Query psy14059
Match_columns 220
No_of_seqs 19 out of 21
Neff 2.4
Searched_HMMs 46136
Date Fri Aug 16 18:30:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14059.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14059hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03271 EB1: EB1-like C-termi 47.6 11 0.00024 25.6 1.2 12 70-81 7-18 (43)
2 PF06288 DUF1040: Protein of u 32.6 20 0.00043 28.4 0.7 48 64-119 30-77 (86)
3 PF12286 DUF3622: Protein of u 27.3 32 0.00069 26.5 1.0 15 190-204 18-32 (71)
4 PF08459 UvrC_HhH_N: UvrC Heli 23.3 26 0.00057 29.4 -0.1 12 88-99 144-155 (155)
5 PF10226 DUF2216: Uncharacteri 20.9 85 0.0018 28.1 2.6 28 56-83 91-124 (195)
6 PF09185 DUF1948: Domain of un 18.3 1.3E+02 0.0028 25.4 3.0 64 45-110 30-93 (140)
7 TIGR03751 conj_TIGR03751 conju 17.5 49 0.0011 27.4 0.3 8 96-103 108-115 (116)
8 KOG4153|consensus 16.7 81 0.0018 30.2 1.6 30 94-123 26-55 (358)
9 PF03270 DUF269: Protein of un 15.4 90 0.002 25.9 1.4 26 90-116 84-118 (122)
10 PF03980 Nnf1: Nnf1 ; InterPr 12.2 6.5E+02 0.014 19.0 6.2 21 75-97 35-55 (109)
No 1
>PF03271 EB1: EB1-like C-terminal motif; InterPro: IPR004953 A group of microtubule-associated proteins called +TIPs (plus end tracking proteins), including EB1 (end-binding protein 1) family proteins, label growing microtubules ends specifically in diverse organisms and are implicated in spindle dynamics, chromosome segregation, and directing microtubules toward cortical sites. EB1 members have a bipartite composition: the N-terminal CH domain (IPR001715 from INTERPRO) mediates microtubule plus end localization and a C-terminal cargo binding domain (EB1-C) that captures cell polarity determinants. The EB1-C domain comprises a unique EB1-like sequence motif that acts as a binding site for other +TIP proteins. It interacts with the carboxy terminus of the adenomatous polyposis coli (APC) tumor suppressor, a well conserved +TIP phosphoprotein with a pivotal function in cell cycle regulation. Another binding partner of the EB1-C domain is the well conserved +TIP protein dynactin, a component of the large cytoplasmic dynein/dynactin complex [, , ]. The ~80-residue EB1-C domain starts with a long smoothly curved helix (alpha1), which is followed by a hairpin connection leading to a short second helix (alpha2) running antiparallel to alpha1. The two parallel alpha1 helices of the EB1-C domain dimer wrap around each other in a slightly left-handed supercoil. The two alpha2 helices run antiparallel to helices alpha1 and form a similar fork in the opposite orientation and rotated by 90 degrees. As a result, two helical segments from each monomer form a four-helix bundle. The side chain forming the hydrophobic core of this bundle are highly conserved [, , ]. Some protein known to contain an EB1-C domain are listed below: Yeast protein BIM1. Fission yeast microtubule integrity protein mal3. Vertebrate microtubule-associated protein RP/EB family member 1 (EB1). Vertebrate microtubule-associated protein RP/EB family member 2 (EB2 or RP1). Vertebrate microtubule-associated protein RP/EB family member 3 (EBF3). ; GO: 0008017 microtubule binding; PDB: 3TQ7_B 4E61_B 2HKQ_A 1YIG_B 3GJO_B 2HL5_B 1YIB_A 1WU9_A 1TXQ_B.
Probab=47.57 E-value=11 Score=25.64 Aligned_cols=12 Identities=42% Similarity=0.725 Sum_probs=9.8
Q ss_pred hHHHHHhhhhhH
Q psy14059 70 EDYYNKLSKLEE 81 (220)
Q Consensus 70 edYYnKL~~LE~ 81 (220)
+=|||||..+|-
T Consensus 7 dFYf~KLR~IE~ 18 (43)
T PF03271_consen 7 DFYFNKLRDIEI 18 (43)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 459999999874
No 2
>PF06288 DUF1040: Protein of unknown function (DUF1040); InterPro: IPR009383 This family consists of several bacterial YihD proteins of unknown function [].; PDB: 2KO6_A.
Probab=32.65 E-value=20 Score=28.45 Aligned_cols=48 Identities=25% Similarity=0.441 Sum_probs=30.0
Q ss_pred HhhhcchHHHHHhhhhhHHHHHHHhhhhhccccccCCCchhhhhhHHHHHHHHhHH
Q psy14059 64 VKTRKTEDYYNKLSKLEEDQLIREARIREASHQVGIPQERVSVSSKAAQKYERDLE 119 (220)
Q Consensus 64 VK~KK~edYYnKL~~LE~eQ~~KE~~lRe~sHQfAIPgEKvv~~S~AAq~YEe~Le 119 (220)
+|--..-.|...|..|.++-|+=--+||.+.-.=.|||=| ..||+++-
T Consensus 30 qkLa~eag~~~~l~~LtDdvLIYhLKMr~s~k~e~iPGlk--------KDye~DFK 77 (86)
T PF06288_consen 30 QKLAQEAGFDGPLEDLTDDVLIYHLKMRNSDKDEMIPGLK--------KDYEDDFK 77 (86)
T ss_dssp HHHHHHTT-SS-TTS--HHHHHHHHHHHHHTTSSS-SS----------------HH
T ss_pred HHHHHhcCCCCchhhccHHHHHHHHHhcCCCccCcCCccc--------hhhHHHHH
Confidence 4555566788999999999999999999999999999965 67777664
No 3
>PF12286 DUF3622: Protein of unknown function (DUF3622); InterPro: IPR022069 This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif.
Probab=27.29 E-value=32 Score=26.45 Aligned_cols=15 Identities=33% Similarity=0.463 Sum_probs=12.2
Q ss_pred CCceeeeeeccceee
Q psy14059 190 GDKEIVRKITATETT 204 (220)
Q Consensus 190 GD~EItRkITATETT 204 (220)
=--||||++|+.-|.
T Consensus 18 W~aEItR~vTsrkTv 32 (71)
T PF12286_consen 18 WTAEITRRVTSRKTV 32 (71)
T ss_pred eeeeeeeeecCceeE
Confidence 345999999998874
No 4
>PF08459 UvrC_HhH_N: UvrC Helix-hairpin-helix N-terminal; InterPro: IPR001162 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. Proteins that contain the UvrC homology region 1, IPR000305 from INTERPRO, are listed below: Prokaryotic UvrC proteins. Bacteriophage T4 END2 protein. Small subunit of ribonucleotide reductase enzyme. T4 TEV1 protein. Endonuclease specific to the thymidylate synthase (td) gene splice junction. Found in putative intron-homing endonucleases encoded by group I introns of fungi and phage. Mycobacterium hypothetical protein Y002. Exonuclease by similarity. Bacillus subtilis hypothetical protein YURQ. ; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3C65_A 2NRZ_A 2NRR_A 2NRX_A 2NRV_A 2NRT_A 2NRW_A.
Probab=23.30 E-value=26 Score=29.38 Aligned_cols=12 Identities=42% Similarity=0.808 Sum_probs=10.5
Q ss_pred hhhhhccccccC
Q psy14059 88 ARIREASHQVGI 99 (220)
Q Consensus 88 ~~lRe~sHQfAI 99 (220)
++||...|.|||
T Consensus 144 q~irDEaHRFAI 155 (155)
T PF08459_consen 144 QRIRDEAHRFAI 155 (155)
T ss_dssp HHHHHHHHHHCC
T ss_pred HHHHHHHHhccC
Confidence 578899999998
No 5
>PF10226 DUF2216: Uncharacterized conserved proteins (DUF2216); InterPro: IPR019359 Proteins in this entry are found in Metazoa and contain a coiled-coil domain. Some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed.
Probab=20.94 E-value=85 Score=28.09 Aligned_cols=28 Identities=32% Similarity=0.615 Sum_probs=23.4
Q ss_pred CChhHHH------HHhhhcchHHHHHhhhhhHHH
Q psy14059 56 KEPEWTQ------AVKTRKTEDYYNKLSKLEEDQ 83 (220)
Q Consensus 56 ~etEWQk------~VK~KK~edYYnKL~~LE~eQ 83 (220)
-..|||+ +|=.+.-.-|-+||++||.-|
T Consensus 91 larEWQrFGryta~vmr~eV~~Y~~KL~eLE~kq 124 (195)
T PF10226_consen 91 LAREWQRFGRYTASVMRQEVAQYQQKLKELEDKQ 124 (195)
T ss_pred HhHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5678996 577888899999999998755
No 6
>PF09185 DUF1948: Domain of unknown function (DUF1948); InterPro: IPR015268 Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with one central alpha-helix surrounded by five others, in a NusB-like fold. Their function has not, as yet, been determined []. ; PDB: 1Q8C_A.
Probab=18.25 E-value=1.3e+02 Score=25.38 Aligned_cols=64 Identities=22% Similarity=0.373 Sum_probs=32.6
Q ss_pred hhhccccccCCCChhHHHHHhhhcchHHHHHhhhhhHHHHHHHhhhhhccccccCCCchhhhhhHH
Q psy14059 45 ADMIKRDKIQKKEPEWTQAVKTRKTEDYYNKLSKLEEDQLIREARIREASHQVGIPQERVSVSSKA 110 (220)
Q Consensus 45 ~~~lk~k~~ke~etEWQk~VK~KK~edYYnKL~~LE~eQ~~KE~~lRe~sHQfAIPgEKvv~~S~A 110 (220)
|++|.-+...-+-.+||+.+-+-=+|.-+.-+..+|+.|+-.-..+ .+.---|.|-||---..|
T Consensus 30 a~fl~yd~~er~ln~wqk~ivk~fse~~~~f~~~ie~qq~~nq~ei--q~kynkisgkkidllt~a 93 (140)
T PF09185_consen 30 ADFLDYDTPERQLNDWQKEIVKVFSENCFSFQKKIENQQQRNQAEI--QSKYNKISGKKIDLLTKA 93 (140)
T ss_dssp HHHHHT--TTT---HHHHHHHHHHHHHHHHHHHHHHHHHHH---S----------------HHHHH
T ss_pred HHHHhcCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHhcccccchhhHHHHH
Confidence 4577777777788999999998889998888888888776543332 233345778887655555
No 7
>TIGR03751 conj_TIGR03751 conjugative transfer region lipoprotein, TIGR03751 family. Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=17.54 E-value=49 Score=27.39 Aligned_cols=8 Identities=50% Similarity=0.825 Sum_probs=6.0
Q ss_pred cccCCCch
Q psy14059 96 QVGIPQER 103 (220)
Q Consensus 96 QfAIPgEK 103 (220)
|||.|||.
T Consensus 108 QYAlPGEr 115 (116)
T TIGR03751 108 QYALPGER 115 (116)
T ss_pred eeccCCCc
Confidence 77777775
No 8
>KOG4153|consensus
Probab=16.74 E-value=81 Score=30.19 Aligned_cols=30 Identities=27% Similarity=0.346 Sum_probs=24.4
Q ss_pred cccccCCCchhhhhhHHHHHHHHhHHHhhc
Q psy14059 94 SHQVGIPQERVSVSSKAAQKYERDLEAAKK 123 (220)
Q Consensus 94 sHQfAIPgEKvv~~S~AAq~YEe~Le~~~~ 123 (220)
-|-||||.=-|++||.|-.+-|+-++....
T Consensus 26 eh~fAipainvtsSstA~aaleaar~~~sp 55 (358)
T KOG4153|consen 26 EHKFAIPAINVTSSSTAVAALEAARDSKSP 55 (358)
T ss_pred ccccccceeeeechHHHHHHHHHHHhccCC
Confidence 489999999999999996677776666554
No 9
>PF03270 DUF269: Protein of unknown function, DUF269; InterPro: IPR004952 This family includes several proteins of unknown function. Members of this family may be involved in nitrogen fixation, since they are found within nitrogen fixation operons.; PDB: 3NJ2_B 3G7P_A.
Probab=15.35 E-value=90 Score=25.93 Aligned_cols=26 Identities=19% Similarity=0.445 Sum_probs=18.1
Q ss_pred hhhccccccCC--------CchhhhhhHH-HHHHHH
Q psy14059 90 IREASHQVGIP--------QERVSVSSKA-AQKYER 116 (220)
Q Consensus 90 lRe~sHQfAIP--------gEKvv~~S~A-Aq~YEe 116 (220)
|| +.|-|+.+ |+|+++..++ ..+|-+
T Consensus 84 LR-DvHRFGF~SlekL~~~G~klv~~av~~i~~~pe 118 (122)
T PF03270_consen 84 LR-DVHRFGFESLEKLAEEGEKLVSKAVELIEKFPE 118 (122)
T ss_dssp E--SGGG--BSSHHHHHHHHHHHHHHHHHHHHH-HH
T ss_pred HH-HHHhcCCccHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 44 89999988 8999999888 777754
No 10
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=12.22 E-value=6.5e+02 Score=18.96 Aligned_cols=21 Identities=48% Similarity=0.635 Sum_probs=16.0
Q ss_pred HhhhhhHHHHHHHhhhhhccccc
Q psy14059 75 KLSKLEEDQLIREARIREASHQV 97 (220)
Q Consensus 75 KL~~LE~eQ~~KE~~lRe~sHQf 97 (220)
||.+| +.|+.|++.|...+.-
T Consensus 35 kLneL--d~Li~eA~~r~~~~~~ 55 (109)
T PF03980_consen 35 KLNEL--DKLIEEAKERKNSGER 55 (109)
T ss_pred HHHHH--HHHHHHHHHhHhcccc
Confidence 66666 4689999999887664
Done!