Query 038029
Match_columns 101
No_of_seqs 105 out of 137
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 06:49:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038029.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038029hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04690 YABBY: YABBY protein; 100.0 7.5E-37 1.6E-41 227.7 2.5 100 1-101 31-134 (170)
2 PF11331 DUF3133: Protein of u 87.9 0.34 7.5E-06 29.4 1.5 17 4-20 29-45 (46)
3 PF10122 Mu-like_Com: Mu-like 85.1 0.28 6.1E-06 30.6 0.1 14 5-18 3-16 (51)
4 PF13719 zinc_ribbon_5: zinc-r 84.4 0.59 1.3E-05 26.5 1.2 15 4-18 23-37 (37)
5 PF13717 zinc_ribbon_4: zinc-r 74.8 1.9 4.1E-05 24.4 1.2 13 4-16 23-35 (36)
6 KOG4684 Uncharacterized conser 73.2 1.8 3.8E-05 34.7 1.1 17 4-20 168-184 (275)
7 TIGR02098 MJ0042_CXXC MJ0042 f 72.1 2.4 5.2E-05 23.5 1.2 14 5-18 24-37 (38)
8 COG4416 Com Mu-like prophage p 67.5 1.3 2.8E-05 28.3 -0.6 14 4-17 2-15 (60)
9 PF01020 Ribosomal_L40e: Ribos 63.1 2.9 6.3E-05 26.1 0.4 9 8-16 38-46 (52)
10 PF05180 zf-DNL: DNL zinc fing 60.6 5.3 0.00011 25.9 1.3 13 3-15 26-38 (66)
11 PF13408 Zn_ribbon_recom: Reco 55.9 5.9 0.00013 23.1 0.8 14 6-19 5-18 (58)
12 TIGR01053 LSD1 zinc finger dom 52.4 6.4 0.00014 21.8 0.6 15 7-21 2-16 (31)
13 COG4357 Zinc finger domain con 52.0 4.2 9E-05 28.7 -0.3 19 2-20 58-76 (105)
14 PF03811 Zn_Tnp_IS1: InsA N-te 49.4 13 0.00029 21.1 1.6 17 3-19 2-18 (36)
15 PF09788 Tmemb_55A: Transmembr 48.0 11 0.00024 30.3 1.4 17 4-20 155-171 (256)
16 PF15227 zf-C3HC4_4: zinc fing 44.9 12 0.00026 21.4 1.0 10 2-11 9-18 (42)
17 TIGR02064 dsrA sulfite reducta 44.9 8 0.00017 32.4 0.3 9 7-15 275-283 (402)
18 TIGR03114 cas_csf1 CRISPR-asso 39.7 8.1 0.00018 30.0 -0.4 15 6-20 32-46 (202)
19 KOG1404 Alanine-glyoxylate ami 39.2 16 0.00035 31.4 1.2 12 3-14 58-69 (442)
20 COG1756 Mra1 Uncharacterized c 38.6 8.4 0.00018 30.4 -0.5 10 91-100 102-111 (223)
21 PF02150 RNA_POL_M_15KD: RNA p 36.2 16 0.00035 20.4 0.6 12 8-19 3-14 (35)
22 PF04690 YABBY: YABBY protein; 36.0 17 0.00037 27.4 0.8 18 5-22 11-28 (170)
23 PF05495 zf-CHY: CHY zinc fing 35.8 18 0.00038 23.0 0.8 15 6-20 41-55 (71)
24 PF06397 Desulfoferrod_N: Desu 32.3 20 0.00043 20.6 0.5 12 7-18 7-18 (36)
25 cd00246 RabGEF Nucleotide exch 31.0 25 0.00055 24.7 1.0 12 6-17 2-13 (103)
26 PF12028 DUF3515: Protein of u 27.5 31 0.00067 25.4 1.0 8 3-10 79-86 (163)
27 PF04810 zf-Sec23_Sec24: Sec23 27.4 28 0.00061 19.7 0.6 10 7-16 3-12 (40)
28 PF15288 zf-CCHC_6: Zinc knuck 23.4 31 0.00068 20.4 0.3 9 7-15 2-10 (40)
29 PF05634 APO_RNA-bind: APO RNA 22.4 43 0.00093 26.1 0.9 15 1-15 92-107 (204)
30 PF11017 DUF2855: Protein of u 22.1 32 0.0007 28.1 0.2 15 86-100 81-95 (314)
31 PF02258 SLT_beta: Shiga-like 20.9 77 0.0017 20.9 1.8 13 3-15 49-61 (70)
32 PF00518 E6: Early Protein (E6 20.8 51 0.0011 22.7 1.0 18 2-19 67-84 (110)
33 PF04502 DUF572: Family of unk 20.7 39 0.00085 27.2 0.4 10 6-15 40-49 (324)
No 1
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=100.00 E-value=7.5e-37 Score=227.70 Aligned_cols=100 Identities=41% Similarity=0.548 Sum_probs=54.7
Q ss_pred CCceeeEeCCCCCCccccccCccccc-ccc--ccccCCCCCChhhhhhchhhHHhhhhhcCCCCc-cccCCCCccccccC
Q 038029 1 MSMVVTVRCGHCTSLLSVNMMKASFV-PLH--LLASFSHDDEPKEEFRKEEVQADQKAFKRFSPS-ILTSSDNEEEDTGS 76 (101)
Q Consensus 1 l~~iVTVRCGHCtnLlSVNm~~~~~~-P~~--~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ss~~~~~~~~~ 76 (101)
||+|||||||||||||||||++++++ |.+ +.+++..+..+..............+.++.+.+ .......++ +...
T Consensus 31 L~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 109 (170)
T PF04690_consen 31 LLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQSQELQFQPENFGSNSSSSSSSSSSSSSSSMSFSE-EEEI 109 (170)
T ss_pred hhhhhceeccCccceeeeeccccccCCCcccchhccccccccccccccccccccccccCCCccccccccccCccc-cccc
Confidence 79999999999999999999976432 322 111111111000000000000000011111111 111111222 3367
Q ss_pred ccCCCCCCCCCccCCCCcccccCCC
Q 038029 77 VINHVVSKPPEKRQRAPSAYNRFIK 101 (101)
Q Consensus 77 p~~~~v~rPPEKRQRvPSAYNRFIK 101 (101)
|+.+.|+||||||||+|||||||||
T Consensus 110 pr~~~v~kPPEKRqR~psaYn~f~k 134 (170)
T PF04690_consen 110 PRAPPVNKPPEKRQRVPSAYNRFMK 134 (170)
T ss_pred cccccccCCccccCCCchhHHHHHH
Confidence 8888899999999999999999998
No 2
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=87.89 E-value=0.34 Score=29.43 Aligned_cols=17 Identities=35% Similarity=0.899 Sum_probs=14.3
Q ss_pred eeeEeCCCCCCcccccc
Q 038029 4 VVTVRCGHCTSLLSVNM 20 (101)
Q Consensus 4 iVTVRCGHCtnLlSVNm 20 (101)
.-.+|||.|..++++.+
T Consensus 29 ~~klrCGaCs~vl~~s~ 45 (46)
T PF11331_consen 29 QQKLRCGACSEVLSFSL 45 (46)
T ss_pred eeEEeCCCCceeEEEec
Confidence 45789999999998875
No 3
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=85.11 E-value=0.28 Score=30.56 Aligned_cols=14 Identities=50% Similarity=1.179 Sum_probs=11.5
Q ss_pred eeEeCCCCCCcccc
Q 038029 5 VTVRCGHCTSLLSV 18 (101)
Q Consensus 5 VTVRCGHCtnLlSV 18 (101)
=.+|||||.-||--
T Consensus 3 ~eiRC~~CnklLa~ 16 (51)
T PF10122_consen 3 KEIRCGHCNKLLAK 16 (51)
T ss_pred cceeccchhHHHhh
Confidence 36899999999754
No 4
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=84.45 E-value=0.59 Score=26.50 Aligned_cols=15 Identities=33% Similarity=0.680 Sum_probs=11.9
Q ss_pred eeeEeCCCCCCcccc
Q 038029 4 VVTVRCGHCTSLLSV 18 (101)
Q Consensus 4 iVTVRCGHCtnLlSV 18 (101)
...|||++|...+.|
T Consensus 23 ~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 23 GRKVRCPKCGHVFRV 37 (37)
T ss_pred CcEEECCCCCcEeeC
Confidence 357999999988654
No 5
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=74.82 E-value=1.9 Score=24.38 Aligned_cols=13 Identities=31% Similarity=0.754 Sum_probs=10.9
Q ss_pred eeeEeCCCCCCcc
Q 038029 4 VVTVRCGHCTSLL 16 (101)
Q Consensus 4 iVTVRCGHCtnLl 16 (101)
.+.|||+.|.+.+
T Consensus 23 g~~v~C~~C~~~f 35 (36)
T PF13717_consen 23 GRKVRCSKCGHVF 35 (36)
T ss_pred CcEEECCCCCCEe
Confidence 4789999999875
No 6
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=73.24 E-value=1.8 Score=34.67 Aligned_cols=17 Identities=35% Similarity=0.800 Sum_probs=13.1
Q ss_pred eeeEeCCCCCCcccccc
Q 038029 4 VVTVRCGHCTSLLSVNM 20 (101)
Q Consensus 4 iVTVRCGHCtnLlSVNm 20 (101)
-+-|+||||.+..--|.
T Consensus 168 gcRV~CgHC~~tFLfnt 184 (275)
T KOG4684|consen 168 GCRVKCGHCNETFLFNT 184 (275)
T ss_pred ceEEEecCccceeehhh
Confidence 37899999999765553
No 7
>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=72.12 E-value=2.4 Score=23.47 Aligned_cols=14 Identities=36% Similarity=0.788 Sum_probs=11.1
Q ss_pred eeEeCCCCCCcccc
Q 038029 5 VTVRCGHCTSLLSV 18 (101)
Q Consensus 5 VTVRCGHCtnLlSV 18 (101)
..|+|++|.+.+.|
T Consensus 24 ~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 24 GKVRCGKCGHVWYA 37 (38)
T ss_pred CEEECCCCCCEEEe
Confidence 46999999987654
No 8
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=67.50 E-value=1.3 Score=28.28 Aligned_cols=14 Identities=43% Similarity=1.051 Sum_probs=11.6
Q ss_pred eeeEeCCCCCCccc
Q 038029 4 VVTVRCGHCTSLLS 17 (101)
Q Consensus 4 iVTVRCGHCtnLlS 17 (101)
+-|.||-||.-||-
T Consensus 2 ~~tiRC~~CnKlLa 15 (60)
T COG4416 2 MQTIRCAKCNKLLA 15 (60)
T ss_pred ceeeehHHHhHHHH
Confidence 45899999999853
No 9
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 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 contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=63.10 E-value=2.9 Score=26.15 Aligned_cols=9 Identities=44% Similarity=1.113 Sum_probs=5.5
Q ss_pred eCCCCCCcc
Q 038029 8 RCGHCTSLL 16 (101)
Q Consensus 8 RCGHCtnLl 16 (101)
+|||++||-
T Consensus 38 kCGhsn~LR 46 (52)
T PF01020_consen 38 KCGHSNNLR 46 (52)
T ss_dssp SCTS-S-EE
T ss_pred cCCCCcccC
Confidence 499999983
No 10
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=60.65 E-value=5.3 Score=25.89 Aligned_cols=13 Identities=38% Similarity=0.677 Sum_probs=8.6
Q ss_pred ceeeEeCCCCCCc
Q 038029 3 MVVTVRCGHCTSL 15 (101)
Q Consensus 3 ~iVTVRCGHCtnL 15 (101)
-+|-|||+.|.|.
T Consensus 26 GvViv~C~gC~~~ 38 (66)
T PF05180_consen 26 GVVIVQCPGCKNR 38 (66)
T ss_dssp SEEEEE-TTS--E
T ss_pred CeEEEECCCCcce
Confidence 3799999999996
No 11
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=55.86 E-value=5.9 Score=23.07 Aligned_cols=14 Identities=43% Similarity=1.009 Sum_probs=11.2
Q ss_pred eEeCCCCCCccccc
Q 038029 6 TVRCGHCTSLLSVN 19 (101)
Q Consensus 6 TVRCGHCtnLlSVN 19 (101)
.|+||+|..-+...
T Consensus 5 ~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 5 LLRCGHCGSKMTRR 18 (58)
T ss_pred cEEcccCCcEeEEE
Confidence 47999999886664
No 12
>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=52.44 E-value=6.4 Score=21.83 Aligned_cols=15 Identities=40% Similarity=0.673 Sum_probs=12.0
Q ss_pred EeCCCCCCccccccC
Q 038029 7 VRCGHCTSLLSVNMM 21 (101)
Q Consensus 7 VRCGHCtnLlSVNm~ 21 (101)
|.||+|..+|..--+
T Consensus 2 ~~C~~C~t~L~yP~g 16 (31)
T TIGR01053 2 VVCGGCRTLLMYPRG 16 (31)
T ss_pred cCcCCCCcEeecCCC
Confidence 689999999876543
No 13
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=51.98 E-value=4.2 Score=28.66 Aligned_cols=19 Identities=26% Similarity=0.448 Sum_probs=14.8
Q ss_pred CceeeEeCCCCCCcccccc
Q 038029 2 SMVVTVRCGHCTSLLSVNM 20 (101)
Q Consensus 2 ~~iVTVRCGHCtnLlSVNm 20 (101)
++.=.|-||+|-++|+++=
T Consensus 58 ~~~~~iiCGvC~~~LT~~E 76 (105)
T COG4357 58 FNPKAIICGVCRKLLTRAE 76 (105)
T ss_pred cCCccEEhhhhhhhhhHHH
Confidence 3445688999999999873
No 14
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=49.36 E-value=13 Score=21.13 Aligned_cols=17 Identities=29% Similarity=0.577 Sum_probs=14.3
Q ss_pred ceeeEeCCCCCCccccc
Q 038029 3 MVVTVRCGHCTSLLSVN 19 (101)
Q Consensus 3 ~iVTVRCGHCtnLlSVN 19 (101)
.+|+|.|-+|.+-.+|.
T Consensus 2 a~i~v~CP~C~s~~~v~ 18 (36)
T PF03811_consen 2 AKIDVHCPRCQSTEGVK 18 (36)
T ss_pred CcEeeeCCCCCCCCcce
Confidence 57999999999887664
No 15
>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=47.97 E-value=11 Score=30.32 Aligned_cols=17 Identities=35% Similarity=0.778 Sum_probs=13.3
Q ss_pred eeeEeCCCCCCcccccc
Q 038029 4 VVTVRCGHCTSLLSVNM 20 (101)
Q Consensus 4 iVTVRCGHCtnLlSVNm 20 (101)
..-|+||||.+-..-|.
T Consensus 155 ~~rv~CghC~~~Fl~~~ 171 (256)
T PF09788_consen 155 SCRVICGHCSNTFLFNT 171 (256)
T ss_pred ceeEECCCCCCcEeccC
Confidence 35699999999876664
No 16
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=44.92 E-value=12 Score=21.44 Aligned_cols=10 Identities=40% Similarity=0.840 Sum_probs=6.9
Q ss_pred CceeeEeCCC
Q 038029 2 SMVVTVRCGH 11 (101)
Q Consensus 2 ~~iVTVRCGH 11 (101)
-+-||..|||
T Consensus 9 ~~Pv~l~CGH 18 (42)
T PF15227_consen 9 KDPVSLPCGH 18 (42)
T ss_dssp SSEEE-SSSS
T ss_pred CCccccCCcC
Confidence 4568888888
No 17
>TIGR02064 dsrA sulfite reductase, dissimilatory-type alpha subunit. This model describes the alpha subunit of sulfite reductase.
Probab=44.88 E-value=8 Score=32.41 Aligned_cols=9 Identities=56% Similarity=1.176 Sum_probs=8.1
Q ss_pred EeCCCCCCc
Q 038029 7 VRCGHCTSL 15 (101)
Q Consensus 7 VRCGHCtnL 15 (101)
||||||-|.
T Consensus 275 ~~Cm~Ci~~ 283 (402)
T TIGR02064 275 VRCMHCINK 283 (402)
T ss_pred CcCcccccc
Confidence 799999995
No 18
>TIGR03114 cas_csf1 CRISPR-associated protein, Csf1 family. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf1 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies closest to the repeats.
Probab=39.72 E-value=8.1 Score=30.00 Aligned_cols=15 Identities=53% Similarity=1.143 Sum_probs=12.1
Q ss_pred eEeCCCCCCcccccc
Q 038029 6 TVRCGHCTSLLSVNM 20 (101)
Q Consensus 6 TVRCGHCtnLlSVNm 20 (101)
+--||||+-|+|-.|
T Consensus 32 ~~vCG~C~al~skd~ 46 (202)
T TIGR03114 32 GMVCGHCTALMSKDM 46 (202)
T ss_pred CeeecccHHHhhHHH
Confidence 346999999998665
No 19
>KOG1404 consensus Alanine-glyoxylate aminotransferase AGT2 [Amino acid transport and metabolism]
Probab=39.20 E-value=16 Score=31.41 Aligned_cols=12 Identities=50% Similarity=0.872 Sum_probs=10.3
Q ss_pred ceeeEeCCCCCC
Q 038029 3 MVVTVRCGHCTS 14 (101)
Q Consensus 3 ~iVTVRCGHCtn 14 (101)
-+|||-||||-=
T Consensus 58 Gi~tvslGHchP 69 (442)
T KOG1404|consen 58 GIVTVSLGHCHP 69 (442)
T ss_pred CeEEEEcCCCCh
Confidence 489999999964
No 20
>COG1756 Mra1 Uncharacterized conserved protein [Function unknown]
Probab=38.56 E-value=8.4 Score=30.39 Aligned_cols=10 Identities=70% Similarity=1.261 Sum_probs=9.1
Q ss_pred CCCcccccCC
Q 038029 91 RAPSAYNRFI 100 (101)
Q Consensus 91 RvPSAYNRFI 100 (101)
|+|--|||||
T Consensus 102 R~Prny~RFi 111 (223)
T COG1756 102 RLPRNYNRFI 111 (223)
T ss_pred cCCCCHHHHH
Confidence 5999999997
No 21
>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=36.18 E-value=16 Score=20.42 Aligned_cols=12 Identities=33% Similarity=0.653 Sum_probs=9.3
Q ss_pred eCCCCCCccccc
Q 038029 8 RCGHCTSLLSVN 19 (101)
Q Consensus 8 RCGHCtnLlSVN 19 (101)
-|..|.|||.+-
T Consensus 3 FCp~C~nlL~p~ 14 (35)
T PF02150_consen 3 FCPECGNLLYPK 14 (35)
T ss_dssp BETTTTSBEEEE
T ss_pred eCCCCCccceEc
Confidence 388999998753
No 22
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=35.95 E-value=17 Score=27.44 Aligned_cols=18 Identities=28% Similarity=0.667 Sum_probs=15.1
Q ss_pred eeEeCCCCCCccccccCc
Q 038029 5 VTVRCGHCTSLLSVNMMK 22 (101)
Q Consensus 5 VTVRCGHCtnLlSVNm~~ 22 (101)
--|+|+.|+-+|=|+...
T Consensus 11 CYVhCnFC~TiLaVsVP~ 28 (170)
T PF04690_consen 11 CYVHCNFCNTILAVSVPC 28 (170)
T ss_pred EEEEcCCcCeEEEEecch
Confidence 469999999999998753
No 23
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=35.82 E-value=18 Score=23.05 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=10.6
Q ss_pred eEeCCCCCCcccccc
Q 038029 6 TVRCGHCTSLLSVNM 20 (101)
Q Consensus 6 TVRCGHCtnLlSVNm 20 (101)
.|.||.|...++++-
T Consensus 41 ~v~Cg~C~~~~~~~~ 55 (71)
T PF05495_consen 41 RVICGKCRTEQPIDE 55 (71)
T ss_dssp EEEETTT--EEES-S
T ss_pred CeECCCCCCccChhh
Confidence 799999999998874
No 24
>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=32.35 E-value=20 Score=20.63 Aligned_cols=12 Identities=33% Similarity=1.049 Sum_probs=6.8
Q ss_pred EeCCCCCCcccc
Q 038029 7 VRCGHCTSLLSV 18 (101)
Q Consensus 7 VRCGHCtnLlSV 18 (101)
-||-||.|+--|
T Consensus 7 YkC~~CGniVev 18 (36)
T PF06397_consen 7 YKCEHCGNIVEV 18 (36)
T ss_dssp EE-TTT--EEEE
T ss_pred EEccCCCCEEEE
Confidence 589999998653
No 25
>cd00246 RabGEF Nucleotide exchange factor for Rab-like small GTPases (RabGEF), Mss4 type; RabGEF positely regulates the function of Rab GTPase by promoting exchange of GDP for GTP; members of the Rab subfamily of Ras GTPases are important in vesicular transport;
Probab=31.03 E-value=25 Score=24.66 Aligned_cols=12 Identities=33% Similarity=0.639 Sum_probs=9.8
Q ss_pred eEeCCCCCCccc
Q 038029 6 TVRCGHCTSLLS 17 (101)
Q Consensus 6 TVRCGHCtnLlS 17 (101)
+|+|.||.++.-
T Consensus 2 ~v~C~~C~S~VL 13 (103)
T cd00246 2 AVLCQRCGSRVL 13 (103)
T ss_pred ceECCCCCCEEE
Confidence 689999999643
No 26
>PF12028 DUF3515: Protein of unknown function (DUF3515); InterPro: IPR021903 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 166 to 214 amino acids in length. This protein has a conserved RCG sequence motif.
Probab=27.54 E-value=31 Score=25.42 Aligned_cols=8 Identities=50% Similarity=1.007 Sum_probs=6.7
Q ss_pred ceeeEeCC
Q 038029 3 MVVTVRCG 10 (101)
Q Consensus 3 ~iVTVRCG 10 (101)
.-|++|||
T Consensus 79 ~~vvlRCG 86 (163)
T PF12028_consen 79 EPVVLRCG 86 (163)
T ss_pred CcEEEECC
Confidence 36899999
No 27
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=27.44 E-value=28 Score=19.75 Aligned_cols=10 Identities=50% Similarity=1.185 Sum_probs=4.9
Q ss_pred EeCCCCCCcc
Q 038029 7 VRCGHCTSLL 16 (101)
Q Consensus 7 VRCGHCtnLl 16 (101)
|||.+|...+
T Consensus 3 ~rC~~C~ayl 12 (40)
T PF04810_consen 3 VRCRRCRAYL 12 (40)
T ss_dssp -B-TTT--BS
T ss_pred cccCCCCCEE
Confidence 7999998774
No 28
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=23.36 E-value=31 Score=20.35 Aligned_cols=9 Identities=33% Similarity=1.154 Sum_probs=7.7
Q ss_pred EeCCCCCCc
Q 038029 7 VRCGHCTSL 15 (101)
Q Consensus 7 VRCGHCtnL 15 (101)
|||+.|..+
T Consensus 2 ~kC~~CG~~ 10 (40)
T PF15288_consen 2 VKCKNCGAF 10 (40)
T ss_pred ccccccccc
Confidence 789999876
No 29
>PF05634 APO_RNA-bind: APO RNA-binding; InterPro: IPR008512 This family consists of plant APO (accumulation of photosystem 1) proteins.
Probab=22.43 E-value=43 Score=26.13 Aligned_cols=15 Identities=33% Similarity=0.771 Sum_probs=11.4
Q ss_pred CCceeeE-eCCCCCCc
Q 038029 1 MSMVVTV-RCGHCTSL 15 (101)
Q Consensus 1 l~~iVTV-RCGHCtnL 15 (101)
|+++++| .||.|.-+
T Consensus 92 Lm~v~pV~~C~~C~EV 107 (204)
T PF05634_consen 92 LMKVYPVKACGYCPEV 107 (204)
T ss_pred HheeeeeeecCCCCCe
Confidence 5677777 49999875
No 30
>PF11017 DUF2855: Protein of unknown function (DUF2855); InterPro: IPR021276 This family of proteins has no known function.
Probab=22.07 E-value=32 Score=28.14 Aligned_cols=15 Identities=27% Similarity=0.689 Sum_probs=13.1
Q ss_pred CCccCCCCcccccCC
Q 038029 86 PEKRQRAPSAYNRFI 100 (101)
Q Consensus 86 PEKRQRvPSAYNRFI 100 (101)
-|-||=+|..||||.
T Consensus 81 s~hR~~l~~~YN~Y~ 95 (314)
T PF11017_consen 81 SPHRAGLPPIYNQYL 95 (314)
T ss_pred hhhhCcCchhhhcee
Confidence 477999999999985
No 31
>PF02258 SLT_beta: Shiga-like toxin beta subunit; InterPro: IPR003189 This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of Escherichia coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT s are composed of one enzymatic A subunit and five cell binding B subunits.; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region; PDB: 2GA4_B 1R4P_D 1BOS_I 4ULL_A 2C5C_I 1QNU_C 1CZW_F 1D1I_C 1CZG_D 2XSC_D ....
Probab=20.91 E-value=77 Score=20.87 Aligned_cols=13 Identities=38% Similarity=0.639 Sum_probs=11.3
Q ss_pred ceeeEeCCCCCCc
Q 038029 3 MVVTVRCGHCTSL 15 (101)
Q Consensus 3 ~iVTVRCGHCtnL 15 (101)
++||++|--|.+=
T Consensus 49 ~~vTi~~~sc~sG 61 (70)
T PF02258_consen 49 MTVTIKTNSCESG 61 (70)
T ss_dssp SEEEEESSSSSTT
T ss_pred eEEEEEeecccCC
Confidence 5899999999874
No 32
>PF00518 E6: Early Protein (E6); InterPro: IPR001334 The papillomavirus E6 oncoproteins are small zinc-binding proteins that share a conserved zinc-binding CXXC motif and do not have identified intrinsic enzymatic activity. E6 proteins are thought to act as adapter proteins, thereby altering the function of E6-associated cellular proteins. This model for E6 function is best supported by observations of human papillomavirus type 16 (HPV-16) E6 (16E6), which can alter the metabolism of the p53 tumor suppressor through association with a cellular E3 ubiquitin ligase called E6AP. HPV-16 E6 interacts with an 18-amino-acid sequence in E6AP, and in an as yet ill-defined fashion the E6AP-16E6 complex binds to p53, inducing the ubiquitin-dependent degradation of the trimolecular complex. 16E6 apparently functions as an adapter protein in the complex with p53, since E6AP does not interact with p53 in the absence of E6 and since the degradation of p53 requires both E6 and E6AP. Despite the similarity in structure of the E6 oncoproteins, studies have indicated surprising biochemical diversity among E6 oncoproteins of different papillomavirus types. E6 from the cancer-associated human papillomaviruses (HPVs) complex with a cellular protein termed E6-AP and together with E6-AP bind to the p53 tumor suppressor protein thereby degrading p53 through ubiquitin-mediated proteolysis. E6 from the non-cancer-associated HPV types do not bind E6-AP or degrade p53. Bovine papilloma virus E6 (BE6) binds E6-AP but fails either to complex with p53 or to degrade associated proteins, implying that BE6 might transform cells through a mechanism different from that of the HPVs. In addition to targeting p53, E6 of both cancer-associated HPVs and BPV-1 have been shown to associate with a cellular-calcium-binding protein localized to the endoplasmic reticulum [, ].; GO: 0003677 DNA binding, 0042025 host cell nucleus; PDB: 2LJY_B 2LJX_A 2LJZ_A 2FK4_A 3PY7_A.
Probab=20.77 E-value=51 Score=22.67 Aligned_cols=18 Identities=22% Similarity=0.405 Sum_probs=11.0
Q ss_pred CceeeEeCCCCCCccccc
Q 038029 2 SMVVTVRCGHCTSLLSVN 19 (101)
Q Consensus 2 ~~iVTVRCGHCtnLlSVN 19 (101)
+.-+.|||-+|-.+|+..
T Consensus 67 l~~i~iRC~~C~k~L~~~ 84 (110)
T PF00518_consen 67 LSDIIIRCYYCLKPLTPS 84 (110)
T ss_dssp CCCSEEEETTT--B--HH
T ss_pred eeEEEEEhHHcCCcCCHH
Confidence 346899999999987754
No 33
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=20.75 E-value=39 Score=27.23 Aligned_cols=10 Identities=20% Similarity=0.807 Sum_probs=5.2
Q ss_pred eEeCCCCCCc
Q 038029 6 TVRCGHCTSL 15 (101)
Q Consensus 6 TVRCGHCtnL 15 (101)
+|||.+|.+-
T Consensus 40 ~i~C~~C~~~ 49 (324)
T PF04502_consen 40 NIWCNTCGEY 49 (324)
T ss_pred cCcCCCCccc
Confidence 4455555554
Done!