Query psy15221
Match_columns 70
No_of_seqs 103 out of 623
Neff 5.0
Searched_HMMs 46136
Date Sat Aug 17 00:19:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15221.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15221hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00270 rpsU 30S ribosomal pr 99.9 9.6E-26 2.1E-30 134.9 8.1 62 1-62 1-62 (64)
2 COG0828 RpsU Ribosomal protein 99.9 2.4E-25 5.2E-30 134.8 8.2 66 1-66 1-66 (67)
3 TIGR00030 S21p ribosomal prote 99.9 3.4E-25 7.3E-30 130.4 7.1 57 2-58 1-57 (58)
4 PF01165 Ribosomal_S21: Riboso 99.7 8.6E-22 1.9E-26 114.4 -11.1 57 2-58 1-57 (57)
5 TIGR03595 Obg_CgtA_exten Obg f 71.0 6.5 0.00014 23.2 3.0 24 12-35 29-52 (69)
6 PF14044 NETI: NETI protein 67.2 6.5 0.00014 23.2 2.4 18 4-21 2-19 (57)
7 PF09269 DUF1967: Domain of un 66.2 4.9 0.00011 23.7 1.8 23 13-35 30-52 (69)
8 COG1356 tfx Transcriptional re 63.6 6.8 0.00015 26.8 2.3 27 2-28 68-94 (143)
9 PF02196 RBD: Raf-like Ras-bin 54.0 16 0.00034 21.5 2.5 17 2-18 13-29 (71)
10 TIGR03884 sel_bind_Methan sele 50.3 26 0.00056 21.6 3.0 24 4-27 19-42 (74)
11 smart00878 Biotin_carb_C Bioti 49.6 22 0.00047 22.6 2.8 25 2-27 52-76 (107)
12 PRK13780 phosphocarrier protei 48.7 26 0.00056 21.4 2.9 26 2-28 61-86 (88)
13 PF10516 SHNi-TPR: SHNi-TPR; 44.4 23 0.0005 18.7 2.0 16 8-23 13-28 (38)
14 COG2816 NPY1 NTP pyrophosphohy 41.0 18 0.0004 27.1 1.6 14 5-18 176-189 (279)
15 COG2061 ACT-domain-containing 39.6 24 0.00052 24.9 1.9 29 1-29 133-161 (170)
16 PF11393 IcmL: Macrophage kill 38.9 31 0.00068 21.7 2.3 28 13-40 52-79 (108)
17 PF14601 TFX_C: DNA_binding pr 38.6 45 0.00096 20.7 2.9 27 2-28 15-41 (84)
18 PF00571 CBS: CBS domain CBS d 35.3 52 0.0011 17.0 2.5 18 4-21 10-27 (57)
19 PF12221 HflK_N: Bacterial mem 35.3 41 0.00088 18.4 2.1 15 11-25 22-36 (42)
20 smart00257 LysM Lysin motif. 34.6 45 0.00097 15.1 2.0 17 4-20 2-18 (44)
21 TIGR02663 nifX nitrogen fixati 31.5 55 0.0012 20.5 2.5 22 6-27 90-111 (119)
22 PF02785 Biotin_carb_C: Biotin 30.2 51 0.0011 20.9 2.2 25 2-27 52-76 (107)
23 PF10865 DUF2703: Domain of un 30.0 32 0.0007 22.6 1.3 21 9-29 22-42 (120)
24 cd00118 LysM Lysin domain, fou 29.1 69 0.0015 14.7 2.4 17 3-19 2-18 (46)
25 cd04661 MRP_L46 Mitochondrial 28.4 47 0.001 20.8 1.8 18 2-19 31-48 (132)
26 smart00455 RBD Raf-like Ras-bi 28.2 71 0.0015 18.7 2.5 17 2-18 12-28 (70)
27 PF03681 UPF0150: Uncharacteri 26.9 68 0.0015 16.8 2.0 18 7-24 26-43 (48)
28 cd01760 RBD Ubiquitin-like dom 26.6 60 0.0013 19.3 2.0 23 3-28 13-35 (72)
29 cd04678 Nudix_Hydrolase_19 Mem 26.4 52 0.0011 20.0 1.7 14 5-18 36-49 (129)
30 TIGR00756 PPR pentatricopeptid 26.3 29 0.00062 15.7 0.4 22 5-28 10-31 (35)
31 cd04684 Nudix_Hydrolase_25 Con 26.0 53 0.0012 19.5 1.7 14 5-18 33-46 (128)
32 PF04921 XAP5: XAP5, circadian 25.3 1.4E+02 0.0031 21.9 4.1 29 3-33 114-142 (239)
33 PF08461 HTH_12: Ribonuclease 24.7 62 0.0013 18.7 1.7 22 9-30 27-49 (66)
34 PF07660 STN: Secretin and Ton 24.5 37 0.00081 17.9 0.7 12 8-19 21-32 (52)
35 PF14559 TPR_19: Tetratricopep 23.6 78 0.0017 16.7 1.9 19 8-27 4-22 (68)
36 COG1071 AcoA Pyruvate/2-oxoglu 23.3 1.2E+02 0.0025 23.5 3.4 25 1-26 223-247 (358)
37 PF02271 UCR_14kD: Ubiquinol-c 23.2 73 0.0016 20.5 2.0 27 8-34 38-64 (105)
38 PF03732 Retrotrans_gag: Retro 22.8 1.3E+02 0.0029 16.7 2.9 28 8-35 59-88 (96)
39 PF01535 PPR: PPR repeat; Int 22.6 35 0.00076 15.3 0.3 19 5-24 10-28 (31)
40 PF13812 PPR_3: Pentatricopept 22.3 40 0.00087 15.5 0.5 21 6-28 12-32 (34)
41 PF14207 DpnD-PcfM: DpnD/PcfM- 22.3 89 0.0019 17.4 2.0 26 3-29 13-38 (48)
42 COG1051 ADP-ribose pyrophospha 21.9 67 0.0015 20.9 1.7 15 4-18 42-56 (145)
43 PHA02754 hypothetical protein; 21.9 66 0.0014 19.3 1.5 18 11-28 15-32 (67)
44 cd04669 Nudix_Hydrolase_11 Mem 21.7 78 0.0017 19.3 1.9 14 5-18 33-46 (121)
45 PRK15434 GDP-mannose mannosyl 21.4 87 0.0019 20.9 2.2 23 4-28 50-72 (159)
46 PF01877 RNA_binding: RNA bind 20.6 1.5E+02 0.0033 18.9 3.1 31 3-34 49-79 (120)
47 cd03430 GDPMH GDP-mannose glyc 20.4 83 0.0018 20.1 1.8 14 5-18 46-59 (144)
No 1
>PRK00270 rpsU 30S ribosomal protein S21; Reviewed
Probab=99.93 E-value=9.6e-26 Score=134.91 Aligned_cols=62 Identities=55% Similarity=0.872 Sum_probs=59.0
Q ss_pred CcEeeccCCCcHHHHHHHHHHHHHhhchHHHHHHHHhccChhHHHHHHHHHHHHHHHHHHHh
Q psy15221 1 MTIIRVKENEPFEVAIRRFKRTIEKTGLLTDLRAREFYEKPTTVRKRKLAAAIKRHYKRIRS 62 (70)
Q Consensus 1 M~~V~V~~~E~ie~Alrrfkr~~~k~Gil~e~rrrr~yeKPs~krkrk~~ea~rR~rk~~r~ 62 (70)
|++|.|++|||||.||++|+++|+++|||.|+++++||||||++++++..+|.++.+++.+.
T Consensus 1 M~~V~V~~~e~ie~Alrrfkr~~~k~gil~e~r~r~~yekPs~krkrk~~~a~rr~~k~~~~ 62 (64)
T PRK00270 1 MPQVKVRENESIDKALRRFKRKVEKAGILRELRRREFYEKPSEKRKRKKAAARKRRRKKLAR 62 (64)
T ss_pred CCeeEeCCCChHHHHHHHHHHHHHHcchHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHhh
Confidence 89999999999999999999999999999999999999999999999999999998875543
No 2
>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=2.4e-25 Score=134.75 Aligned_cols=66 Identities=55% Similarity=0.926 Sum_probs=63.4
Q ss_pred CcEeeccCCCcHHHHHHHHHHHHHhhchHHHHHHHHhccChhHHHHHHHHHHHHHHHHHHHhhcCC
Q psy15221 1 MTIIRVKENEPFEVAIRRFKRTIEKTGLLTDLRAREFYEKPTTVRKRKLAAAIKRHYKRIRSQQLP 66 (70)
Q Consensus 1 M~~V~V~~~E~ie~Alrrfkr~~~k~Gil~e~rrrr~yeKPs~krkrk~~ea~rR~rk~~r~~~~~ 66 (70)
|++|.|++|||||.||++||++|+++|||.|++.++|||+||++++++..+|.++..+++++.++.
T Consensus 1 M~~v~V~ene~~d~ALrrFKr~~~k~gil~e~k~r~~yEkPs~krkrK~a~a~kr~~k~~~k~~~~ 66 (67)
T COG0828 1 MPQVKVRENEPLDKALRRFKRKVEKEGILREMKEREFYEKPSEKRKRKKAAARKRKFKRLRKEQQR 66 (67)
T ss_pred CCeeeecCCChHHHHHHHHHHHHHHHHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999999999999999999999999999999999999999999999999887653
No 3
>TIGR00030 S21p ribosomal protein S21. This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents.
Probab=99.92 E-value=3.4e-25 Score=130.40 Aligned_cols=57 Identities=49% Similarity=0.812 Sum_probs=54.8
Q ss_pred cEeeccCCCcHHHHHHHHHHHHHhhchHHHHHHHHhccChhHHHHHHHHHHHHHHHH
Q psy15221 2 TIIRVKENEPFEVAIRRFKRTIEKTGLLTDLRAREFYEKPTTVRKRKLAAAIKRHYK 58 (70)
Q Consensus 2 ~~V~V~~~E~ie~Alrrfkr~~~k~Gil~e~rrrr~yeKPs~krkrk~~ea~rR~rk 58 (70)
++|.|++|||||+||++|+++|+++||++|+++++||||||++++++..+|++++++
T Consensus 1 ~~V~V~~~e~ie~alrrfkr~~~~~gil~e~r~r~~yeKPs~krkrk~~~a~rr~~k 57 (58)
T TIGR00030 1 PTVKVKEGESIDSALRRFKRKLEKEGILRELKKRRYYEKPSERRRRKEKAAAKRIRK 57 (58)
T ss_pred CeeEeCCCCcHHHHHHHHHHHHHHcchHHHHHHHHhhcCHHHHHHHHHHHHHHHHhc
Confidence 589999999999999999999999999999999999999999999999999998764
No 4
>PF01165 Ribosomal_S21: Ribosomal protein S21; InterPro: IPR001911 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 [, ]. Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryote ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA []. The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S21 contains 55-70 amino acid residues, and has only been found in eubacteria to date, though it has been reported that plant chloroplasts and mammalian mitochondria contain ribosomal subunit protein S21. Experimental evidence has revealed that S21 is well exposed on the surface of the Escherichia coli ribosome [], and is one of the 'split proteins': these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2VHO_U 3J18_U 2AVY_U 3OFO_U 3OFP_U 2WWL_U 3J0X_X 3IZV_Y 3ORA_U 3IZW_Y ....
Probab=99.73 E-value=8.6e-22 Score=114.36 Aligned_cols=57 Identities=44% Similarity=0.832 Sum_probs=50.8
Q ss_pred cEeeccCCCcHHHHHHHHHHHHHhhchHHHHHHHHhccChhHHHHHHHHHHHHHHHH
Q psy15221 2 TIIRVKENEPFEVAIRRFKRTIEKTGLLTDLRAREFYEKPTTVRKRKLAAAIKRHYK 58 (70)
Q Consensus 2 ~~V~V~~~E~ie~Alrrfkr~~~k~Gil~e~rrrr~yeKPs~krkrk~~ea~rR~rk 58 (70)
++|.|.+|||||.||++|+++|+++||+.+++.++|||+||++++++..++.++..+
T Consensus 1 v~V~V~~~~~~e~Alrr~~r~~~~~gi~~~~r~r~~yekps~kRkrk~~~~~rr~~k 57 (57)
T PF01165_consen 1 VTVKVRDGEDVERALRRFKRKVRRNGILKELRKRRFYEKPSEKRKRKRSERWRRRFK 57 (57)
T ss_dssp ---EEESSSSSSSSSGTTCCTSSTTHHHTTTSSSB-SSSCCCCTTHCCCCCTHHHHH
T ss_pred CeeecCCCCCHHHHHHHHHHHHHHcChHHHHHHHHhcCCHHHHHHHHHHHHHHHHhC
Confidence 589999999999999999999999999999999999999999999999999888754
No 5
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=70.96 E-value=6.5 Score=23.19 Aligned_cols=24 Identities=33% Similarity=0.555 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHhhchHHHHHHH
Q psy15221 12 FEVAIRRFKRTIEKTGLLTDLRAR 35 (70)
Q Consensus 12 ie~Alrrfkr~~~k~Gil~e~rrr 35 (70)
-+.|+.+|.+.+.+.||...+++.
T Consensus 29 ~~e~~~~f~~~L~~~Gv~~~L~~~ 52 (69)
T TIGR03595 29 NDENLRRFARKLKKLGVEDALRKA 52 (69)
T ss_pred CHHHHHHHHHHHHHCCHHHHHHHc
Confidence 357899999999999999998763
No 6
>PF14044 NETI: NETI protein
Probab=67.16 E-value=6.5 Score=23.19 Aligned_cols=18 Identities=33% Similarity=0.562 Sum_probs=15.3
Q ss_pred eeccCCCcHHHHHHHHHH
Q psy15221 4 IRVKENEPFEVAIRRFKR 21 (70)
Q Consensus 4 V~V~~~E~ie~Alrrfkr 21 (70)
..|.+||+|++.|-|.+.
T Consensus 2 FeV~enETI~~CL~RM~~ 19 (57)
T PF14044_consen 2 FEVEENETISDCLARMKK 19 (57)
T ss_pred eeccCCCcHHHHHHHHHH
Confidence 468999999999998764
No 7
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=66.16 E-value=4.9 Score=23.67 Aligned_cols=23 Identities=39% Similarity=0.696 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHhhchHHHHHHH
Q psy15221 13 EVAIRRFKRTIEKTGLLTDLRAR 35 (70)
Q Consensus 13 e~Alrrfkr~~~k~Gil~e~rrr 35 (70)
+.|+.+|.+.+.+.||...+++.
T Consensus 30 ~e~~~rf~~~L~~~Gv~~~L~~~ 52 (69)
T PF09269_consen 30 EESLRRFQRKLKKMGVEKALRKA 52 (69)
T ss_dssp GGGHHHHHHHHHHTTHHHHHHTT
T ss_pred HHHHHHHHHHHHHCCHHHHHHHc
Confidence 36789999999999999999753
No 8
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=63.57 E-value=6.8 Score=26.82 Aligned_cols=27 Identities=22% Similarity=0.369 Sum_probs=24.8
Q ss_pred cEeeccCCCcHHHHHHHHHHHHHhhch
Q psy15221 2 TIIRVKENEPFEVAIRRFKRTIEKTGL 28 (70)
Q Consensus 2 ~~V~V~~~E~ie~Alrrfkr~~~k~Gi 28 (70)
+.|.|+.||+||....++=.+-+.+||
T Consensus 68 v~i~v~aGe~~dei~e~l~k~adeagi 94 (143)
T COG1356 68 VSITVKAGEDIDEIPERLFKEADEAGI 94 (143)
T ss_pred eEEEecCCCcHHHHHHHHHHhcccccc
Confidence 468999999999999999999999997
No 9
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=54.02 E-value=16 Score=21.51 Aligned_cols=17 Identities=18% Similarity=0.403 Sum_probs=13.4
Q ss_pred cEeeccCCCcHHHHHHH
Q psy15221 2 TIIRVKENEPFEVAIRR 18 (70)
Q Consensus 2 ~~V~V~~~E~ie~Alrr 18 (70)
+.|.|++|+++..||..
T Consensus 13 t~V~vrpg~ti~d~L~~ 29 (71)
T PF02196_consen 13 TVVQVRPGMTIRDALSK 29 (71)
T ss_dssp EEEEE-TTSBHHHHHHH
T ss_pred EEEEEcCCCCHHHHHHH
Confidence 36899999999999864
No 10
>TIGR03884 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus.
Probab=50.34 E-value=26 Score=21.62 Aligned_cols=24 Identities=13% Similarity=0.378 Sum_probs=18.3
Q ss_pred eeccCCCcHHHHHHHHHHHHHhhc
Q psy15221 4 IRVKENEPFEVAIRRFKRTIEKTG 27 (70)
Q Consensus 4 V~V~~~E~ie~Alrrfkr~~~k~G 27 (70)
|....|+|+|+||.++.....+-|
T Consensus 19 iv~~~~~d~d~Al~eM~e~A~~lG 42 (74)
T TIGR03884 19 IVSTESDNVDEIVENLREKVKAKG 42 (74)
T ss_pred EEEEecCCHHHHHHHHHHHHHHcC
Confidence 455678899999999987665543
No 11
>smart00878 Biotin_carb_C Biotin carboxylase C-terminal domain. Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain.
Probab=49.59 E-value=22 Score=22.60 Aligned_cols=25 Identities=28% Similarity=0.394 Sum_probs=20.9
Q ss_pred cEeeccCCCcHHHHHHHHHHHHHhhc
Q psy15221 2 TIIRVKENEPFEVAIRRFKRTIEKTG 27 (70)
Q Consensus 2 ~~V~V~~~E~ie~Alrrfkr~~~k~G 27 (70)
+.|.|. |++-+.|+.++.+.+...-
T Consensus 52 AKliv~-g~~R~~A~~rl~~aL~e~~ 76 (107)
T smart00878 52 AKLIVH-GETREEAIARLRRALDEFR 76 (107)
T ss_pred eEEEEE-cCCHHHHHHHHHHHHHhCE
Confidence 467777 8899999999999997654
No 12
>PRK13780 phosphocarrier protein HPr; Provisional
Probab=48.74 E-value=26 Score=21.40 Aligned_cols=26 Identities=31% Similarity=0.367 Sum_probs=21.0
Q ss_pred cEeeccCCCcHHHHHHHHHHHHHhhch
Q psy15221 2 TIIRVKENEPFEVAIRRFKRTIEKTGL 28 (70)
Q Consensus 2 ~~V~V~~~E~ie~Alrrfkr~~~k~Gi 28 (70)
++|.+ +|++-+.|+..+...+..+|+
T Consensus 61 v~i~a-~G~De~~Al~~l~~~l~~~~l 86 (88)
T PRK13780 61 ITISA-EGADAADAIAAIEETMKKEGL 86 (88)
T ss_pred EEEEE-eCcCHHHHHHHHHHHHHhccc
Confidence 34555 699999999999999987764
No 13
>PF10516 SHNi-TPR: SHNi-TPR; InterPro: IPR019544 The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. This entry represents SHNi-TPR (Sim3-Hif1-NASP interrupted TPR), a sequence that is an interrupted form of TPR repeat [].
Probab=44.40 E-value=23 Score=18.71 Aligned_cols=16 Identities=44% Similarity=0.794 Sum_probs=14.0
Q ss_pred CCCcHHHHHHHHHHHH
Q psy15221 8 ENEPFEVAIRRFKRTI 23 (70)
Q Consensus 8 ~~E~ie~Alrrfkr~~ 23 (70)
++|++++|+.-|...+
T Consensus 13 e~e~f~qA~~D~~~aL 28 (38)
T PF10516_consen 13 ENENFEQAIEDYEKAL 28 (38)
T ss_pred HhccHHHHHHHHHHHH
Confidence 5789999999998876
No 14
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=40.95 E-value=18 Score=27.08 Aligned_cols=14 Identities=36% Similarity=0.446 Sum_probs=12.1
Q ss_pred eccCCCcHHHHHHH
Q psy15221 5 RVKENEPFEVAIRR 18 (70)
Q Consensus 5 ~V~~~E~ie~Alrr 18 (70)
+|..|||||+|..|
T Consensus 176 FVE~GETlE~AV~R 189 (279)
T COG2816 176 FVEPGETLEQAVAR 189 (279)
T ss_pred cccCCccHHHHHHH
Confidence 57889999999875
No 15
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=39.60 E-value=24 Score=24.86 Aligned_cols=29 Identities=28% Similarity=0.343 Sum_probs=22.3
Q ss_pred CcEeeccCCCcHHHHHHHHHHHHHhhchH
Q psy15221 1 MTIIRVKENEPFEVAIRRFKRTIEKTGLL 29 (70)
Q Consensus 1 M~~V~V~~~E~ie~Alrrfkr~~~k~Gil 29 (70)
|++|.+-+-|+++.|+.+|+-.+..-+++
T Consensus 133 ~iti~a~~~e~l~ea~~~l~ev~~eK~Ll 161 (170)
T COG2061 133 RITIIAVGKEKLDEALRRLKEVAMEKDLL 161 (170)
T ss_pred eEEEEEcChhHHHHHHHHHHHHHhhcCcE
Confidence 35666656679999999999988776653
No 16
>PF11393 IcmL: Macrophage killing protein with similarity to conjugation protein; InterPro: IPR021055 IcmL contains two amphipathic beta-sheet regions, required for the pore-forming ability which may be related to the transfer of this protein into a host cell membrane []. The icmL gene shows significant similarity to plasmid genes involved in conjugation however IcmL is thought to be required for macrophage killing. It is unknown whether conjugation plays a role in macrophage killing [].
Probab=38.91 E-value=31 Score=21.67 Aligned_cols=28 Identities=14% Similarity=0.476 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHhhchHHHHHHHHhccC
Q psy15221 13 EVAIRRFKRTIEKTGLLTDLRAREFYEK 40 (70)
Q Consensus 13 e~Alrrfkr~~~k~Gil~e~rrrr~yeK 40 (70)
+.+...|...+++.|+|..++.++....
T Consensus 52 ~~g~~~f~~aL~~Sg~l~~ik~~~l~~~ 79 (108)
T PF11393_consen 52 DEGWNSFQKALQKSGILDAIKDKRLNLS 79 (108)
T ss_pred HHHHHHHHHHHHHCCCHHHHHhcceEEe
Confidence 4567789999999999999998877654
No 17
>PF14601 TFX_C: DNA_binding protein, TFX, C-term; PDB: 1NR3_A.
Probab=38.61 E-value=45 Score=20.68 Aligned_cols=27 Identities=7% Similarity=0.085 Sum_probs=21.8
Q ss_pred cEeeccCCCcHHHHHHHHHHHHHhhch
Q psy15221 2 TIIRVKENEPFEVAIRRFKRTIEKTGL 28 (70)
Q Consensus 2 ~~V~V~~~E~ie~Alrrfkr~~~k~Gi 28 (70)
+.|.|..|.++-.+=...=++++++||
T Consensus 15 v~i~i~~GtDl~diP~~if~~aDe~gI 41 (84)
T PF14601_consen 15 VRITIPAGTDLFDIPEIIFKEADEAGI 41 (84)
T ss_dssp EEEEE--GGGHHHHHHHHHHHHHHHS-
T ss_pred EEEEEcCCCcHHHhHHHHHHHHhHcCC
Confidence 358899999999999999999999997
No 18
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=35.26 E-value=52 Score=16.99 Aligned_cols=18 Identities=22% Similarity=0.482 Sum_probs=15.5
Q ss_pred eeccCCCcHHHHHHHHHH
Q psy15221 4 IRVKENEPFEVAIRRFKR 21 (70)
Q Consensus 4 V~V~~~E~ie~Alrrfkr 21 (70)
+.|.++.++..|+..|.+
T Consensus 10 ~~v~~~~~l~~~~~~~~~ 27 (57)
T PF00571_consen 10 ITVSPDDSLEEALEIMRK 27 (57)
T ss_dssp EEEETTSBHHHHHHHHHH
T ss_pred EEEcCcCcHHHHHHHHHH
Confidence 567889999999999875
No 19
>PF12221 HflK_N: Bacterial membrane protein N terminal; InterPro: IPR020980 HflK is a bacterial membrane protein which is thought, together with the HflC protein, to form a membrane protease complex whose activity is modulated by the GTPase HflX []. This entry represents the N-terminal, membrane-spanning, region of of HflK responsible for anchoring the protein in the bacterial membrane. It is often found in association with PF01145 from PFAM.
Probab=35.25 E-value=41 Score=18.40 Aligned_cols=15 Identities=7% Similarity=0.301 Sum_probs=12.8
Q ss_pred cHHHHHHHHHHHHHh
Q psy15221 11 PFEVAIRRFKRTIEK 25 (70)
Q Consensus 11 ~ie~Alrrfkr~~~k 25 (70)
++|.+++.|.+++..
T Consensus 22 DLdel~r~l~~kl~~ 36 (42)
T PF12221_consen 22 DLDELFRKLQDKLGG 36 (42)
T ss_pred CHHHHHHHHHHHHhc
Confidence 699999999998843
No 20
>smart00257 LysM Lysin motif.
Probab=34.65 E-value=45 Score=15.15 Aligned_cols=17 Identities=24% Similarity=0.454 Sum_probs=13.2
Q ss_pred eeccCCCcHHHHHHHHH
Q psy15221 4 IRVKENEPFEVAIRRFK 20 (70)
Q Consensus 4 V~V~~~E~ie~Alrrfk 20 (70)
+.|..|+++.....+|.
T Consensus 2 ~~v~~gdt~~~ia~~~~ 18 (44)
T smart00257 2 YTVKKGDTLSSIARRYG 18 (44)
T ss_pred eEeCCCCCHHHHHHHhC
Confidence 56888999998877664
No 21
>TIGR02663 nifX nitrogen fixation protein NifX. Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the Pfam family pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor.
Probab=31.50 E-value=55 Score=20.52 Aligned_cols=22 Identities=18% Similarity=0.369 Sum_probs=17.3
Q ss_pred ccCCCcHHHHHHHHHHHHHhhc
Q psy15221 6 VKENEPFEVAIRRFKRTIEKTG 27 (70)
Q Consensus 6 V~~~E~ie~Alrrfkr~~~k~G 27 (70)
+..+++||.||..|.+.|....
T Consensus 90 ~~~~~~v~eal~~l~~~~~~~~ 111 (119)
T TIGR02663 90 VNEPESISELLERLQKMLKGNP 111 (119)
T ss_pred cCCCccHHHHHHHHHHHHcCCC
Confidence 3556689999999999886543
No 22
>PF02785 Biotin_carb_C: Biotin carboxylase C-terminal domain; InterPro: IPR005482 Acetyl-CoA carboxylase is found in all animals, plants, and bacteria and catalyzes the first committed step in fatty acid synthesis. It is a multicomponent enzyme containing a biotin carboxylase activity, a biotin carboxyl carrier protein, and a carboxyltransferase functionality. The "B-domain" extends from the main body of the subunit where it folds into two alpha-helical regions and three strands of beta-sheet. Following the excursion into the B-domain, the polypeptide chain folds back into the body of the protein where it forms an eight-stranded antiparallel beta-sheet. In addition to this major secondary structural element, the C-terminal domain also contains a smaller three-stranded antiparallel beta-sheet and seven alpha-helices []. ; GO: 0016874 ligase activity; PDB: 1W96_B 1W93_A 3VA7_A 2GPW_A 2W70_A 3G8D_A 1DV2_A 2VR1_B 2J9G_B 1DV1_A ....
Probab=30.15 E-value=51 Score=20.93 Aligned_cols=25 Identities=28% Similarity=0.325 Sum_probs=20.3
Q ss_pred cEeeccCCCcHHHHHHHHHHHHHhhc
Q psy15221 2 TIIRVKENEPFEVAIRRFKRTIEKTG 27 (70)
Q Consensus 2 ~~V~V~~~E~ie~Alrrfkr~~~k~G 27 (70)
+.|.|. |.+-+.|+.++.+.++..-
T Consensus 52 aKliv~-g~~R~~Ai~~l~~AL~e~~ 76 (107)
T PF02785_consen 52 AKLIVH-GPDREEAIARLRRALAETV 76 (107)
T ss_dssp EEEEEE-ESSHHHHHHHHHHHHHHHE
T ss_pred hhheee-ccchHHHHHHHHhhcceEE
Confidence 457776 7799999999999997653
No 23
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=29.99 E-value=32 Score=22.58 Aligned_cols=21 Identities=14% Similarity=0.341 Sum_probs=18.7
Q ss_pred CCcHHHHHHHHHHHHHhhchH
Q psy15221 9 NEPFEVAIRRFKRTIEKTGLL 29 (70)
Q Consensus 9 ~E~ie~Alrrfkr~~~k~Gil 29 (70)
|++++.|+..++..+...||-
T Consensus 22 g~~L~~av~~l~~~L~~~Gie 42 (120)
T PF10865_consen 22 GETLREAVKELAPVLAPLGIE 42 (120)
T ss_pred HHHHHHHHHHHHHHHHhCCcE
Confidence 568999999999999999973
No 24
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=29.15 E-value=69 Score=14.67 Aligned_cols=17 Identities=18% Similarity=0.401 Sum_probs=14.1
Q ss_pred EeeccCCCcHHHHHHHH
Q psy15221 3 IIRVKENEPFEVAIRRF 19 (70)
Q Consensus 3 ~V~V~~~E~ie~Alrrf 19 (70)
.+.|..|+++.....+|
T Consensus 2 ~~~v~~gdt~~~ia~~~ 18 (46)
T cd00118 2 TYTVKKGDTLSSIAQRY 18 (46)
T ss_pred EEEECCCCCHHHHHHHH
Confidence 46788999999888877
No 25
>cd04661 MRP_L46 Mitochondrial ribosomal protein L46 (MRP L46) is a component of the large subunit (39S) of the mammalian mitochondrial ribosome and a member of the Nudix hydrolase superfamily. MRPs are thought to be involved in the maintenance of the mitochondrial DNA. In general, members of the Nudix superfamily require a divalent cation, such as Mg2+ or Mn2+, for activity and contain the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. MRP L46 appears to contain a modified nudix motif.
Probab=28.39 E-value=47 Score=20.81 Aligned_cols=18 Identities=17% Similarity=0.130 Sum_probs=13.3
Q ss_pred cEeeccCCCcHHHHHHHH
Q psy15221 2 TIIRVKENEPFEVAIRRF 19 (70)
Q Consensus 2 ~~V~V~~~E~ie~Alrrf 19 (70)
|.-.|..||++++|+.|-
T Consensus 31 PgG~ve~gEt~~eaa~RE 48 (132)
T cd04661 31 PQGKREEGETLRQTAERT 48 (132)
T ss_pred CcccccCCCCHHHHHHHH
Confidence 445678899999887653
No 26
>smart00455 RBD Raf-like Ras-binding domain.
Probab=28.21 E-value=71 Score=18.67 Aligned_cols=17 Identities=18% Similarity=0.464 Sum_probs=14.5
Q ss_pred cEeeccCCCcHHHHHHH
Q psy15221 2 TIIRVKENEPFEVAIRR 18 (70)
Q Consensus 2 ~~V~V~~~E~ie~Alrr 18 (70)
+.|.|++|.++..+|..
T Consensus 12 ~~V~vrpg~tl~e~L~~ 28 (70)
T smart00455 12 TVVKVRPGKTVRDALAK 28 (70)
T ss_pred EEEEECCCCCHHHHHHH
Confidence 57999999999998864
No 27
>PF03681 UPF0150: Uncharacterised protein family (UPF0150); InterPro: IPR005357 This family of small proteins is uncharacterised. In Q9A3L8 from SWISSPROT this domain is found next to a DNA binding helix-turn-helix domain IPR002145 from INTERPRO, which suggests that this is some kind of ligand binding domain.; PDB: 2DSY_C 2YZT_A 3KWR_A.
Probab=26.86 E-value=68 Score=16.85 Aligned_cols=18 Identities=22% Similarity=0.425 Sum_probs=14.4
Q ss_pred cCCCcHHHHHHHHHHHHH
Q psy15221 7 KENEPFEVAIRRFKRTIE 24 (70)
Q Consensus 7 ~~~E~ie~Alrrfkr~~~ 24 (70)
-.|+|+|.|+..++-.+.
T Consensus 26 t~G~t~eea~~~~~eal~ 43 (48)
T PF03681_consen 26 TQGDTLEEALENAKEALE 43 (48)
T ss_dssp EEESSHHHHHHHHHHHHH
T ss_pred hcCCCHHHHHHHHHHHHH
Confidence 358899999999887663
No 28
>cd01760 RBD Ubiquitin-like domain of RBD-like S/T kinases. The ras-binding domain (RBD) of the serine/threonine kinase raf is structurally quite similar to the beta-grasp fold of ubiquitin. A raf-like RBD is also present in RGS12 and other members of a family of GTPase activating proteins and TIAM1, a guanine nucleotide exchange protein.
Probab=26.63 E-value=60 Score=19.31 Aligned_cols=23 Identities=17% Similarity=0.387 Sum_probs=16.6
Q ss_pred EeeccCCCcHHHHHHHHHHHHHhhch
Q psy15221 3 IIRVKENEPFEVAIRRFKRTIEKTGL 28 (70)
Q Consensus 3 ~V~V~~~E~ie~Alrrfkr~~~k~Gi 28 (70)
.|.|++|.++..+|-. .|.+-|+
T Consensus 13 ~V~vrpg~ti~d~L~~---~c~kr~l 35 (72)
T cd01760 13 VVPVRPGMSVRDVLAK---ACKKRGL 35 (72)
T ss_pred EEEECCCCCHHHHHHH---HHHHcCC
Confidence 6899999999988753 4444443
No 29
>cd04678 Nudix_Hydrolase_19 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=26.41 E-value=52 Score=19.95 Aligned_cols=14 Identities=29% Similarity=0.396 Sum_probs=11.2
Q ss_pred eccCCCcHHHHHHH
Q psy15221 5 RVKENEPFEVAIRR 18 (70)
Q Consensus 5 ~V~~~E~ie~Alrr 18 (70)
.|..||++++|+.|
T Consensus 36 ~ve~gEt~~~Aa~R 49 (129)
T cd04678 36 HLEFGESFEECAAR 49 (129)
T ss_pred cccCCCCHHHHHHH
Confidence 56789999998855
No 30
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=26.27 E-value=29 Score=15.72 Aligned_cols=22 Identities=32% Similarity=0.475 Sum_probs=15.3
Q ss_pred eccCCCcHHHHHHHHHHHHHhhch
Q psy15221 5 RVKENEPFEVAIRRFKRTIEKTGL 28 (70)
Q Consensus 5 ~V~~~E~ie~Alrrfkr~~~k~Gi 28 (70)
.++.| .++.|+.-|....+ .|+
T Consensus 10 ~~~~~-~~~~a~~~~~~M~~-~g~ 31 (35)
T TIGR00756 10 LCKAG-RVEEALELFKEMLE-RGI 31 (35)
T ss_pred HHHCC-CHHHHHHHHHHHHH-cCC
Confidence 34555 79999999987553 454
No 31
>cd04684 Nudix_Hydrolase_25 Contains a crystal structure of the Nudix hydrolase from Enterococcus faecalis, which has an unknown function. In general, members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity. They also contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability
Probab=26.01 E-value=53 Score=19.49 Aligned_cols=14 Identities=29% Similarity=0.373 Sum_probs=10.7
Q ss_pred eccCCCcHHHHHHH
Q psy15221 5 RVKENEPFEVAIRR 18 (70)
Q Consensus 5 ~V~~~E~ie~Alrr 18 (70)
.|..||+++.|+.|
T Consensus 33 ~ve~gE~~~~aa~R 46 (128)
T cd04684 33 GIEPGESPEEALHR 46 (128)
T ss_pred ccCCCCCHHHHHHH
Confidence 36778988888765
No 32
>PF04921 XAP5: XAP5, circadian clock regulator; InterPro: IPR007005 These proteins are found in a wide range of eukaryotes. Their function is uncertain though they are nuclear proteins, possibly with DNA-binding activity.; GO: 0005634 nucleus
Probab=25.34 E-value=1.4e+02 Score=21.88 Aligned_cols=29 Identities=21% Similarity=0.469 Sum_probs=23.9
Q ss_pred EeeccCCCcHHHHHHHHHHHHHhhchHHHHH
Q psy15221 3 IIRVKENEPFEVAIRRFKRTIEKTGLLTDLR 33 (70)
Q Consensus 3 ~V~V~~~E~ie~Alrrfkr~~~k~Gil~e~r 33 (70)
+|.|+.|.+|-.-|-+.++.+.++ +.|++
T Consensus 114 ~v~vKKGdtI~~FL~~~r~~l~~~--f~el~ 142 (239)
T PF04921_consen 114 TVRVKKGDTIWQFLEKCRKQLAKE--FRELR 142 (239)
T ss_pred eEEEcCCCCHHHHHHHHHHHHHHH--hHHHH
Confidence 588999999999999999988765 55554
No 33
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=24.67 E-value=62 Score=18.68 Aligned_cols=22 Identities=41% Similarity=0.607 Sum_probs=19.0
Q ss_pred CCcH-HHHHHHHHHHHHhhchHH
Q psy15221 9 NEPF-EVAIRRFKRTIEKTGLLT 30 (70)
Q Consensus 9 ~E~i-e~Alrrfkr~~~k~Gil~ 30 (70)
|+++ +.|+++.=+.+++.|+..
T Consensus 27 g~~~se~avRrrLr~me~~Glt~ 49 (66)
T PF08461_consen 27 GEELSEEAVRRRLRAMERDGLTR 49 (66)
T ss_pred ChhhhHHHHHHHHHHHHHCCCcc
Confidence 7778 899999999999999654
No 34
>PF07660 STN: Secretin and TonB N terminus short domain; InterPro: IPR011662 This is a conserved region found at the N-terminal region of bacterial proteins involved in either protein secretion or the uptake of selective substrates, including: Bundle-forming pilus protein B, an outer-membrane protein absolutely required for pilus biogenesis, and for enteropathogenic Escherichia coli localized adherence and autoaggregation []. PilQ, which is required for type IV pilus biogenesis and competence and is thought to function both as a pore for exit of the pilus and as a channel for entry of haem and antimicrobial agents and uptake of transforming DNA []. PupB, a specific receptor for the siderophores ferric pseudobactin BN8 and ferric pseudobactin BN7, iron chelating molecules that allow the organism to extract iron from the environment, especially under iron-restricted conditions []. TonB, which couples the electrochemical potential of the cytoplasmic membrane to the active transport of iron-siderophores and vitamin B12 across the outer membrane []. ; GO: 0019867 outer membrane; PDB: 2D1U_A 1ZZV_A 2W75_B 2O5P_A 2W77_A 2W16_A 2W6U_B 2W6T_A 2W76_B 2W78_B ....
Probab=24.46 E-value=37 Score=17.89 Aligned_cols=12 Identities=25% Similarity=0.432 Sum_probs=8.5
Q ss_pred CCCcHHHHHHHH
Q psy15221 8 ENEPFEVAIRRF 19 (70)
Q Consensus 8 ~~E~ie~Alrrf 19 (70)
.+.|+|+||..+
T Consensus 21 ~~~~~~~~L~~l 32 (52)
T PF07660_consen 21 KNMSLEEALDQL 32 (52)
T ss_dssp EEE-HHHHHHHH
T ss_pred CCcCHHHHHHHH
Confidence 467999998764
No 35
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=23.64 E-value=78 Score=16.73 Aligned_cols=19 Identities=11% Similarity=0.431 Sum_probs=14.6
Q ss_pred CCCcHHHHHHHHHHHHHhhc
Q psy15221 8 ENEPFEVAIRRFKRTIEKTG 27 (70)
Q Consensus 8 ~~E~ie~Alrrfkr~~~k~G 27 (70)
.| +.+.|+..|+..++...
T Consensus 4 ~~-~~~~A~~~~~~~l~~~p 22 (68)
T PF14559_consen 4 QG-DYDEAIELLEKALQRNP 22 (68)
T ss_dssp TT-HHHHHHHHHHHHHHHTT
T ss_pred cc-CHHHHHHHHHHHHHHCC
Confidence 44 78899999988887654
No 36
>COG1071 AcoA Pyruvate/2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, eukaryotic type, alpha subunit [Energy production and conversion]
Probab=23.32 E-value=1.2e+02 Score=23.54 Aligned_cols=25 Identities=16% Similarity=0.283 Sum_probs=22.0
Q ss_pred CcEeeccCCCcHHHHHHHHHHHHHhh
Q psy15221 1 MTIIRVKENEPFEVAIRRFKRTIEKT 26 (70)
Q Consensus 1 M~~V~V~~~E~ie~Alrrfkr~~~k~ 26 (70)
|+.|.| ||.++...+..++..++.+
T Consensus 223 ipgv~V-DG~D~~avy~~~~~A~e~A 247 (358)
T COG1071 223 IPGVRV-DGNDVLAVYEAAKEAVERA 247 (358)
T ss_pred CCeEEE-CCcCHHHHHHHHHHHHHHH
Confidence 688999 7889999999999998765
No 37
>PF02271 UCR_14kD: Ubiquinol-cytochrome C reductase complex 14kD subunit; InterPro: IPR003197 The cytochrome bd type terminal oxidases catalyse quinol dependent, Na+ independent oxygen uptake []. Members of this family are integral membrane proteins and contain a protoheame IX centre B558. Cytochrome bd may play an important role in microaerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae, where it is expressed under all conditions that permit diazotrophy []. The 14 kDa (or VI) subunit of the complex is not directly involved in electron transfer, but has a role in assembly of the complex [].; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0006122 mitochondrial electron transport, ubiquinol to cytochrome c; PDB: 3L74_F 3H1K_F 3L72_F 3H1L_S 3L71_S 3L70_S 3L73_F 3L75_F 1P84_G 3CXH_G ....
Probab=23.16 E-value=73 Score=20.53 Aligned_cols=27 Identities=22% Similarity=0.193 Sum_probs=20.9
Q ss_pred CCCcHHHHHHHHHHHHHhhchHHHHHH
Q psy15221 8 ENEPFEVAIRRFKRTIEKTGLLTDLRA 34 (70)
Q Consensus 8 ~~E~ie~Alrrfkr~~~k~Gil~e~rr 34 (70)
++.+|..||+||-..+..+..++-.|.
T Consensus 38 ~~~~v~eAl~RLp~~~~~~R~~Ri~RA 64 (105)
T PF02271_consen 38 EDPDVQEALRRLPPDEQYDRNFRIKRA 64 (105)
T ss_dssp -SHHHHHHHHHS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 478899999999999988877776654
No 38
>PF03732 Retrotrans_gag: Retrotransposon gag protein ; InterPro: IPR005162 Transposable elements (TEs) promote various chromosomal rearrangements more efficiently, and often more specifically, than other cellular processes. Retrotransposons are structurally similar to retroviruses and are bounded by long terminal repeats. This entry represents eukaryotic Gag or capsid-related retrotranspon-related proteins. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Probab=22.76 E-value=1.3e+02 Score=16.74 Aligned_cols=28 Identities=14% Similarity=0.288 Sum_probs=21.0
Q ss_pred CCCcHHHHHHHHHHHHHhhc--hHHHHHHH
Q psy15221 8 ENEPFEVAIRRFKRTIEKTG--LLTDLRAR 35 (70)
Q Consensus 8 ~~E~ie~Alrrfkr~~~k~G--il~e~rrr 35 (70)
+||+|+.-+.+|...+...+ +-.+..-.
T Consensus 59 ~~esv~~y~~rf~~l~~~~~~~~~e~~~v~ 88 (96)
T PF03732_consen 59 GNESVREYVNRFRELARRAPPPMDEEMLVE 88 (96)
T ss_pred cCCcHHHHHHHHHHHHHHCCCCcCHHHHHH
Confidence 58899999999999988887 44444433
No 39
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=22.63 E-value=35 Score=15.30 Aligned_cols=19 Identities=32% Similarity=0.359 Sum_probs=13.0
Q ss_pred eccCCCcHHHHHHHHHHHHH
Q psy15221 5 RVKENEPFEVAIRRFKRTIE 24 (70)
Q Consensus 5 ~V~~~E~ie~Alrrfkr~~~ 24 (70)
..+.| .+|.|+.-|....+
T Consensus 10 ~~~~~-~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 10 YCKMG-QFEEALEVFDEMRE 28 (31)
T ss_pred HHccc-hHHHHHHHHHHHhH
Confidence 34455 68888888877654
No 40
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=22.34 E-value=40 Score=15.50 Aligned_cols=21 Identities=24% Similarity=0.377 Sum_probs=14.1
Q ss_pred ccCCCcHHHHHHHHHHHHHhhch
Q psy15221 6 VKENEPFEVAIRRFKRTIEKTGL 28 (70)
Q Consensus 6 V~~~E~ie~Alrrfkr~~~k~Gi 28 (70)
++.| ++|.|+.-|....+ .||
T Consensus 12 ~~~g-~~~~a~~~~~~M~~-~gv 32 (34)
T PF13812_consen 12 AKAG-DPDAALQLFDEMKE-QGV 32 (34)
T ss_pred HHCC-CHHHHHHHHHHHHH-hCC
Confidence 4445 78888888877554 554
No 41
>PF14207 DpnD-PcfM: DpnD/PcfM-like protein
Probab=22.33 E-value=89 Score=17.44 Aligned_cols=26 Identities=15% Similarity=0.341 Sum_probs=19.6
Q ss_pred EeeccCCCcHHHHHHHHHHHHHhhchH
Q psy15221 3 IIRVKENEPFEVAIRRFKRTIEKTGLL 29 (70)
Q Consensus 3 ~V~V~~~E~ie~Alrrfkr~~~k~Gil 29 (70)
+|.|..+ |.+.|+...+.....+-|+
T Consensus 13 ~V~VeA~-s~eeA~~~v~~~y~~~eiv 38 (48)
T PF14207_consen 13 VVTVEAE-SEEEAIEKVRDAYRNEEIV 38 (48)
T ss_pred EEEEEeC-CHHHHHHHHHHHHhCCCEE
Confidence 4667655 9999999988888766543
No 42
>COG1051 ADP-ribose pyrophosphatase [Nucleotide transport and metabolism]
Probab=21.94 E-value=67 Score=20.91 Aligned_cols=15 Identities=40% Similarity=0.290 Sum_probs=11.7
Q ss_pred eeccCCCcHHHHHHH
Q psy15221 4 IRVKENEPFEVAIRR 18 (70)
Q Consensus 4 V~V~~~E~ie~Alrr 18 (70)
=.|..||+++.|..|
T Consensus 42 G~ve~GEt~eeaa~R 56 (145)
T COG1051 42 GFVEIGETLEEAARR 56 (145)
T ss_pred ccCCCCCCHHHHHHH
Confidence 357889999988754
No 43
>PHA02754 hypothetical protein; Provisional
Probab=21.91 E-value=66 Score=19.33 Aligned_cols=18 Identities=28% Similarity=0.632 Sum_probs=15.5
Q ss_pred cHHHHHHHHHHHHHhhch
Q psy15221 11 PFEVAIRRFKRTIEKTGL 28 (70)
Q Consensus 11 ~ie~Alrrfkr~~~k~Gi 28 (70)
++..|+|.++-.++..||
T Consensus 15 ~Fke~MRelkD~LSe~Gi 32 (67)
T PHA02754 15 DFKEAMRELKDILSEAGI 32 (67)
T ss_pred HHHHHHHHHHHHHhhCce
Confidence 688889999999988886
No 44
>cd04669 Nudix_Hydrolase_11 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate
Probab=21.66 E-value=78 Score=19.30 Aligned_cols=14 Identities=36% Similarity=0.427 Sum_probs=10.9
Q ss_pred eccCCCcHHHHHHH
Q psy15221 5 RVKENEPFEVAIRR 18 (70)
Q Consensus 5 ~V~~~E~ie~Alrr 18 (70)
.|..||+++.|+.|
T Consensus 33 ~ve~gEs~~~a~~R 46 (121)
T cd04669 33 GIEEGETPEEAAKR 46 (121)
T ss_pred eccCCCCHHHHHHH
Confidence 46788999988854
No 45
>PRK15434 GDP-mannose mannosyl hydrolase NudD; Provisional
Probab=21.39 E-value=87 Score=20.87 Aligned_cols=23 Identities=39% Similarity=0.637 Sum_probs=15.3
Q ss_pred eeccCCCcHHHHHHHHHHHHHhhch
Q psy15221 4 IRVKENEPFEVAIRRFKRTIEKTGL 28 (70)
Q Consensus 4 V~V~~~E~ie~Alrrfkr~~~k~Gi 28 (70)
=.|..|||++.|+.|= ..+..|+
T Consensus 50 G~VE~GEt~~~Aa~RE--l~EEtGl 72 (159)
T PRK15434 50 GRVQKDETLEAAFERL--TMAELGL 72 (159)
T ss_pred eecCCCCCHHHHHHHH--HHHHHCC
Confidence 3578899999998652 2233466
No 46
>PF01877 RNA_binding: RNA binding; InterPro: IPR002739 The proteins in this entry are functionally uncharacterised.; PDB: 2WNY_B 2NWU_A 2NRQ_A 2OGK_A 3D7A_B 3C9G_B 2PZZ_D.
Probab=20.58 E-value=1.5e+02 Score=18.85 Aligned_cols=31 Identities=10% Similarity=0.313 Sum_probs=24.0
Q ss_pred EeeccCCCcHHHHHHHHHHHHHhhchHHHHHH
Q psy15221 3 IIRVKENEPFEVAIRRFKRTIEKTGLLTDLRA 34 (70)
Q Consensus 3 ~V~V~~~E~ie~Alrrfkr~~~k~Gil~e~rr 34 (70)
.+.+. |+....+|.+|...+....|+..++.
T Consensus 49 ~~~i~-~~~~~~~l~~l~~~l~~~~i~d~~~~ 79 (120)
T PF01877_consen 49 EVRIE-GKEALKSLKKLHELLRDQEILDTARS 79 (120)
T ss_dssp EEEEE-ECHHHHHHHHHHHHHHHTTHHHHHHH
T ss_pred EEEEe-cccHHHHHHHHHHHHhhhhhhhHHHH
Confidence 34443 44789999999999999999877754
No 47
>cd03430 GDPMH GDP-mannose glycosyl hydrolase (AKA GDP-mannose mannosyl hydrolase (GDPMH)) is a member of the Nudix hydrolase superfamily. This class of enzymes is unique from other members of the superfamily in two aspects. First, it contains a modified Nudix signature sequence. The slight changes to the conserved sequence motif, GX5EX7REUXEEXGU, where U = I, L or V), are believed to contribute to the removal of all magnesium binding sites but one, retaining only the metal site that coordinates the pyrophosphate of the substrate. Secondly, it is not a pyrophosphatase that substitutes at a phosphorus; instead, it hydrolyzes nucleotide sugars such as GDP-mannose to GDP and mannose, cleaving the phosphoglycosyl bond by substituting at a carbon position. GDP-mannose provides mannosyl components for cell wall synthesis and is required for the synthesis of other glycosyl donors (such as GDP-fucose and colitose) for the cell wall. The importance of GDP-sugar hydrolase activities is thus close
Probab=20.36 E-value=83 Score=20.05 Aligned_cols=14 Identities=36% Similarity=0.660 Sum_probs=10.9
Q ss_pred eccCCCcHHHHHHH
Q psy15221 5 RVKENEPFEVAIRR 18 (70)
Q Consensus 5 ~V~~~E~ie~Alrr 18 (70)
.|..|||++.|+.|
T Consensus 46 ~ve~gEs~~~aa~R 59 (144)
T cd03430 46 RIRKNETLTEAFER 59 (144)
T ss_pred eecCCCCHHHHHHH
Confidence 56789999988764
Done!