Query psy2280
Match_columns 162
No_of_seqs 169 out of 716
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 20:40:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2280.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2280hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1101|consensus 100.0 9.3E-31 2E-35 204.8 6.2 102 27-128 5-109 (147)
2 smart00238 BIR Baculoviral inh 99.9 1.9E-26 4.2E-31 158.0 6.7 69 36-105 1-70 (71)
3 PF00653 BIR: Inhibitor of Apo 99.9 1.1E-26 2.3E-31 159.9 3.7 66 40-105 1-70 (70)
4 cd00022 BIR Baculoviral inhibi 99.9 6.5E-26 1.4E-30 154.6 5.7 67 38-105 1-68 (69)
5 PF07967 zf-C3HC: C3HC zinc fi 97.3 0.00031 6.8E-09 53.6 3.7 50 33-82 3-54 (133)
6 KOG4765|consensus 92.1 0.097 2.1E-06 47.2 2.2 100 28-127 45-160 (419)
7 KOG3497|consensus 82.4 0.45 9.7E-06 32.7 0.2 15 71-85 4-19 (69)
8 PF08600 Rsm1: Rsm1-like; Int 78.3 0.72 1.6E-05 33.2 0.2 36 70-108 18-65 (91)
9 PF11682 DUF3279: Protein of u 75.6 1.7 3.7E-05 33.6 1.6 51 54-109 16-74 (128)
10 PLN00032 DNA-directed RNA poly 71.9 1.1 2.5E-05 31.3 -0.2 12 71-82 4-15 (71)
11 PRK04016 DNA-directed RNA poly 68.8 1.5 3.3E-05 30.0 -0.1 13 71-83 4-16 (62)
12 COG1644 RPB10 DNA-directed RNA 60.3 4.4 9.6E-05 27.8 0.9 12 71-82 4-15 (63)
13 PF01194 RNA_pol_N: RNA polyme 53.8 3.6 7.8E-05 27.9 -0.4 11 72-82 5-15 (60)
14 KOG3533|consensus 43.6 63 0.0014 34.6 6.2 49 70-118 2583-2636(2706)
15 PF15463 ECM11: Extracellular 31.7 2.2E+02 0.0048 21.7 6.4 49 112-160 78-131 (139)
16 PF07295 DUF1451: Protein of u 30.8 40 0.00087 26.4 2.2 27 56-82 93-123 (146)
17 PRK11032 hypothetical protein; 27.7 45 0.00097 26.7 2.0 26 58-83 107-136 (160)
18 PF02748 PyrI_C: Aspartate car 26.0 24 0.00052 23.0 0.1 25 58-82 20-46 (52)
19 PRK00464 nrdR transcriptional 24.6 24 0.00051 28.0 -0.1 30 73-103 2-36 (154)
20 PRK14127 cell division protein 24.2 3.1E+02 0.0067 20.5 6.0 59 89-153 7-67 (109)
21 COG3599 DivIVA Cell division i 23.2 3.3E+02 0.0073 22.6 6.5 58 89-157 7-64 (212)
22 PRK08476 F0F1 ATP synthase sub 22.8 3.4E+02 0.0075 20.5 6.1 35 125-159 106-140 (141)
23 PF01195 Pept_tRNA_hydro: Pept 22.0 2.2E+02 0.0048 22.7 5.1 58 101-158 123-184 (184)
24 PF05178 Kri1: KRI1-like famil 21.1 1.6E+02 0.0036 21.5 3.8 26 135-160 8-33 (101)
25 PF15290 Syntaphilin: Golgi-lo 20.9 2.8E+02 0.006 24.5 5.6 24 133-156 120-143 (305)
26 COG4416 Com Mu-like prophage p 20.2 57 0.0012 21.9 1.1 37 57-95 12-48 (60)
No 1
>KOG1101|consensus
Probab=99.96 E-value=9.3e-31 Score=204.79 Aligned_cols=102 Identities=36% Similarity=0.680 Sum_probs=87.9
Q ss_pred CCCCCCCCccHHHHHhchhhCccCCC-CCCHHHHHhccceecC-CCeEEEeecCCccCCCCCCCChHHHhhhcCCCCccc
Q psy2280 27 NIEIASPMMFYTNRLATFTNWTFKSG-NCTAEHMAHAGFYLIQ-DDCTKCVFCYKELDGWEVTDYPWDEHKSHKPDCPFV 104 (162)
Q Consensus 27 ~~~~~~~~~~~~~Rl~TF~~WP~~~~-~~spe~LA~AGFyytg-~D~V~Cf~C~~~L~~We~~DdP~~EH~r~sP~C~Fv 104 (162)
..+.++.|..+++|++||.+||+... .|+|+.||+|||||+| .|.|+||+|+++|.+|+++||||.||.+|+|.|.|+
T Consensus 5 ~~~~~~~~~~~~aRl~TF~~Wp~~~~~~c~p~~lA~AGFy~~g~~D~~~Cf~C~~~L~~We~~DDPW~EH~k~~p~C~F~ 84 (147)
T KOG1101|consen 5 FDPQNPKMAREEARLKTFKNWPYSDMDKCTPEQLAEAGFYYTGKQDCVKCFFCSGGLDDWEPGDDPWEEHAKWSPECEFL 84 (147)
T ss_pred ccccchhHHHHHHHHhhhhcCCCCCCCCcCHHHHHhCCceeeCCCCceECcccCcccccCCCCCCcHHHHHhhCCCCcee
Confidence 34678899999999999999999975 5999999999999999 999999999999999999999999999999999999
Q ss_pred cccccCCCcccHHHHHH-HHHHHHH
Q psy2280 105 QLNKRDLTTCHIDEFIV-LNSAVVK 128 (162)
Q Consensus 105 ~~~k~d~~~~tv~efl~-l~~~r~~ 128 (162)
+..|+++.-.+|..... +.....+
T Consensus 85 ~~~k~~e~~~~v~~~~~~~~~~~~~ 109 (147)
T KOG1101|consen 85 KLKKGREFLGTVQSTARALLALKEK 109 (147)
T ss_pred ecccchhhhhHHHHhHhhhhhccCC
Confidence 99999555555555554 4333333
No 2
>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=99.93 E-value=1.9e-26 Score=157.98 Aligned_cols=69 Identities=51% Similarity=1.013 Sum_probs=64.5
Q ss_pred cHHHHHhchhhCccCCCCCCHHHHHhccceecC-CCeEEEeecCCccCCCCCCCChHHHhhhcCCCCcccc
Q psy2280 36 FYTNRLATFTNWTFKSGNCTAEHMAHAGFYLIQ-DDCTKCVFCYKELDGWEVTDYPWDEHKSHKPDCPFVQ 105 (162)
Q Consensus 36 ~~~~Rl~TF~~WP~~~~~~spe~LA~AGFyytg-~D~V~Cf~C~~~L~~We~~DdP~~EH~r~sP~C~Fv~ 105 (162)
+++.|++||.+||+.. ...++.||.|||||+| +|.|+|++|+++|++|+++|+||.+|++++|+|+|++
T Consensus 1 ~~~~R~~sF~~w~~~~-~~~~~~LA~~Gfyy~~~~d~v~C~~C~~~l~~w~~~d~p~~~H~~~~p~C~fv~ 70 (71)
T smart00238 1 SEEARLKTFQNWPYNS-KLTPEQLAEAGFYYTGVGDEVKCFFCGGELDNWEPGDDPWEEHKKWSPNCPFVR 70 (71)
T ss_pred CHHHHHHHHHcCCCCc-cCCHHHHHHcCCeECCCCCEEEeCCCCCCcCCCCCCCCHHHHHhHhCcCCcCcc
Confidence 4789999999999743 3789999999999999 9999999999999999999999999999999999986
No 3
>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=99.93 E-value=1.1e-26 Score=159.90 Aligned_cols=66 Identities=47% Similarity=1.066 Sum_probs=58.1
Q ss_pred HHhchh-hCccCCC--CCCHHHHHhccceecC-CCeEEEeecCCccCCCCCCCChHHHhhhcCCCCcccc
Q psy2280 40 RLATFT-NWTFKSG--NCTAEHMAHAGFYLIQ-DDCTKCVFCYKELDGWEVTDYPWDEHKSHKPDCPFVQ 105 (162)
Q Consensus 40 Rl~TF~-~WP~~~~--~~spe~LA~AGFyytg-~D~V~Cf~C~~~L~~We~~DdP~~EH~r~sP~C~Fv~ 105 (162)
|++||. +||+... .++++.||.|||||+| +|.|+|++|+++|++|+++|||+.+|.+++|+|+|++
T Consensus 1 Rl~SF~~~wp~~~~~~~~~~~~LA~aGFyy~~~~d~v~C~~C~~~l~~w~~~Ddp~~~H~~~sp~C~f~k 70 (70)
T PF00653_consen 1 RLKSFRSNWPHSNDHDPVSPEKLARAGFYYTGTGDRVRCFYCGLELDNWEPNDDPWEEHKRHSPNCPFVK 70 (70)
T ss_dssp HHHGGTTGSSTTTTTSSSHHHHHHHTTEEEESSTTEEEETTTTEEEES-STT--HHHHHHHHSTTBHHHH
T ss_pred ChhHHCCcccCccccCCCCHHHHHHCCCEEcCCCCEEEEeccCCEEeCCCCCCCHHHHHHHHCcCCeecC
Confidence 899995 5997542 5789999999999999 9999999999999999999999999999999999974
No 4
>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=99.92 E-value=6.5e-26 Score=154.56 Aligned_cols=67 Identities=49% Similarity=0.987 Sum_probs=63.1
Q ss_pred HHHHhchhhCccCCCCCCHHHHHhccceecC-CCeEEEeecCCccCCCCCCCChHHHhhhcCCCCcccc
Q psy2280 38 TNRLATFTNWTFKSGNCTAEHMAHAGFYLIQ-DDCTKCVFCYKELDGWEVTDYPWDEHKSHKPDCPFVQ 105 (162)
Q Consensus 38 ~~Rl~TF~~WP~~~~~~spe~LA~AGFyytg-~D~V~Cf~C~~~L~~We~~DdP~~EH~r~sP~C~Fv~ 105 (162)
+.|++||.+||++. ...++.||.|||||+| +|.|+|++|++++++|+++|+|+.+|.+++|+|+|++
T Consensus 1 ~~R~~TF~~w~~~~-~~~~~~La~~Gfyy~~~~d~v~C~~C~~~~~~w~~~d~p~~~H~~~~p~C~fv~ 68 (69)
T cd00022 1 EARLKTFKNWPISL-KVTPEKLAEAGFYYTGRGDEVKCFFCGLELKNWEPGDDPWEEHKRWSPNCPFVL 68 (69)
T ss_pred ChHHHHHHcCCCCc-cCCHHHHHHcCCeEcCCCCEEEeCCCCCCccCCCCCCCHHHHHhHhCcCCcCcc
Confidence 47999999999983 3789999999999999 8999999999999999999999999999999999986
No 5
>PF07967 zf-C3HC: C3HC zinc finger-like ; InterPro: IPR012935 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 zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) and other proteins. NIPA is thought to perform an antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signalling events []. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe protein containing this domain (O94506 from SWISSPROT) is involved in mRNA export from the nucleus []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=97.26 E-value=0.00031 Score=53.58 Aligned_cols=50 Identities=26% Similarity=0.355 Sum_probs=40.7
Q ss_pred CCccHHHHHhchhh--CccCCCCCCHHHHHhccceecCCCeEEEeecCCccC
Q psy2280 33 PMMFYTNRLATFTN--WTFKSGNCTAEHMAHAGFYLIQDDCTKCVFCYKELD 82 (162)
Q Consensus 33 ~~~~~~~Rl~TF~~--WP~~~~~~spe~LA~AGFyytg~D~V~Cf~C~~~L~ 82 (162)
+...+-.||+||.. |...-..++|-.+|+.||...+.|.++|..|+..+.
T Consensus 3 ~r~~~l~RL~Tf~~~~W~~kp~~lspl~cA~~GW~~~~~d~l~C~~C~~~l~ 54 (133)
T PF07967_consen 3 DREDFLRRLETFKSLTWFPKPPWLSPLECARRGWICVSKDMLKCESCGARLC 54 (133)
T ss_pred CHHHHHHHHHHcccccccCCCcccCHHHHHHcCCCcCCCCEEEeCCCCCEEE
Confidence 34567799999974 932222689999999999999999999999999764
No 6
>KOG4765|consensus
Probab=92.07 E-value=0.097 Score=47.17 Aligned_cols=100 Identities=21% Similarity=0.191 Sum_probs=66.7
Q ss_pred CCCCCCCccHHHHHhchhh--CccCCCCCCHHHHHhccceecCCCeEEEeecCCccCC------CCCC---CChHHHhhh
Q psy2280 28 IEIASPMMFYTNRLATFTN--WTFKSGNCTAEHMAHAGFYLIQDDCTKCVFCYKELDG------WEVT---DYPWDEHKS 96 (162)
Q Consensus 28 ~~~~~~~~~~~~Rl~TF~~--WP~~~~~~spe~LA~AGFyytg~D~V~Cf~C~~~L~~------We~~---DdP~~EH~r 96 (162)
+-.+.++..+-.|++||+. |-..-..++|-+.|..||.....|.++|-+|+.-|.- |+.+ .-+-.-|++
T Consensus 45 l~k~wdred~lrRl~Tfks~tWygkp~~iS~lnCA~~GWv~vd~D~lkCe~C~a~L~~s~pq~s~s~d~~n~~~ek~~kk 124 (419)
T KOG4765|consen 45 LCKPWDREDLLRRLATFKSRTWYGKPFEISPLNCAKYGWVCVDCDMLKCESCGAFLCASLPQQSFSFDRYNQRCEKFKKK 124 (419)
T ss_pred ccCcccHHHHHHHHHhccCchhccCCcccchHHHhhcCeeeccCCeeehhhhhhHHhccCCccccChHHHHhHHHHHHHH
Confidence 3366778888899999974 6432115899999999998888999999999987643 3322 122222222
Q ss_pred ----cCCCCcccccccc-CCCcccHHHHHHHHHHHH
Q psy2280 97 ----HKPDCPFVQLNKR-DLTTCHIDEFIVLNSAVV 127 (162)
Q Consensus 97 ----~sP~C~Fv~~~k~-d~~~~tv~efl~l~~~r~ 127 (162)
|-..|++.--... +..++++.+=+.++..|.
T Consensus 125 LetaHe~~C~W~~~s~pe~i~e~p~~~p~~lV~r~~ 160 (419)
T KOG4765|consen 125 LETAHEKFCPWRDSSCPERIVELPLDEPADLVGRRL 160 (419)
T ss_pred HHHHHhhcCcCCCCCCchhhccCCCccHHHHHHHHH
Confidence 3456888654332 246677777777776654
No 7
>KOG3497|consensus
Probab=82.44 E-value=0.45 Score=32.69 Aligned_cols=15 Identities=33% Similarity=0.844 Sum_probs=12.3
Q ss_pred eEEEeecCCccCC-CC
Q psy2280 71 CTKCVFCYKELDG-WE 85 (162)
Q Consensus 71 ~V~Cf~C~~~L~~-We 85 (162)
.++||.||+++.+ |+
T Consensus 4 PiRCFtCGKvig~KWe 19 (69)
T KOG3497|consen 4 PIRCFTCGKVIGDKWE 19 (69)
T ss_pred eeEeeeccccccccHH
Confidence 4799999999864 66
No 8
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=78.29 E-value=0.72 Score=33.21 Aligned_cols=36 Identities=28% Similarity=0.767 Sum_probs=27.4
Q ss_pred CeEEEeecCCccCCCCCC------------CChHHHhhhcCCCCccccccc
Q psy2280 70 DCTKCVFCYKELDGWEVT------------DYPWDEHKSHKPDCPFVQLNK 108 (162)
Q Consensus 70 D~V~Cf~C~~~L~~We~~------------DdP~~EH~r~sP~C~Fv~~~k 108 (162)
..+.|-+|...+.=|.-. =||..||..+ ||++....
T Consensus 18 ~~~~C~~C~Rr~GLW~f~~~~ss~~~~~~~~d~~~eHr~~---CPwv~~~~ 65 (91)
T PF08600_consen 18 GLLSCSYCFRRLGLWMFKSKESSDSDPMSPFDPLEEHREY---CPWVNPST 65 (91)
T ss_pred CeEEccccCcEeeeeecccCccCCCCcCCCCCCccccccc---CCccCCcc
Confidence 589999999988767432 3788999765 99987643
No 9
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=75.58 E-value=1.7 Score=33.59 Aligned_cols=51 Identities=29% Similarity=0.452 Sum_probs=36.7
Q ss_pred CCHHHHHhccceecCCCeEEEeecCCccCCC--CCCCChHHHhhhcCC------CCcccccccc
Q psy2280 54 CTAEHMAHAGFYLIQDDCTKCVFCYKELDGW--EVTDYPWDEHKSHKP------DCPFVQLNKR 109 (162)
Q Consensus 54 ~spe~LA~AGFyytg~D~V~Cf~C~~~L~~W--e~~DdP~~EH~r~sP------~C~Fv~~~k~ 109 (162)
+++...+.+ +.|...|.+|+..|.-= ..+..||-||...+. .|+|+.-..+
T Consensus 16 v~A~~a~~~-----~~~~~tC~~Cg~~L~lh~~~~~~~pWFEH~~~~~~~~~l~~C~yl~pe~k 74 (128)
T PF11682_consen 16 VGARTAASA-----PYDHWTCHSCGCPLILHPGTDTEPPWFEHDQHSLAENGLMQCPYLDPEEK 74 (128)
T ss_pred EehhhhhhC-----CCCeEEEecCCceEEEecCCcCCCCccccCccccChhhcccCceECcccc
Confidence 455555555 36999999999977533 456799999987652 4999886554
No 10
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=71.91 E-value=1.1 Score=31.34 Aligned_cols=12 Identities=25% Similarity=0.575 Sum_probs=10.6
Q ss_pred eEEEeecCCccC
Q psy2280 71 CTKCVFCYKELD 82 (162)
Q Consensus 71 ~V~Cf~C~~~L~ 82 (162)
-|+||.||+.+.
T Consensus 4 PVRCFTCGkvig 15 (71)
T PLN00032 4 PVRCFTCGKVIG 15 (71)
T ss_pred ceeecCCCCCcH
Confidence 389999999996
No 11
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=68.82 E-value=1.5 Score=29.96 Aligned_cols=13 Identities=23% Similarity=0.501 Sum_probs=11.1
Q ss_pred eEEEeecCCccCC
Q psy2280 71 CTKCVFCYKELDG 83 (162)
Q Consensus 71 ~V~Cf~C~~~L~~ 83 (162)
-|+||.||+.+.+
T Consensus 4 PvRCFTCGkvi~~ 16 (62)
T PRK04016 4 PVRCFTCGKVIAE 16 (62)
T ss_pred CeEecCCCCChHH
Confidence 4899999999973
No 12
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=60.28 E-value=4.4 Score=27.76 Aligned_cols=12 Identities=25% Similarity=0.559 Sum_probs=10.5
Q ss_pred eEEEeecCCccC
Q psy2280 71 CTKCVFCYKELD 82 (162)
Q Consensus 71 ~V~Cf~C~~~L~ 82 (162)
-|+||.||+.+.
T Consensus 4 PiRCFsCGkvi~ 15 (63)
T COG1644 4 PVRCFSCGKVIG 15 (63)
T ss_pred ceEeecCCCCHH
Confidence 389999999986
No 13
>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=53.82 E-value=3.6 Score=27.93 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=9.0
Q ss_pred EEEeecCCccC
Q psy2280 72 TKCVFCYKELD 82 (162)
Q Consensus 72 V~Cf~C~~~L~ 82 (162)
|+||.||+.+.
T Consensus 5 VRCFTCGkvi~ 15 (60)
T PF01194_consen 5 VRCFTCGKVIG 15 (60)
T ss_dssp SS-STTTSBTC
T ss_pred eecCCCCCChh
Confidence 78999999996
No 14
>KOG3533|consensus
Probab=43.58 E-value=63 Score=34.62 Aligned_cols=49 Identities=20% Similarity=0.193 Sum_probs=33.8
Q ss_pred CeEEEeecCCccCCCCCCCChHHHhhh-----cCCCCccccccccCCCcccHHH
Q psy2280 70 DCTKCVFCYKELDGWEVTDYPWDEHKS-----HKPDCPFVQLNKRDLTTCHIDE 118 (162)
Q Consensus 70 D~V~Cf~C~~~L~~We~~DdP~~EH~r-----~sP~C~Fv~~~k~d~~~~tv~e 118 (162)
-+..||.||.+-+.+....-.++||.+ |.--|..|.+.-.|+.++|-.|
T Consensus 2583 LKttCFICgLeR~kFDNktVsFEeHik~EHNmWhYLyfIVlvkvKd~Te~TGPE 2636 (2706)
T KOG3533|consen 2583 LKTTCFICGLERSKFDNKTVTFEEHIKTEHNMWHYLYFIVLVKVKDETEFTGPE 2636 (2706)
T ss_pred HhcceeEeecchhhccCceeeHHHhhhhhhhhHHhhheeEEEEecCCccccChH
Confidence 457899999999988887777777755 3333544444433578887654
No 15
>PF15463 ECM11: Extracellular mutant protein 11
Probab=31.66 E-value=2.2e+02 Score=21.69 Aligned_cols=49 Identities=6% Similarity=0.183 Sum_probs=29.7
Q ss_pred CcccHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHhHHHHHHHhhhc
Q psy2280 112 TTCHIDEFIVLNSAVVKNK-----MMETLQQGKEELTRMFDDFKAKITEKINRV 160 (162)
Q Consensus 112 ~~~tv~efl~l~~~r~~~~-----~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (162)
.++-+++|-.|...-.+.+ +-+.++..+.+=.+.+.....+|-+||+++
T Consensus 78 Gd~~l~qf~~l~~kl~~~R~~~r~~~~~fe~eI~~R~eav~~~~~~l~~kL~~m 131 (139)
T PF15463_consen 78 GDWFLEQFSELMQKLKEARRKLRKKFAVFEDEINRRAEAVRAQGEQLDRKLEKM 131 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444556655544333332 444566666666677778888888888764
No 16
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=30.82 E-value=40 Score=26.44 Aligned_cols=27 Identities=26% Similarity=0.506 Sum_probs=23.1
Q ss_pred HHHHHhccceecC----CCeEEEeecCCccC
Q psy2280 56 AEHMAHAGFYLIQ----DDCTKCVFCYKELD 82 (162)
Q Consensus 56 pe~LA~AGFyytg----~D~V~Cf~C~~~L~ 82 (162)
.+.+-.+|-|.+| +..-.|--||..+.
T Consensus 93 ~~d~~h~g~Y~sGE~~g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 93 AQDLEHHGVYHSGEVVGPGTLVCENCGHEVE 123 (146)
T ss_pred HHHHHhcCCeecCcEecCceEecccCCCEEE
Confidence 3456689999999 89999999999886
No 17
>PRK11032 hypothetical protein; Provisional
Probab=27.66 E-value=45 Score=26.67 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=22.1
Q ss_pred HHHhccceecC----CCeEEEeecCCccCC
Q psy2280 58 HMAHAGFYLIQ----DDCTKCVFCYKELDG 83 (162)
Q Consensus 58 ~LA~AGFyytg----~D~V~Cf~C~~~L~~ 83 (162)
.+-..|-|.+| ...-.|--||-.+.-
T Consensus 107 dl~h~g~Y~sGEvvg~G~LvC~~Cg~~~~~ 136 (160)
T PRK11032 107 DLNHHGVYHSGEVVGLGNLVCEKCHHHLAF 136 (160)
T ss_pred HhhhcCeeecceeeecceEEecCCCCEEEe
Confidence 45568999999 899999999998863
No 18
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=26.03 E-value=24 Score=22.98 Aligned_cols=25 Identities=20% Similarity=0.539 Sum_probs=15.8
Q ss_pred HHHhccceecC--CCeEEEeecCCccC
Q psy2280 58 HMAHAGFYLIQ--DDCTKCVFCYKELD 82 (162)
Q Consensus 58 ~LA~AGFyytg--~D~V~Cf~C~~~L~ 82 (162)
.-+...|+... +...+|.||+..+.
T Consensus 20 E~v~~~F~v~~~~~~~~rC~YCe~~~~ 46 (52)
T PF02748_consen 20 EPVESRFYVIDKEPIKLRCHYCERIIT 46 (52)
T ss_dssp SSS--EEEEEETTTCEEEETTT--EEE
T ss_pred CCCCceEEEEeCCCCEEEeeCCCCEec
Confidence 34456787644 99999999998764
No 19
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.64 E-value=24 Score=27.97 Aligned_cols=30 Identities=20% Similarity=0.417 Sum_probs=19.2
Q ss_pred EEeecC----CccCCCCCCC-ChHHHhhhcCCCCcc
Q psy2280 73 KCVFCY----KELDGWEVTD-YPWDEHKSHKPDCPF 103 (162)
Q Consensus 73 ~Cf~C~----~~L~~We~~D-dP~~EH~r~sP~C~F 103 (162)
+|.||| ..++.|.-.+ +....| ++.|+|++
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~-~~c~~c~~ 36 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRR-RECLACGK 36 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeee-eeccccCC
Confidence 699999 4556664443 344555 66778877
No 20
>PRK14127 cell division protein GpsB; Provisional
Probab=24.23 E-value=3.1e+02 Score=20.52 Aligned_cols=59 Identities=17% Similarity=0.129 Sum_probs=36.2
Q ss_pred ChHHHhhhcCCCCccccccccCCCcccHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHhHHHH
Q psy2280 89 YPWDEHKSHKPDCPFVQLNKRDLTTCHIDEFIVLNSAVVKNKMMET--LQQGKEELTRMFDDFKAKI 153 (162)
Q Consensus 89 dP~~EH~r~sP~C~Fv~~~k~d~~~~tv~efl~l~~~r~~~~~~k~--~~~~~~~~~~~~~~~~~~~ 153 (162)
.|...|.+.++. ..+| ...--|++||+.+..-+...+... +....+.++..+.+++.++
T Consensus 7 Tp~DI~~KeF~~-----~~RG-Yd~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~ 67 (109)
T PRK14127 7 TPKDILEKEFKT-----SMRG-YDQDEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQV 67 (109)
T ss_pred CHHHHhhCccCC-----CCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 477777766642 2356 566678999999988777664322 4444445555555555443
No 21
>COG3599 DivIVA Cell division initiation protein [Cell division and chromosome partitioning]
Probab=23.23 E-value=3.3e+02 Score=22.59 Aligned_cols=58 Identities=17% Similarity=0.173 Sum_probs=36.3
Q ss_pred ChHHHhhhcCCCCccccccccCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHh
Q psy2280 89 YPWDEHKSHKPDCPFVQLNKRDLTTCHIDEFIVLNSAVVKNKMMETLQQGKEELTRMFDDFKAKITEKI 157 (162)
Q Consensus 89 dP~~EH~r~sP~C~Fv~~~k~d~~~~tv~efl~l~~~r~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~ 157 (162)
.|...|.+-+.. ..+| ...=-|.+||+++...+...+ +..+.+++.+++.+.+|-++=
T Consensus 7 ~~~dI~ek~F~~-----~~rG-y~~eEVdeFLD~V~~dye~~l-----~e~~~l~~~i~~L~~~l~~~~ 64 (212)
T COG3599 7 SPKDITEKEFGT-----GFRG-YDEEEVDEFLDDVIDDYEQLL-----DENEDLEDEIDELKEELKEAA 64 (212)
T ss_pred CHHHHHHHHhcc-----cccC-CCHHHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHhh
Confidence 466667665443 3455 555578999999999988876 334444555555555554443
No 22
>PRK08476 F0F1 ATP synthase subunit B'; Validated
Probab=22.79 E-value=3.4e+02 Score=20.53 Aligned_cols=35 Identities=20% Similarity=0.376 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHhhh
Q psy2280 125 AVVKNKMMETLQQGKEELTRMFDDFKAKITEKINR 159 (162)
Q Consensus 125 ~r~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (162)
......++....+....++..++++..+|-.||..
T Consensus 106 ~~a~~~l~~e~~~~~~~l~~qv~~~~~~~~~~~~~ 140 (141)
T PRK08476 106 EAFAKQLANQKQELKEQLLSQMPEFKEALNAKLSK 140 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHhhc
Confidence 33444556666667777778888888888888753
No 23
>PF01195 Pept_tRNA_hydro: Peptidyl-tRNA hydrolase; InterPro: IPR001328 Peptidyl-tRNA hydrolase (3.1.1.29 from EC) (PTH) is a bacterial enzyme that cleaves peptidyl-tRNA or N-acyl-aminoacyl-tRNA to yield free peptides or N-acyl-amino acids and tRNA. The natural substrate for this enzyme may be peptidyl-tRNA which drop off the ribosome during protein synthesis [, ]. Bacterial PTH has been found to be evolutionary related to a yeast protein [].; GO: 0004045 aminoacyl-tRNA hydrolase activity; PDB: 3KJZ_A 3KK0_A 3P2J_A 3V2I_A 3TCN_A 3TD6_A 2Z2K_A 3TD2_A 2Z2J_B 2JRC_A ....
Probab=22.03 E-value=2.2e+02 Score=22.72 Aligned_cols=58 Identities=14% Similarity=0.191 Sum_probs=38.3
Q ss_pred Ccccccccc---CCCcccHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHhHHHHHHHhh
Q psy2280 101 CPFVQLNKR---DLTTCHIDEFIVLNSAVVK-NKMMETLQQGKEELTRMFDDFKAKITEKIN 158 (162)
Q Consensus 101 C~Fv~~~k~---d~~~~tv~efl~l~~~r~~-~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (162)
-.|.+++-| +...-++.+|.--.-...+ ..+.+.+.+..+.++.++..-..+.|+++|
T Consensus 123 ~~f~RlrIGIGrp~~~~~v~~yVL~~f~~~E~~~l~~~~~~a~~~l~~~i~~~~~~~mn~~n 184 (184)
T PF01195_consen 123 EDFPRLRIGIGRPPSKEDVADYVLSKFSPEERELLDKVIPQAAEALEQIIEGGFEKAMNKFN 184 (184)
T ss_dssp SGSEEEEEEE--TSTTSGHHHHHTSB-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccceeEEEecCCCCCcchHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHhC
Confidence 556655422 1334466666543333322 246678889999999999999999999987
No 24
>PF05178 Kri1: KRI1-like family; InterPro: IPR018034 The Kri1 protein is also known as KRR1-interacting protein 1. The Saccharomyces cerevisiae member of this family is found to be required for the assembly of preribosomal 40S subunits in the nucleolus []. KRR1 is highly expressed in dividing cells and its expression ceases almost completely when cells enter the stationary phase.
Probab=21.08 E-value=1.6e+02 Score=21.55 Aligned_cols=26 Identities=31% Similarity=0.469 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHhhhc
Q psy2280 135 LQQGKEELTRMFDDFKAKITEKINRV 160 (162)
Q Consensus 135 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (162)
-.+..+++.++-+-.++.|++||..+
T Consensus 8 k~~k~eElkrlK~lK~~Ei~~kl~ki 33 (101)
T PF05178_consen 8 KQEKEEELKRLKNLKRKEIEEKLEKI 33 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566777777777777887877754
No 25
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=20.90 E-value=2.8e+02 Score=24.53 Aligned_cols=24 Identities=13% Similarity=0.411 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHH
Q psy2280 133 ETLQQGKEELTRMFDDFKAKITEK 156 (162)
Q Consensus 133 k~~~~~~~~~~~~~~~~~~~~~~~ 156 (162)
|+..+.|..|+..++-+|..|+||
T Consensus 120 KEARkEIkQLkQvieTmrssL~ek 143 (305)
T PF15290_consen 120 KEARKEIKQLKQVIETMRSSLAEK 143 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhhhchh
Confidence 555667778888999999999998
No 26
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=20.17 E-value=57 Score=21.92 Aligned_cols=37 Identities=19% Similarity=0.063 Sum_probs=24.5
Q ss_pred HHHHhccceecCCCeEEEeecCCccCCCCCCCChHHHhh
Q psy2280 57 EHMAHAGFYLIQDDCTKCVFCYKELDGWEVTDYPWDEHK 95 (162)
Q Consensus 57 e~LA~AGFyytg~D~V~Cf~C~~~L~~We~~DdP~~EH~ 95 (162)
.-||+||+- +--.++|.-|...-.-..+.+-|-..|+
T Consensus 12 KlLa~a~~~--~yle~KCPrCK~vN~~~~~~e~~t~~~k 48 (60)
T COG4416 12 KLLAEAEGQ--AYLEKKCPRCKEVNEFYIKEEATTQIHK 48 (60)
T ss_pred HHHHhcccc--eeeeecCCccceeeeeecccccchhhhh
Confidence 457788763 2346778888776555666677777775
Done!