA-binding transcription factors such as the Mad family of repressors, Mnt/Rox, PLZF, MeCP2, p53, REST/NRSF, MNFbeta, Sp1, TGIF and Ume6 []. Sin3 acts as a scaffold protein that in turn recruits histone-binding proteins RbAp46/RbAp48 and histone deacetylases HDAC1/HDAC2, which deacetylate the core histones resulting in a repressed state of the chromatin []. The PAH domains are protein-protein interaction domains through which Sin3 fulfils its role as a scaffold. The PAH2 domain of Sin3 can interact with a wide range of unrelated and structurally diverse transcription factors that bind using different interaction motifs. For example, the Sin3 PAH2 domain can interact with the unrelated Mad and HBP1 factors using alternative interaction motifs that involve binding in opposite helical orientations [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1S5Q_B 2L9S_B 1G1E_B 1S5R_B 2CR7_A 2CZY_A 2LD7_B 2RMR_A 2RMS_A 1PD7_A ....
Probab=37.59 E-value=35 Score=16.84 Aligned_cols=19 Identities=21% Similarity=0.559 Sum_probs=12.2
Q ss_pred hHHhhhcCC-hHHHHHHHHH
Q psy16544 4 QYIHSILSD-QALFEKYEDF 22 (63)
Q Consensus 4 ~~I~~ll~d-~~~~~kY~~~ 22 (63)
+.|..|+.+ +++.+.|.+|
T Consensus 26 ~~v~~Ll~~hpdLl~~F~~F 45 (47)
T PF02671_consen 26 EEVSELLRGHPDLLEEFNRF 45 (47)
T ss_dssp HHHHHHTTT-HHHHHHHHHH
T ss_pred HHHHHHHccCHHHHHHHHhh
Confidence 345666664 6777777665
No 29
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=36.66 E-value=28 Score=16.08 Aligned_cols=17 Identities=24% Similarity=0.356 Sum_probs=9.1
Q ss_pred eeEeCCCCCcceEEccCCC
Q psy16544 34 ARWCPTPDCGKVFDGQFLV 52 (63)
Q Consensus 34 ~rWCP~p~C~~av~~~~~~ 52 (63)
-+|||. |+........+
T Consensus 3 ~rfC~~--CG~~t~~~~~g 19 (32)
T PF09297_consen 3 HRFCGR--CGAPTKPAPGG 19 (32)
T ss_dssp TSB-TT--T--BEEE-SSS
T ss_pred CcccCc--CCccccCCCCc
Confidence 368887 88887776665
No 30
>PF14369 zf-RING_3: zinc-finger
Probab=36.40 E-value=27 Score=16.81 Aligned_cols=23 Identities=17% Similarity=0.365 Sum_probs=15.4
Q ss_pred eEeCCCCCcceEEccCCCceeeEec
Q psy16544 35 RWCPTPDCGKVFDGQFLVPKHVLRS 59 (63)
Q Consensus 35 rWCP~p~C~~av~~~~~~~~~V~c~ 59 (63)
=||=. |...|.........|.|+
T Consensus 3 ywCh~--C~~~V~~~~~~~~~~~CP 25 (35)
T PF14369_consen 3 YWCHQ--CNRFVRIAPSPDSDVACP 25 (35)
T ss_pred EeCcc--CCCEeEeCcCCCCCcCCc
Confidence 38865 898888865544455665
No 31
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=35.13 E-value=43 Score=15.81 Aligned_cols=22 Identities=18% Similarity=0.173 Sum_probs=14.8
Q ss_pred EeCCCCCcceEEccCCCceeeEecC
Q psy16544 36 WCPTPDCGKVFDGQFLVPKHVLRSL 60 (63)
Q Consensus 36 WCP~p~C~~av~~~~~~~~~V~c~~ 60 (63)
+|. +|+........ ++.|.|+.
T Consensus 3 ~C~--~C~t~L~yP~g-A~~vrCs~ 24 (31)
T TIGR01053 3 VCG--GCRTLLMYPRG-ASSVRCAL 24 (31)
T ss_pred CcC--CCCcEeecCCC-CCeEECCC
Confidence 454 48777766554 47899875
No 32
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=32.84 E-value=15 Score=16.42 Aligned_cols=8 Identities=63% Similarity=1.688 Sum_probs=4.2
Q ss_pred CCeeEeCC
Q psy16544 32 PDARWCPT 39 (63)
Q Consensus 32 ~~~rWCP~ 39 (63)
++.++||.
T Consensus 14 ~~~~fC~~ 21 (26)
T PF13248_consen 14 PDAKFCPN 21 (26)
T ss_pred cccccChh
Confidence 44556654
No 33
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=31.47 E-value=16 Score=16.02 Aligned_cols=11 Identities=55% Similarity=1.528 Sum_probs=6.4
Q ss_pred CCeeEeCCCCCcc
Q psy16544 32 PDARWCPTPDCGK 44 (63)
Q Consensus 32 ~~~rWCP~p~C~~ 44 (63)
++.++||. ||.
T Consensus 11 ~~~~fC~~--CG~ 21 (23)
T PF13240_consen 11 DDAKFCPN--CGT 21 (23)
T ss_pred CcCcchhh--hCC
Confidence 45667764 654
No 34
>TIGR02177 PorB_KorB 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of beta subunits, representing mostly pyruvate and 2-ketoisovalerate specific enzymes.
Probab=31.20 E-value=20 Score=24.90 Aligned_cols=9 Identities=56% Similarity=1.870 Sum_probs=6.9
Q ss_pred eEeCCCCCcce
Q psy16544 35 RWCPTPDCGKV 45 (63)
Q Consensus 35 rWCP~p~C~~a 45 (63)
.|||+ |++.
T Consensus 2 ~~CpG--Cg~~ 10 (287)
T TIGR02177 2 DWCPG--CGDF 10 (287)
T ss_pred CcCCC--CCCh
Confidence 49986 9883
No 35
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=30.23 E-value=53 Score=16.25 Aligned_cols=11 Identities=36% Similarity=0.746 Sum_probs=4.9
Q ss_pred eEeCCCCCcceEE
Q psy16544 35 RWCPTPDCGKVFD 47 (63)
Q Consensus 35 rWCP~p~C~~av~ 47 (63)
.-||. |+.-+.
T Consensus 22 ~~Cp~--CG~~~~ 32 (46)
T PRK00398 22 VRCPY--CGYRIL 32 (46)
T ss_pred eECCC--CCCeEE
Confidence 34543 554443
No 36
>PRK09628 oorB 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed
Probab=30.15 E-value=29 Score=23.92 Aligned_cols=9 Identities=44% Similarity=1.354 Sum_probs=7.0
Q ss_pred eeEeCCCCCcc
Q psy16544 34 ARWCPTPDCGK 44 (63)
Q Consensus 34 ~rWCP~p~C~~ 44 (63)
..|||+ |+.
T Consensus 16 ~~~CpG--Cg~ 24 (277)
T PRK09628 16 TLWCWG--CGD 24 (277)
T ss_pred CCcCCC--CCC
Confidence 579987 775
No 37
>PF10426 zf-RAG1: Recombination-activating protein 1 zinc-finger domain; InterPro: IPR019485 During lymphocyte development, the genes encoding immunoglobulins and T-cell receptors are assembled from variable (V), diversity (D), and joining (J) gene segments. This combinatorial process, known as V(D)J recombination, allows the generation of an enormous range of binding specificities from a limited amount of genetic information. The V(D)J recombination-activating proteins 1 and 2 (RAG1 and RAG2) form a complex that initiates this process by binding to the conserved recombination signal sequences (RSS) and introducing a double-strand break between the RSS and the adjacent coding segment. These breaks are generated in two steps, nicking of one strand (hydrolysis), followed by hairpin formation (transesterification). RAG1/2 has also been shown to function as a transposase in vitro, and to possess RSS-independent endonuclease activity (end processing) and hairpin opening. RAG1 alone can bind to RSS but stable, efficient binding requires RAG2. All known catalytic activities require the presence of both proteins. For more information see []. 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 domain found in the RAG1 protein. The structure contains the characteristic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with an adjacent RING-type zinc finger domain, helps to stabilise the whole of the dimerisation region of recombination activating protein 1 (RAG1) []. The function of the whole is to bind double-stranded DNA. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0016881 acid-amino acid ligase activity; PDB: 1RMD_A.
Probab=30.04 E-value=28 Score=16.64 Aligned_cols=14 Identities=29% Similarity=0.636 Sum_probs=6.5
Q ss_pred eEeCCCCCcceEEc
Q psy16544 35 RWCPTPDCGKVFDG 48 (63)
Q Consensus 35 rWCP~p~C~~av~~ 48 (63)
-=||..+|+--|..
T Consensus 3 vrCPvkdC~EEv~l 16 (30)
T PF10426_consen 3 VRCPVKDCDEEVSL 16 (30)
T ss_dssp EE--STT---EEEH
T ss_pred cccccccCcchhhh
Confidence 35999999987764
No 38
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=30.03 E-value=51 Score=15.80 Aligned_cols=23 Identities=22% Similarity=0.306 Sum_probs=15.3
Q ss_pred EeCCCCCcceEEccC----CCceeeEecC
Q psy16544 36 WCPTPDCGKVFDGQF----LVPKHVLRSL 60 (63)
Q Consensus 36 WCP~p~C~~av~~~~----~~~~~V~c~~ 60 (63)
=||. |+.....+. +..+.|+|+-
T Consensus 4 ~Cp~--C~~~y~i~d~~ip~~g~~v~C~~ 30 (36)
T PF13717_consen 4 TCPN--CQAKYEIDDEKIPPKGRKVRCSK 30 (36)
T ss_pred ECCC--CCCEEeCCHHHCCCCCcEEECCC
Confidence 3654 888877743 4566788863
No 39
>PF01233 NMT: Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain; InterPro: IPR022676 Myristoyl-CoA:protein N-myristoyltransferase (2.3.1.97 from EC) (Nmt) [] is the enzyme responsible for transferring a myristate group on the N-terminal glycine of a number of cellular eukaryotics and viral proteins. Nmt is a monomeric protein of about 50 to 60kDa whose sequence appears to be well conserved. The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold. This entry represents the N-terminal region. ; GO: 0004379 glycylpeptide N-tetradecanoyltransferase activity; PDB: 2P6G_B 2P6F_F 2P6E_A 1IIC_A 1IID_A 2NMT_A 4A33_A 3H5Z_A 4A2Z_A 2WSA_A ....
Probab=29.86 E-value=53 Score=21.36 Aligned_cols=21 Identities=5% Similarity=0.154 Sum_probs=17.3
Q ss_pred ChHHHHHHHHHHHHhHHhhCC
Q psy16544 12 DQALFEKYEDFMVRRVLSIEP 32 (63)
Q Consensus 12 d~~~~~kY~~~~~~~~V~~~~ 32 (63)
|++..+...+||-++||+++.
T Consensus 33 d~~~l~ely~lL~~nYVEDdd 53 (162)
T PF01233_consen 33 DDEELKELYELLNENYVEDDD 53 (162)
T ss_dssp SHHHHHHHHHHHHHHSSBTTT
T ss_pred CHHHHHHHHHHHHhcCccCCc
Confidence 567777888999999999864
No 40
>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=29.70 E-value=24 Score=18.54 Aligned_cols=11 Identities=36% Similarity=0.866 Sum_probs=7.9
Q ss_pred eEeCCCCCcce
Q psy16544 35 RWCPTPDCGKV 45 (63)
Q Consensus 35 rWCP~p~C~~a 45 (63)
-=||+|+|-.-
T Consensus 7 l~C~Np~CITn 17 (52)
T PF02748_consen 7 LKCPNPNCITN 17 (52)
T ss_dssp SE-SSTTBTTT
T ss_pred EEcCCCCcccC
Confidence 35999999766
No 41
>PRK11869 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=29.54 E-value=20 Score=24.79 Aligned_cols=11 Identities=45% Similarity=1.259 Sum_probs=7.8
Q ss_pred eEeCCCCCcceEE
Q psy16544 35 RWCPTPDCGKVFD 47 (63)
Q Consensus 35 rWCP~p~C~~av~ 47 (63)
.|||+ |++...
T Consensus 9 ~~CpG--Cg~~~i 19 (280)
T PRK11869 9 AWCPG--CGNFGI 19 (280)
T ss_pred CCCcC--CCCHHH
Confidence 49986 987543
No 42
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=29.01 E-value=61 Score=18.20 Aligned_cols=23 Identities=26% Similarity=0.228 Sum_probs=17.7
Q ss_pred eEeCCCCCcceEEccCCCceeeEec
Q psy16544 35 RWCPTPDCGKVFDGQFLVPKHVLRS 59 (63)
Q Consensus 35 rWCP~p~C~~av~~~~~~~~~V~c~ 59 (63)
.=|| ||++.-.+-+...-.|.|.
T Consensus 20 VkCp--dC~N~q~vFshast~V~C~ 42 (67)
T COG2051 20 VKCP--DCGNEQVVFSHASTVVTCL 42 (67)
T ss_pred EECC--CCCCEEEEeccCceEEEec
Confidence 4586 5999988877777788884
No 43
>PRK05778 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated
Probab=28.52 E-value=23 Score=24.76 Aligned_cols=13 Identities=38% Similarity=0.979 Sum_probs=9.4
Q ss_pred eeEeCCCCCcceEEc
Q psy16544 34 ARWCPTPDCGKVFDG 48 (63)
Q Consensus 34 ~rWCP~p~C~~av~~ 48 (63)
-.|||+ |++....
T Consensus 18 ~~~CpG--Cg~~~i~ 30 (301)
T PRK05778 18 TTWCPG--CGNFGIL 30 (301)
T ss_pred CCCCCC--CCChHHH
Confidence 369986 9986543
No 44
>PF10952 DUF2753: Protein of unknown function (DUF2753); InterPro: IPR020206 This entry represents a group of uncharacterised proteins.
Probab=28.16 E-value=75 Score=20.22 Aligned_cols=35 Identities=29% Similarity=0.640 Sum_probs=26.3
Q ss_pred CChHHHHHHHHHHHHhHHhhCCCeeEeCCCCCcceEEc
Q psy16544 11 SDQALFEKYEDFMVRRVLSIEPDARWCPTPDCGKVFDG 48 (63)
Q Consensus 11 ~d~~~~~kY~~~~~~~~V~~~~~~rWCP~p~C~~av~~ 48 (63)
.|++.--||-++.-+.-+-.-|+ ||..+|+-.|..
T Consensus 64 gd~~yELkYLqlASE~VltLiPQ---Cp~~~C~afi~s 98 (140)
T PF10952_consen 64 GDSDYELKYLQLASEKVLTLIPQ---CPNTECEAFIDS 98 (140)
T ss_pred CChHHHHHHHHHHHHHHHHhccC---CCCcchHHHHHh
Confidence 45544458999888888777886 999999976543
No 45
>PF12773 DZR: Double zinc ribbon
Probab=27.99 E-value=18 Score=18.07 Aligned_cols=15 Identities=40% Similarity=1.081 Sum_probs=8.6
Q ss_pred CCCeeEeCCCCCcceEE
Q psy16544 31 EPDARWCPTPDCGKVFD 47 (63)
Q Consensus 31 ~~~~rWCP~p~C~~av~ 47 (63)
.++.++||. |+..+.
T Consensus 9 ~~~~~fC~~--CG~~l~ 23 (50)
T PF12773_consen 9 PDDAKFCPH--CGTPLP 23 (50)
T ss_pred CccccCChh--hcCChh
Confidence 344566654 666655
No 46
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 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 [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=27.20 E-value=37 Score=17.72 Aligned_cols=20 Identities=25% Similarity=0.506 Sum_probs=13.0
Q ss_pred CeeEeCCCCCcceE-EccCCC
Q psy16544 33 DARWCPTPDCGKVF-DGQFLV 52 (63)
Q Consensus 33 ~~rWCP~p~C~~av-~~~~~~ 52 (63)
.-+-||.+.|+-.| .++..+
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~d 37 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKD 37 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SS
T ss_pred hhhcCCCcccCCceEeeecCC
Confidence 45899999999864 555544
No 47
>PF12564 TypeIII_RM_meth: Type III restriction/modification enzyme methylation subunit; InterPro: IPR022221 This domain family is found in bacteria, and is approximately 60 amino acids in length. It is found in association with PF01555 from PFAM. There are two completely conserved residues (F and S) that may be functionally important. It is found in bacterial phage resistance proteins, in particular in the methylation subunit of the type III restriction/modification enzyme complex [].
Probab=26.35 E-value=73 Score=17.20 Aligned_cols=19 Identities=21% Similarity=0.448 Sum_probs=13.1
Q ss_pred CChhHHhhhcCChHHHHHH
Q psy16544 1 MKIQYIHSILSDQALFEKY 19 (63)
Q Consensus 1 ~~~~~I~~ll~d~~~~~kY 19 (63)
|.++-|..||+++.+.+.|
T Consensus 1 yD~~Li~~LL~~~~ik~~F 19 (57)
T PF12564_consen 1 YDEELIKALLSNELIKEHF 19 (57)
T ss_pred CCHHHHHHHHcCHHHHHHH
Confidence 4566777888777666655
No 48
>PF12894 Apc4_WD40: Anaphase-promoting complex subunit 4 WD40 domain
Probab=26.30 E-value=40 Score=17.15 Aligned_cols=9 Identities=56% Similarity=1.257 Sum_probs=6.9
Q ss_pred CeeEeCCCC
Q psy16544 33 DARWCPTPD 41 (63)
Q Consensus 33 ~~rWCP~p~ 41 (63)
.+.|||.-|
T Consensus 16 ~~~w~P~md 24 (47)
T PF12894_consen 16 CMSWCPTMD 24 (47)
T ss_pred EEEECCCCC
Confidence 579999844
No 49
>PF02184 HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107 The HAT (Half A TPR) repeat has a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs (tetratricopeptide repeats), though they lack the highly conserved alanine and glycine residues found in TPRs. The number of HAT repeats found in different proteins varies between 9 and 12. HAT-repeat-containing proteins appear to be components of macromolecular complexes that are required for RNA processing []. The repeats may be involved in protein-protein interactions. The HAT motif has striking structural similarities to HEAT repeats (IPR000357 from INTERPRO), being of a similar length and consisting of two short helices connected by a loop domain, as in HEAT repeats.; GO: 0006396 RNA processing, 0005622 intracellular
Probab=26.18 E-value=65 Score=15.46 Aligned_cols=12 Identities=17% Similarity=0.562 Sum_probs=7.1
Q ss_pred HHHhHHhhCCCe
Q psy16544 23 MVRRVLSIEPDA 34 (63)
Q Consensus 23 ~~~~~V~~~~~~ 34 (63)
+.++||..+|..
T Consensus 9 IyeR~v~~hp~~ 20 (32)
T PF02184_consen 9 IYERFVLVHPEV 20 (32)
T ss_pred HHHHHHHhCCCc
Confidence 445566667764
No 50
>COG1013 PorB Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion]
Probab=25.56 E-value=21 Score=24.83 Aligned_cols=12 Identities=50% Similarity=1.500 Sum_probs=8.6
Q ss_pred eeEeCCCCCcceEE
Q psy16544 34 ARWCPTPDCGKVFD 47 (63)
Q Consensus 34 ~rWCP~p~C~~av~ 47 (63)
-+|||| |+..+.
T Consensus 15 ~~~CpG--CG~~~~ 26 (294)
T COG1013 15 TRWCPG--CGEFII 26 (294)
T ss_pred CCcCCC--CCchHH
Confidence 379986 887643
No 51
>PF11709 Mit_ribos_Mrp51: Mitochondrial ribosomal protein subunit ; InterPro: IPR016712 The function of mitochondrial ribosomal small-subunit protein MRP51 is not entirely clear, but deletion of the MRP51 gene completely blocks mitochondrial gene expression [].
Probab=25.40 E-value=65 Score=22.58 Aligned_cols=30 Identities=10% Similarity=0.166 Sum_probs=20.7
Q ss_pred CChhHHhhhcCC-hHHHHHHHHHHHHhHHhh
Q psy16544 1 MKIQYIHSILSD-QALFEKYEDFMVRRVLSI 30 (63)
Q Consensus 1 ~~~~~I~~ll~d-~~~~~kY~~~~~~~~V~~ 30 (63)
|++.++.++|.. ..+...|++|+.+.+.+.
T Consensus 143 mt~~ef~~yL~kvr~~R~eF~~~L~~~~~e~ 173 (312)
T PF11709_consen 143 MTEGEFERYLKKVRPLRPEFKKWLREKHPES 173 (312)
T ss_pred CCHHHHHHHHHHhHHHHHHHHHHHHHhChhh
Confidence 677788888753 456667777787776554
No 52
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=25.07 E-value=81 Score=14.34 Aligned_cols=20 Identities=20% Similarity=0.383 Sum_probs=7.8
Q ss_pred eCCCCCcceEEccCCCceeeEec
Q psy16544 37 CPTPDCGKVFDGQFLVPKHVLRS 59 (63)
Q Consensus 37 CP~p~C~~av~~~~~~~~~V~c~ 59 (63)
||. |+..+....++. .+.|.
T Consensus 2 CP~--C~s~l~~~~~ev-~~~C~ 21 (28)
T PF03119_consen 2 CPV--CGSKLVREEGEV-DIRCP 21 (28)
T ss_dssp -TT--T--BEEE-CCTT-CEEE-
T ss_pred cCC--CCCEeEcCCCCE-eEECC
Confidence 554 777766554443 44443
No 53
>PF13963 Transpos_assoc: Transposase-associated domain
Probab=25.06 E-value=69 Score=17.70 Aligned_cols=29 Identities=17% Similarity=0.313 Sum_probs=18.5
Q ss_pred HHHHHHHHhHHhhCCCeeEeCCCCCcceEEc
Q psy16544 18 KYEDFMVRRVLSIEPDARWCPTPDCGKVFDG 48 (63)
Q Consensus 18 kY~~~~~~~~V~~~~~~rWCP~p~C~~av~~ 48 (63)
.|-.|.+......+ .-+||=.+|.+....
T Consensus 23 ~Fi~~A~~~~~~~~--~i~CPC~~C~N~~~~ 51 (77)
T PF13963_consen 23 EFIDFAFSNPSNDN--MIRCPCRKCKNEKRQ 51 (77)
T ss_pred HHHHHHHhcccCCC--ceECCchhhccCccC
Confidence 44444444443333 679999999987764
No 54
>PRK11866 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional
Probab=23.10 E-value=31 Score=23.85 Aligned_cols=11 Identities=45% Similarity=1.428 Sum_probs=8.2
Q ss_pred CeeEeCCCCCcce
Q psy16544 33 DARWCPTPDCGKV 45 (63)
Q Consensus 33 ~~rWCP~p~C~~a 45 (63)
.-.|||+ |+..
T Consensus 6 ~~~~CpG--Cg~~ 16 (279)
T PRK11866 6 PPIWCPG--CGNY 16 (279)
T ss_pred CCCCCCC--CCCh
Confidence 3479986 8875
No 55
>PF09872 DUF2099: Uncharacterized protein conserved in archaea (DUF2099); InterPro: IPR009181 The exact function of this protein is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=22.85 E-value=33 Score=23.91 Aligned_cols=10 Identities=40% Similarity=0.883 Sum_probs=8.2
Q ss_pred hCCCeeEeCC
Q psy16544 30 IEPDARWCPT 39 (63)
Q Consensus 30 ~~~~~rWCP~ 39 (63)
..|.++|||-
T Consensus 22 geP~I~~CPL 31 (258)
T PF09872_consen 22 GEPLIKYCPL 31 (258)
T ss_pred cCcccccCcc
Confidence 3788999995
No 56
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=22.70 E-value=58 Score=16.01 Aligned_cols=18 Identities=11% Similarity=0.198 Sum_probs=8.8
Q ss_pred CCcceEEccCCCceeeEe
Q psy16544 41 DCGKVFDGQFLVPKHVLR 58 (63)
Q Consensus 41 ~C~~av~~~~~~~~~V~c 58 (63)
.|+++|.+-.+..-.++|
T Consensus 11 ~CGniVev~~~g~g~lvC 28 (36)
T PF06397_consen 11 HCGNIVEVVHDGGGPLVC 28 (36)
T ss_dssp TT--EEEEEE--SS-EEE
T ss_pred CCCCEEEEEECCCCCEEe
Confidence 499999886554444555
No 57
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=22.49 E-value=83 Score=18.88 Aligned_cols=25 Identities=20% Similarity=0.485 Sum_probs=14.9
Q ss_pred CeeEeCCCCCcceEEccCC-CceeeEec
Q psy16544 33 DARWCPTPDCGKVFDGQFL-VPKHVLRS 59 (63)
Q Consensus 33 ~~rWCP~p~C~~av~~~~~-~~~~V~c~ 59 (63)
.|++||. |+..+....+ ......|+
T Consensus 1 ~m~FCp~--Cgsll~p~~~~~~~~l~C~ 26 (113)
T COG1594 1 SMRFCPK--CGSLLYPKKDDEGGKLVCR 26 (113)
T ss_pred CccccCC--ccCeeEEeEcCCCcEEECC
Confidence 3688975 8888776332 22255554
No 58
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=22.38 E-value=50 Score=17.82 Aligned_cols=35 Identities=17% Similarity=0.211 Sum_probs=22.0
Q ss_pred HHHHHHHhHHhhCC-CeeEeCC-----CCCcceEEccCCCc
Q psy16544 19 YEDFMVRRVLSIEP-DARWCPT-----PDCGKVFDGQFLVP 53 (63)
Q Consensus 19 Y~~~~~~~~V~~~~-~~rWCP~-----p~C~~av~~~~~~~ 53 (63)
++-+.+++.+..+. ..+=-|. .+||.+++....+.
T Consensus 12 ~~a~~~ek~lk~~gi~~~liP~P~~i~~~CG~al~~~~~d~ 52 (73)
T PF11823_consen 12 HDAMKAEKLLKKNGIPVRLIPTPREISAGCGLALRFEPEDL 52 (73)
T ss_pred HHHHHHHHHHHHCCCcEEEeCCChhccCCCCEEEEEChhhH
Confidence 34444555555543 4566664 58999999977543
No 59
>PRK14102 nifW nitrogenase stabilizing/protective protein; Provisional
Probab=22.10 E-value=89 Score=18.90 Aligned_cols=20 Identities=25% Similarity=0.293 Sum_probs=15.4
Q ss_pred cCChHHHHHHHHHHHHhHHh
Q psy16544 10 LSDQALFEKYEDFMVRRVLS 29 (63)
Q Consensus 10 l~d~~~~~kY~~~~~~~~V~ 29 (63)
+++.+.+++|+..+.++|=+
T Consensus 55 ~~e~~~~~~yr~~L~~AY~d 74 (105)
T PRK14102 55 LSEEEKLEKYQLALEEAYQV 74 (105)
T ss_pred CCHHHHHHHHHHHHHHHHHH
Confidence 34567789999999988854
No 60
>COG5220 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=21.99 E-value=17 Score=25.53 Aligned_cols=34 Identities=26% Similarity=0.623 Sum_probs=19.7
Q ss_pred ChHHHHHHHHHHHHhHHhhCCCeeEeCCCCCcceEE
Q psy16544 12 DQALFEKYEDFMVRRVLSIEPDARWCPTPDCGKVFD 47 (63)
Q Consensus 12 d~~~~~kY~~~~~~~~V~~~~~~rWCP~p~C~~av~ 47 (63)
+|+-+.|.-+--+.+....-| .-||.+||+.+.+
T Consensus 31 nPECyHrmCESCvdRIFs~Gp--AqCP~~gC~kILR 64 (314)
T COG5220 31 NPECYHRMCESCVDRIFSRGP--AQCPYKGCGKILR 64 (314)
T ss_pred CHHHHHHHHHHHHHHHhcCCC--CCCCCccHHHHHH
Confidence 565555543333333333333 5799999998765
No 61
>KOG0801|consensus
Probab=21.91 E-value=64 Score=21.46 Aligned_cols=24 Identities=29% Similarity=0.479 Sum_probs=20.9
Q ss_pred eCCCCCcceEEccCCCceeeEecCCC
Q psy16544 37 CPTPDCGKVFDGQFLVPKHVLRSLEP 62 (63)
Q Consensus 37 CP~p~C~~av~~~~~~~~~V~c~~~~ 62 (63)
||. |...|-.+..+...|+|--.|
T Consensus 141 CPv--C~K~V~sDd~e~HlvMCLtkP 164 (205)
T KOG0801|consen 141 CPV--CHKVVPSDDAEIHLVMCLTKP 164 (205)
T ss_pred CCc--cccccCCCcceEEEEEEeccc
Confidence 876 999999999999999996544
No 62
>PF14982 UPF0731: UPF0731 family
Probab=21.81 E-value=38 Score=19.37 Aligned_cols=17 Identities=29% Similarity=0.655 Sum_probs=13.0
Q ss_pred CCCeeEeCCCCCcceEE
Q psy16544 31 EPDARWCPTPDCGKVFD 47 (63)
Q Consensus 31 ~~~~rWCP~p~C~~av~ 47 (63)
+..+|-||+..|-.+--
T Consensus 40 ~RqLrRCpgsHCLTitd 56 (79)
T PF14982_consen 40 TRQLRRCPGSHCLTITD 56 (79)
T ss_pred cchhccCCCcceeEeec
Confidence 44689999999976543
No 63
>PF03206 NifW: Nitrogen fixation protein NifW; InterPro: IPR004893 Nitrogenase is a complex metalloenzyme composed of two proteins designated the Fe-protein and the MoFe-protein. Apart from these two proteins, a number of accessory proteins are essential for the maturation and assembly of nitrogenase. Even though experimental evidence suggests that these accessory proteins are required for nitrogenase activity, the exact roles played by many of these proteins in the functions of nitrogenase are unclear []. Using yeast two-hybrid screening it has been shown that NifW can interact with itself as well as NifZ. ; GO: 0009399 nitrogen fixation
Probab=21.07 E-value=1e+02 Score=18.46 Aligned_cols=18 Identities=11% Similarity=0.224 Sum_probs=14.5
Q ss_pred ChHHHHHHHHHHHHhHHh
Q psy16544 12 DQALFEKYEDFMVRRVLS 29 (63)
Q Consensus 12 d~~~~~kY~~~~~~~~V~ 29 (63)
+.+.++.|++++.++|=+
T Consensus 56 e~~~~~~~R~~L~~AY~d 73 (105)
T PF03206_consen 56 EEEDWAAYRRALERAYQD 73 (105)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 457788999999988854
No 64
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=20.50 E-value=97 Score=15.34 Aligned_cols=22 Identities=32% Similarity=0.462 Sum_probs=12.7
Q ss_pred CChhHHhhhc----CChHHHHHHHHH
Q psy16544 1 MKIQYIHSIL----SDQALFEKYEDF 22 (63)
Q Consensus 1 ~~~~~I~~ll----~d~~~~~kY~~~ 22 (63)
|+.+++..++ .|+.+.+++...
T Consensus 1 MS~~~l~~Fl~~~~~d~~l~~~l~~~ 26 (49)
T PF07862_consen 1 MSIESLKAFLEKVKSDPELREQLKAC 26 (49)
T ss_pred CCHHHHHHHHHHHhcCHHHHHHHHhc
Confidence 4555554444 467777777653
No 65
>PRK10353 3-methyl-adenine DNA glycosylase I; Provisional
Probab=20.17 E-value=1.4e+02 Score=19.67 Aligned_cols=18 Identities=11% Similarity=0.370 Sum_probs=13.8
Q ss_pred CChhHHhhhcCChHHHHH
Q psy16544 1 MKIQYIHSILSDQALFEK 18 (63)
Q Consensus 1 ~~~~~I~~ll~d~~~~~k 18 (63)
|++++|..|+.|+.+...
T Consensus 71 ~~e~die~Ll~d~~IIRn 88 (187)
T PRK10353 71 MQEEDVERLVQDAGIIRH 88 (187)
T ss_pred CCHHHHHHHhcCchhHHh
Confidence 578899999998866543
No 66
>COG5627 MMS21 DNA repair protein MMS21 [DNA replication, recombination, and repair]
Probab=20.09 E-value=78 Score=22.17 Aligned_cols=35 Identities=23% Similarity=0.204 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhHHhhCCCeeEeCCCCCcceEEccC
Q psy16544 15 LFEKYEDFMVRRVLSIEPDARWCPTPDCGKVFDGQF 50 (63)
Q Consensus 15 ~~~kY~~~~~~~~V~~~~~~rWCP~p~C~~av~~~~ 50 (63)
--.+|++=+++++++..+ .|=||..+|...+...+
T Consensus 208 cnh~~e~D~I~~~lq~~~-trvcp~~~Csq~~~~~~ 242 (275)
T COG5627 208 CNHKPEMDLINKKLQVEC-TRVCPRLICSQKEVVDP 242 (275)
T ss_pred hcccccHHHHHHHhcCCc-eeecchhhcchheeccc
Confidence 335788888999998776 78999999977665543
No 67
>cd07357 HN_L-whirlin_R2_like Second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains. This subgroup contains the second of two harmonin_N_like domains found in the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. The short whirlin isoform, derived from an alternative start ATG, lacks the first harmonin_N_like domain but has in common with the long isoform, this second harmonin_N_like domain (designated repeat 2, included in this subgroup) and PDZ3. This second harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=20.04 E-value=1.1e+02 Score=17.72 Aligned_cols=20 Identities=20% Similarity=0.592 Sum_probs=11.6
Q ss_pred HHhhhcCChHHHHHHHHHHHH
Q psy16544 5 YIHSILSDQALFEKYEDFMVR 25 (63)
Q Consensus 5 ~I~~ll~d~~~~~kY~~~~~~ 25 (63)
+|..+++ |....+|..+.++
T Consensus 60 EiR~lI~-p~Dl~RFD~LVlr 79 (81)
T cd07357 60 EIRELIS-PQDLDRFDDLVLR 79 (81)
T ss_pred HHHHhcC-hhhhhHHHHHHHc
Confidence 4555663 5556666666554
Done!