Query 033174
Match_columns 125
No_of_seqs 57 out of 59
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 10:43:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033174.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033174hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10764 Gin: Inhibitor of sig 88.0 0.34 7.3E-06 30.9 1.6 28 69-111 1-28 (46)
2 PF14471 DUF4428: Domain of un 81.5 0.53 1.2E-05 30.3 0.3 30 69-111 1-30 (51)
3 cd00085 HNHc HNH nucleases; HN 76.4 0.62 1.3E-05 27.3 -0.5 43 68-111 12-56 (57)
4 KOG4628 Predicted E3 ubiquitin 72.7 3 6.5E-05 36.4 2.5 42 68-109 230-275 (348)
5 COG2174 RPL34A Ribosomal prote 68.4 2.8 6.1E-05 30.8 1.2 45 62-110 29-80 (93)
6 PF00412 LIM: LIM domain; Int 60.8 4.1 8.8E-05 24.7 0.7 16 66-81 25-40 (58)
7 KOG2893 Zn finger protein [Gen 58.6 5.1 0.00011 34.7 1.2 23 65-87 32-54 (341)
8 KOG1829 Uncharacterized conser 58.4 2.8 6.2E-05 38.8 -0.4 36 67-110 340-375 (580)
9 PRK00807 50S ribosomal protein 56.5 7.1 0.00015 25.2 1.3 43 68-121 2-46 (52)
10 PHA02565 49 recombination endo 56.0 8 0.00017 30.7 1.8 38 69-109 22-63 (157)
11 PF13831 PHD_2: PHD-finger; PD 54.8 4.2 9.1E-05 24.4 0.1 32 65-108 2-36 (36)
12 smart00507 HNHc HNH nucleases. 51.5 11 0.00023 21.4 1.5 39 68-108 11-51 (52)
13 PF01844 HNH: HNH endonuclease 50.2 6.8 0.00015 22.9 0.5 43 70-112 1-45 (47)
14 KOG2316 Predicted ATPase (PP-l 38.9 13 0.00029 31.7 0.7 28 17-44 67-96 (277)
15 cd00350 rubredoxin_like Rubred 37.1 19 0.00042 20.8 1.0 15 100-114 16-30 (33)
16 PF12874 zf-met: Zinc-finger o 36.0 2.8 6E-05 22.0 -2.5 20 68-87 1-20 (25)
17 KOG2177 Predicted E3 ubiquitin 35.4 7.9 0.00017 27.9 -1.0 45 62-108 8-54 (386)
18 smart00451 ZnF_U1 U1-like zinc 34.7 6.5 0.00014 21.8 -1.3 21 66-86 2-22 (35)
19 PF13639 zf-RING_2: Ring finge 34.3 14 0.00031 21.7 0.1 18 69-86 2-19 (44)
20 PF05947 DUF879: Bacterial pro 34.2 28 0.0006 31.7 2.0 76 18-95 19-114 (602)
21 KOG3013 Exosomal 3'-5' exoribo 33.8 10 0.00022 32.8 -0.7 37 17-53 124-164 (301)
22 smart00746 TRASH metallochaper 32.5 27 0.00058 17.5 1.0 16 70-85 1-17 (39)
23 PF10742 DUF2555: Protein of u 32.0 19 0.0004 24.4 0.4 22 38-59 5-27 (57)
24 PF04671 Ag332: Erythrocyte me 32.0 20 0.00044 20.0 0.5 11 38-48 3-13 (21)
25 PF12643 MazG-like: MazG-like 31.5 23 0.00049 25.5 0.8 13 47-59 48-60 (98)
26 PF06827 zf-FPG_IleRS: Zinc fi 28.8 20 0.00043 20.0 0.1 10 100-109 20-29 (30)
27 KOG0303 Actin-binding protein 27.6 24 0.00052 32.3 0.5 20 93-112 178-197 (472)
28 cd05700 S1_Rrp5_repeat_hs9 S1_ 26.6 13 0.00028 25.9 -1.1 15 38-52 7-21 (65)
29 smart00132 LIM Zinc-binding do 26.5 58 0.0013 17.5 1.8 35 69-110 1-36 (39)
30 COG2075 RPL24A Ribosomal prote 26.1 31 0.00066 24.0 0.7 23 68-90 4-28 (66)
31 cd00730 rubredoxin Rubredoxin; 26.1 50 0.0011 21.2 1.6 43 68-114 2-47 (50)
32 PF01199 Ribosomal_L34e: Ribos 25.8 30 0.00065 25.1 0.6 42 65-110 39-87 (94)
33 cd00472 Ribosomal_L24e_L24 Rib 24.9 32 0.00069 22.6 0.6 16 68-83 4-19 (54)
34 PRK13267 archaemetzincin-like 24.8 21 0.00045 28.0 -0.4 13 100-112 162-174 (179)
35 PF06677 Auto_anti-p27: Sjogre 23.9 30 0.00065 21.5 0.3 35 39-73 5-40 (41)
36 PF14284 PcfJ: PcfJ-like prote 23.8 26 0.00056 26.8 -0.0 17 33-49 77-93 (169)
37 PF00301 Rubredoxin: Rubredoxi 23.6 40 0.00086 21.5 0.8 42 68-113 2-46 (47)
38 PF13912 zf-C2H2_6: C2H2-type 23.4 6.8 0.00015 20.8 -2.4 12 67-78 1-12 (27)
39 PF01246 Ribosomal_L24e: Ribos 22.7 35 0.00076 23.6 0.4 18 67-84 3-20 (71)
40 smart00531 TFIIE Transcription 22.2 21 0.00046 26.5 -0.7 39 64-112 96-134 (147)
41 KOG0478 DNA replication licens 21.9 30 0.00065 33.6 0.0 36 66-114 263-298 (804)
42 PF02323 ELH: Egg-laying hormo 21.4 30 0.00065 29.3 -0.1 50 57-107 5-54 (255)
43 KOG3032 Uncharacterized conser 21.1 41 0.00089 28.8 0.6 28 62-90 30-57 (264)
44 PF10926 DUF2800: Protein of u 20.7 28 0.00061 30.5 -0.4 54 36-90 84-147 (372)
45 PF09641 DUF2026: Protein of u 20.1 32 0.00069 28.5 -0.2 37 17-53 116-162 (204)
No 1
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=87.97 E-value=0.34 Score=30.91 Aligned_cols=28 Identities=36% Similarity=0.985 Sum_probs=21.8
Q ss_pred cceeeecccCCCCceeeecCCCCCCCCCCCCCceecccchhhh
Q 033174 69 TCAVCQIDLAPSEGISVHAGSIFSTSSKPWQGPFLCADCRNKK 111 (125)
Q Consensus 69 ~CAvCqvdl~~~egISvh~gs~~~~~~~pW~GPFLC~sCq~KK 111 (125)
.|.|| +.+..+||-|. |-|+|.+|.++-
T Consensus 1 ~CiiC--~~~~~~GI~I~-------------~~fIC~~CE~~i 28 (46)
T PF10764_consen 1 KCIIC--GKEKEEGIHIY-------------GKFICSDCEKEI 28 (46)
T ss_pred CeEeC--CCcCCCCEEEE-------------CeEehHHHHHHh
Confidence 48888 66777799886 568999998763
No 2
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=81.49 E-value=0.53 Score=30.30 Aligned_cols=30 Identities=33% Similarity=0.750 Sum_probs=20.7
Q ss_pred cceeeecccCCCCceeeecCCCCCCCCCCCCCceecccchhhh
Q 033174 69 TCAVCQIDLAPSEGISVHAGSIFSTSSKPWQGPFLCADCRNKK 111 (125)
Q Consensus 69 ~CAvCqvdl~~~egISvh~gs~~~~~~~pW~GPFLC~sCq~KK 111 (125)
.||||.-++ |.+.. ++==|| |+|.+|.+|-
T Consensus 1 ~C~iCg~ki----------gl~~~--~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKI----------GLFKR--FKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCcccccc----------ccccc--eeccCc-cchHHHHHHh
Confidence 589996555 33322 444578 9999999984
No 3
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=76.39 E-value=0.62 Score=27.27 Aligned_cols=43 Identities=23% Similarity=0.332 Sum_probs=30.9
Q ss_pred ccceeeecccCCCCceeeec-CCC-CCCCCCCCCCceecccchhhh
Q 033174 68 FTCAVCQIDLAPSEGISVHA-GSI-FSTSSKPWQGPFLCADCRNKK 111 (125)
Q Consensus 68 f~CAvCqvdl~~~egISvh~-gs~-~~~~~~pW~GPFLC~sCq~KK 111 (125)
..|++|...+ .+..+.||- -+. ..+...+++.-.+|..|...|
T Consensus 12 ~~C~~c~~~~-~~~~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch~~~ 56 (57)
T cd00085 12 GLCPYCGKPG-GTEGLEVDHIIPLSDGGNNDLDNLVLLCRKCHRKK 56 (57)
T ss_pred CcCccCCCcC-CCCCceEEeecchhhCCCCchHHhHHHHHHHhhcc
Confidence 5799999988 455677765 222 235667888899999998653
No 4
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.71 E-value=3 Score=36.44 Aligned_cols=42 Identities=24% Similarity=0.642 Sum_probs=35.6
Q ss_pred ccceeeecccCCCCceeeec-CCCCCCCC-CCCCCce--ecccchh
Q 033174 68 FTCAVCQIDLAPSEGISVHA-GSIFSTSS-KPWQGPF--LCADCRN 109 (125)
Q Consensus 68 f~CAvCqvdl~~~egISvh~-gs~~~~~~-~pW~GPF--LC~sCq~ 109 (125)
+.||||+.|-+.|+.+-+=- ...|+... +||=+.. -|.-|+-
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~r~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQTRTFCPVCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhcCccCCCCCC
Confidence 79999999999999988855 77777776 9998887 4888876
No 5
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=68.43 E-value=2.8 Score=30.82 Aligned_cols=45 Identities=27% Similarity=0.617 Sum_probs=28.3
Q ss_pred ccCCCcccceeeecccCCCCceeeec-----CCCC--CCCCCCCCCceecccchhh
Q 033174 62 QSTSGLFTCAVCQIDLAPSEGISVHA-----GSIF--STSSKPWQGPFLCADCRNK 110 (125)
Q Consensus 62 ~~~~~lf~CAvCqvdl~~~egISvh~-----gs~~--~~~~~pW~GPFLC~sCq~K 110 (125)
..-.+...||+|...| .||.--- .... -...+|+.| +||++|-.+
T Consensus 29 kK~~~~p~C~~cg~pL---~Gi~r~RP~e~~r~skt~krp~RpYGG-~lc~~c~~~ 80 (93)
T COG2174 29 KKKPTIPKCAICGRPL---GGIPRGRPREFRRLSKTKKRPERPYGG-YLCANCVRE 80 (93)
T ss_pred eccCCCCcccccCCcc---CCccCCCcHHHHhccccccCcCCCcCc-eecHHHHHH
Confidence 4455778999998776 3444320 1122 334478766 899999765
No 6
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=60.84 E-value=4.1 Score=24.72 Aligned_cols=16 Identities=25% Similarity=0.615 Sum_probs=10.8
Q ss_pred CcccceeeecccCCCC
Q 033174 66 GLFTCAVCQIDLAPSE 81 (125)
Q Consensus 66 ~lf~CAvCqvdl~~~e 81 (125)
.=|.|++|+..|..+.
T Consensus 25 ~Cf~C~~C~~~l~~~~ 40 (58)
T PF00412_consen 25 ECFKCSKCGKPLNDGD 40 (58)
T ss_dssp TTSBETTTTCBTTTSS
T ss_pred cccccCCCCCccCCCe
Confidence 4467888877776553
No 7
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=58.64 E-value=5.1 Score=34.72 Aligned_cols=23 Identities=30% Similarity=0.772 Sum_probs=20.8
Q ss_pred CCcccceeeecccCCCCceeeec
Q 033174 65 SGLFTCAVCQIDLAPSEGISVHA 87 (125)
Q Consensus 65 ~~lf~CAvCqvdl~~~egISvh~ 87 (125)
-+-|.|-||-..|-+|-|+|||-
T Consensus 32 akhfkchichkkl~sgpglsihc 54 (341)
T KOG2893|consen 32 AKHFKCHICHKKLFSGPGLSIHC 54 (341)
T ss_pred hccceeeeehhhhccCCCceeeh
Confidence 37799999999999999999984
No 8
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=58.38 E-value=2.8 Score=38.83 Aligned_cols=36 Identities=22% Similarity=0.532 Sum_probs=27.8
Q ss_pred cccceeeecccCCCCceeeecCCCCCCCCCCCCCceecccchhh
Q 033174 67 LFTCAVCQIDLAPSEGISVHAGSIFSTSSKPWQGPFLCADCRNK 110 (125)
Q Consensus 67 lf~CAvCqvdl~~~egISvh~gs~~~~~~~pW~GPFLC~sCq~K 110 (125)
=|+||.|+..+.+ ..+.-.++-...|-|.|..|..-
T Consensus 340 ~~~CAgC~~~i~~--------~~~~~~R~C~y~G~y~C~~Ch~~ 375 (580)
T KOG1829|consen 340 NFRCAGCGHTIGP--------DLEQRPRLCRYLGKYFCDCCHQN 375 (580)
T ss_pred CceecccCCCccc--------ccccchhHhhhhhhhhCchhccc
Confidence 3699999555543 45557777889999999999875
No 9
>PRK00807 50S ribosomal protein L24e; Validated
Probab=56.46 E-value=7.1 Score=25.22 Aligned_cols=43 Identities=28% Similarity=0.616 Sum_probs=28.4
Q ss_pred ccceeeecccCCCCcee-eec-CCCCCCCCCCCCCceecccchhhhhhccCCCCCC
Q 033174 68 FTCAVCQIDLAPSEGIS-VHA-GSIFSTSSKPWQGPFLCADCRNKKDAMEGKRPSG 121 (125)
Q Consensus 68 f~CAvCqvdl~~~egIS-vh~-gs~~~~~~~pW~GPFLC~sCq~KKdAmEGKr~~~ 121 (125)
..|++|.-.+.||.|+. |.. |..+ =|+|+.|+.- -+-++-|+.
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~---------~Fcs~KC~~~--f~~~~nprk 46 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTIL---------YFCSSKCEKN--YKLGRVPRK 46 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEE---------EEeCHHHHHH--HHccCCCCc
Confidence 36999999999999987 644 4433 2677788542 244444544
No 10
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=55.98 E-value=8 Score=30.67 Aligned_cols=38 Identities=24% Similarity=0.508 Sum_probs=21.5
Q ss_pred cceeeecccCCC-CceeeecCCCCCCCCCCCCCc---eecccchh
Q 033174 69 TCAVCQIDLAPS-EGISVHAGSIFSTSSKPWQGP---FLCADCRN 109 (125)
Q Consensus 69 ~CAvCqvdl~~~-egISvh~gs~~~~~~~pW~GP---FLC~sCq~ 109 (125)
+|||||..+... .+. |-.... .-.-||-|- -||..|..
T Consensus 22 ~CaiC~~~l~~~~~~~--~vDHDH-~l~g~~TG~VRGLLC~~CN~ 63 (157)
T PHA02565 22 ICPLCKRELDGDVSKN--HLDHDH-ELNGPNAGRVRGLLCNLCNA 63 (157)
T ss_pred cCCCCCCccCCCcccc--ccCCCC-CCCCcccccccccCchhhhh
Confidence 799999887532 232 222211 001255665 69999965
No 11
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=54.76 E-value=4.2 Score=24.40 Aligned_cols=32 Identities=28% Similarity=0.703 Sum_probs=13.6
Q ss_pred CCcccceeeecccCCCCceeeec---CCCCCCCCCCCCCceecccch
Q 033174 65 SGLFTCAVCQIDLAPSEGISVHA---GSIFSTSSKPWQGPFLCADCR 108 (125)
Q Consensus 65 ~~lf~CAvCqvdl~~~egISvh~---gs~~~~~~~pW~GPFLC~sCq 108 (125)
+.++.|.-| +|.||. |-....... .++|.-|+
T Consensus 2 n~ll~C~~C--------~v~VH~~CYGv~~~~~~~----~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNC--------NVAVHQSCYGVSEVPDGD----DWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS----------EEEHHHHT-SS--SS---------HHH-
T ss_pred CceEEeCCC--------CCcCChhhCCcccCCCCC----cEECCcCC
Confidence 456778888 899999 554433222 36887764
No 12
>smart00507 HNHc HNH nucleases.
Probab=51.52 E-value=11 Score=21.42 Aligned_cols=39 Identities=21% Similarity=0.359 Sum_probs=25.7
Q ss_pred ccceeeecccCCCCceeeec-CCCC-CCCCCCCCCceecccch
Q 033174 68 FTCAVCQIDLAPSEGISVHA-GSIF-STSSKPWQGPFLCADCR 108 (125)
Q Consensus 68 f~CAvCqvdl~~~egISvh~-gs~~-~~~~~pW~GPFLC~sCq 108 (125)
+.|++|...+.. .+.||- -+.. .+....++.=.+|..|.
T Consensus 11 ~~C~~C~~~~~~--~~~v~Hi~p~~~~~~~~~~Nl~~~c~~ch 51 (52)
T smart00507 11 GVCAYCGKPASE--GLEVDHIIPLSDGGNDDLDNLVLLCPKCH 51 (52)
T ss_pred CCCcCCcCCCCC--CeEEEecCChhcCCCCChHhCeecChhhC
Confidence 589999877765 455543 2222 24557777888888885
No 13
>PF01844 HNH: HNH endonuclease; InterPro: IPR002711 HNH endonuclease is found in bacteria and viruses [, , ]. This family includes pyocins, colicins and anaredoxins.; GO: 0003676 nucleic acid binding, 0004519 endonuclease activity; PDB: 2QGP_C.
Probab=50.19 E-value=6.8 Score=22.86 Aligned_cols=43 Identities=23% Similarity=0.337 Sum_probs=23.9
Q ss_pred ceeeecccCCCCceeeecCCCC--CCCCCCCCCceecccchhhhh
Q 033174 70 CAVCQIDLAPSEGISVHAGSIF--STSSKPWQGPFLCADCRNKKD 112 (125)
Q Consensus 70 CAvCqvdl~~~egISvh~gs~~--~~~~~pW~GPFLC~sCq~KKd 112 (125)
|.+|...+...+.+.||==-+. .+...+.+-=.||.+|..+|-
T Consensus 1 C~~C~~~~~~~~~~~v~Hi~~~~~gg~~~~~Nl~~lC~~Ch~~k~ 45 (47)
T PF01844_consen 1 CQYCGKPGSDNESLHVHHIIPRSKGGKNDLENLILLCPSCHRKKH 45 (47)
T ss_dssp -TTT--B--GG-GEEEEESS-TTTT---STTTEEEEEHHHHHHHH
T ss_pred CCCCCCcCccCcceEeECcCchhcCCCCCHHHHHHHhHHHHHHhc
Confidence 6778777766666777652222 456678888899999988764
No 14
>KOG2316 consensus Predicted ATPase (PP-loop superfamily) [General function prediction only]
Probab=38.90 E-value=13 Score=31.73 Aligned_cols=28 Identities=29% Similarity=0.456 Sum_probs=20.8
Q ss_pred hhccccccch--hhhccccCCCCchhhhhc
Q 033174 17 LFRKKSLDSA--NKLSKKLSAVGIVEELFE 44 (125)
Q Consensus 17 ~F~rks~~s~--~~~~~~~~~~~vVEElFE 44 (125)
+|||+.+..+ .+++-.-.+-|.||+|||
T Consensus 67 lyrr~i~g~s~nq~l~Y~~t~~DEvEDLy~ 96 (277)
T KOG2316|consen 67 LYRRRIRGRSINQKLQYTKTEGDEVEDLYE 96 (277)
T ss_pred eeeeeccCcccccccccccCCCchHHHHHH
Confidence 5999998755 233445678899999997
No 15
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=37.08 E-value=19 Score=20.79 Aligned_cols=15 Identities=33% Similarity=0.913 Sum_probs=11.1
Q ss_pred Cceecccchhhhhhc
Q 033174 100 GPFLCADCRNKKDAM 114 (125)
Q Consensus 100 GPFLC~sCq~KKdAm 114 (125)
-|+.|..|...|++.
T Consensus 16 ~~~~CP~Cg~~~~~F 30 (33)
T cd00350 16 APWVCPVCGAPKDKF 30 (33)
T ss_pred CCCcCcCCCCcHHHc
Confidence 455899998877753
No 16
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=36.04 E-value=2.8 Score=21.96 Aligned_cols=20 Identities=20% Similarity=0.682 Sum_probs=12.7
Q ss_pred ccceeeecccCCCCceeeec
Q 033174 68 FTCAVCQIDLAPSEGISVHA 87 (125)
Q Consensus 68 f~CAvCqvdl~~~egISvh~ 87 (125)
|.|.||++..........|-
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~ 20 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHL 20 (25)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCCCCCCcCCHHHHHHHH
Confidence 56888877776555444443
No 17
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.39 E-value=7.9 Score=27.91 Aligned_cols=45 Identities=24% Similarity=0.690 Sum_probs=30.4
Q ss_pred ccCCCcccceeeecccCCCCceeeecCCCCCCCC--CCCCCceecccch
Q 033174 62 QSTSGLFTCAVCQIDLAPSEGISVHAGSIFSTSS--KPWQGPFLCADCR 108 (125)
Q Consensus 62 ~~~~~lf~CAvCqvdl~~~egISvh~gs~~~~~~--~pW~GPFLC~sCq 108 (125)
...-..+.|.||.-.+..- ...+-|..|-... ..|++++.|..|+
T Consensus 8 ~~~~~~~~C~iC~~~~~~p--~~l~C~H~~c~~C~~~~~~~~~~Cp~cr 54 (386)
T KOG2177|consen 8 EVLQEELTCPICLEYFREP--VLLPCGHNFCRACLTRSWEGPLSCPVCR 54 (386)
T ss_pred hhccccccChhhHHHhhcC--ccccccchHhHHHHHHhcCCCcCCcccC
Confidence 3455778999998877444 4444465552222 5666999999999
No 18
>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=34.66 E-value=6.5 Score=21.82 Aligned_cols=21 Identities=24% Similarity=0.710 Sum_probs=12.6
Q ss_pred CcccceeeecccCCCCceeee
Q 033174 66 GLFTCAVCQIDLAPSEGISVH 86 (125)
Q Consensus 66 ~lf~CAvCqvdl~~~egISvh 86 (125)
+.|.|.+|++.+.....+-.|
T Consensus 2 ~~~~C~~C~~~~~~~~~~~~H 22 (35)
T smart00451 2 GGFYCKLCNVTFTDEISVEAH 22 (35)
T ss_pred cCeEccccCCccCCHHHHHHH
Confidence 457788887777643333333
No 19
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=34.28 E-value=14 Score=21.74 Aligned_cols=18 Identities=17% Similarity=0.508 Sum_probs=13.7
Q ss_pred cceeeecccCCCCceeee
Q 033174 69 TCAVCQIDLAPSEGISVH 86 (125)
Q Consensus 69 ~CAvCqvdl~~~egISvh 86 (125)
.|+||+.++..++.+-+-
T Consensus 2 ~C~IC~~~~~~~~~~~~l 19 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKL 19 (44)
T ss_dssp CETTTTCBHHTTSCEEEE
T ss_pred CCcCCChhhcCCCeEEEc
Confidence 599999999887665443
No 20
>PF05947 DUF879: Bacterial protein of unknown function (DUF879); InterPro: IPR010272 This entry represents a protein family associated with type VI secretion in a number of pathogenic bacteria [, ]. Mutation is associated with impaired virulence, such as impaired infection of plants by Rhizobium leguminosarum.
Probab=34.22 E-value=28 Score=31.66 Aligned_cols=76 Identities=25% Similarity=0.385 Sum_probs=52.5
Q ss_pred hccccccchhhhc---cccCCCCchhhhhccCchhhHhH----hcCCCcc-----cc-----cCCCcccceeeecccCCC
Q 033174 18 FRKKSLDSANKLS---KKLSAVGIVEELFEEGSAMLAER----LGNEENV-----VQ-----STSGLFTCAVCQIDLAPS 80 (125)
Q Consensus 18 F~rks~~s~~~~~---~~~~~~~vVEElFEEGSAmLseR----L~~~yp~-----~~-----~~~~lf~CAvCqvdl~~~ 80 (125)
|-++.......++ .+..+|+| |-|.| |-|.|+-| |+-+||- +. -......|+|-|.+..++
T Consensus 19 FA~~~P~iA~~L~l~~~~~~DP~V-ERLlE-gfAfLtAri~~kLDd~~Pe~t~~LL~~L~P~~lrP~PS~tivqf~p~~~ 96 (602)
T PF05947_consen 19 FAREYPKIARRLGLSADESEDPHV-ERLLE-GFAFLTARIRQKLDDEFPELTESLLEVLYPHYLRPIPSMTIVQFDPDPG 96 (602)
T ss_pred HHHHChhhhhhhcCCCCCCCCchH-HHHHH-HHHHHHHHHHHHHhccCHHHHHHHHHhhhhhhcCCccceeEEEEeeChh
Confidence 5555555554443 56777775 88884 88888877 7888875 11 123666888988888777
Q ss_pred ---CceeeecCCCCCCCC
Q 033174 81 ---EGISVHAGSIFSTSS 95 (125)
Q Consensus 81 ---egISvh~gs~~~~~~ 95 (125)
+++.|-.|....+..
T Consensus 97 ~~~~~~~iprGt~l~s~~ 114 (602)
T PF05947_consen 97 KLTEGYTIPRGTELSSKP 114 (602)
T ss_pred hccCceEECCCCEEeccC
Confidence 888888888774443
No 21
>KOG3013 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification]
Probab=33.82 E-value=10 Score=32.81 Aligned_cols=37 Identities=27% Similarity=0.372 Sum_probs=25.4
Q ss_pred hhccccccchhhh----ccccCCCCchhhhhccCchhhHhH
Q 033174 17 LFRKKSLDSANKL----SKKLSAVGIVEELFEEGSAMLAER 53 (125)
Q Consensus 17 ~F~rks~~s~~~~----~~~~~~~~vVEElFEEGSAmLseR 53 (125)
++|||+.....+. .....-...|..+|.+||++|--|
T Consensus 124 ~~RRk~~~DEl~MR~fl~egDLi~AEVQ~v~~dGs~sLhTR 164 (301)
T KOG3013|consen 124 IQRRKSEEDELQMRSFLKEGDLIVAEVQNVFHDGSLSLHTR 164 (301)
T ss_pred hhhccchhhHHHHHHHhhccCeehHHHHHhccCCeEEEEec
Confidence 4888887654222 233333445788999999999888
No 22
>smart00746 TRASH metallochaperone-like domain.
Probab=32.55 E-value=27 Score=17.54 Aligned_cols=16 Identities=44% Similarity=0.976 Sum_probs=11.3
Q ss_pred ceeeecccC-CCCceee
Q 033174 70 CAVCQIDLA-PSEGISV 85 (125)
Q Consensus 70 CAvCqvdl~-~~egISv 85 (125)
|++|...+. +..++..
T Consensus 1 c~~C~~~~~~~~~~~~~ 17 (39)
T smart00746 1 CSFCGKDIYNPGTGIMV 17 (39)
T ss_pred CCCCCCCccCCCCceEE
Confidence 889988887 5555443
No 23
>PF10742 DUF2555: Protein of unknown function (DUF2555); InterPro: IPR019678 This entry represents conserved proteins found in Cyanobacteria. The function is not known.
Probab=31.97 E-value=19 Score=24.42 Aligned_cols=22 Identities=32% Similarity=0.333 Sum_probs=17.7
Q ss_pred chhhhhccCchhhHhHh-cCCCc
Q 033174 38 IVEELFEEGSAMLAERL-GNEEN 59 (125)
Q Consensus 38 vVEElFEEGSAmLseRL-~~~yp 59 (125)
.+.-..||..|-||+|| .-+|+
T Consensus 5 ~~~~~t~~~va~LA~RLE~DdY~ 27 (57)
T PF10742_consen 5 DLAAFTEEDVAKLAKRLEEDDYP 27 (57)
T ss_pred hHhhcCHHHHHHHHHhhhhccCC
Confidence 45567789999999999 56777
No 24
>PF04671 Ag332: Erythrocyte membrane-associated giant protein antigen 332 ; InterPro: IPR006763 To date many different Plasmodium antigens recognised by the hyperimmune system human sera have been cloned, sequenced and characterised. The majority contain tandemly repeated amino acid sequences which make up a considerable portion of the protein sequence. It has been suggested that these repeat-containing antigens may provide an immunological smokescreen to the parasite in order to evade the human immune system. This repeat is found exclusively in the Plasmodium falciparum Ag332 protein and occupies most of its length [].
Probab=31.96 E-value=20 Score=19.96 Aligned_cols=11 Identities=55% Similarity=0.887 Sum_probs=9.3
Q ss_pred chhhhhccCch
Q 033174 38 IVEELFEEGSA 48 (125)
Q Consensus 38 vVEElFEEGSA 48 (125)
+-|||-||||.
T Consensus 3 v~EEiveegs~ 13 (21)
T PF04671_consen 3 VTEEIVEEGSV 13 (21)
T ss_pred chHHHHhccch
Confidence 56899999986
No 25
>PF12643 MazG-like: MazG-like family
Probab=31.46 E-value=23 Score=25.55 Aligned_cols=13 Identities=38% Similarity=0.549 Sum_probs=11.2
Q ss_pred chhhHhHhcCCCc
Q 033174 47 SAMLAERLGNEEN 59 (125)
Q Consensus 47 SAmLseRL~~~yp 59 (125)
|.|||+|||.+|.
T Consensus 48 ~ylLa~rLGid~~ 60 (98)
T PF12643_consen 48 CYLLADRLGIDFR 60 (98)
T ss_pred HHHHHHHhCCCHH
Confidence 6799999999974
No 26
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=28.82 E-value=20 Score=20.01 Aligned_cols=10 Identities=30% Similarity=1.162 Sum_probs=6.2
Q ss_pred Cceecccchh
Q 033174 100 GPFLCADCRN 109 (125)
Q Consensus 100 GPFLC~sCq~ 109 (125)
.+|+|..||+
T Consensus 20 ~~~~C~rCq~ 29 (30)
T PF06827_consen 20 STYLCPRCQK 29 (30)
T ss_dssp EEEE-TTTCC
T ss_pred CCeECcCCcC
Confidence 4677887774
No 27
>KOG0303 consensus Actin-binding protein Coronin, contains WD40 repeats [Cytoskeleton]
Probab=27.60 E-value=24 Score=32.25 Aligned_cols=20 Identities=35% Similarity=0.707 Sum_probs=16.7
Q ss_pred CCCCCCCCceecccchhhhh
Q 033174 93 TSSKPWQGPFLCADCRNKKD 112 (125)
Q Consensus 93 ~~~~pW~GPFLC~sCq~KKd 112 (125)
+.+..|+|-.||+.|++||-
T Consensus 178 S~sfn~dGs~l~TtckDKkv 197 (472)
T KOG0303|consen 178 SMSFNRDGSLLCTTCKDKKV 197 (472)
T ss_pred EEEeccCCceeeeeccccee
Confidence 34467999999999999964
No 28
>cd05700 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=26.55 E-value=13 Score=25.86 Aligned_cols=15 Identities=33% Similarity=0.718 Sum_probs=12.9
Q ss_pred chhhhhccCchhhHh
Q 033174 38 IVEELFEEGSAMLAE 52 (125)
Q Consensus 38 vVEElFEEGSAmLse 52 (125)
+|++.-|+||+|++-
T Consensus 7 vV~~~~edgsv~fs~ 21 (65)
T cd05700 7 VVQDVTEDGSVMFSG 21 (65)
T ss_pred EEeeeccCCcEEEec
Confidence 688999999999864
No 29
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=26.54 E-value=58 Score=17.52 Aligned_cols=35 Identities=26% Similarity=0.645 Sum_probs=17.3
Q ss_pred cceeeecccCCCCceeeec-CCCCCCCCCCCCCceecccchhh
Q 033174 69 TCAVCQIDLAPSEGISVHA-GSIFSTSSKPWQGPFLCADCRNK 110 (125)
Q Consensus 69 ~CAvCqvdl~~~egISvh~-gs~~~~~~~pW~GPFLC~sCq~K 110 (125)
+|+.|...+.+++ ..+.+ |..++. .=|-|..|+..
T Consensus 1 ~C~~C~~~i~~~~-~~~~~~~~~~H~------~Cf~C~~C~~~ 36 (39)
T smart00132 1 KCAGCGKPIRGGE-LVLRALGKVWHP------ECFKCSKCGKP 36 (39)
T ss_pred CccccCCcccCCc-EEEEeCCccccc------cCCCCcccCCc
Confidence 4777766666552 22222 232222 23667777654
No 30
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=26.14 E-value=31 Score=24.00 Aligned_cols=23 Identities=26% Similarity=0.722 Sum_probs=18.7
Q ss_pred ccceeeecccCCCCc-eeeec-CCC
Q 033174 68 FTCAVCQIDLAPSEG-ISVHA-GSI 90 (125)
Q Consensus 68 f~CAvCqvdl~~~eg-ISvh~-gs~ 90 (125)
-.|.-|.-+|+||.| +-|+. |..
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v 28 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKV 28 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeE
Confidence 468899999999999 67777 544
No 31
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=26.09 E-value=50 Score=21.21 Aligned_cols=43 Identities=26% Similarity=0.633 Sum_probs=29.9
Q ss_pred ccceeeecccCCCCceeeec---CCCCCCCCCCCCCceecccchhhhhhc
Q 033174 68 FTCAVCQIDLAPSEGISVHA---GSIFSTSSKPWQGPFLCADCRNKKDAM 114 (125)
Q Consensus 68 f~CAvCqvdl~~~egISvh~---gs~~~~~~~pW~GPFLC~sCq~KKdAm 114 (125)
|+|-+|.-.-.+..|-..++ |..|..-... |.|..|...|+..
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~----w~CP~C~a~K~~F 47 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPGTPFEDLPDD----WVCPVCGAGKDDF 47 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCCCCHhHCCCC----CCCCCCCCcHHHc
Confidence 68999998888888866554 5444332233 5799998887754
No 32
>PF01199 Ribosomal_L34e: Ribosomal protein L34e; InterPro: IPR008195 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaebacterial ribosomal proteins belong to the L34e family. These include, vertebrate L34, mosquito L31 [], plant L34 [], yeast putative ribosomal protein YIL052c and archaebacterial L34e.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_i 3IZS_i 4A19_L 4A1D_L 4A18_L 4A1B_L.
Probab=25.76 E-value=30 Score=25.10 Aligned_cols=42 Identities=26% Similarity=0.416 Sum_probs=21.9
Q ss_pred CCcccceeeecccCCCCce---eeec--CCCC--CCCCCCCCCceecccchhh
Q 033174 65 SGLFTCAVCQIDLAPSEGI---SVHA--GSIF--STSSKPWQGPFLCADCRNK 110 (125)
Q Consensus 65 ~~lf~CAvCqvdl~~~egI---Svh~--gs~~--~~~~~pW~GPFLC~sCq~K 110 (125)
.....|++|...|. || -.++ .... -...++.+| .||+.|-..
T Consensus 39 ~~~pkC~~cg~~L~---Gi~~~rp~~~~rl~k~~k~vsRaYGG-~lc~~cvr~ 87 (94)
T PF01199_consen 39 PKKPKCGDCGKPLN---GIPALRPVELRRLSKRQKTVSRAYGG-SLCHKCVRE 87 (94)
T ss_dssp TT--BSTSSS-BSS---SS-SS-SSTTGTS-CHCH--CCTSSS-S-HHHHHHH
T ss_pred CCCCCcCccCCccc---ccccccHHHHhhcccCCCCCCCCCCc-cchHHHHHH
Confidence 34557999988774 44 2222 2222 345578777 699999765
No 33
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=24.89 E-value=32 Score=22.59 Aligned_cols=16 Identities=25% Similarity=0.681 Sum_probs=14.2
Q ss_pred ccceeeecccCCCCce
Q 033174 68 FTCAVCQIDLAPSEGI 83 (125)
Q Consensus 68 f~CAvCqvdl~~~egI 83 (125)
-.|+.|.-.+.||.|+
T Consensus 4 ~~C~f~g~~I~PG~G~ 19 (54)
T cd00472 4 EKCSFCGYKIYPGHGK 19 (54)
T ss_pred EEecCcCCeecCCCcc
Confidence 4799999999999994
No 34
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=24.77 E-value=21 Score=28.04 Aligned_cols=13 Identities=31% Similarity=0.905 Sum_probs=11.2
Q ss_pred Cceecccchhhhh
Q 033174 100 GPFLCADCRNKKD 112 (125)
Q Consensus 100 GPFLC~sCq~KKd 112 (125)
.+++|..|+.|-+
T Consensus 162 ~~~lC~~C~~kL~ 174 (179)
T PRK13267 162 EPNFCGSCQRKLE 174 (179)
T ss_pred CcccCHHHHHHHH
Confidence 5799999999865
No 35
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=23.86 E-value=30 Score=21.53 Aligned_cols=35 Identities=23% Similarity=0.459 Sum_probs=18.2
Q ss_pred hhhhhccCchhhHhHh-cCCCcccccCCCcccceee
Q 033174 39 VEELFEEGSAMLAERL-GNEENVVQSTSGLFTCAVC 73 (125)
Q Consensus 39 VEElFEEGSAmLseRL-~~~yp~~~~~~~lf~CAvC 73 (125)
+-|+.-.|-+||++.= .=+.|..++-.+-..|.+|
T Consensus 5 m~~~LL~G~~ML~~~Cp~C~~PL~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 5 MGEYLLQGWTMLDEHCPDCGTPLMRDKDGKIYCVSC 40 (41)
T ss_pred HHHHHHHhHhHhcCccCCCCCeeEEecCCCEECCCC
Confidence 4456666777777652 2334433333344446655
No 36
>PF14284 PcfJ: PcfJ-like protein
Probab=23.81 E-value=26 Score=26.81 Aligned_cols=17 Identities=47% Similarity=0.624 Sum_probs=15.0
Q ss_pred cCCCCchhhhhccCchh
Q 033174 33 LSAVGIVEELFEEGSAM 49 (125)
Q Consensus 33 ~~~~~vVEElFEEGSAm 49 (125)
...|..++||++||.+|
T Consensus 77 i~~~~s~~eL~~EG~~m 93 (169)
T PF14284_consen 77 IRVPKSVEELIKEGKAM 93 (169)
T ss_pred EEeCCCHHHHHHHHHHH
Confidence 56788899999999998
No 37
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=23.60 E-value=40 Score=21.48 Aligned_cols=42 Identities=24% Similarity=0.612 Sum_probs=26.5
Q ss_pred ccceeeecccCCCCceeeec---CCCCCCCCCCCCCceecccchhhhhh
Q 033174 68 FTCAVCQIDLAPSEGISVHA---GSIFSTSSKPWQGPFLCADCRNKKDA 113 (125)
Q Consensus 68 f~CAvCqvdl~~~egISvh~---gs~~~~~~~pW~GPFLC~sCq~KKdA 113 (125)
++|.+|+-.-.+..|-..++ |-.|..-... |.|..|.-.|+.
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~----w~CP~C~a~K~~ 46 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDD----WVCPVCGAPKSD 46 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-----B-TTTSSBGGG
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCC----CcCcCCCCcccc
Confidence 67999998888888876554 5555444344 478888877653
No 38
>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=23.37 E-value=6.8 Score=20.80 Aligned_cols=12 Identities=25% Similarity=0.706 Sum_probs=5.9
Q ss_pred cccceeeecccC
Q 033174 67 LFTCAVCQIDLA 78 (125)
Q Consensus 67 lf~CAvCqvdl~ 78 (125)
+|.|.+|+....
T Consensus 1 ~~~C~~C~~~F~ 12 (27)
T PF13912_consen 1 PFECDECGKTFS 12 (27)
T ss_dssp SEEETTTTEEES
T ss_pred CCCCCccCCccC
Confidence 355555544433
No 39
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=22.66 E-value=35 Score=23.56 Aligned_cols=18 Identities=17% Similarity=0.346 Sum_probs=12.4
Q ss_pred cccceeeecccCCCCcee
Q 033174 67 LFTCAVCQIDLAPSEGIS 84 (125)
Q Consensus 67 lf~CAvCqvdl~~~egIS 84 (125)
...|+.|.-.|.||.|+-
T Consensus 3 ~~~C~Fsg~~I~PG~G~~ 20 (71)
T PF01246_consen 3 TEKCSFSGYKIYPGHGKM 20 (71)
T ss_dssp SEE-TTT-SEE-SSSSEE
T ss_pred eEEecccCCccCCCCCeE
Confidence 457999999999999943
No 40
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.16 E-value=21 Score=26.53 Aligned_cols=39 Identities=21% Similarity=0.527 Sum_probs=25.7
Q ss_pred CCCcccceeeecccCCCCceeeecCCCCCCCCCCCCCceecccchhhhh
Q 033174 64 TSGLFTCAVCQIDLAPSEGISVHAGSIFSTSSKPWQGPFLCADCRNKKD 112 (125)
Q Consensus 64 ~~~lf~CAvCqvdl~~~egISvh~gs~~~~~~~pW~GPFLC~sCq~KKd 112 (125)
...-|.|..|.......+-+.. ..+ +|-|.|..|...-+
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~---------~d~-~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQL---------LDM-DGTFTCPRCGEELE 134 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHh---------cCC-CCcEECCCCCCEEE
Confidence 4567899999766665431111 124 68899999988754
No 41
>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]
Probab=21.95 E-value=30 Score=33.59 Aligned_cols=36 Identities=25% Similarity=0.735 Sum_probs=23.3
Q ss_pred CcccceeeecccCCCCceeeecCCCCCCCCCCCCCceecccchhhhhhc
Q 033174 66 GLFTCAVCQIDLAPSEGISVHAGSIFSTSSKPWQGPFLCADCRNKKDAM 114 (125)
Q Consensus 66 ~lf~CAvCqvdl~~~egISvh~gs~~~~~~~pW~GPFLC~sCq~KKdAm 114 (125)
.-|+|.||+..+.... - +.. -.=|.+|..|-.+ +.|
T Consensus 263 afFrC~vC~~~~~ve~----d-rg~-------i~eP~~C~~C~~~-~~~ 298 (804)
T KOG0478|consen 263 AFFRCSVCGHEIAVES----D-RGR-------IKEPMLCKECGTT-NSF 298 (804)
T ss_pred HhhhhhhcCceEEEEe----e-cCc-------cCCCcccccccCc-ccc
Confidence 4589999988765432 0 111 2348899999777 554
No 42
>PF02323 ELH: Egg-laying hormone precursor ; InterPro: IPR003424 This family consists of egg-laying hormone (ELH) precursor and atrial gland peptides from the little (Aplysia parvula) and california (Aplysia californica) sea hares. The family also includes ovulation prohormone precursor from the great pond snail (Lymnaea stagnalis). This family thus represents a conserved gastropoda ovulation and egg production prohormone. Note that many of the proteins present are further cleaved to give individual peptides []. Neuropeptidergic bag cells of the marine mollusc A. californica synthesize an egg-laying hormone (ELH) precursor protein which is cleaved to generate several bioacitve peptides including ELH, bag cell peptides (BCP) and acidic peptide (AP) [].; GO: 0005179 hormone activity, 0007275 multicellular organismal development, 0005576 extracellular region
Probab=21.40 E-value=30 Score=29.29 Aligned_cols=50 Identities=16% Similarity=0.196 Sum_probs=36.1
Q ss_pred CCcccccCCCcccceeeecccCCCCceeeecCCCCCCCCCCCCCceecccc
Q 033174 57 EENVVQSTSGLFTCAVCQIDLAPSEGISVHAGSIFSTSSKPWQGPFLCADC 107 (125)
Q Consensus 57 ~yp~~~~~~~lf~CAvCqvdl~~~egISvh~gs~~~~~~~pW~GPFLC~sC 107 (125)
+|-++..|| +-.|-+|-.--...+.|+||+-.+-.-..---.|||+-.+=
T Consensus 5 ~y~~a~~mf-vi~Cl~lSslc~ss~S~sv~Gk~f~~~Ravk~ss~~vv~s~ 54 (255)
T PF02323_consen 5 DYRVANTMF-VILCLWLSSLCVSSQSISVHGKDFYTNRAVKSSSPEVVLSP 54 (255)
T ss_pred CccchhhhH-HHHHHHHhhhhhhhhhhhccccccccccccccCCceEEeCc
Confidence 454478899 77788886666889999999866654444444789987653
No 43
>KOG3032 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.15 E-value=41 Score=28.76 Aligned_cols=28 Identities=36% Similarity=0.640 Sum_probs=20.7
Q ss_pred ccCCCcccceeeecccCCCCceeeecCCC
Q 033174 62 QSTSGLFTCAVCQIDLAPSEGISVHAGSI 90 (125)
Q Consensus 62 ~~~~~lf~CAvCqvdl~~~egISvh~gs~ 90 (125)
.|-++...|+||-+.|+|. =-.||-++-
T Consensus 30 yn~sgql~C~vCn~piKp~-lW~vHvnsK 57 (264)
T KOG3032|consen 30 YNESGQLVCRVCNVPIKPS-LWDVHVNSK 57 (264)
T ss_pred cCCCCCeeEEEecCcccHH-HHHHHhccH
Confidence 3477888999999999954 456776543
No 44
>PF10926 DUF2800: Protein of unknown function (DUF2800); InterPro: IPR021229 This entry is represented by Bacteriophage APSE-1, protein 51. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins found in bacteria and viruses. Some members of this family are annotated as being Phi APSE P51-like proteins.
Probab=20.71 E-value=28 Score=30.45 Aligned_cols=54 Identities=28% Similarity=0.416 Sum_probs=41.5
Q ss_pred CCchhhhhc---cCchhhHhHhcCCCcccccCCCccccee------eecccCCCCceeeec-CCC
Q 033174 36 VGIVEELFE---EGSAMLAERLGNEENVVQSTSGLFTCAV------CQIDLAPSEGISVHA-GSI 90 (125)
Q Consensus 36 ~~vVEElFE---EGSAmLseRL~~~yp~~~~~~~lf~CAv------Cqvdl~~~egISvh~-gs~ 90 (125)
+|.|.|+++ ++--++.+|++...- +...||--.|.| .-+|++-|.|+-|.+ ++.
T Consensus 84 vd~v~e~~~~~~~~~v~vEqrvd~s~~-vp~~fGT~D~vii~~~~L~IiDlKyG~GV~V~Ae~Np 147 (372)
T PF10926_consen 84 VDYVRELIEEAKDPEVLVEQRVDFSRY-VPEGFGTADCVIIADDTLHIIDLKYGKGVPVSAEENP 147 (372)
T ss_pred HHHHHHHHHhcCCCeEEEEEEeccccc-CCCCCCceeEEEEeCCeEEEEECCCCCCCcccCCCCH
Confidence 577888888 566667778765543 455899999998 789999999998888 443
No 45
>PF09641 DUF2026: Protein of unknown function (DUF2026); InterPro: IPR018599 This protein of approx. 100 residues is found in bacteria. It contains up to five alpha helices and up to seven beta strands and is probably monomeric. Its function is unknown. ; PDB: 2HLY_A.
Probab=20.06 E-value=32 Score=28.47 Aligned_cols=37 Identities=22% Similarity=0.418 Sum_probs=23.2
Q ss_pred hhccccccch---hhhccc-----cCCCCchhhhhcc--CchhhHhH
Q 033174 17 LFRKKSLDSA---NKLSKK-----LSAVGIVEELFEE--GSAMLAER 53 (125)
Q Consensus 17 ~F~rks~~s~---~~~~~~-----~~~~~vVEElFEE--GSAmLseR 53 (125)
||.|+..+-. +.+.+. ++++++-+|||.+ .++|+..=
T Consensus 116 MfQr~L~~ma~~~~~L~~~GDFfy~~d~~~t~~l~~~~~~~~~~~Dl 162 (204)
T PF09641_consen 116 MFQRRLDDMAPSPDDLQQSGDFFYHPDPDVTAELLADFFQSPMIGDL 162 (204)
T ss_dssp BEEEEGGG--SSTT---STT-EEEEE-HHHHHHHTTTGGG-HHHHHH
T ss_pred HHhchhhhhcCCHHHhcCCCceEecCCHHHHHHHHHHHHHhHHHHHH
Confidence 6999988522 333332 6789999999998 88887653
Done!