Query 034388
Match_columns 96
No_of_seqs 88 out of 90
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 12:55:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034388.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034388hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03242 LEA_3: Late embryogen 100.0 2.2E-41 4.8E-46 232.0 5.3 90 1-90 1-93 (93)
2 PF02736 Myosin_N: Myosin N-te 82.7 0.43 9.3E-06 27.9 0.2 13 58-70 2-14 (42)
3 PF09996 DUF2237: Uncharacteri 66.3 2.5 5.5E-05 30.6 0.6 10 63-72 14-23 (117)
4 COG3651 Uncharacterized protei 64.4 2.5 5.4E-05 30.8 0.3 10 62-71 20-29 (125)
5 PRK09936 hypothetical protein; 50.3 10 0.00022 31.2 1.6 26 64-89 133-159 (296)
6 PF10948 DUF2635: Protein of u 46.2 21 0.00045 21.8 2.2 14 62-75 9-22 (47)
7 PF10500 SR-25: Nuclear RNA-sp 44.6 8.4 0.00018 30.6 0.3 22 58-79 171-192 (225)
8 PF12904 Collagen_bind_2: Puta 36.8 10 0.00022 25.8 -0.2 16 58-74 50-65 (93)
9 PF03195 DUF260: Protein of un 33.0 17 0.00037 25.1 0.4 17 58-74 65-81 (101)
10 TIGR03054 photo_alph_chp1 puta 30.1 31 0.00067 25.2 1.3 25 62-86 109-133 (135)
11 PF09803 DUF2346: Uncharacteri 30.0 19 0.00041 24.1 0.2 32 61-92 34-65 (80)
12 PF12230 PRP21_like_P: Pre-mRN 29.0 18 0.0004 27.2 0.0 36 58-93 165-208 (229)
13 COG4953 PbpC Membrane carboxyp 27.7 37 0.0008 31.2 1.6 27 66-92 365-392 (733)
14 PF13405 EF-hand_6: EF-hand do 26.8 39 0.00084 17.6 1.0 17 73-89 11-27 (31)
15 PF07886 BA14K: BA14K-like pro 26.6 32 0.0007 19.4 0.7 12 64-75 14-25 (31)
16 TIGR02697 WPE_wolbac Wolbachia 26.3 29 0.00062 20.6 0.5 12 65-76 3-14 (36)
17 PF07846 Metallothio_Cad: Meta 23.1 39 0.00084 17.9 0.6 7 63-69 12-18 (21)
18 COG3375 Uncharacterized conser 22.8 50 0.0011 27.0 1.4 13 62-74 178-190 (266)
19 PHA00542 putative Cro-like pro 22.6 82 0.0018 20.3 2.2 26 65-92 6-31 (82)
20 PF14317 YcxB: YcxB-like prote 21.5 29 0.00063 19.6 -0.1 27 62-88 35-61 (62)
21 PF00986 DNA_gyraseB_C: DNA gy 21.3 72 0.0016 20.7 1.7 19 76-94 14-32 (65)
22 PF13597 NRDD: Anaerobic ribon 20.6 47 0.001 28.7 0.9 24 64-87 519-542 (546)
23 COG4982 3-oxoacyl-[acyl-carrie 20.4 99 0.0022 28.9 2.9 30 58-88 761-790 (866)
No 1
>PF03242 LEA_3: Late embryogenesis abundant protein; InterPro: IPR004926 Late-embryogenesis abundant (LEA) genes encode a diverse group of proteins that accumulate to high levels during the maturation phase of seed development []. This group includes LEA-5 [], whose expression is induced by salt, drought and heat stress [], and related proteins. ; GO: 0006950 response to stress
Probab=100.00 E-value=2.2e-41 Score=232.00 Aligned_cols=90 Identities=53% Similarity=0.737 Sum_probs=72.4
Q ss_pred CchhhhhHHHHHHHHhhhhhhhhh-hhhhhhcCCCcc--cccccccccCCCcccccccCCccccccCCCCcccccCCCCC
Q 034388 1 MARSLFKAKLLLAPVADGISLSIG-RGYAAAAPLGTI--SRTGIMEKNDLTPAVREDSGASSAWAPDPITGYYRPENRAV 77 (96)
Q Consensus 1 MARSlsnak~lsalv~d~iS~~i~-RgYAAAa~~~~~--~~~~~~~~~~~~~~~~e~~~~~~~W~~DP~TG~~~Pe~~~~ 77 (96)
|||||+|+|+||++++|.|++.++ |||+++++.... .+.+.+....+..+.++..++++|||||||||||||||||+
T Consensus 1 MArsls~ak~lsal~~~~~s~~~~rRgYaaaA~~~~~sa~r~g~~~~~~~~~~~~~~~~~~~~W~pDPvTGyyrPen~~~ 80 (93)
T PF03242_consen 1 MARSLSNAKVLSALVSDAFSSLISRRGYAAAAAAVRSSAARGGAAGKAKMASKAGEDSKEKSSWMPDPVTGYYRPENHFG 80 (93)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhhcccccccccchhhhhcccccccccccccCCCCccccCCCCCC
Confidence 999999999999999999999988 999998885111 12222222223333445567899999999999999999999
Q ss_pred CCCHHHHHHHHhc
Q 034388 78 EIDPAELREMLLN 90 (96)
Q Consensus 78 e~D~aelR~~lL~ 90 (96)
|||+||||++||+
T Consensus 81 EiD~AeLR~~lL~ 93 (93)
T PF03242_consen 81 EIDAAELRAKLLK 93 (93)
T ss_pred CCCHHHHHHHHhC
Confidence 9999999999996
No 2
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=82.75 E-value=0.43 Score=27.88 Aligned_cols=13 Identities=38% Similarity=1.012 Sum_probs=10.7
Q ss_pred ccccccCCCCccc
Q 034388 58 SSAWAPDPITGYY 70 (96)
Q Consensus 58 ~~~W~~DP~TG~~ 70 (96)
+..|+|||..||=
T Consensus 2 ~~vWvpD~~egfv 14 (42)
T PF02736_consen 2 KWVWVPDPKEGFV 14 (42)
T ss_dssp TEEEEEESSSSEE
T ss_pred CEEEEeCCcccEE
Confidence 4569999999984
No 3
>PF09996 DUF2237: Uncharacterized protein conserved in bacteria (DUF2237); InterPro: IPR018714 This family of hypothetical proteins has no known function.; PDB: 2LQ3_A 3USH_B.
Probab=66.28 E-value=2.5 Score=30.59 Aligned_cols=10 Identities=60% Similarity=1.361 Sum_probs=7.6
Q ss_pred cCCCCccccc
Q 034388 63 PDPITGYYRP 72 (96)
Q Consensus 63 ~DP~TG~~~P 72 (96)
.||.|||||=
T Consensus 14 ~~P~TGf~Rd 23 (117)
T PF09996_consen 14 TDPMTGFYRD 23 (117)
T ss_dssp TTTT-STTSS
T ss_pred CCCCcccccC
Confidence 4999999993
No 4
>COG3651 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.36 E-value=2.5 Score=30.80 Aligned_cols=10 Identities=60% Similarity=1.411 Sum_probs=8.7
Q ss_pred ccCCCCcccc
Q 034388 62 APDPITGYYR 71 (96)
Q Consensus 62 ~~DP~TG~~~ 71 (96)
--||+||+||
T Consensus 20 ~~dPlTGFYR 29 (125)
T COG3651 20 CTDPLTGFYR 29 (125)
T ss_pred cCCcchhhhc
Confidence 3599999999
No 5
>PRK09936 hypothetical protein; Provisional
Probab=50.34 E-value=10 Score=31.25 Aligned_cols=26 Identities=27% Similarity=0.451 Sum_probs=16.4
Q ss_pred CCCCcccccCCCCC-CCCHHHHHHHHh
Q 034388 64 DPITGYYRPENRAV-EIDPAELREMLL 89 (96)
Q Consensus 64 DP~TG~~~Pe~~~~-e~D~aelR~~lL 89 (96)
=|++|||+|..--. .-..++-|+.|+
T Consensus 133 ~~v~GWYiP~ElDd~~W~~~~rR~~L~ 159 (296)
T PRK09936 133 VPVDGWYLPAELDDLNWRDEARRQPLL 159 (296)
T ss_pred CCCCeEEeeeccchhcccCHHHHHHHH
Confidence 46799999964321 122266688777
No 6
>PF10948 DUF2635: Protein of unknown function (DUF2635); InterPro: IPR024400 This family consists of uncharacterised proteins found in bacteria and bacteriophages. It includes protein Gp38 from Enterobacteria phage Mu.
Probab=46.22 E-value=21 Score=21.85 Aligned_cols=14 Identities=36% Similarity=0.487 Sum_probs=11.9
Q ss_pred ccCCCCcccccCCC
Q 034388 62 APDPITGYYRPENR 75 (96)
Q Consensus 62 ~~DP~TG~~~Pe~~ 75 (96)
||||.||-+.|+..
T Consensus 9 VrdP~~g~~Lp~eG 22 (47)
T PF10948_consen 9 VRDPDTGQLLPAEG 22 (47)
T ss_pred cCCCCCCCccCccc
Confidence 78999999888875
No 7
>PF10500 SR-25: Nuclear RNA-splicing-associated protein; InterPro: IPR019532 SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing []. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see IPR019093 from INTERPRO) signalling pathway [].
Probab=44.61 E-value=8.4 Score=30.65 Aligned_cols=22 Identities=32% Similarity=0.181 Sum_probs=19.0
Q ss_pred ccccccCCCCcccccCCCCCCC
Q 034388 58 SSAWAPDPITGYYRPENRAVEI 79 (96)
Q Consensus 58 ~~~W~~DP~TG~~~Pe~~~~e~ 79 (96)
-+-||-||+||-+|=....+||
T Consensus 171 vIRrVvDpETGRtRLIkGdGEi 192 (225)
T PF10500_consen 171 VIRRVVDPETGRTRLIKGDGEI 192 (225)
T ss_pred hheeeecCCCCceeeecccchH
Confidence 4669999999999998887876
No 8
>PF12904 Collagen_bind_2: Putative collagen-binding domain of a collagenase ; InterPro: IPR024749 This domain is likely to be the collagen-binding domain of a family of bacterial collagenase enzymes. The structure of one family member, Q8A905 from SWISSPROT, has been characterised. The domain occurs in the C-terminal region of the protein.; PDB: 3KZS_D.
Probab=36.83 E-value=10 Score=25.81 Aligned_cols=16 Identities=38% Similarity=0.596 Sum_probs=12.4
Q ss_pred ccccccCCCCcccccCC
Q 034388 58 SSAWAPDPITGYYRPEN 74 (96)
Q Consensus 58 ~~~W~~DP~TG~~~Pe~ 74 (96)
+.+|+ ||.||-|.+..
T Consensus 50 ~a~Wf-dPR~G~~~~~g 65 (93)
T PF12904_consen 50 KAWWF-DPRTGKYTYIG 65 (93)
T ss_dssp EEEEE-ETTT-BEEEEE
T ss_pred eEEEE-cCCCCCEEEee
Confidence 67788 99999998754
No 9
>PF03195 DUF260: Protein of unknown function DUF260; InterPro: IPR004883 The lateral organ boundaries (LOB) gene is expressed at the adaxial base of initiating lateral organs and encodes a plant-specific protein of unknown function. The N-terminal one half of the LOB protein contains a conserved approximately 100-amino acid domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins and in proteins from a variety of other plant species. Genes encoding LOB domain (LBD) proteins are expressed in a variety of temporal- and tissue-specific patterns, suggesting that they may function in diverse processes [] The LOB domain contains conserved blocks of amino acids that identify the LBD gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is defining feature of the LOB domain, is present in all LBD proteins. It is possible that this motif forms a new zinc finger [].
Probab=32.96 E-value=17 Score=25.11 Aligned_cols=17 Identities=29% Similarity=0.343 Sum_probs=13.3
Q ss_pred ccccccCCCCcccccCC
Q 034388 58 SSAWAPDPITGYYRPEN 74 (96)
Q Consensus 58 ~~~W~~DP~TG~~~Pe~ 74 (96)
-..|..||+.|.+--..
T Consensus 65 A~~R~~dPv~Gc~G~i~ 81 (101)
T PF03195_consen 65 ANARARDPVYGCVGIIS 81 (101)
T ss_pred HHhhccCCCcchHHHHH
Confidence 46799999999986544
No 10
>TIGR03054 photo_alph_chp1 putative photosynthetic complex assembly protein. In twenty or so anoxygenic photosynthetic alpha-Proteobacteria known so far, a gene for a member of this protein family is present and is found in the vicinity of puhA, which encodes a component of the photosynthetic reaction center, and other genes associated with photosynthesis. This protein family is suggested, consequently, as a probable assembly factor for the photosynthetic reaction center, but its seems its actual function has not yet been demonstrated.
Probab=30.13 E-value=31 Score=25.25 Aligned_cols=25 Identities=24% Similarity=0.235 Sum_probs=21.4
Q ss_pred ccCCCCcccccCCCCCCCCHHHHHH
Q 034388 62 APDPITGYYRPENRAVEIDPAELRE 86 (96)
Q Consensus 62 ~~DP~TG~~~Pe~~~~e~D~aelR~ 86 (96)
+-||.||..+.-+.|+....+...+
T Consensus 109 L~Dp~Tg~~i~L~aFG~dN~aaFa~ 133 (135)
T TIGR03054 109 LTDPATGWSIELNAFGADNAAAFER 133 (135)
T ss_pred EEcCCCCcEEEEeecCCchHHHHHh
Confidence 5699999999999999988876544
No 11
>PF09803 DUF2346: Uncharacterized conserved protein (DUF2346); InterPro: IPR018625 Members of this family of proteins have no known function.
Probab=30.00 E-value=19 Score=24.09 Aligned_cols=32 Identities=25% Similarity=0.496 Sum_probs=23.6
Q ss_pred cccCCCCcccccCCCCCCCCHHHHHHHHhccc
Q 034388 61 WAPDPITGYYRPENRAVEIDPAELREMLLNHK 92 (96)
Q Consensus 61 W~~DP~TG~~~Pe~~~~e~D~aelR~~lL~~~ 92 (96)
||.+-...+|.|++....-...++++.+..++
T Consensus 34 ~v~~~~~~~~ppe~~~~~~ele~~~~~~~~k~ 65 (80)
T PF09803_consen 34 WVIKRKRELYPPENEEIREELEEFKEELRKKR 65 (80)
T ss_pred HhHHHhcccCCCCCcccHHHHHHHHHHHHHHH
Confidence 77777788999998765555677777776544
No 12
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=28.99 E-value=18 Score=27.17 Aligned_cols=36 Identities=28% Similarity=0.359 Sum_probs=0.0
Q ss_pred ccccccCCCCcccccCCCCCC------CCHH--HHHHHHhcccc
Q 034388 58 SSAWAPDPITGYYRPENRAVE------IDPA--ELREMLLNHKV 93 (96)
Q Consensus 58 ~~~W~~DP~TG~~~Pe~~~~e------~D~a--elR~~lL~~~~ 93 (96)
..-|+..|.||-.+|++-+.| +||. |-|++++.++.
T Consensus 165 ~~~~~~cPitGe~IP~~e~~eHmRi~LlDP~wkEqr~~~~~k~~ 208 (229)
T PF12230_consen 165 KEKMIICPITGEMIPADEMDEHMRIELLDPRWKEQRDRYEAKRK 208 (229)
T ss_dssp --------------------------------------------
T ss_pred cccccccccccccccccccccccccccccccccccccccccccc
Confidence 456999999999999999887 5663 55666555443
No 13
>COG4953 PbpC Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell envelope biogenesis, outer membrane]
Probab=27.68 E-value=37 Score=31.25 Aligned_cols=27 Identities=37% Similarity=0.539 Sum_probs=21.3
Q ss_pred CCcccccCCCCCC-CCHHHHHHHHhccc
Q 034388 66 ITGYYRPENRAVE-IDPAELREMLLNHK 92 (96)
Q Consensus 66 ~TG~~~Pe~~~~e-~D~aelR~~lL~~~ 92 (96)
.+|+|+|+|...- ..+.-.|+.|+++.
T Consensus 365 ~fg~YrP~Nfd~~F~G~VsvreAL~~SL 392 (733)
T COG4953 365 RFGDYRPENFDSNFHGPVSVREALIKSL 392 (733)
T ss_pred cccCcCCccccccccCcchHHHHHHHhc
Confidence 4699999997554 78888888888754
No 14
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=26.76 E-value=39 Score=17.56 Aligned_cols=17 Identities=35% Similarity=0.323 Sum_probs=13.2
Q ss_pred CCCCCCCCHHHHHHHHh
Q 034388 73 ENRAVEIDPAELREMLL 89 (96)
Q Consensus 73 e~~~~e~D~aelR~~lL 89 (96)
.|..+.||..||+..|-
T Consensus 11 ~d~dG~I~~~el~~~l~ 27 (31)
T PF13405_consen 11 KDGDGFIDFEELRAILR 27 (31)
T ss_dssp TTSSSEEEHHHHHHHHH
T ss_pred CCCCCcCcHHHHHHHHH
Confidence 35568899999998763
No 15
>PF07886 BA14K: BA14K-like protein; InterPro: IPR012413 The sequences found in this family are similar to the BA14K proteins expressed by Brucella abortus (Q44701 from SWISSPROT) and by Brucella suis (Q8FVU0 from SWISSPROT). BA14K was found to be strongly immunoreactive; it induces both humoral and cellular responses in hosts throughout the infective process [].
Probab=26.56 E-value=32 Score=19.40 Aligned_cols=12 Identities=33% Similarity=0.661 Sum_probs=10.4
Q ss_pred CCCCcccccCCC
Q 034388 64 DPITGYYRPENR 75 (96)
Q Consensus 64 DP~TG~~~Pe~~ 75 (96)
||.||.|+|-+.
T Consensus 14 ~p~~~Ty~~~~G 25 (31)
T PF07886_consen 14 DPRDNTYQPYDG 25 (31)
T ss_pred CCCCCcEeCCCC
Confidence 899999999764
No 16
>TIGR02697 WPE_wolbac Wolbachia palindromic element (WPE) domain. This domain conceptually resembles TIGR01045, the Rickettsial palindromic element (RPE) domain. In both cases, a protein-coding palindromic element spreads through a genome, inserting usually in protein-coding regions. The additional protein coding sequence is thought to allow function of the host protein because of location in surface-exposed regions of the protein structure. Note that this model appears to work better in fragment mode.
Probab=26.35 E-value=29 Score=20.58 Aligned_cols=12 Identities=33% Similarity=0.650 Sum_probs=10.1
Q ss_pred CCCcccccCCCC
Q 034388 65 PITGYYRPENRA 76 (96)
Q Consensus 65 P~TG~~~Pe~~~ 76 (96)
||-+||-|||-.
T Consensus 3 PV~~hwDp~~li 14 (36)
T TIGR02697 3 PVPRHWDPENLI 14 (36)
T ss_pred ccccccCcchhh
Confidence 788999999863
No 17
>PF07846 Metallothio_Cad: Metallothionein family; InterPro: IPR012484 The sequence making up family 7 of the metallothionein superfamily are found repeated in metallothionein proteins expressed by two Tetrahymena species. Metallothioneins are low molecular mass, cysteine-rich metal-binding proteins that are thought to be involved in the regulation of levels of trace metals, and detoxification of these metals when present in excess []. Some of the metallothioneins found in this family (for example, Q8T6B3 from SWISSPROT) are known to be induced by cadmium and are thought to be involved in the cellular sequestration of toxic metal ions. The high proportion of cysteine residues allows the metal ions to be bound by the formation of clusters of metal-thiolate complexes []. Tetrahymena spp. metallothioneins differ from other eukaryotic metallothioneins mainly in the length of their sequences and in the cysteine-containing motifs they exhibit. ; GO: 0046870 cadmium ion binding
Probab=23.13 E-value=39 Score=17.89 Aligned_cols=7 Identities=43% Similarity=0.819 Sum_probs=5.8
Q ss_pred cCCCCcc
Q 034388 63 PDPITGY 69 (96)
Q Consensus 63 ~DP~TG~ 69 (96)
-||.|||
T Consensus 12 ~DPnsG~ 18 (21)
T PF07846_consen 12 TDPNSGC 18 (21)
T ss_pred cCCCCcc
Confidence 4999997
No 18
>COG3375 Uncharacterized conserved protein [Function unknown]
Probab=22.84 E-value=50 Score=26.97 Aligned_cols=13 Identities=38% Similarity=0.506 Sum_probs=11.1
Q ss_pred ccCCCCcccccCC
Q 034388 62 APDPITGYYRPEN 74 (96)
Q Consensus 62 ~~DP~TG~~~Pe~ 74 (96)
.++++||||||..
T Consensus 178 in~~~~g~~rp~~ 190 (266)
T COG3375 178 INPGGTGYLRPVE 190 (266)
T ss_pred cCCCCcccccccc
Confidence 4469999999988
No 19
>PHA00542 putative Cro-like protein
Probab=22.61 E-value=82 Score=20.25 Aligned_cols=26 Identities=27% Similarity=0.252 Sum_probs=17.9
Q ss_pred CCCcccccCCCCCCCCHHHHHHHHhccc
Q 034388 65 PITGYYRPENRAVEIDPAELREMLLNHK 92 (96)
Q Consensus 65 P~TG~~~Pe~~~~e~D~aelR~~lL~~~ 92 (96)
|.+|.|||.-+.. ++.++...+..++
T Consensus 6 ~~~~~~Rp~~~~~--~~~~l~~~l~~~g 31 (82)
T PHA00542 6 PATTPTIPAAYTQ--RPDELVCALIRAG 31 (82)
T ss_pred cccCCcCCcccCc--CHHHHHHHHHHCC
Confidence 5689999997755 4557776665443
No 20
>PF14317 YcxB: YcxB-like protein
Probab=21.54 E-value=29 Score=19.61 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=21.8
Q ss_pred ccCCCCcccccCCCCCCCCHHHHHHHH
Q 034388 62 APDPITGYYRPENRAVEIDPAELREML 88 (96)
Q Consensus 62 ~~DP~TG~~~Pe~~~~e~D~aelR~~l 88 (96)
.-++..++.+|-..+.+-|..++++.|
T Consensus 35 ~~~~~~~~~iPk~~f~~~e~~~f~~~l 61 (62)
T PF14317_consen 35 YLGKNQAFIIPKRAFSEEEKEEFREFL 61 (62)
T ss_pred EECCCeEEEEEHHHCCHhHHHHHHHHh
Confidence 458889999999998877778887654
No 21
>PF00986 DNA_gyraseB_C: DNA gyrase B subunit, carboxyl terminus The Prosite motif does not match this Pfam entry.; InterPro: IPR002288 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils []. Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions, domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA []. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication []. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB. This entry represents the C-terminal region (C-terminal part of domain 2) of subunit B found in topoisomerase II (gyrB) and topoisomerase IV (parE), which are primarily of bacterial origin. It does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. This region is involved in subunit interaction, which accounts for the difference between subunit B and single polypeptide topoisomerase II. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome; PDB: 3LTN_D 3RAF_C 3FOF_C 3RAE_C 3KSA_D 3RAD_C 3FOE_D 3KSB_D 3K9F_D 2XCT_D ....
Probab=21.25 E-value=72 Score=20.70 Aligned_cols=19 Identities=26% Similarity=0.470 Sum_probs=14.3
Q ss_pred CCCCCHHHHHHHHhccccc
Q 034388 76 AVEIDPAELREMLLNHKVR 94 (96)
Q Consensus 76 ~~e~D~aelR~~lL~~~~~ 94 (96)
-+|+||.+|++.-+....|
T Consensus 14 LGEM~p~qL~eTTmdP~~R 32 (65)
T PF00986_consen 14 LGEMNPDQLWETTMDPETR 32 (65)
T ss_dssp GGGS-HHHHHHHHTSTTTT
T ss_pred cccCCHHHHHHHccCccce
Confidence 4799999999998876543
No 22
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=20.56 E-value=47 Score=28.71 Aligned_cols=24 Identities=33% Similarity=0.535 Sum_probs=8.1
Q ss_pred CCCCcccccCCCCCCCCHHHHHHH
Q 034388 64 DPITGYYRPENRAVEIDPAELREM 87 (96)
Q Consensus 64 DP~TG~~~Pe~~~~e~D~aelR~~ 87 (96)
.-+||||+|.+.+.+-=-+|++.+
T Consensus 519 ~Rv~GYl~~v~~~n~gK~~E~~~R 542 (546)
T PF13597_consen 519 SRVTGYLRPVSRWNKGKQAEFKDR 542 (546)
T ss_dssp B-SSSS-BTTS-------------
T ss_pred EEeeccccCccccCHHHHHHHHHh
Confidence 359999999998887777777654
No 23
>COG4982 3-oxoacyl-[acyl-carrier protein]
Probab=20.35 E-value=99 Score=28.90 Aligned_cols=30 Identities=20% Similarity=0.574 Sum_probs=24.8
Q ss_pred ccccccCCCCcccccCCCCCCCCHHHHHHHH
Q 034388 58 SSAWAPDPITGYYRPENRAVEIDPAELREML 88 (96)
Q Consensus 58 ~~~W~~DP~TG~~~Pe~~~~e~D~aelR~~l 88 (96)
-.+|--||.+|.|--+.. ..||-.|+-++.
T Consensus 761 lI~w~~dP~pgWyDt~sg-e~Vde~dv~~rY 790 (866)
T COG4982 761 LISWENDPYPGWYDTKSG-EPVDEKDVKARY 790 (866)
T ss_pred hhhccCCCCCCceeCCCC-CcCCHHHHHHHH
Confidence 367899999999988775 679999988764
Done!