Query psy13302
Match_columns 88
No_of_seqs 100 out of 196
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 16:00:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13302.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13302hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3533|consensus 100.0 3.3E-31 7.2E-36 230.3 2.2 84 1-84 2583-2666(2706)
2 KOG2243|consensus 99.8 4.9E-21 1.1E-25 167.9 4.0 84 1-84 4936-5019(5019)
3 cd00350 rubredoxin_like Rubred 62.8 2.3 4.9E-05 22.5 -0.1 15 3-17 18-32 (33)
4 PF00653 BIR: Inhibitor of Apo 57.7 2.8 6.1E-05 25.2 -0.4 26 3-28 37-62 (70)
5 KOG1101|consensus 56.8 7.8 0.00017 27.3 1.7 26 3-28 52-77 (147)
6 PF00253 Ribosomal_S14: Riboso 54.5 5.9 0.00013 23.3 0.7 19 1-19 15-33 (55)
7 cd00729 rubredoxin_SM Rubredox 54.2 4.2 9E-05 21.8 -0.0 15 3-17 19-33 (34)
8 smart00265 BH4 BH4 Bcl-2 homol 48.6 16 0.00034 19.1 1.7 18 53-70 9-26 (27)
9 COG1773 Rubredoxin [Energy pro 46.2 8.3 0.00018 23.3 0.4 16 4-19 38-53 (55)
10 smart00238 BIR Baculoviral inh 44.9 15 0.00033 21.6 1.5 26 3-28 37-62 (71)
11 PF10764 Gin: Inhibitor of sig 44.4 12 0.00026 21.5 0.9 11 4-14 1-11 (46)
12 cd00730 rubredoxin Rubredoxin; 43.6 7.1 0.00015 22.8 -0.2 14 4-17 36-49 (50)
13 PRK08061 rpsN 30S ribosomal pr 43.1 15 0.00032 22.5 1.2 19 1-19 20-38 (61)
14 PF03904 DUF334: Domain of unk 42.9 15 0.00032 28.0 1.4 19 25-43 190-208 (230)
15 PF09963 DUF2197: Uncharacteri 41.4 13 0.00029 22.5 0.8 10 1-10 1-10 (56)
16 PRK05766 rps14P 30S ribosomal 40.7 14 0.00031 21.8 0.8 18 2-19 14-31 (52)
17 cd00022 BIR Baculoviral inhibi 39.5 22 0.00047 20.8 1.5 26 3-28 35-60 (69)
18 PF02180 BH4: Bcl-2 homology r 37.9 25 0.00053 18.4 1.4 18 53-70 9-26 (27)
19 PF13894 zf-C2H2_4: C2H2-type 34.1 11 0.00023 17.0 -0.4 11 20-30 14-24 (24)
20 PRK06911 rpsN 30S ribosomal pr 33.9 18 0.00039 23.9 0.6 19 1-19 59-77 (100)
21 PRK13619 psbV cytochrome c-550 33.4 15 0.00032 26.6 0.1 38 45-82 102-139 (160)
22 KOG4477|consensus 32.3 20 0.00042 27.1 0.6 17 3-19 39-55 (228)
23 PF14392 zf-CCHC_4: Zinc knuck 32.1 16 0.00034 20.8 0.1 10 1-10 30-39 (49)
24 PF01702 TGT: Queuine tRNA-rib 31.9 8.7 0.00019 28.1 -1.3 54 4-59 178-235 (238)
25 PF00098 zf-CCHC: Zinc knuckle 28.9 15 0.00031 17.1 -0.4 7 4-10 2-8 (18)
26 COG1644 RPB10 DNA-directed RNA 28.0 25 0.00054 21.9 0.5 15 47-61 34-48 (63)
27 KOG3497|consensus 27.5 27 0.00059 21.8 0.6 8 3-10 5-12 (69)
28 PF03802 CitX: Apo-citrate lya 27.3 21 0.00045 25.5 0.0 11 3-13 133-143 (170)
29 PF09706 Cas_CXXC_CXXC: CRISPR 26.1 25 0.00054 21.6 0.2 9 2-10 5-13 (69)
30 TIGR03124 ctirate_citX holo-AC 26.1 28 0.0006 24.9 0.5 11 3-13 131-141 (165)
31 PF10664 NdhM: Cyanobacterial 26.0 47 0.001 22.6 1.5 26 51-76 73-98 (108)
32 CHL00074 rps14 ribosomal prote 25.7 28 0.00061 23.0 0.4 19 1-19 59-77 (100)
33 TIGR00009 L28 ribosomal protei 25.6 36 0.00078 20.1 0.9 11 1-11 1-11 (56)
34 PRK08881 rpsN 30S ribosomal pr 25.0 26 0.00056 23.1 0.2 19 1-19 60-78 (101)
35 PLN00032 DNA-directed RNA poly 24.7 27 0.0006 22.1 0.2 8 3-10 5-12 (71)
36 TIGR03523 GldN gliding motilit 24.7 24 0.00052 27.5 -0.1 10 26-35 269-278 (278)
37 PRK04016 DNA-directed RNA poly 24.4 28 0.00061 21.5 0.2 9 3-11 5-13 (62)
38 PRK01392 citX 2'-(5''-triphosp 23.3 32 0.0007 24.9 0.4 12 3-14 140-151 (180)
39 PRK01008 queuine tRNA-ribosylt 22.8 41 0.00088 27.1 0.9 41 4-44 320-365 (372)
40 COG0199 RpsN Ribosomal protein 22.4 39 0.00084 20.7 0.6 16 2-17 21-36 (61)
41 PF01194 RNA_pol_N: RNA polyme 22.1 25 0.00053 21.6 -0.4 6 4-9 6-11 (60)
42 PF06084 Cytomega_TRL10: Cytom 21.3 27 0.00058 24.6 -0.3 19 35-54 74-92 (150)
43 smart00547 ZnF_RBZ Zinc finger 20.2 39 0.00084 16.3 0.2 9 3-11 17-25 (26)
No 1
>KOG3533|consensus
Probab=99.96 E-value=3.3e-31 Score=230.29 Aligned_cols=84 Identities=36% Similarity=0.708 Sum_probs=80.2
Q ss_pred CCceeeeeCCCccccccCCCChHHHhhhhccchhHHHHHHHhccCCCCCCChhhHHHHHHHhcCCCCeeecchhhhhhch
Q psy13302 1 MESNCFICGIGKDYFDKVPHGFDTHVQQEHNLANYMFFLMHLINKPDTEFTGQETYVWNMYQQRCWDFFPVGDCFRKQYE 80 (88)
Q Consensus 1 ~kn~CFICgi~r~~fd~~~~~F~~Hi~~eHn~WnYl~fi~yL~~K~~~e~tg~E~yV~~~i~~~d~swfP~~~~~~l~~~ 80 (88)
+|++|||||++|+.||++...|++||+.|||||||+|||+.++-|++|||||+||||.+++++++++|||..||+||+..
T Consensus 2583 LKttCFICgLeR~kFDNktVsFEeHik~EHNmWhYLyfIVlvkvKd~Te~TGPESYVaqmvk~~nLdWFPRmrAmSLvs~ 2662 (2706)
T KOG3533|consen 2583 LKTTCFICGLERSKFDNKTVTFEEHIKTEHNMWHYLYFIVLVKVKDETEFTGPESYVAQMVKDRNLDWFPRMRAMSLVSS 2662 (2706)
T ss_pred HhcceeEeecchhhccCceeeHHHhhhhhhhhHHhhheeEEEEecCCccccChHHHHHHHHHhcccchhhhhHhhhhhcc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999876
Q ss_pred hhhc
Q psy13302 81 EDLG 84 (88)
Q Consensus 81 ~~~~ 84 (88)
+.-+
T Consensus 2663 e~dg 2666 (2706)
T KOG3533|consen 2663 ELDG 2666 (2706)
T ss_pred cccc
Confidence 6443
No 2
>KOG2243|consensus
Probab=99.82 E-value=4.9e-21 Score=167.85 Aligned_cols=84 Identities=77% Similarity=1.528 Sum_probs=81.8
Q ss_pred CCceeeeeCCCccccccCCCChHHHhhhhccchhHHHHHHHhccCCCCCCChhhHHHHHHHhcCCCCeeecchhhhhhch
Q psy13302 1 MESNCFICGIGKDYFDKVPHGFDTHVQQEHNLANYMFFLMHLINKPDTEFTGQETYVWNMYQQRCWDFFPVGDCFRKQYE 80 (88)
Q Consensus 1 ~kn~CFICgi~r~~fd~~~~~F~~Hi~~eHn~WnYl~fi~yL~~K~~~e~tg~E~yV~~~i~~~d~swfP~~~~~~l~~~ 80 (88)
|+.+||||||..+.||..+.||+.|..+|||+-||+||++||-.|++||.||.|+||+++.+++-++|||.+.|+..|.+
T Consensus 4936 metkcficgigndyfdt~phgfethtlqehnlanylfflmylinkdetehtgqesyvwkmyqercwdffpagdcfrkqye 5015 (5019)
T KOG2243|consen 4936 METKCFICGIGNDYFDTTPHGFETHTLQEHNLANYLFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYE 5015 (5019)
T ss_pred hhcceEEeccccccccCCCCcccccchhhhhHHHHHHHHHHHhcccccccccchhHHHHHHHHHHHhhCCchhhHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhc
Q psy13302 81 EDLG 84 (88)
Q Consensus 81 ~~~~ 84 (88)
++++
T Consensus 5016 dql~ 5019 (5019)
T KOG2243|consen 5016 DQLG 5019 (5019)
T ss_pred hhcC
Confidence 8874
No 3
>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=62.80 E-value=2.3 Score=22.53 Aligned_cols=15 Identities=47% Similarity=0.882 Sum_probs=12.2
Q ss_pred ceeeeeCCCcccccc
Q psy13302 3 SNCFICGIGKDYFDK 17 (88)
Q Consensus 3 n~CFICgi~r~~fd~ 17 (88)
-+|-+||..++.|..
T Consensus 18 ~~CP~Cg~~~~~F~~ 32 (33)
T cd00350 18 WVCPVCGAPKDKFEK 32 (33)
T ss_pred CcCcCCCCcHHHcEE
Confidence 379999999988864
No 4
>PF00653 BIR: Inhibitor of Apoptosis domain; InterPro: IPR001370 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The baculovirus inhibitor of apoptosis protein repeat (BIR) is a domain of tandem repeats separated by a variable length linker that seems to confer cell death-preventing activity [, ]. The BIR domains characterise the Inhibitor of Apoptosis (IAP) family of proteins (MEROPS proteinase inhibitor family I32, clan IV) that suppress apoptosis by interacting with and inhibiting the enzymatic activity of both initiator and effector caspases (MEROPS peptidase family C14, IPR002398 from INTERPRO). Several distinct mammalian IAPs including XIAP, c-IAP1, c-IAP2, and ML-IAP, have been identified, and they all exhibit antiapoptotic activity in cell culture. The functional unit in each IAP protein is the baculoviral IAP repeat (BIR), which contains approximately 80 amino acids folded around a zinc atom. Most mammalian IAPs have more than one BIR domain, with the different BIR domains performing distinct functions. For example, in XIAP, the third BIR domain (BIR3) potently inhibits the catalytic activity of caspase-9, whereas the linker sequences immediately preceding the second BIR domain (BIR2) selectively targets caspase-3 or -7. The first-recognised members of family MEROPS inhibitor family I32 were viral proteins that inhibited the apoptosis of infected cells: Cp-IAP from Cydia pomonella granulosis virus (CpGV) [] and Op-IAP from Orgyia pseudotsugata multicapsid polyhedrosis virus(OpMNPV) []. The discovery of homologous proteins in mammals followed soon after with the recognition that mutations in the gene for neuronal apoptosis inhibitory protein (NIAP) underlie spinal muscular atrophy []. The inhibitors in family I32 all possess one or more 80-residue domains known as BIR (baculovirus inhibitor repeat) domains and have accordingly been termed 'BIR-containing' or 'BIRC' proteins as well as IAP proteins. The mechanism of inhibition of caspases by the IAP proteins is complex, and reactive site residues cannot yet be identified with any confidence. Despite the conservation of the BIR or IAP (inhibitor of apoptosis) domains throughout the family it seems clear that other parts of the molecules also make essential contributions to inhibitory activity. Homologs of most components in the mammalian apoptotic pathway have been identified in fruit flies. The Drosophila Apaf-1, known as Dapaf-1, HAC-1 or Dark, shares significant sequence similarity with its mammalian counterpart, and is critically important for the activation of the Drosophila initiator caspase Dronc. Dronc, in turn, cleaves and activates the effector caspase DrICE. The Drosophila IAP, DIAP1, binds to and in-activates both DrICE and Dronc through its BIR1 and BIR2 domains. During apoptosis, the anti-death function of DIAP1 is countered by at least four pro-apoptotic proteins, Reaper, Hid, Grim, and sickle, through direct physical interactions. These four proteins represent the functional homologs of the mammalian protein Smac, and they all share a conserved IAP-binding motif at their N termini. The three proteins Reaper, Hid, and Grim are collectively referred to as the RHG proteins [, ]. Both XIAP and DIAP1 contain a RING domain at their C termini, and can act as an E3 ubiquitin ligase. Indeed, both XIAP and DIAP1 have been shown to promote self-ubiquitination and degradation as well as to negatively regulate the target caspases. Nonetheless, important differences exist between XIAP and DIAP1. The primary function of XIAP is thought to inhibit the catalytic activities of caspases; to what extent the ubiquitinating activity of XIAP contributes to its function remains unclear. For DIAP1, however, the ubiquitinating activity appears to be essential for its function. Recently a Drosophila p53 protein has been identified that mediates apoptosis via a novel pathway involving the activation of the Reaper gene and subsequent inhibition of the inhibitors of apoptosis (IAPs). CIAP1, a major mammalian homologue of Drosophila IAPs, is irreversibly inhibited (cleaved) during p53-dependent apoptosis and this cleavage is mediated by a serine protease. Serine protease inhibitors that block CIAP1 cleavage inhibit p53-dependent apoptosis. Furthermore, activation of the p53 protein increases the transcription of the HTRA2 gene, which encodes a serine protease that interacts with CIAP1 and potentiates apoptosis. Therefore mammalian p53 protein activates apoptosis through a novel pathway functionally similar to that in Drosophila, which involves HTRA2 and subsequent inhibition of CIAP1 by cleavage [].; GO: 0005622 intracellular; PDB: 3HL5_B 3UW5_A 3CM7_A 1G3F_A 1G73_C 3G76_G 3CM2_C 2VSL_A 2OPZ_B 3CLX_A ....
Probab=57.72 E-value=2.8 Score=25.22 Aligned_cols=26 Identities=23% Similarity=0.682 Sum_probs=19.2
Q ss_pred ceeeeeCCCccccccCCCChHHHhhh
Q psy13302 3 SNCFICGIGKDYFDKVPHGFDTHVQQ 28 (88)
Q Consensus 3 n~CFICgi~r~~fd~~~~~F~~Hi~~ 28 (88)
-+||-||+.-+.++....-++.|.+.
T Consensus 37 v~C~~C~~~l~~w~~~Ddp~~~H~~~ 62 (70)
T PF00653_consen 37 VRCFYCGLELDNWEPNDDPWEEHKRH 62 (70)
T ss_dssp EEETTTTEEEES-STT--HHHHHHHH
T ss_pred EEEeccCCEEeCCCCCCCHHHHHHHH
Confidence 47999999998888777788888775
No 5
>KOG1101|consensus
Probab=56.83 E-value=7.8 Score=27.33 Aligned_cols=26 Identities=23% Similarity=0.574 Sum_probs=23.9
Q ss_pred ceeeeeCCCccccccCCCChHHHhhh
Q psy13302 3 SNCFICGIGKDYFDKVPHGFDTHVQQ 28 (88)
Q Consensus 3 n~CFICgi~r~~fd~~~~~F~~Hi~~ 28 (88)
-+||-||..=...|.....|.+|-+.
T Consensus 52 ~~Cf~C~~~L~~We~~DDPW~EH~k~ 77 (147)
T KOG1101|consen 52 VKCFFCSGGLDDWEPGDDPWEEHAKW 77 (147)
T ss_pred eECcccCcccccCCCCCCcHHHHHhh
Confidence 47999999999999999999999885
No 6
>PF00253 Ribosomal_S14: Ribosomal protein S14p/S29e; InterPro: IPR001209 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 [, ]. S14 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S14 is known to be required for the assembly of 30S particles and may also be responsible for determining the conformation of 16S rRNA at the A site. It belongs to a family of ribosomal proteins [, ] that include, bacterial, algal and plant chloroplast, yeast mitochondrial, cyanelle and archael, Methanococcus vannielii S14's, as well as yeast mitochondrial MRP2, yeast YS29A/B and mammalian S29.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_N 2XZM_N 1S1H_N 3IZ6_N 2YKR_N 2QBB_N 3I1Z_N 3OAQ_N 3R8O_N 2Z4K_N ....
Probab=54.49 E-value=5.9 Score=23.33 Aligned_cols=19 Identities=21% Similarity=0.504 Sum_probs=15.7
Q ss_pred CCceeeeeCCCccccccCC
Q psy13302 1 MESNCFICGIGKDYFDKVP 19 (88)
Q Consensus 1 ~kn~CFICgi~r~~fd~~~ 19 (88)
..|.|.+||-.|..+-+.+
T Consensus 15 ~~nrC~~tGR~rgv~r~f~ 33 (55)
T PF00253_consen 15 IKNRCVITGRSRGVIRKFG 33 (55)
T ss_dssp SCSSBSSSCSSSSBETTTS
T ss_pred CCeecccCCCceeeecccc
Confidence 3689999999999887654
No 7
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, 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), 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=54.20 E-value=4.2 Score=21.84 Aligned_cols=15 Identities=40% Similarity=0.957 Sum_probs=11.8
Q ss_pred ceeeeeCCCcccccc
Q psy13302 3 SNCFICGIGKDYFDK 17 (88)
Q Consensus 3 n~CFICgi~r~~fd~ 17 (88)
..|-|||-.++.|++
T Consensus 19 ~~CP~Cg~~~~~F~~ 33 (34)
T cd00729 19 EKCPICGAPKEKFEE 33 (34)
T ss_pred CcCcCCCCchHHcEE
Confidence 478889888888764
No 8
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=48.61 E-value=16 Score=19.09 Aligned_cols=18 Identities=17% Similarity=0.167 Sum_probs=15.9
Q ss_pred hhHHHHHHHhcCCCCeee
Q psy13302 53 QETYVWNMYQQRCWDFFP 70 (88)
Q Consensus 53 ~E~yV~~~i~~~d~swfP 70 (88)
++.||.-||.++...|.|
T Consensus 9 V~~yv~yKLsQrgy~w~~ 26 (27)
T smart00265 9 VVDYVTYKLSQNGYEWDA 26 (27)
T ss_pred HHHHHHHHHhhcCCCCCC
Confidence 688999999999998875
No 9
>COG1773 Rubredoxin [Energy production and conversion]
Probab=46.20 E-value=8.3 Score=23.28 Aligned_cols=16 Identities=38% Similarity=0.879 Sum_probs=13.3
Q ss_pred eeeeeCCCccccccCC
Q psy13302 4 NCFICGIGKDYFDKVP 19 (88)
Q Consensus 4 ~CFICgi~r~~fd~~~ 19 (88)
.|-.||.+++.|++..
T Consensus 38 ~CP~Cg~~K~~F~~~~ 53 (55)
T COG1773 38 VCPECGVGKKDFEMID 53 (55)
T ss_pred CCCCCCCCHhHeeecc
Confidence 5888999999998764
No 10
>smart00238 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes.
Probab=44.90 E-value=15 Score=21.63 Aligned_cols=26 Identities=23% Similarity=0.553 Sum_probs=19.4
Q ss_pred ceeeeeCCCccccccCCCChHHHhhh
Q psy13302 3 SNCFICGIGKDYFDKVPHGFDTHVQQ 28 (88)
Q Consensus 3 n~CFICgi~r~~fd~~~~~F~~Hi~~ 28 (88)
-+||.||+.=+..+....-+..|.+.
T Consensus 37 v~C~~C~~~l~~w~~~d~p~~~H~~~ 62 (71)
T smart00238 37 VKCFFCGGELDNWEPGDDPWEEHKKW 62 (71)
T ss_pred EEeCCCCCCcCCCCCCCCHHHHHhHh
Confidence 47999999877766666778887553
No 11
>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=44.35 E-value=12 Score=21.53 Aligned_cols=11 Identities=45% Similarity=1.081 Sum_probs=8.3
Q ss_pred eeeeeCCCccc
Q psy13302 4 NCFICGIGKDY 14 (88)
Q Consensus 4 ~CFICgi~r~~ 14 (88)
+|+|||-.+..
T Consensus 1 ~CiiC~~~~~~ 11 (46)
T PF10764_consen 1 KCIICGKEKEE 11 (46)
T ss_pred CeEeCCCcCCC
Confidence 59999877664
No 12
>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=43.55 E-value=7.1 Score=22.85 Aligned_cols=14 Identities=50% Similarity=1.111 Sum_probs=12.0
Q ss_pred eeeeeCCCcccccc
Q psy13302 4 NCFICGIGKDYFDK 17 (88)
Q Consensus 4 ~CFICgi~r~~fd~ 17 (88)
+|-+||..|+.|.+
T Consensus 36 ~CP~C~a~K~~F~~ 49 (50)
T cd00730 36 VCPVCGAGKDDFEP 49 (50)
T ss_pred CCCCCCCcHHHcEe
Confidence 79999999998864
No 13
>PRK08061 rpsN 30S ribosomal protein S14; Reviewed
Probab=43.09 E-value=15 Score=22.53 Aligned_cols=19 Identities=21% Similarity=0.426 Sum_probs=15.7
Q ss_pred CCceeeeeCCCccccccCC
Q psy13302 1 MESNCFICGIGKDYFDKVP 19 (88)
Q Consensus 1 ~kn~CFICgi~r~~fd~~~ 19 (88)
.+|.|.+||-.|..+-+-+
T Consensus 20 ~~nRC~~tGR~rgvir~fg 38 (61)
T PRK08061 20 AYTRCERCGRPHSVYRKFG 38 (61)
T ss_pred cceeeecCCCCcceeccCC
Confidence 3689999999998887654
No 14
>PF03904 DUF334: Domain of unknown function (DUF334); InterPro: IPR005602 This is a family of proteins found in Staphylococcus aureus plasmid with no characterised function.
Probab=42.91 E-value=15 Score=28.04 Aligned_cols=19 Identities=11% Similarity=0.557 Sum_probs=15.9
Q ss_pred HhhhhccchhHHHHHHHhc
Q psy13302 25 HVQQEHNLANYMFFLMHLI 43 (88)
Q Consensus 25 Hi~~eHn~WnYl~fi~yL~ 43 (88)
-|+..|..|-||+||+|+-
T Consensus 190 ~ik~se~~~~~lwyi~Y~v 208 (230)
T PF03904_consen 190 KIKASESFWTYLWYIAYLV 208 (230)
T ss_pred HHhhhHhHHHHHHHHHHhh
Confidence 3667788999999999974
No 15
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=41.38 E-value=13 Score=22.47 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=8.0
Q ss_pred CCceeeeeCC
Q psy13302 1 MESNCFICGI 10 (88)
Q Consensus 1 ~kn~CFICgi 10 (88)
|+-+|.|||-
T Consensus 1 m~vkC~lCdk 10 (56)
T PF09963_consen 1 MRVKCILCDK 10 (56)
T ss_pred CeeEEEecCC
Confidence 6778999964
No 16
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=40.72 E-value=14 Score=21.81 Aligned_cols=18 Identities=22% Similarity=0.457 Sum_probs=15.1
Q ss_pred CceeeeeCCCccccccCC
Q psy13302 2 ESNCFICGIGKDYFDKVP 19 (88)
Q Consensus 2 kn~CFICgi~r~~fd~~~ 19 (88)
.|.|.+||-.|..+.+-+
T Consensus 14 ~nrC~~~Gr~rgvirkf~ 31 (52)
T PRK05766 14 ARECQRCGRKQGLIRKYG 31 (52)
T ss_pred CceeecCCCCceeHHhhC
Confidence 689999999998877654
No 17
>cd00022 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger.
Probab=39.46 E-value=22 Score=20.85 Aligned_cols=26 Identities=19% Similarity=0.593 Sum_probs=19.4
Q ss_pred ceeeeeCCCccccccCCCChHHHhhh
Q psy13302 3 SNCFICGIGKDYFDKVPHGFDTHVQQ 28 (88)
Q Consensus 3 n~CFICgi~r~~fd~~~~~F~~Hi~~ 28 (88)
-+|+-||+.=+..+....-++.|.+.
T Consensus 35 v~C~~C~~~~~~w~~~d~p~~~H~~~ 60 (69)
T cd00022 35 VKCFFCGLELKNWEPGDDPWEEHKRW 60 (69)
T ss_pred EEeCCCCCCccCCCCCCCHHHHHhHh
Confidence 47999999877766666677777654
No 18
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=37.95 E-value=25 Score=18.41 Aligned_cols=18 Identities=22% Similarity=0.240 Sum_probs=15.5
Q ss_pred hhHHHHHHHhcCCCCeee
Q psy13302 53 QETYVWNMYQQRCWDFFP 70 (88)
Q Consensus 53 ~E~yV~~~i~~~d~swfP 70 (88)
+|.||.-||.++...|.+
T Consensus 9 V~~yi~yKLsQrgy~w~~ 26 (27)
T PF02180_consen 9 VEDYISYKLSQRGYVWEE 26 (27)
T ss_dssp HHHHHHHHHHHTTSTSTT
T ss_pred HHHHHHHHhhhcCCCCCC
Confidence 688999999999888865
No 19
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=34.11 E-value=11 Score=17.01 Aligned_cols=11 Identities=18% Similarity=0.492 Sum_probs=7.7
Q ss_pred CChHHHhhhhc
Q psy13302 20 HGFDTHVQQEH 30 (88)
Q Consensus 20 ~~F~~Hi~~eH 30 (88)
..+..|+...|
T Consensus 14 ~~l~~H~~~~H 24 (24)
T PF13894_consen 14 SELRQHMRTHH 24 (24)
T ss_dssp HHHHHHHHHHS
T ss_pred HHHHHHHHhhC
Confidence 56778887754
No 20
>PRK06911 rpsN 30S ribosomal protein S14; Reviewed
Probab=33.87 E-value=18 Score=23.95 Aligned_cols=19 Identities=21% Similarity=0.466 Sum_probs=15.8
Q ss_pred CCceeeeeCCCccccccCC
Q psy13302 1 MESNCFICGIGKDYFDKVP 19 (88)
Q Consensus 1 ~kn~CFICgi~r~~fd~~~ 19 (88)
++|.|.++|-.|..+-+-+
T Consensus 59 ~rNRC~~TGR~Rgv~r~Fg 77 (100)
T PRK06911 59 YVTRCKQCGRPHAVYRKFN 77 (100)
T ss_pred hhcccCCCCCCcccccccC
Confidence 4799999999999887654
No 21
>PRK13619 psbV cytochrome c-550; Provisional
Probab=33.41 E-value=15 Score=26.62 Aligned_cols=38 Identities=24% Similarity=0.215 Sum_probs=25.5
Q ss_pred CCCCCCChhhHHHHHHHhcCCCCeeecchhhhhhchhh
Q psy13302 45 KPDTEFTGQETYVWNMYQQRCWDFFPVGDCFRKQYEED 82 (88)
Q Consensus 45 K~~~e~tg~E~yV~~~i~~~d~swfP~~~~~~l~~~~~ 82 (88)
|+++-|+|.|++..-.-.-...+-||..|.|+-+.-..
T Consensus 102 k~PtsyDG~~~~a~~hpsi~~~di~P~mr~LtdedL~~ 139 (160)
T PRK13619 102 KHPTSYDGEDDYSELHPNVSRPDIFPELRNFTEDDLYD 139 (160)
T ss_pred hCCcccccchhhhhhcccccccccccccCCCCHHHHHH
Confidence 78999999998654332224456788888887654433
No 22
>KOG4477|consensus
Probab=32.32 E-value=20 Score=27.07 Aligned_cols=17 Identities=29% Similarity=0.794 Sum_probs=12.2
Q ss_pred ceeeeeCCCccccccCC
Q psy13302 3 SNCFICGIGKDYFDKVP 19 (88)
Q Consensus 3 n~CFICgi~r~~fd~~~ 19 (88)
-+|||||.-+-.=-+++
T Consensus 39 fkC~vCdvRKGTSTRkp 55 (228)
T KOG4477|consen 39 FKCFVCDVRKGTSTRKP 55 (228)
T ss_pred hheeeecccccccccCC
Confidence 37999998776655553
No 23
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=32.11 E-value=16 Score=20.75 Aligned_cols=10 Identities=40% Similarity=1.032 Sum_probs=7.5
Q ss_pred CCceeeeeCC
Q psy13302 1 MESNCFICGI 10 (88)
Q Consensus 1 ~kn~CFICgi 10 (88)
+.+.||.||.
T Consensus 30 lp~~C~~C~~ 39 (49)
T PF14392_consen 30 LPRFCFHCGR 39 (49)
T ss_pred cChhhcCCCC
Confidence 3467999985
No 24
>PF01702 TGT: Queuine tRNA-ribosyltransferase; InterPro: IPR002616 This is a family of queuine, archaeosine and general tRNA-ribosyltransferases 2.4.2.29 from EC, also known as tRNA-guanine transglycosylase and guanine insertion enzyme. Queuine tRNA-ribosyltransferase modifies tRNAs for asparagine, aspartic acid, histidine and tyrosine with queuine at position 34 and with archaeosine at position 15 in archaeal tRNAs. In bacterial it catalyses the exchange of guanine-34 at the wobble position with 7-aminomethyl-7-deazaguanine, and the addition of a cyclopentenediol moiety to 7-aminomethyl-7-deazaguanine-34 tRNA; giving a hypermodified base queuine in the wobble position [, ]. The aligned region contains a zinc binding motif C-x-C-x2-C-x29-H, and important tRNA and 7-aminomethyl-7deazaguanine binding residues [].; GO: 0008479 queuine tRNA-ribosyltransferase activity, 0006400 tRNA modification, 0008616 queuosine biosynthetic process; PDB: 2ASH_A 1J2B_A 1IT8_A 1IT7_B 1IQ8_A 1R5Y_A 1P0B_A 3BL3_A 3EOS_A 1EFZ_A ....
Probab=31.92 E-value=8.7 Score=28.07 Aligned_cols=54 Identities=17% Similarity=0.338 Sum_probs=28.1
Q ss_pred eeeee-CCCcccccc---CCCChHHHhhhhccchhHHHHHHHhccCCCCCCChhhHHHHH
Q psy13302 4 NCFIC-GIGKDYFDK---VPHGFDTHVQQEHNLANYMFFLMHLINKPDTEFTGQETYVWN 59 (88)
Q Consensus 4 ~CFIC-gi~r~~fd~---~~~~F~~Hi~~eHn~WnYl~fi~yL~~K~~~e~tg~E~yV~~ 59 (88)
.|++| ..+|..+-. ...--.......||+|.|.-|+.-++..=.++- ++.|+.+
T Consensus 178 ~C~~C~~~trayl~hL~~~~e~l~~~Ll~~HNl~~~~~~~~~iR~~I~~~~--~~~~~~~ 235 (238)
T PF01702_consen 178 SCPTCRNYTRAYLHHLLKAKEMLGPVLLSIHNLHHYLRFFKEIREAIRNGT--LREFVEE 235 (238)
T ss_dssp -SHHHHH-BHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHH
T ss_pred CCCCCcccCHHHHHHHHcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC--HHHHHHH
Confidence 57888 333333321 111222234467999999999887775433332 4444443
No 25
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=28.94 E-value=15 Score=17.09 Aligned_cols=7 Identities=57% Similarity=1.516 Sum_probs=5.2
Q ss_pred eeeeeCC
Q psy13302 4 NCFICGI 10 (88)
Q Consensus 4 ~CFICgi 10 (88)
+||.||-
T Consensus 2 ~C~~C~~ 8 (18)
T PF00098_consen 2 KCFNCGE 8 (18)
T ss_dssp BCTTTSC
T ss_pred cCcCCCC
Confidence 5888864
No 26
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=28.04 E-value=25 Score=21.85 Aligned_cols=15 Identities=13% Similarity=0.091 Sum_probs=9.0
Q ss_pred CCCCChhhHHHHHHH
Q psy13302 47 DTEFTGQETYVWNMY 61 (88)
Q Consensus 47 ~~e~tg~E~yV~~~i 61 (88)
-.+--|++.|....+
T Consensus 34 vLDdLGv~RYCCRRM 48 (63)
T COG1644 34 VLDDLGVKRYCCRRM 48 (63)
T ss_pred HHHHhCcHHHHHHHH
Confidence 345567777765543
No 27
>KOG3497|consensus
Probab=27.46 E-value=27 Score=21.84 Aligned_cols=8 Identities=50% Similarity=1.348 Sum_probs=6.0
Q ss_pred ceeeeeCC
Q psy13302 3 SNCFICGI 10 (88)
Q Consensus 3 n~CFICgi 10 (88)
-+||.||-
T Consensus 5 iRCFtCGK 12 (69)
T KOG3497|consen 5 IRCFTCGK 12 (69)
T ss_pred eEeeeccc
Confidence 37999973
No 28
>PF03802 CitX: Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase; InterPro: IPR005551 Members of this protein family are annotated as CitX, containing the CitX domain, the domain is also found in the CitXG bifunctional protein, of the citrate lyase system. CitX transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein. This enzyme may be designated holo-ACP synthase, holo-citrate lyase synthase, or apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. In a few genera, including Haemophilus, this protein occurs as a fusion protein with CitG (2.7.8.25 from EC), an enzyme involved in prosthetic group biosynthesis. This CitX family is easily separated from the holo-ACP synthases of other enzyme systems.; GO: 0051191 prosthetic group biosynthetic process
Probab=27.33 E-value=21 Score=25.48 Aligned_cols=11 Identities=36% Similarity=0.963 Sum_probs=7.9
Q ss_pred ceeeeeCCCcc
Q psy13302 3 SNCFICGIGKD 13 (88)
Q Consensus 3 n~CFICgi~r~ 13 (88)
-+|||||-+.-
T Consensus 133 R~CliC~~~Ak 143 (170)
T PF03802_consen 133 RRCLICGRPAK 143 (170)
T ss_pred CcccCCChhHH
Confidence 47999976543
No 29
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=26.14 E-value=25 Score=21.57 Aligned_cols=9 Identities=44% Similarity=1.184 Sum_probs=7.2
Q ss_pred CceeeeeCC
Q psy13302 2 ESNCFICGI 10 (88)
Q Consensus 2 kn~CFICgi 10 (88)
+..|++||-
T Consensus 5 ~~~C~~Cg~ 13 (69)
T PF09706_consen 5 KYNCIFCGE 13 (69)
T ss_pred CCcCcCCCC
Confidence 468999994
No 30
>TIGR03124 ctirate_citX holo-ACP synthase CitX. Members of this protein family are the CitX protein, or CitX domain of the CitXG bifunctional protein, of the citrate lyase system. CitX transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein. This enzyme may be designated holo-ACP synthase, holo-citrate lyase synthase, or apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. In a few genera, including Haemophilus, this protein occurs as a fusion protein with CitG (2.7.8.25), an enzyme involved in prosthetic group biosynthesis. This CitX family is easily separated from the holo-ACP synthases of other enzyme systems.
Probab=26.05 E-value=28 Score=24.90 Aligned_cols=11 Identities=18% Similarity=0.761 Sum_probs=7.9
Q ss_pred ceeeeeCCCcc
Q psy13302 3 SNCFICGIGKD 13 (88)
Q Consensus 3 n~CFICgi~r~ 13 (88)
-+|||||-+.-
T Consensus 131 R~CliC~~~Ak 141 (165)
T TIGR03124 131 RKCLLCEEDAK 141 (165)
T ss_pred CeeecCCchHH
Confidence 47999976543
No 31
>PF10664 NdhM: Cyanobacterial and plastid NDH-1 subunit M; InterPro: IPR018922 The NADH dehydrogenase I complex shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in plants is believed to be plastoquinone. The NADH dehydrogenase I complex couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. This entry represents subunit M of the NADH dehydrogenase I complex in cyanobacteria and plant chloroplasts []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=25.96 E-value=47 Score=22.59 Aligned_cols=26 Identities=8% Similarity=0.130 Sum_probs=21.9
Q ss_pred ChhhHHHHHHHhcCCCCeeecchhhh
Q psy13302 51 TGQETYVWNMYQQRCWDFFPVGDCFR 76 (88)
Q Consensus 51 tg~E~yV~~~i~~~d~swfP~~~~~~ 76 (88)
+.+|-||+++++...|++=|-.|.+.
T Consensus 73 SdLE~~iR~LLq~GeisYNl~~RVlN 98 (108)
T PF10664_consen 73 SDLEHFIRSLLQAGEISYNLDSRVLN 98 (108)
T ss_pred cHHHHHHHHHHHCCceeeCCCcceec
Confidence 36899999999999999988777543
No 32
>CHL00074 rps14 ribosomal protein S14
Probab=25.73 E-value=28 Score=22.96 Aligned_cols=19 Identities=16% Similarity=0.579 Sum_probs=15.5
Q ss_pred CCceeeeeCCCccccccCC
Q psy13302 1 MESNCFICGIGKDYFDKVP 19 (88)
Q Consensus 1 ~kn~CFICgi~r~~fd~~~ 19 (88)
++|.|.++|-.|..+-.-+
T Consensus 59 i~NRC~~TGR~Rgv~r~F~ 77 (100)
T CHL00074 59 LHNRCFLTGRPRGNYRDFG 77 (100)
T ss_pred HhccccCCCCCCccccCcC
Confidence 3689999999999887653
No 33
>TIGR00009 L28 ribosomal protein L28. This model describes bacterial and chloroplast forms of the 50S ribosomal protein L28, a polypeptide about 60 amino acids in length. Mitochondrial homologs differ substantially in architecture and are not included.
Probab=25.62 E-value=36 Score=20.13 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=7.8
Q ss_pred CCceeeeeCCC
Q psy13302 1 MESNCFICGIG 11 (88)
Q Consensus 1 ~kn~CFICgi~ 11 (88)
|...|-|||-.
T Consensus 1 Ms~~C~i~GK~ 11 (56)
T TIGR00009 1 MSRKCQLTGKG 11 (56)
T ss_pred CCCEeeeCCCc
Confidence 55679999743
No 34
>PRK08881 rpsN 30S ribosomal protein S14; Reviewed
Probab=24.97 E-value=26 Score=23.14 Aligned_cols=19 Identities=21% Similarity=0.597 Sum_probs=15.4
Q ss_pred CCceeeeeCCCccccccCC
Q psy13302 1 MESNCFICGIGKDYFDKVP 19 (88)
Q Consensus 1 ~kn~CFICgi~r~~fd~~~ 19 (88)
++|.|+++|-.|..+-.-+
T Consensus 60 i~NRC~~TGR~Rgv~r~F~ 78 (101)
T PRK08881 60 LRNRCELTGRPRGYYRKFG 78 (101)
T ss_pred HhccccCCCCCCccccCcC
Confidence 3689999999998887653
No 35
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=24.69 E-value=27 Score=22.10 Aligned_cols=8 Identities=50% Similarity=1.381 Sum_probs=5.8
Q ss_pred ceeeeeCC
Q psy13302 3 SNCFICGI 10 (88)
Q Consensus 3 n~CFICgi 10 (88)
-.||-||-
T Consensus 5 VRCFTCGk 12 (71)
T PLN00032 5 VRCFTCGK 12 (71)
T ss_pred eeecCCCC
Confidence 36999973
No 36
>TIGR03523 GldN gliding motility associated protien GldN. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldN is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldN abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein also include those which are not believed to express the gliding phenotype, such as Prevotella intermedia and Porphyromonas gingivales.
Probab=24.66 E-value=24 Score=27.47 Aligned_cols=10 Identities=30% Similarity=0.541 Sum_probs=7.8
Q ss_pred hhhhccchhH
Q psy13302 26 VQQEHNLANY 35 (88)
Q Consensus 26 i~~eHn~WnY 35 (88)
...||+||+|
T Consensus 269 ~~fE~dmW~y 278 (278)
T TIGR03523 269 LEFEDDLWEY 278 (278)
T ss_pred HHHHHhhhcC
Confidence 3468999987
No 37
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=24.42 E-value=28 Score=21.47 Aligned_cols=9 Identities=44% Similarity=1.106 Sum_probs=6.3
Q ss_pred ceeeeeCCC
Q psy13302 3 SNCFICGIG 11 (88)
Q Consensus 3 n~CFICgi~ 11 (88)
-.||-||-.
T Consensus 5 vRCFTCGkv 13 (62)
T PRK04016 5 VRCFTCGKV 13 (62)
T ss_pred eEecCCCCC
Confidence 369999743
No 38
>PRK01392 citX 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate lyase; Reviewed
Probab=23.28 E-value=32 Score=24.93 Aligned_cols=12 Identities=25% Similarity=0.880 Sum_probs=8.4
Q ss_pred ceeeeeCCCccc
Q psy13302 3 SNCFICGIGKDY 14 (88)
Q Consensus 3 n~CFICgi~r~~ 14 (88)
-+|||||-+.-.
T Consensus 140 R~CliC~~~Ak~ 151 (180)
T PRK01392 140 RRCLLCGQDAKV 151 (180)
T ss_pred CeeecCCchHHH
Confidence 479999765433
No 39
>PRK01008 queuine tRNA-ribosyltransferase; Provisional
Probab=22.81 E-value=41 Score=27.07 Aligned_cols=41 Identities=17% Similarity=0.355 Sum_probs=28.9
Q ss_pred eeeeeC--CCccccccC---CCChHHHhhhhccchhHHHHHHHhcc
Q psy13302 4 NCFICG--IGKDYFDKV---PHGFDTHVQQEHNLANYMFFLMHLIN 44 (88)
Q Consensus 4 ~CFICg--i~r~~fd~~---~~~F~~Hi~~eHn~WnYl~fi~yL~~ 44 (88)
.|+.|. .+|..+-.- ..---......||++.|.-++..+++
T Consensus 320 ~C~~C~~~ytraYLhHL~~~~E~l~~~LltiHNl~~~~~l~~~iR~ 365 (372)
T PRK01008 320 SCLACSSGISRAYLRHLFKVHEPNAGIWASIHNLHHMQQVMKEIRE 365 (372)
T ss_pred CCcCcCCCCCHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 599993 677754332 33355677788999999888877653
No 40
>COG0199 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]
Probab=22.41 E-value=39 Score=20.71 Aligned_cols=16 Identities=25% Similarity=0.567 Sum_probs=13.6
Q ss_pred CceeeeeCCCcccccc
Q psy13302 2 ESNCFICGIGKDYFDK 17 (88)
Q Consensus 2 kn~CFICgi~r~~fd~ 17 (88)
.|.|-+||-.|..+-+
T Consensus 21 ~nRC~~cGRprg~~Rk 36 (61)
T COG0199 21 RNRCRRCGRPRGVIRK 36 (61)
T ss_pred cccccccCCCccchhh
Confidence 6899999998888766
No 41
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=22.06 E-value=25 Score=21.57 Aligned_cols=6 Identities=67% Similarity=2.012 Sum_probs=4.0
Q ss_pred eeeeeC
Q psy13302 4 NCFICG 9 (88)
Q Consensus 4 ~CFICg 9 (88)
+||-||
T Consensus 6 RCFTCG 11 (60)
T PF01194_consen 6 RCFTCG 11 (60)
T ss_dssp S-STTT
T ss_pred ecCCCC
Confidence 688887
No 42
>PF06084 Cytomega_TRL10: Cytomegalovirus TRL10 protein; InterPro: IPR009284 This family consists of several Cytomegalovirus TRL10 proteins. TRL10 represents a structural component of the virus particle and like the other HCMV envelope glycoproteins, is present in a disulphide-linked complex [].
Probab=21.26 E-value=27 Score=24.56 Aligned_cols=19 Identities=21% Similarity=0.478 Sum_probs=15.6
Q ss_pred HHHHHHHhccCCCCCCChhh
Q psy13302 35 YMFFLMHLINKPDTEFTGQE 54 (88)
Q Consensus 35 Yl~fi~yL~~K~~~e~tg~E 54 (88)
-|||++|-+..+.++ ||.|
T Consensus 74 viffviy~re~~~~~-~gt~ 92 (150)
T PF06084_consen 74 VIFFVIYSREEEKNN-NGTE 92 (150)
T ss_pred HHhheeEeccccccC-CCce
Confidence 579999999988777 7765
No 43
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=20.21 E-value=39 Score=16.25 Aligned_cols=9 Identities=56% Similarity=1.346 Sum_probs=6.7
Q ss_pred ceeeeeCCC
Q psy13302 3 SNCFICGIG 11 (88)
Q Consensus 3 n~CFICgi~ 11 (88)
..|++||-.
T Consensus 17 ~~C~~C~~p 25 (26)
T smart00547 17 SKCFACGAP 25 (26)
T ss_pred ccccccCCc
Confidence 579999753
Done!