Query psy1257
Match_columns 125
No_of_seqs 168 out of 880
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 22:43:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1257.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1257hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03392 OS-D: Insect pheromon 99.9 2E-22 4.4E-27 134.1 5.4 58 2-59 38-95 (95)
2 KOG3589|consensus 99.9 1.4E-21 3E-26 147.2 7.7 76 50-125 68-151 (221)
3 smart00315 RGS Regulator of G 99.7 5.3E-17 1.1E-21 109.1 6.7 62 64-125 9-70 (118)
4 PF00615 RGS: Regulator of G p 99.6 2.7E-15 5.8E-20 99.9 6.8 62 64-125 9-70 (118)
5 PF09128 RGS-like: Regulator o 97.9 2.1E-05 4.5E-10 58.3 4.9 60 64-124 15-74 (188)
6 KOG3590|consensus 97.1 0.00063 1.4E-08 56.1 4.0 61 64-124 325-392 (602)
7 KOG0986|consensus 97.0 0.0012 2.6E-08 55.2 5.2 54 64-118 61-115 (591)
8 KOG3590|consensus 96.0 0.012 2.6E-07 48.7 4.8 32 64-95 122-153 (602)
9 PF04818 CTD_bind: RNA polymer 80.5 3.7 8E-05 24.5 3.8 36 2-37 25-60 (64)
10 PF11919 DUF3437: Domain of un 75.8 2.7 5.9E-05 27.5 2.4 47 7-53 27-75 (90)
11 PF01418 HTH_6: Helix-turn-hel 74.4 18 0.00039 22.4 6.1 70 10-79 5-75 (77)
12 PF15182 OTOS: Otospiralin 72.1 6.4 0.00014 24.3 3.2 30 84-113 26-55 (69)
13 PF02184 HAT: HAT (Half-A-TPR) 64.6 5.3 0.00012 21.2 1.5 14 103-116 4-17 (32)
14 TIGR03826 YvyF flagellar opero 58.6 11 0.00025 26.5 2.8 53 10-62 15-69 (137)
15 PF14194 Cys_rich_VLP: Cystein 46.0 21 0.00046 21.4 2.1 21 20-40 1-21 (56)
16 COG4790 EscR Type III secretor 43.4 46 0.001 25.1 4.0 40 54-93 83-122 (214)
17 PF08910 Aida_N: Aida N-termin 42.3 50 0.0011 22.3 3.8 32 4-35 31-63 (106)
18 smart00582 RPR domain present 40.7 47 0.001 21.9 3.5 34 3-36 74-107 (121)
19 PF13713 BRX_N: Transcription 39.6 15 0.00034 20.3 0.8 19 1-20 21-39 (39)
20 KOG3364|consensus 36.2 33 0.00072 24.5 2.2 70 6-95 5-85 (149)
21 KOG0210|consensus 35.3 24 0.00052 31.8 1.7 89 6-96 751-844 (1051)
22 PF12725 DUF3810: Protein of u 35.1 96 0.0021 24.7 5.0 31 80-118 272-302 (318)
23 PLN03190 aminophospholipid tra 33.6 46 0.00099 31.4 3.3 30 4-33 835-868 (1178)
24 PF06530 Phage_antitermQ: Phag 31.3 38 0.00082 23.1 1.9 45 4-49 31-75 (125)
25 TIGR02765 crypto_DASH cryptoch 31.2 22 0.00047 29.1 0.8 14 47-60 413-426 (429)
26 COG4133 CcmA ABC-type transpor 29.2 33 0.00072 25.9 1.4 17 76-92 88-105 (209)
27 KOG0063|consensus 29.1 50 0.0011 28.3 2.5 32 64-95 494-525 (592)
28 KOG4304|consensus 28.3 76 0.0017 24.5 3.3 15 1-15 51-65 (250)
29 PF01805 Surp: Surp module; I 27.8 1.2E+02 0.0026 17.4 3.4 30 23-52 1-32 (55)
30 PF09494 Slx4: Slx4 endonuclea 27.0 1.5E+02 0.0032 17.7 4.9 29 32-61 6-35 (64)
31 PF07583 PSCyt2: Protein of un 26.8 1.3E+02 0.0029 22.5 4.3 51 29-79 44-111 (208)
32 PF04512 Baculo_PEP_N: Baculov 26.2 73 0.0016 21.1 2.5 54 30-83 32-87 (97)
33 PF07278 DUF1441: Protein of u 25.8 1.3E+02 0.0028 21.6 3.9 34 5-39 110-143 (152)
34 TIGR02766 crypt_chrom_pln cryp 25.4 32 0.0007 28.6 0.8 18 46-63 409-426 (475)
35 PHA02754 hypothetical protein; 25.1 25 0.00055 21.4 0.1 11 1-11 20-30 (67)
36 PF09764 Nt_Gln_amidase: N-ter 25.1 48 0.001 24.6 1.6 16 77-94 5-20 (184)
37 PF10589 NADH_4Fe-4S: NADH-ubi 24.4 46 0.00099 18.8 1.1 14 10-23 10-23 (46)
38 PF05823 Gp-FAR-1: Nematode fa 24.1 1.3E+02 0.0028 21.4 3.6 45 2-46 4-61 (154)
39 TIGR02887 spore_ger_x_C germin 23.7 35 0.00075 27.2 0.7 45 2-46 297-344 (371)
40 PF09759 Atx10homo_assoc: Spin 23.6 1.3E+02 0.0028 20.1 3.3 69 4-90 2-72 (102)
41 PRK10803 tol-pal system protei 23.5 2.5E+02 0.0054 21.6 5.4 45 64-113 160-207 (263)
42 PF13174 TPR_6: Tetratricopept 23.4 1E+02 0.0022 14.6 2.3 18 23-40 15-32 (33)
43 PRK10410 hypothetical protein; 23.1 85 0.0018 20.9 2.4 21 13-33 56-81 (100)
44 PHA00447 lysozyme 23.0 86 0.0019 21.9 2.5 24 18-41 93-116 (142)
45 PF10774 DUF4226: Domain of un 22.7 45 0.00097 22.7 1.0 23 56-78 60-84 (112)
46 cd03562 CID CID (CTD-Interacti 22.2 1.1E+02 0.0025 19.9 2.9 22 17-38 89-110 (114)
47 PF03441 FAD_binding_7: FAD bi 21.4 38 0.00081 26.2 0.4 17 47-63 209-225 (277)
48 PRK15482 transcriptional regul 21.2 2.8E+02 0.006 21.1 5.2 53 27-79 18-75 (285)
49 PF11467 LEDGF: Lens epitheliu 21.1 2.3E+02 0.0049 19.0 4.2 17 98-114 61-77 (106)
50 KOG4342|consensus 21.0 80 0.0017 28.4 2.3 57 31-87 333-400 (1078)
51 PRK10674 deoxyribodipyrimidine 20.8 44 0.00095 27.9 0.7 18 46-63 406-423 (472)
52 COG4748 Uncharacterized conser 20.6 2.2E+02 0.0047 23.2 4.5 48 68-115 175-227 (365)
53 PF14615 Rsa3: Ribosome-assemb 20.2 1.2E+02 0.0026 17.4 2.3 41 30-70 6-46 (47)
54 TIGR03556 photolyase_8HDF deox 20.1 45 0.00097 27.9 0.7 18 46-63 410-427 (471)
No 1
>PF03392 OS-D: Insect pheromone-binding family, A10/OS-D; InterPro: IPR005055 A class of small (14-20 Kd) water-soluble proteins, called odorant binding proteins (OBPs), first discovered in the insect sensillar lymph but also in the mucus of vertebrates, is postulated to mediate the solubilisation of hydrophobic odorant molecules, and thereby to facilitate their transport to the receptor neurons. The product of a gene expressed in the olfactory system of Drosophila melanogaster (Fruit fly), OS-D, shares features common to vertebrate odorant-binding proteins, but has a primary structure unlike odorant-binding proteins []. OS-D derivatives have subsequently been found in chemosensory organs of phylogenetically distinct insects, including cockroaches, phasmids and moths, suggesting that OS-D-like proteins seem to be conserved in the insect phylum.; PDB: 1KX9_A 1N8U_A 1KX8_A 1K19_A 1N8V_A 2GVS_A 2JNT_A.
Probab=99.87 E-value=2e-22 Score=134.14 Aligned_cols=58 Identities=48% Similarity=0.978 Sum_probs=54.2
Q ss_pred hhHHhhhhHHHHhcCccCCHHHHhHHHHHHHHHHhhChhHHHHHhhcCCCCchhhhhH
Q psy1257 2 SECRENIPTVLQTLCEKCTPSQTDKAVMVIRRLKKDYPEEWKILLEKWDPKGEYTRKF 59 (125)
Q Consensus 2 ~~~k~~lpea~~~~C~kCt~~Qk~~~~kvi~~l~~~~P~~W~~l~~k~dP~~~~v~kw 59 (125)
++||++|||||+|+|+||||+||+++++|++||++++|+.|+.|..+|||+++|..+|
T Consensus 38 ~~lK~~ipeal~t~C~KCt~kQK~~~~kv~~~l~~~~P~~w~~l~~KyDp~~~y~~ky 95 (95)
T PF03392_consen 38 KELKKVIPEALKTNCAKCTPKQKENARKVIKFLKKNYPDEWEELVKKYDPEGKYRKKY 95 (95)
T ss_dssp HHHHHHHHHHHHCTTTTS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT-TTHHHH
T ss_pred HHHHHHHHHHHHccccCCCHHHHHHHHHHHHHHHHcCHHHHHHHHHHHCCCcchhhcC
Confidence 6899999999999999999999999999999999999999999999999999998875
No 2
>KOG3589|consensus
Probab=99.85 E-value=1.4e-21 Score=147.17 Aligned_cols=76 Identities=41% Similarity=0.719 Sum_probs=72.6
Q ss_pred CCCchhhhhHHhhh------cccHHHHHHHHHHhhcHHHHHHHHHHHHhhcCCCH--HHHHHHHHHHHHHHcCCCCCCcc
Q psy1257 50 DPKGEYTRKFQEKF------GDTYKLFREFLRCEYSEENILFWLACEDLKKESNP--DVIEEKARFIYEDYISILSPKEV 121 (125)
Q Consensus 50 dP~~~~v~kw~~s~------~~g~~~F~~FL~~e~s~ENl~Fw~a~e~~k~~~~~--~~~~~~a~~Iy~~yi~~~sp~ev 121 (125)
.|..+++.+|+.|| +.|+..|..||++|||+|||+||+||++|++.... ..+...|+.||++||+++||.+|
T Consensus 68 ~~~~e~~~~w~~sf~~L~~~~~G~~~F~~fLk~e~Seeni~FW~ace~~k~~~~~~~~~~~~~a~~i~~~f~~~~ap~~v 147 (221)
T KOG3589|consen 68 LPSREEVESWAKSFEKLLADEAGRAVFAEFLKSEFSEENLEFWLACEEFKKRRSEKSTKMSEKAKEIYEEFSAPAAPKEV 147 (221)
T ss_pred CCCHHHHHHHHHhHHHHhhChhhHHHHHHHHHHHhhHhHHHHHHHHHHHHhCcCchhhhhhHHHHHHHHHHhccCCCCCC
Confidence 78999999999999 99999999999999999999999999999998775 67899999999999999999999
Q ss_pred CCCC
Q psy1257 122 TQDP 125 (125)
Q Consensus 122 Nid~ 125 (125)
|||+
T Consensus 148 n~d~ 151 (221)
T KOG3589|consen 148 NLDS 151 (221)
T ss_pred CCch
Confidence 9996
No 3
>smart00315 RGS Regulator of G protein signalling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits.
Probab=99.69 E-value=5.3e-17 Score=109.07 Aligned_cols=62 Identities=47% Similarity=0.703 Sum_probs=59.3
Q ss_pred cccHHHHHHHHHHhhcHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHcCCCCCCccCCCC
Q psy1257 64 GDTYKLFREFLRCEYSEENILFWLACEDLKKESNPDVIEEKARFIYEDYISILSPKEVTQDP 125 (125)
Q Consensus 64 ~~g~~~F~~FL~~e~s~ENl~Fw~a~e~~k~~~~~~~~~~~a~~Iy~~yi~~~sp~evNid~ 125 (125)
|.|+.+|++||++++|.|||.||.+|+.|+.......+...|+.||++||.++||.+|||++
T Consensus 9 ~~~~~~F~~fl~~~~~~e~l~F~~~v~~~~~~~~~~~~~~~a~~I~~~yi~~~s~~~~ni~~ 70 (118)
T smart00315 9 PIGRLLFREFLESEFSEENLEFWLAVEEFKKAEDDEERIAKAREIYDKFLSPNAPKEVNLDS 70 (118)
T ss_pred hHHHHHHHHHHHHhcchHhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhCCCCCCceeCCH
Confidence 88999999999999999999999999999999886788999999999999999999999974
No 4
>PF00615 RGS: Regulator of G protein signaling domain; InterPro: IPR000342 RGS (Regulator of G Protein Signalling) proteins are multi-functional, GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways []. Upon activation by GPCRs, heterotrimeric G proteins exchange GDP for GTP, are released from the receptor, and dissociate into free, active GTP-bound alpha subunit and beta-gamma dimer, both of which activate downstream effectors. The response is terminated upon GTP hydrolysis by the alpha subunit (IPR001019 from INTERPRO), which can then bind the beta-gamma dimer (IPR001632 from INTERPRO, IPR001770 from INTERPRO) and the receptor. RGS proteins markedly reduce the lifespan of GTP-bound alpha subunits by stabilising the G protein transition state. All RGS proteins contain an 'RGS-box' (or RGS domain), which is required for activity. Some small RGS proteins such as RGS1 and RGS4 are comprised of little more than an RGS domain, while others also contain additional domains that confer further functionality []. RGS domains can be found in conjunction with a variety of domains, including: DEP for membrane targeting (IPR000591 from INTERPRO), PDZ for binding to GPCRs (IPR001478 from INTERPRO), PTB for phosphotyrosine-binding (IPR006020 from INTERPRO), RBD for Ras-binding (IPR003116 from INTERPRO), GoLoco for guanine nucleotide inhibitor activity (IPR003109 from INTERPRO), PX for phosphatidylinositol-binding (IPR001683 from INTERPRO), PXA that is associated with PX (IPR003114 from INTERPRO), PH for stimulating guanine nucleotide exchange (IPR001849 from INTERPRO), and GGL (G protein gamma subunit-like) for binding G protein beta subunits (IPR001770 from INTERPRO) []. Those RGS proteins that contain GGL domains can interact with G protein beta subunits to form novel dimers that prevent G protein gamma subunit binding and G protein alpha subunit association, thereby preventing heterotrimer formation.; GO: 0004871 signal transducer activity; PDB: 2BCJ_A 3PSC_A 3PVU_A 1YM7_B 3PVW_A 1OMW_A 2EBZ_A 2BV1_B 2GTP_D 1CMZ_A ....
Probab=99.60 E-value=2.7e-15 Score=99.92 Aligned_cols=62 Identities=35% Similarity=0.599 Sum_probs=59.0
Q ss_pred cccHHHHHHHHHHhhcHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHcCCCCCCccCCCC
Q psy1257 64 GDTYKLFREFLRCEYSEENILFWLACEDLKKESNPDVIEEKARFIYEDYISILSPKEVTQDP 125 (125)
Q Consensus 64 ~~g~~~F~~FL~~e~s~ENl~Fw~a~e~~k~~~~~~~~~~~a~~Iy~~yi~~~sp~evNid~ 125 (125)
|.|+.+|..||+++++.+||.||++|+.|++..+...+...|+.||++||+++||.+|||++
T Consensus 9 ~~~~~~F~~Fl~~~~~~~~l~F~~~v~~~~~~~~~~~~~~~a~~I~~~fi~~~s~~~l~i~~ 70 (118)
T PF00615_consen 9 PEGLELFKEFLEKENCEENLQFWLEVEEFKSSESEEQRKKLAQQIYNKFISPGSPNELNIPS 70 (118)
T ss_dssp HHHHHHHHHHHHHTTTTHHHHHHHHHHHHHTSCSHHHHHHHHHHHHHHHTSTTSTTCCSSTH
T ss_pred hHHHHHHHHHHhHCCCHHHHHHHHHHHHHHhhcchhhHHHHHHHHHHHHhcccccccccccH
Confidence 77999999999999999999999999999999777888999999999999999999999973
No 5
>PF09128 RGS-like: Regulator of G protein signalling-like domain; InterPro: IPR015212 This entry represents a domain consisting of twelve helices that fold into a compact structure that contains the overall structural scaffold observed in other regulator of G protein signalling (RGS) proteins and three additional helical elements that pack closely to it. Helices 1-9 comprise the RGS fold, in which helices 4-7 form a classic antiparallel bundle adjacent to the other helices. Like other RGS structures, helices 7 and 8 span the length of the folded domain and form essentially one continuous helix with a kink in the middle. Helices 10-12 form an apparently stable C-terminal extension of the structural domain, and although other RGS proteins lack this structure, these elements are intimately associated with the rest of the structural framework by hydrophobic interactions. This domain binds to active G-alpha proteins, promoting GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways []. ; GO: 0005089 Rho guanyl-nucleotide exchange factor activity, 0005737 cytoplasm; PDB: 3CX6_B 3CX8_B 3CX7_B 1HTJ_F 1SHZ_C 3AB3_D 1IAP_A.
Probab=97.90 E-value=2.1e-05 Score=58.34 Aligned_cols=60 Identities=15% Similarity=0.272 Sum_probs=48.4
Q ss_pred cccHHHHHHHHHHhhcHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHcCCCCCCccCCC
Q psy1257 64 GDTYKLFREFLRCEYSEENILFWLACEDLKKESNPDVIEEKARFIYEDYISILSPKEVTQD 124 (125)
Q Consensus 64 ~~g~~~F~~FL~~e~s~ENl~Fw~a~e~~k~~~~~~~~~~~a~~Iy~~yi~~~sp~evNid 124 (125)
|+-...|..|+-+.+.-.-|+|++-.+-|+.... +++++.|.+||.+||.++||..|+++
T Consensus 15 PaHlaVFl~yv~sq~dP~~LLfyL~~d~yk~~~~-Ke~rk~~~ei~stFL~~~ApL~v~v~ 74 (188)
T PF09128_consen 15 PAHLAVFLNYVLSQFDPSPLLFYLIADLYKQGNA-KEMRKWAYEIHSTFLDPGAPLRVNVP 74 (188)
T ss_dssp HHHHHHHHHHHHHHS-SHHHHHHHHHHHHTTS-T-TCHHHHHHHHHHHHTSTT-TT-----
T ss_pred cHHHHHHHHHHHhcCCcchHHHHHHHHHHhccCH-HHHHHHHHHHHHHHcCCCCCceecCC
Confidence 7778999999999999999999999999999665 56899999999999999999999875
No 6
>KOG3590|consensus
Probab=97.09 E-value=0.00063 Score=56.07 Aligned_cols=61 Identities=20% Similarity=0.450 Sum_probs=51.3
Q ss_pred cccHHHHHHHHHHhhcHHHHHHHHHHHHhhcCC-------CHHHHHHHHHHHHHHHcCCCCCCccCCC
Q psy1257 64 GDTYKLFREFLRCEYSEENILFWLACEDLKKES-------NPDVIEEKARFIYEDYISILSPKEVTQD 124 (125)
Q Consensus 64 ~~g~~~F~~FL~~e~s~ENl~Fw~a~e~~k~~~-------~~~~~~~~a~~Iy~~yi~~~sp~evNid 124 (125)
...+-+|.+||+++-..|-|.||++|..|++.- +.++...-|-.||++|.+-.|.+.+.++
T Consensus 325 e~aLfyF~Ey~e~~~~~~~lqFwl~adnF~~~la~~E~~~d~~eAq~DAMilYdKYFSlQat~~l~~~ 392 (602)
T KOG3590|consen 325 ESALFYFSEYMEKEDAVNILQFWLAADNFQSQLAAKEGQYDGQEAQNDAMILYDKYFSLQATHPLGFD 392 (602)
T ss_pred hHHHHHHHHHHHHHhHHHHHHHHHHhhhHHHhhhhcccccchhhhhcchhHHHHHHhhhhccCccchh
Confidence 456779999999999999999999999999852 2235566788999999999999988765
No 7
>KOG0986|consensus
Probab=97.03 E-value=0.0012 Score=55.20 Aligned_cols=54 Identities=24% Similarity=0.257 Sum_probs=44.2
Q ss_pred cccHHHHHHHHHHh-hcHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHcCCCCC
Q psy1257 64 GDTYKLFREFLRCE-YSEENILFWLACEDLKKESNPDVIEEKARFIYEDYISILSP 118 (125)
Q Consensus 64 ~~g~~~F~~FL~~e-~s~ENl~Fw~a~e~~k~~~~~~~~~~~a~~Iy~~yi~~~sp 118 (125)
|.|+.+|++||.+- --.--+.||.+|+.|-..++ +.+...|+.|++.||....+
T Consensus 61 pIGrlLFr~Fc~~~~~~~~~i~Fl~~v~eYE~~~~-~~r~~~~~~i~~~~l~~~~~ 115 (591)
T KOG0986|consen 61 PIGRLLFRDFCENRPELRPAIEFLEEVKEYEKADD-DERKDKARQILDAYLMKELL 115 (591)
T ss_pred cHHHHHHHHHHhcCchhhhHHHHHHHHHHHhcCCc-ccchhhHHHHHHHHhhcccc
Confidence 99999999999971 11224689999999999885 56789999999999996544
No 8
>KOG3590|consensus
Probab=96.00 E-value=0.012 Score=48.72 Aligned_cols=32 Identities=25% Similarity=0.392 Sum_probs=30.0
Q ss_pred cccHHHHHHHHHHhhcHHHHHHHHHHHHhhcC
Q psy1257 64 GDTYKLFREFLRCEYSEENILFWLACEDLKKE 95 (125)
Q Consensus 64 ~~g~~~F~~FL~~e~s~ENl~Fw~a~e~~k~~ 95 (125)
|..+.+|-+||...---.-|.||+++|.||+.
T Consensus 122 ~~~LSYFiQYLD~r~~L~LIKFwl~~E~FKs~ 153 (602)
T KOG3590|consen 122 TIVLSYFIQYLDLRRMLHLIKFWLEAESFKST 153 (602)
T ss_pred chHHHHHHHHHHHHhHHHHHHHHHhhhhhhHH
Confidence 88899999999999999999999999999985
No 9
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=80.47 E-value=3.7 Score=24.54 Aligned_cols=36 Identities=8% Similarity=0.183 Sum_probs=29.1
Q ss_pred hhHHhhhhHHHHhcCccCCHHHHhHHHHHHHHHHhh
Q psy1257 2 SECRENIPTVLQTLCEKCTPSQTDKAVMVIRRLKKD 37 (125)
Q Consensus 2 ~~~k~~lpea~~~~C~kCt~~Qk~~~~kvi~~l~~~ 37 (125)
..|...||+++...+....+..++.+.++++-..++
T Consensus 25 ~~F~~~l~~~~~~~~~~~~~~~~~kv~rll~iW~~r 60 (64)
T PF04818_consen 25 PAFSPVLPDAFAHAYKNVDPEVRKKVQRLLNIWEER 60 (64)
T ss_dssp HHHHCCHHHHHHHHCCCS-HHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhCC
Confidence 467889999999999888999999999998765543
No 10
>PF11919 DUF3437: Domain of unknown function (DUF3437); InterPro: IPR021843 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 142 to 163 amino acids in length. ; PDB: 3L5Q_6 1VSY_5.
Probab=75.82 E-value=2.7 Score=27.50 Aligned_cols=47 Identities=17% Similarity=0.340 Sum_probs=36.8
Q ss_pred hhhHHHHhcCccCCHHHH--hHHHHHHHHHHhhChhHHHHHhhcCCCCc
Q psy1257 7 NIPTVLQTLCEKCTPSQT--DKAVMVIRRLKKDYPEEWKILLEKWDPKG 53 (125)
Q Consensus 7 ~lpea~~~~C~kCt~~Qk--~~~~kvi~~l~~~~P~~W~~l~~k~dP~~ 53 (125)
.+|++|..-|...+..|- ..+++.+..+...+.|.|..-..+|.++.
T Consensus 27 w~P~~l~~La~~~~~~~~I~~tvk~tl~eFkrtH~D~W~~~~~~Ft~~q 75 (90)
T PF11919_consen 27 WMPEVLEELARHANDPQPIRTTVKKTLSEFKRTHQDTWHEHKKKFTEDQ 75 (90)
T ss_dssp HHHHHHHHHHTTSSS-SSHHHHTHHHHHHHHHHTSTTHHHHGGG--SST
T ss_pred cHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHhCcccHHHHHHhCCHHH
Confidence 589999998888886553 77889999999999999987777777764
No 11
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=74.35 E-value=18 Score=22.41 Aligned_cols=70 Identities=17% Similarity=0.121 Sum_probs=48.4
Q ss_pred HHHHhcCccCCHHHHhHHHHHHHHHHhhChhHHHHHhhcCCCCchhhhhHHhhh-cccHHHHHHHHHHhhc
Q psy1257 10 TVLQTLCEKCTPSQTDKAVMVIRRLKKDYPEEWKILLEKWDPKGEYTRKFQEKF-GDTYKLFREFLRCEYS 79 (125)
Q Consensus 10 ea~~~~C~kCt~~Qk~~~~kvi~~l~~~~P~~W~~l~~k~dP~~~~v~kw~~s~-~~g~~~F~~FL~~e~s 79 (125)
+-|+..-...|+..+..++-++.+...-.--.-..+...-..+..-+.++...+ =.|...|+..|..+.+
T Consensus 5 ~~i~~~~~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~efk~~l~~~~~ 75 (77)
T PF01418_consen 5 EKIRSQYNSLSPTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFKEFKIALAQELS 75 (77)
T ss_dssp HHHHHHGGGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHHHHHHHHHCHHH
T ss_pred HHHHHHHhhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Confidence 445566677888887777666555544444445666677788888899999999 8899999999988765
No 12
>PF15182 OTOS: Otospiralin
Probab=72.15 E-value=6.4 Score=24.30 Aligned_cols=30 Identities=20% Similarity=0.363 Sum_probs=26.0
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHHHHHHHHc
Q psy1257 84 LFWLACEDLKKESNPDVIEEKARFIYEDYI 113 (125)
Q Consensus 84 ~Fw~a~e~~k~~~~~~~~~~~a~~Iy~~yi 113 (125)
+||--||.|+....-.++..+|+..|..|=
T Consensus 26 DFW~YveyFrtlGAY~~indmARtfFAh~p 55 (69)
T PF15182_consen 26 DFWNYVEYFRTLGAYNQINDMARTFFAHFP 55 (69)
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHHHhhCc
Confidence 799999999998877789999998887663
No 13
>PF02184 HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107 The HAT (Half A TPR) repeat has a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs (tetratricopeptide repeats), though they lack the highly conserved alanine and glycine residues found in TPRs. The number of HAT repeats found in different proteins varies between 9 and 12. HAT-repeat-containing proteins appear to be components of macromolecular complexes that are required for RNA processing []. The repeats may be involved in protein-protein interactions. The HAT motif has striking structural similarities to HEAT repeats (IPR000357 from INTERPRO), being of a similar length and consisting of two short helices connected by a loop domain, as in HEAT repeats.; GO: 0006396 RNA processing, 0005622 intracellular
Probab=64.58 E-value=5.3 Score=21.24 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=12.1
Q ss_pred HHHHHHHHHHcCCC
Q psy1257 103 EKARFIYEDYISIL 116 (125)
Q Consensus 103 ~~a~~Iy~~yi~~~ 116 (125)
..|+.||++||...
T Consensus 4 dRAR~IyeR~v~~h 17 (32)
T PF02184_consen 4 DRARSIYERFVLVH 17 (32)
T ss_pred HHHHHHHHHHHHhC
Confidence 57999999999864
No 14
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=58.65 E-value=11 Score=26.54 Aligned_cols=53 Identities=15% Similarity=0.201 Sum_probs=43.1
Q ss_pred HHHHhcCccCCHHHHhHHHHHHHHHHhhCh--hHHHHHhhcCCCCchhhhhHHhh
Q psy1257 10 TVLQTLCEKCTPSQTDKAVMVIRRLKKDYP--EEWKILLEKWDPKGEYTRKFQEK 62 (125)
Q Consensus 10 ea~~~~C~kCt~~Qk~~~~kvi~~l~~~~P--~~W~~l~~k~dP~~~~v~kw~~s 62 (125)
-+.+..|..|....-+...+|-+||.++.. ..-..+....+.+.+.+.+|-..
T Consensus 15 ~~~~~iCp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~Ire 69 (137)
T TIGR03826 15 KTGRDVCPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIRE 69 (137)
T ss_pred hcCCccCHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHc
Confidence 346678999999999999999999996655 56677777888888888888654
No 15
>PF14194 Cys_rich_VLP: Cysteine-rich VLP
Probab=45.98 E-value=21 Score=21.37 Aligned_cols=21 Identities=29% Similarity=0.453 Sum_probs=17.8
Q ss_pred CHHHHhHHHHHHHHHHhhChh
Q psy1257 20 TPSQTDKAVMVIRRLKKDYPE 40 (125)
Q Consensus 20 t~~Qk~~~~kvi~~l~~~~P~ 40 (125)
|+.|++.+.++++...-|+-+
T Consensus 1 T~~q~r~~~~LV~~~C~Nyd~ 21 (56)
T PF14194_consen 1 TPRQRRRIRKLVRRECCNYDD 21 (56)
T ss_pred CHHHHHHHHHHHHHHcccCCC
Confidence 789999999999988877655
No 16
>COG4790 EscR Type III secretory pathway, component EscR [Intracellular trafficking and secretion]
Probab=43.40 E-value=46 Score=25.05 Aligned_cols=40 Identities=18% Similarity=0.233 Sum_probs=30.9
Q ss_pred hhhhhHHhhhcccHHHHHHHHHHhhcHHHHHHHHHHHHhh
Q psy1257 54 EYTRKFQEKFGDTYKLFREFLRCEYSEENILFWLACEDLK 93 (125)
Q Consensus 54 ~~v~kw~~s~~~g~~~F~~FL~~e~s~ENl~Fw~a~e~~k 93 (125)
.....|......|..-+|+||+|.-.+|+..|+....+=+
T Consensus 83 ~~~~~~~~~~~~~l~pyR~fL~k~t~~~~~~FF~~~~~~~ 122 (214)
T COG4790 83 TNIASVVKFDDKGLSPYRDFLKKNTEEEEVSFFERSAQKK 122 (214)
T ss_pred CcHHHHHHHHHhhhhHHHHHHHHhCcHHHHHHHHHHHHHh
Confidence 3334444444889999999999999999999998876443
No 17
>PF08910 Aida_N: Aida N-terminus; InterPro: IPR015006 This entry represents the axin interactor, dorsalization-associated protein family AIDA [].; PDB: 1UG7_A.
Probab=42.26 E-value=50 Score=22.34 Aligned_cols=32 Identities=13% Similarity=0.065 Sum_probs=21.4
Q ss_pred HHhhhhHHHHh-cCccCCHHHHhHHHHHHHHHH
Q psy1257 4 CRENIPTVLQT-LCEKCTPSQTDKAVMVIRRLK 35 (125)
Q Consensus 4 ~k~~lpea~~~-~C~kCt~~Qk~~~~kvi~~l~ 35 (125)
|-..|..++.. ++..+|+.||+.+.||..-|.
T Consensus 31 La~~l~k~~~~~~~~~fte~qkk~i~Kia~cL~ 63 (106)
T PF08910_consen 31 LARQLKKEVQSHQDSDFTEDQKKTIGKIATCLE 63 (106)
T ss_dssp HHHHHHHHHT-SS--SS-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhcccCCCCCHHHHHHHHHHHHHHH
Confidence 44556666666 999999999999999876654
No 18
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=40.66 E-value=47 Score=21.92 Aligned_cols=34 Identities=9% Similarity=0.080 Sum_probs=27.9
Q ss_pred hHHhhhhHHHHhcCccCCHHHHhHHHHHHHHHHh
Q psy1257 3 ECRENIPTVLQTLCEKCTPSQTDKAVMVIRRLKK 36 (125)
Q Consensus 3 ~~k~~lpea~~~~C~kCt~~Qk~~~~kvi~~l~~ 36 (125)
.|...+++++...+..+.+..++.+.++++-..+
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~~ki~kll~iW~~ 107 (121)
T smart00582 74 ELGPVFQDALRDVLGAANDETKKKIRRLLNIWEE 107 (121)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHhc
Confidence 4566888999999999999999999998866554
No 19
>PF13713 BRX_N: Transcription factor BRX N-terminal domain
Probab=39.56 E-value=15 Score=20.33 Aligned_cols=19 Identities=21% Similarity=0.728 Sum_probs=14.0
Q ss_pred ChhHHhhhhHHHHhcCccCC
Q psy1257 1 MSECRENIPTVLQTLCEKCT 20 (125)
Q Consensus 1 ~~~~k~~lpea~~~~C~kCt 20 (125)
|+++..-+|.+.+ .|..||
T Consensus 21 lK~maekl~~~~~-~~k~~~ 39 (39)
T PF13713_consen 21 LKDMAEKLPGAYR-NCKPCS 39 (39)
T ss_pred HHHHHHhCchhhh-ccCCCC
Confidence 4667777887777 788775
No 20
>KOG3364|consensus
Probab=36.21 E-value=33 Score=24.54 Aligned_cols=70 Identities=13% Similarity=0.160 Sum_probs=46.0
Q ss_pred hhhhHHHHhcCccCCHHHHhHHHHHHHHHHhhChhHHHHHhhcCCCCchhhhhHHhhh---------cccHHHHHHHHHH
Q psy1257 6 ENIPTVLQTLCEKCTPSQTDKAVMVIRRLKKDYPEEWKILLEKWDPKGEYTRKFQEKF---------GDTYKLFREFLRC 76 (125)
Q Consensus 6 ~~lpea~~~~C~kCt~~Qk~~~~kvi~~l~~~~P~~W~~l~~k~dP~~~~v~kw~~s~---------~~g~~~F~~FL~~ 76 (125)
..+|+++.+.-..|-.-|.+.++- |++.+-.-.++--+ ..|...|.+-+++
T Consensus 5 ~~~p~a~~d~~~~~e~~~rq~a~~--------------------~~s~~s~f~lAwaLV~S~~~~dv~~GI~iLe~l~~~ 64 (149)
T KOG3364|consen 5 LKEPWAIEDLIAGQEEILRQAARS--------------------DVSKQSQFNLAWALVRSRDTEDVQEGIVILEDLLKS 64 (149)
T ss_pred ccchhhhhhhhHHHHHHHHHHHhc--------------------cchHHHHHHHHHHHHcccchHHHHHhHHHHHHHhhh
Confidence 456777777777776666666642 33322222222222 6799999999998
Q ss_pred hhcHHHH--HHHHHHHHhhcC
Q psy1257 77 EYSEENI--LFWLACEDLKKE 95 (125)
Q Consensus 77 e~s~ENl--~Fw~a~e~~k~~ 95 (125)
++.++-. .|++|+-.||-.
T Consensus 65 ~~~~~rRe~lyYLAvg~yRlk 85 (149)
T KOG3364|consen 65 AHPERRRECLYYLAVGHYRLK 85 (149)
T ss_pred cCcccchhhhhhhHHHHHHHh
Confidence 8877654 899999988864
No 21
>KOG0210|consensus
Probab=35.25 E-value=24 Score=31.82 Aligned_cols=89 Identities=16% Similarity=0.238 Sum_probs=43.2
Q ss_pred hhhhHHHHhcCccCCHHHHhHHHHHHHHHHhhChhHHHHHhhcCCCCchhhhhHHhhh--cccH--HHHHHHHHHhhcH-
Q psy1257 6 ENIPTVLQTLCEKCTPSQTDKAVMVIRRLKKDYPEEWKILLEKWDPKGEYTRKFQEKF--GDTY--KLFREFLRCEYSE- 80 (125)
Q Consensus 6 ~~lpea~~~~C~kCt~~Qk~~~~kvi~~l~~~~P~~W~~l~~k~dP~~~~v~kw~~s~--~~g~--~~F~~FL~~e~s~- 80 (125)
++.-+.=.--|-.|||.||..+..+++-...++--..-+ -.-|.+.-....-+... ..|. .+=.+|--++||.
T Consensus 751 el~~~~~aVv~CRctPtQKA~v~~llq~~t~krvc~IGD--GGNDVsMIq~A~~GiGI~gkEGkQASLAADfSItqF~Hv 828 (1051)
T KOG0210|consen 751 ELVCELPAVVCCRCTPTQKAQVVRLLQKKTGKRVCAIGD--GGNDVSMIQAADVGIGIVGKEGKQASLAADFSITQFSHV 828 (1051)
T ss_pred HHHHhcCcEEEEecChhHHHHHHHHHHHhhCceEEEEcC--CCccchheeecccceeeecccccccchhccccHHHHHHH
Confidence 333333344677999999999987765544322211100 00111111111111111 2332 1223455666654
Q ss_pred HHHHHHHHHHHhhcCC
Q psy1257 81 ENILFWLACEDLKKES 96 (125)
Q Consensus 81 ENl~Fw~a~e~~k~~~ 96 (125)
--|++|--=..||+..
T Consensus 829 ~rLLl~HGR~SYkrsa 844 (1051)
T KOG0210|consen 829 SRLLLWHGRNSYKRSA 844 (1051)
T ss_pred HHHhhccccchHHHHH
Confidence 3478887777787754
No 22
>PF12725 DUF3810: Protein of unknown function (DUF3810); InterPro: IPR024294 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 333 and 377 amino acids in length and contain a conserved HEXXH sequence motif that is characteristic of metallopeptidases. This family may therefore belong to an as yet uncharacterised family of peptidase enzymes.
Probab=35.14 E-value=96 Score=24.70 Aligned_cols=31 Identities=35% Similarity=0.689 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHcCCCCC
Q psy1257 80 EENILFWLACEDLKKESNPDVIEEKARFIYEDYISILSP 118 (125)
Q Consensus 80 ~ENl~Fw~a~e~~k~~~~~~~~~~~a~~Iy~~yi~~~sp 118 (125)
.+|-.||..-+. .+...+..+|++||..|..
T Consensus 272 ~~~~~fW~~y~~--------~i~~~~~~~yd~yLKaN~q 302 (318)
T PF12725_consen 272 KENRAFWQKYEG--------PIEEVSDFVYDTYLKANNQ 302 (318)
T ss_pred HHHHHHHHHhcc--------hHHHHHHHHHHHHHHhcCc
Confidence 356678854442 3567788999999998753
No 23
>PLN03190 aminophospholipid translocase; Provisional
Probab=33.58 E-value=46 Score=31.35 Aligned_cols=30 Identities=20% Similarity=0.397 Sum_probs=20.4
Q ss_pred HHhhhhHHHHh----cCccCCHHHHhHHHHHHHH
Q psy1257 4 CRENIPTVLQT----LCEKCTPSQTDKAVMVIRR 33 (125)
Q Consensus 4 ~k~~lpea~~~----~C~kCt~~Qk~~~~kvi~~ 33 (125)
+++.+.+++.. -|.+|||.||..+.++++.
T Consensus 835 ~~~~f~~l~~~~~~VI~cR~sP~QKa~IV~~vk~ 868 (1178)
T PLN03190 835 LEEQLFQLASKCSVVLCCRVAPLQKAGIVALVKN 868 (1178)
T ss_pred HHHHHHHHHHhCCEEEEecCCHHHHHHHHHHHHh
Confidence 34445555543 4789999999888776654
No 24
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=31.29 E-value=38 Score=23.12 Aligned_cols=45 Identities=22% Similarity=0.366 Sum_probs=34.0
Q ss_pred HHhhhhHHHHhcCccCCHHHHhHHHHHHHHHHhhChhHHHHHhhcC
Q psy1257 4 CRENIPTVLQTLCEKCTPSQTDKAVMVIRRLKKDYPEEWKILLEKW 49 (125)
Q Consensus 4 ~k~~lpea~~~~C~kCt~~Qk~~~~kvi~~l~~~~P~~W~~l~~k~ 49 (125)
|+.++|..-.... -||+-.--.+..++..|+++.|+.++.+...|
T Consensus 31 f~~~~p~~~~~r~-~csDDdgl~Id~~v~~L~~~~~~~~~ll~~~Y 75 (125)
T PF06530_consen 31 FKGVLPSSSKSRP-SCSDDDGLLIDRCVARLKKRDPEEYDLLILYY 75 (125)
T ss_pred HhcCCCCCCCCCc-eechHHHHHHHHHHHHHHccCHHHHHHHHHHH
Confidence 4555665332222 48888888999999999999999999888654
No 25
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=31.22 E-value=22 Score=29.08 Aligned_cols=14 Identities=36% Similarity=0.921 Sum_probs=12.4
Q ss_pred hcCCCCchhhhhHH
Q psy1257 47 EKWDPKGEYTRKFQ 60 (125)
Q Consensus 47 ~k~dP~~~~v~kw~ 60 (125)
.+|||+|+|+++|-
T Consensus 413 ~k~Dp~g~yir~wv 426 (429)
T TIGR02765 413 QDYDPDGEYVATWV 426 (429)
T ss_pred HhcCCCCCcHHHhc
Confidence 58999999999994
No 26
>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]
Probab=29.18 E-value=33 Score=25.93 Aligned_cols=17 Identities=29% Similarity=0.517 Sum_probs=12.8
Q ss_pred Hhh-cHHHHHHHHHHHHh
Q psy1257 76 CEY-SEENILFWLACEDL 92 (125)
Q Consensus 76 ~e~-s~ENl~Fw~a~e~~ 92 (125)
.|. ..|||.||.+.-..
T Consensus 88 ~eLTa~ENL~F~~~~~~~ 105 (209)
T COG4133 88 TELTALENLHFWQRFHGS 105 (209)
T ss_pred chhhHHHHHHHHHHHhCC
Confidence 444 46999999987665
No 27
>KOG0063|consensus
Probab=29.05 E-value=50 Score=28.30 Aligned_cols=32 Identities=6% Similarity=-0.109 Sum_probs=29.4
Q ss_pred cccHHHHHHHHHHhhcHHHHHHHHHHHHhhcC
Q psy1257 64 GDTYKLFREFLRCEYSEENILFWLACEDLKKE 95 (125)
Q Consensus 64 ~~g~~~F~~FL~~e~s~ENl~Fw~a~e~~k~~ 95 (125)
-.++..+|-+|..+.+++++.+|+.+..|...
T Consensus 494 ~AskvikRfilhakktafvVEhdfImaTYlad 525 (592)
T KOG0063|consen 494 IASKVIKRFILHAKKTAFVVEHDFIMATYLAD 525 (592)
T ss_pred HHHHHHHHHHHhccchhhhhhhHHHHHHhhcc
Confidence 46788999999999999999999999999874
No 28
>KOG4304|consensus
Probab=28.28 E-value=76 Score=24.55 Aligned_cols=15 Identities=27% Similarity=0.468 Sum_probs=13.4
Q ss_pred ChhHHhhhhHHHHhc
Q psy1257 1 MSECRENIPTVLQTL 15 (125)
Q Consensus 1 ~~~~k~~lpea~~~~ 15 (125)
|.+||++|||++.+.
T Consensus 51 L~eLK~Li~e~~~~~ 65 (250)
T KOG4304|consen 51 LDELKDLIPEALKKD 65 (250)
T ss_pred HHHHHHHHHHHHhhc
Confidence 468999999999987
No 29
>PF01805 Surp: Surp module; InterPro: IPR000061 SWAP is derived from the Suppressor-of-White-APricot splicing regulator from Drosophila melanogaster. The domain is found in regulators responsible for pervasive, nonsex-specific alternative pre-mRNA splicing characteristics and has been found in splicing regulatory proteins []. These ancient, conserved SWAP proteins share a colinearly arrayed series of novel sequence motifs [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 2E5Z_A 2DT7_B 2DT6_A 1UG0_A 1X4P_A 2E60_A 1X4O_A 4DGW_B.
Probab=27.76 E-value=1.2e+02 Score=17.39 Aligned_cols=30 Identities=20% Similarity=0.114 Sum_probs=24.9
Q ss_pred HHhHHHHHHHHHHhhChhHHHHHhhcC--CCC
Q psy1257 23 QTDKAVMVIRRLKKDYPEEWKILLEKW--DPK 52 (125)
Q Consensus 23 Qk~~~~kvi~~l~~~~P~~W~~l~~k~--dP~ 52 (125)
|++.|+++..++.++=|+.+..+..+. ||.
T Consensus 1 ~~~~I~~tA~~Va~~G~~fE~~l~~~~~~np~ 32 (55)
T PF01805_consen 1 LREIIDKTAEFVAKNGPEFEEKLRERERNNPQ 32 (55)
T ss_dssp HHHHHHHHHHHHHHCSHHHHHHHHHHTTTSGG
T ss_pred ChHHHHHHHHHHHhcCHHHHHHHHHhcCCCCC
Confidence 578899999999999999998888655 553
No 30
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=26.97 E-value=1.5e+02 Score=17.70 Aligned_cols=29 Identities=21% Similarity=0.432 Sum_probs=19.4
Q ss_pred HHHHhhChhHHHHHhhcCCCCc-hhhhhHHh
Q psy1257 32 RRLKKDYPEEWKILLEKWDPKG-EYTRKFQE 61 (125)
Q Consensus 32 ~~l~~~~P~~W~~l~~k~dP~~-~~v~kw~~ 61 (125)
..+....|+.|+.+. .|+|=. +....|..
T Consensus 6 t~~I~~~p~l~ekIL-~YePI~L~el~~~L~ 35 (64)
T PF09494_consen 6 TKLIRSDPELYEKIL-MYEPINLEELHAWLK 35 (64)
T ss_pred HHHHHcCHHHHHHHH-cCCCccHHHHHHHHH
Confidence 344558888888876 788843 55556655
No 31
>PF07583 PSCyt2: Protein of unknown function (DUF1549); InterPro: IPR011444 The function is not known. It is found associated with IPR022655 from INTERPRO. It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=26.83 E-value=1.3e+02 Score=22.48 Aligned_cols=51 Identities=16% Similarity=0.307 Sum_probs=34.1
Q ss_pred HHHHHHHhhChhHHHHHhhcCCCCchhhhhHHhhh--------c---------ccHHHHHHHHHHhhc
Q psy1257 29 MVIRRLKKDYPEEWKILLEKWDPKGEYTRKFQEKF--------G---------DTYKLFREFLRCEYS 79 (125)
Q Consensus 29 kvi~~l~~~~P~~W~~l~~k~dP~~~~v~kw~~s~--------~---------~g~~~F~~FL~~e~s 79 (125)
.|-.++....|+-|..++...--+..|...|+.-+ . .+...|+.+|...+.
T Consensus 44 Ev~~Fl~d~~~~kr~~lVd~LL~sp~y~e~wa~~W~D~lr~~~~~~~~~d~~~~~~~~~r~wl~~a~~ 111 (208)
T PF07583_consen 44 EVRAFLADPSPDKREKLVDRLLASPEYAERWARHWLDLLRYADSGGYESDNRRPNAWPYRDWLIDAFN 111 (208)
T ss_pred HHHHHHhCCChhHHHHHHHHHHCCcHHHHHHHHHHHHHHccCCCCCCcccccccchhhHHHHHHHHHH
Confidence 34455667788888887777655557888877776 1 245677777776653
No 32
>PF04512 Baculo_PEP_N: Baculovirus polyhedron envelope protein, PEP, N terminus; InterPro: IPR007600 Polyhedra are large crystalline occlusion bodies containing nucleopolyhedrovirus virions, and surrounded by an electron-dense structure called the polyhedron envelope or polyhedron calyx. The polyhedron envelope (associated) protein PEP is thought to be an integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper formation of the periphery of polyhedra. It is thought that PEP may stabilise polyhedra and protect them from fusion or aggregation [].; GO: 0005198 structural molecule activity, 0019028 viral capsid, 0019031 viral envelope
Probab=26.17 E-value=73 Score=21.14 Aligned_cols=54 Identities=9% Similarity=0.116 Sum_probs=36.1
Q ss_pred HHHHHHhhChhHHHHHhhcCCCCchhhhhHHhhhcccHH--HHHHHHHHhhcHHHH
Q psy1257 30 VIRRLKKDYPEEWKILLEKWDPKGEYTRKFQEKFGDTYK--LFREFLRCEYSEENI 83 (125)
Q Consensus 30 vi~~l~~~~P~~W~~l~~k~dP~~~~v~kw~~s~~~g~~--~F~~FL~~e~s~ENl 83 (125)
+++.+-.++...|+++...+|...-++..++..+=.|+. .+..+|..-|=.|++
T Consensus 32 ~l~~iP~~~kk~w~dl~~~~~s~K~Fit~lGv~~L~~r~~~~~~d~l~~~fi~d~~ 87 (97)
T PF04512_consen 32 ALQSIPRSHKKLWKDLEPCVDSNKLFITALGVGVLCNRTNSKLADYLANIFIADVY 87 (97)
T ss_pred HHHHcCHHHHHHHHHhcccCCCceeeeeHHHHHHHHhhcchHHHHHHHHHHHHHHH
Confidence 344667788889999999999999999988877633332 444444444433333
No 33
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=25.79 E-value=1.3e+02 Score=21.61 Aligned_cols=34 Identities=24% Similarity=0.398 Sum_probs=28.5
Q ss_pred HhhhhHHHHhcCccCCHHHHhHHHHHHHHHHhhCh
Q psy1257 5 RENIPTVLQTLCEKCTPSQTDKAVMVIRRLKKDYP 39 (125)
Q Consensus 5 k~~lpea~~~~C~kCt~~Qk~~~~kvi~~l~~~~P 39 (125)
=+.+||.|+..|+ =+|.|...++++|+-++..--
T Consensus 110 LetlPD~LERd~g-L~p~~v~~vQ~~iD~lR~~l~ 143 (152)
T PF07278_consen 110 LETLPDILERDAG-LPPEQVARVQSVIDDLRDQLA 143 (152)
T ss_pred HHHhhHHHHhcCC-CCHHHHHHHHHHHHHHHHHHH
Confidence 3578999999997 489999999999998886543
No 34
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=25.44 E-value=32 Score=28.58 Aligned_cols=18 Identities=39% Similarity=0.794 Sum_probs=15.7
Q ss_pred hhcCCCCchhhhhHHhhh
Q psy1257 46 LEKWDPKGEYTRKFQEKF 63 (125)
Q Consensus 46 ~~k~dP~~~~v~kw~~s~ 63 (125)
..+|||+|+|+++|--.|
T Consensus 409 ~~~~Dp~g~yir~wvPeL 426 (475)
T TIGR02766 409 GYKFDPNGEYVRRWLPEL 426 (475)
T ss_pred HhhcCCCcccHHHhChhh
Confidence 358999999999998776
No 35
>PHA02754 hypothetical protein; Provisional
Probab=25.14 E-value=25 Score=21.35 Aligned_cols=11 Identities=18% Similarity=0.365 Sum_probs=7.3
Q ss_pred ChhHHhhhhHH
Q psy1257 1 MSECRENIPTV 11 (125)
Q Consensus 1 ~~~~k~~lpea 11 (125)
||+||++|.++
T Consensus 20 MRelkD~LSe~ 30 (67)
T PHA02754 20 MRELKDILSEA 30 (67)
T ss_pred HHHHHHHHhhC
Confidence 56777777664
No 36
>PF09764 Nt_Gln_amidase: N-terminal glutamine amidase; InterPro: IPR019161 This entry represents the Protein N-terminal glutamine amidohydrolase (NtQ-amidase) family of proteins. They contain a region of approximately 200 residues carrying several distinctive motifs including a WDYHV motif and one of three cysteines. Protein N-terminal glutamine amidohydrolase is responsible for degradation of N-terminal glutamine [].; GO: 0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides; PDB: 3C9Q_A.
Probab=25.09 E-value=48 Score=24.57 Aligned_cols=16 Identities=44% Similarity=0.833 Sum_probs=11.8
Q ss_pred hhcHHHHHHHHHHHHhhc
Q psy1257 77 EYSEENILFWLACEDLKK 94 (125)
Q Consensus 77 e~s~ENl~Fw~a~e~~k~ 94 (125)
=|||||+ |.-|+.++.
T Consensus 5 cYCEENV--ykLce~~~~ 20 (184)
T PF09764_consen 5 CYCEENV--YKLCEYLRE 20 (184)
T ss_dssp T-HHHHH--HHHHHHHHH
T ss_pred cccHHHH--HHHHHHHHh
Confidence 4899999 778888743
No 37
>PF10589 NADH_4Fe-4S: NADH-ubiquinone oxidoreductase-F iron-sulfur binding region; InterPro: IPR019575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the F subunit of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2. This entry represents the iron-sulphur binding domain of the F subunit.; GO: 0055114 oxidation-reduction process; PDB: 3IAS_S 2FUG_A 3I9V_A 3M9S_1 3IAM_A 2YBB_1.
Probab=24.37 E-value=46 Score=18.75 Aligned_cols=14 Identities=36% Similarity=0.781 Sum_probs=6.3
Q ss_pred HHHHhcCccCCHHH
Q psy1257 10 TVLQTLCEKCTPSQ 23 (125)
Q Consensus 10 ea~~~~C~kCt~~Q 23 (125)
=.-...|.+|+|=-
T Consensus 10 f~~~ESCGkC~PCR 23 (46)
T PF10589_consen 10 FFAHESCGKCTPCR 23 (46)
T ss_dssp HHHHH--S--HHHH
T ss_pred HHHHcCCCCCCCcH
Confidence 34567899998843
No 38
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=24.11 E-value=1.3e+02 Score=21.39 Aligned_cols=45 Identities=24% Similarity=0.338 Sum_probs=26.6
Q ss_pred hhHHhhhhHHHHhcCccCCHHHHhHHHHH-------------HHHHHhhChhHHHHHh
Q psy1257 2 SECRENIPTVLQTLCEKCTPSQTDKAVMV-------------IRRLKKDYPEEWKILL 46 (125)
Q Consensus 2 ~~~k~~lpea~~~~C~kCt~~Qk~~~~kv-------------i~~l~~~~P~~W~~l~ 46 (125)
.++|+.||.=+.+.=..=|+.+|..++.| +..|+++.|.....+.
T Consensus 4 ~~~k~~iP~ev~~~~~~Lt~eeK~~lkev~~~~~~~~~~de~i~~LK~ksP~L~~k~~ 61 (154)
T PF05823_consen 4 EEYKELIPSEVVEFYKNLTPEEKAELKEVAKNYAKFKNEDEMIAALKEKSPSLYEKAE 61 (154)
T ss_dssp HHHHTT--HHHHHHHHH--TTTHHHHHHHHTT-------TTHHHHHHHH-HHHHHHHH
T ss_pred HHHHHhCcHHHHHHHHcCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCHHHHHHHH
Confidence 56788888777777777777777666554 4555677777775533
No 39
>TIGR02887 spore_ger_x_C germination protein, Ger(x)C family. Members of this protein family are restricted to endospore-forming members of the Firmicutes lineage of bacteria, including the genera Bacillus, Clostridium, Thermoanaerobacter, Carboxydothermus, etc. Members are nearly all predicted lipoproteins and belong to probable transport operons, some of which have been characterized as crucial to germination in response to alanine. Members typically have been gene symbols gerKC, gerAC, gerYC, etc.
Probab=23.68 E-value=35 Score=27.18 Aligned_cols=45 Identities=16% Similarity=0.151 Sum_probs=30.4
Q ss_pred hhHHhhhhHHHHhcCccCCHH-HHhHHH--HHHHHHHhhChhHHHHHh
Q psy1257 2 SECRENIPTVLQTLCEKCTPS-QTDKAV--MVIRRLKKDYPEEWKILL 46 (125)
Q Consensus 2 ~~~k~~lpea~~~~C~kCt~~-Qk~~~~--kvi~~l~~~~P~~W~~l~ 46 (125)
++|++.+-+.|+..|.+--.+ |+.+++ .+-++++.++|+.|+.+.
T Consensus 297 ~~le~~~e~~i~~~~~~~i~k~Q~~~~D~~g~g~~~~~~~p~~wk~~~ 344 (371)
T TIGR02887 297 KKIEKEAEKEIEKEIEQLIKKLQKYKIDPLGLGDELYRKHPKLWKKVK 344 (371)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHhChHHHHhhh
Confidence 456777777777777776544 554443 666777888888887543
No 40
>PF09759 Atx10homo_assoc: Spinocerebellar ataxia type 10 protein domain; InterPro: IPR019156 This is the conserved C-terminal 100 residues of Ataxin-10. Ataxin-10 belongs to the family of armadillo repeat proteins and in solution it tends to form homotrimeric complexes, which associate via a tip-to-tip association in a horseshoe-shaped contact with the concave sides of the molecules facing each other. This domain may represent the homo-association site since that is located near the C terminus of Ataxin-10. The protein does not contain a signal sequence for secretion or any subcellular compartment confirming its cytoplasmic localisation, specifically to the olivocerebellar region [].
Probab=23.65 E-value=1.3e+02 Score=20.05 Aligned_cols=69 Identities=19% Similarity=0.223 Sum_probs=47.3
Q ss_pred HHhhhhHHHHhcCccCCHHHHhHHHHHHHHHHhhChhHHHHHhh--cCCCCchhhhhHHhhhcccHHHHHHHHHHhhcHH
Q psy1257 4 CRENIPTVLQTLCEKCTPSQTDKAVMVIRRLKKDYPEEWKILLE--KWDPKGEYTRKFQEKFGDTYKLFREFLRCEYSEE 81 (125)
Q Consensus 4 ~k~~lpea~~~~C~kCt~~Qk~~~~kvi~~l~~~~P~~W~~l~~--k~dP~~~~v~kw~~s~~~g~~~F~~FL~~e~s~E 81 (125)
||..+=.+|.+.|-+|...|-..... +-...+.. .+|+..-+.+.|+.. .-=---|-+.|
T Consensus 2 ~K~~lvrlianl~~~~~~~Qd~vr~~----------~Gi~liL~~c~iD~~nP~irEwai~--------aiRnL~e~n~e 63 (102)
T PF09759_consen 2 FKRDLVRLIANLCYKNKEVQDLVREL----------GGIPLILSCCNIDDHNPFIREWAIF--------AIRNLCEGNPE 63 (102)
T ss_pred cHHHHHHHHHHHHhCCHHHHHHHHHc----------CChHHHHHhcCCCcccHHHHHHHHH--------HHHHHHhCCHH
Confidence 68888999999999998888765421 22333332 579999999999654 21122367888
Q ss_pred HHHHHHHHH
Q psy1257 82 NILFWLACE 90 (125)
Q Consensus 82 Nl~Fw~a~e 90 (125)
|-.|--..+
T Consensus 64 NQ~~I~~L~ 72 (102)
T PF09759_consen 64 NQEFIAQLE 72 (102)
T ss_pred HHHHHHhcc
Confidence 888776555
No 41
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=23.47 E-value=2.5e+02 Score=21.63 Aligned_cols=45 Identities=18% Similarity=0.417 Sum_probs=31.3
Q ss_pred cccHHHHHHHHHHhhcH---HHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHc
Q psy1257 64 GDTYKLFREFLRCEYSE---ENILFWLACEDLKKESNPDVIEEKARFIYEDYI 113 (125)
Q Consensus 64 ~~g~~~F~~FL~~e~s~---ENl~Fw~a~e~~k~~~~~~~~~~~a~~Iy~~yi 113 (125)
......|..|+..-=.+ .|..||++--.|..... ..|...|.+++
T Consensus 160 ~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~~~g~~-----~~A~~~f~~vv 207 (263)
T PRK10803 160 DDAIVAFQNFVKKYPDSTYQPNANYWLGQLNYNKGKK-----DDAAYYFASVV 207 (263)
T ss_pred HHHHHHHHHHHHHCcCCcchHHHHHHHHHHHHHcCCH-----HHHHHHHHHHH
Confidence 45578899999876444 58999999888876442 34445566665
No 42
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=23.35 E-value=1e+02 Score=14.61 Aligned_cols=18 Identities=39% Similarity=0.693 Sum_probs=13.2
Q ss_pred HHhHHHHHHHHHHhhChh
Q psy1257 23 QTDKAVMVIRRLKKDYPE 40 (125)
Q Consensus 23 Qk~~~~kvi~~l~~~~P~ 40 (125)
+.+.+..+++.+.+++|+
T Consensus 15 ~~~~A~~~~~~~~~~~P~ 32 (33)
T PF13174_consen 15 DYDEAIEYFQRLIKRYPD 32 (33)
T ss_dssp HHHHHHHHHHHHHHHSTT
T ss_pred CHHHHHHHHHHHHHHCcC
Confidence 456677778888888886
No 43
>PRK10410 hypothetical protein; Provisional
Probab=23.06 E-value=85 Score=20.90 Aligned_cols=21 Identities=33% Similarity=0.757 Sum_probs=17.6
Q ss_pred HhcCccC-----CHHHHhHHHHHHHH
Q psy1257 13 QTLCEKC-----TPSQTDKAVMVIRR 33 (125)
Q Consensus 13 ~~~C~kC-----t~~Qk~~~~kvi~~ 33 (125)
.+.|.+| .|.+++.+++|++|
T Consensus 56 Kp~C~~C~ihCY~p~~r~ki~~VMr~ 81 (100)
T PRK10410 56 KPTCKKCPVHCYKPAKREKMKQVMRF 81 (100)
T ss_pred CCCCCCCCCcCCCHHHHHHHHHHHHH
Confidence 4678888 48899999999887
No 44
>PHA00447 lysozyme
Probab=23.04 E-value=86 Score=21.92 Aligned_cols=24 Identities=29% Similarity=0.477 Sum_probs=21.2
Q ss_pred cCCHHHHhHHHHHHHHHHhhChhH
Q psy1257 18 KCTPSQTDKAVMVIRRLKKDYPEE 41 (125)
Q Consensus 18 kCt~~Qk~~~~kvi~~l~~~~P~~ 41 (125)
.=|+.|.+.+..++.+|...+|..
T Consensus 93 ~~T~aQ~~al~~Ll~~L~~~~~~~ 116 (142)
T PHA00447 93 NFTPAQMQSLKSLLVTLKAKYPGA 116 (142)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCC
Confidence 349999999999999999999864
No 45
>PF10774 DUF4226: Domain of unknown function (DUF4226); InterPro: IPR019710 This entry represents an uncharacterised family of proteins belonging to Mycobacteria. It was previously incorrectly annotated as Biofilm regulator BssS (also known as YliH).
Probab=22.72 E-value=45 Score=22.70 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=16.9
Q ss_pred hhhHHhhh--cccHHHHHHHHHHhh
Q psy1257 56 TRKFQEKF--GDTYKLFREFLRCEY 78 (125)
Q Consensus 56 v~kw~~s~--~~g~~~F~~FL~~e~ 78 (125)
+..|..++ |.|...|..||....
T Consensus 60 v~~~~~aldTPaG~r~f~~fL~~kl 84 (112)
T PF10774_consen 60 VAAQAPALDTPAGAREFQRFLRGKL 84 (112)
T ss_pred HHhcccccCCHHHHHHHHHHHHHHH
Confidence 33444445 999999999998654
No 46
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=22.22 E-value=1.1e+02 Score=19.88 Aligned_cols=22 Identities=14% Similarity=0.216 Sum_probs=16.4
Q ss_pred ccCCHHHHhHHHHHHHHHHhhC
Q psy1257 17 EKCTPSQTDKAVMVIRRLKKDY 38 (125)
Q Consensus 17 ~kCt~~Qk~~~~kvi~~l~~~~ 38 (125)
.+|.+..++.+.++++-..++.
T Consensus 89 ~~~~~~~r~kl~rl~~iW~~~~ 110 (114)
T cd03562 89 EKVDEKTRKKLERLLNIWEERF 110 (114)
T ss_pred HhCCHHHHHHHHHHHHHccCCC
Confidence 4888888888888877655543
No 47
>PF03441 FAD_binding_7: FAD binding domain of DNA photolyase from Prosite.; InterPro: IPR005101 This entry represents a multi-helical domain composed of two all-alpha subdomains that is found as the C-terminal domain in cryptochrome proteins, as well as at the N-terminal of DNA photolyase where it acts as a FAD-binding domain (the N-terminal of DNA photolyase binds a light-harvesting cofactor). Photolyases and cryptochromes are related flavoproteins that bind FAD. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes (CRY1 and CRY2) are blue light photoreceptors that mediate blue light-induced gene expression [, ]. DNA photolyases are DNA repair enzymes that repair mismatched pyrimidine dimers induced by exposure to ultra-violet light. They bind to UV-damaged DNA containing pyrimidine dimers and, upon absorbing a near-UV photon (300 to 500 nm), they catalyse dimer splitting, breaking the cyclobutane ring joining the two pyrimidines of the dimer so as to split them into the constituent monomers; this process is called photoreactivation. DNA photolyases require two choromophore-cofactors for their activity. All monomers contain a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm [, ].; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 3ZXS_A 1DNP_A 2XRZ_B 2XRY_A 2VTB_A 2J4D_B 2IJG_X 3TVS_A 2E0I_D ....
Probab=21.38 E-value=38 Score=26.21 Aligned_cols=17 Identities=41% Similarity=0.987 Sum_probs=14.8
Q ss_pred hcCCCCchhhhhHHhhh
Q psy1257 47 EKWDPKGEYTRKFQEKF 63 (125)
Q Consensus 47 ~k~dP~~~~v~kw~~s~ 63 (125)
.++||+++|+++|-=.|
T Consensus 209 ~~~Dp~g~~ir~w~PeL 225 (277)
T PF03441_consen 209 KKFDPDGEYIRRWVPEL 225 (277)
T ss_dssp HHHSTTSHHHHHHSGGG
T ss_pred HhhCcHHHHHHHHHHHH
Confidence 47999999999997665
No 48
>PRK15482 transcriptional regulator MurR; Provisional
Probab=21.20 E-value=2.8e+02 Score=21.13 Aligned_cols=53 Identities=19% Similarity=0.209 Sum_probs=36.7
Q ss_pred HHHHHHHHHhhChhH----HHHHhhcCCCCchhhhhHHhhh-cccHHHHHHHHHHhhc
Q psy1257 27 AVMVIRRLKKDYPEE----WKILLEKWDPKGEYTRKFQEKF-GDTYKLFREFLRCEYS 79 (125)
Q Consensus 27 ~~kvi~~l~~~~P~~----W~~l~~k~dP~~~~v~kw~~s~-~~g~~~F~~FL~~e~s 79 (125)
-++|.+|+.++..+. -..+...-..+..-+.++...+ =.|...|+..|..|+.
T Consensus 18 e~~Ia~yIl~n~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk~~l~~~~~ 75 (285)
T PRK15482 18 EQKIADFLRANVSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELRMALIGEYS 75 (285)
T ss_pred HHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHHHHHHHHHh
Confidence 345556666543332 2345556667777888999999 7899999999988765
No 49
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=21.06 E-value=2.3e+02 Score=19.01 Aligned_cols=17 Identities=29% Similarity=0.448 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHcC
Q psy1257 98 PDVIEEKARFIYEDYIS 114 (125)
Q Consensus 98 ~~~~~~~a~~Iy~~yi~ 114 (125)
...++++|..||+.|-.
T Consensus 61 n~~Ir~KA~~lYnkfK~ 77 (106)
T PF11467_consen 61 NQQIRKKATELYNKFKS 77 (106)
T ss_dssp -HHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHH
Confidence 36899999999999854
No 50
>KOG4342|consensus
Probab=20.98 E-value=80 Score=28.40 Aligned_cols=57 Identities=28% Similarity=0.460 Sum_probs=35.8
Q ss_pred HHHHHhhChhHHHHHhh-----cCCCCchhhhhHHhhhcccHHHHHHHHH------HhhcHHHHHHHH
Q psy1257 31 IRRLKKDYPEEWKILLE-----KWDPKGEYTRKFQEKFGDTYKLFREFLR------CEYSEENILFWL 87 (125)
Q Consensus 31 i~~l~~~~P~~W~~l~~-----k~dP~~~~v~kw~~s~~~g~~~F~~FL~------~e~s~ENl~Fw~ 87 (125)
+.|+.+++|+.++++.. +|-|-|-.-..-...+|.|-.+-++||. +||----=.||+
T Consensus 333 ~~WlkedhP~~f~kl~e~~~q~qF~pvGGtWVE~DtNiPsGEslvRQFl~GQ~FFlkeFG~~c~~FWL 400 (1078)
T KOG4342|consen 333 LEWLKEDHPGLFSKLQEFACQGQFVPVGGTWVEMDTNIPSGESLVRQFLQGQNFFLKEFGKMCSEFWL 400 (1078)
T ss_pred HHHHhhhChhHHHHHHHHHhcCceeeccceEEecCCCCCChHHHHHHHHhhhhHHHHHhhhhhcceec
Confidence 57999999999988764 3555443222223334888888777765 455444445665
No 51
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=20.77 E-value=44 Score=27.92 Aligned_cols=18 Identities=28% Similarity=0.678 Sum_probs=16.1
Q ss_pred hhcCCCCchhhhhHHhhh
Q psy1257 46 LEKWDPKGEYTRKFQEKF 63 (125)
Q Consensus 46 ~~k~dP~~~~v~kw~~s~ 63 (125)
..+|||+|+|+++|.-.+
T Consensus 406 ~~k~Dp~g~yIr~w~PeL 423 (472)
T PRK10674 406 GERFDRDGEFIRRWLPEL 423 (472)
T ss_pred HHHhCCCCChHHHhChhh
Confidence 358999999999999888
No 52
>COG4748 Uncharacterized conserved protein [Function unknown]
Probab=20.61 E-value=2.2e+02 Score=23.20 Aligned_cols=48 Identities=21% Similarity=0.271 Sum_probs=36.2
Q ss_pred HHHHHHHHHhh---cHHHHHHHHHHH--HhhcCCCHHHHHHHHHHHHHHHcCC
Q psy1257 68 KLFREFLRCEY---SEENILFWLACE--DLKKESNPDVIEEKARFIYEDYISI 115 (125)
Q Consensus 68 ~~F~~FL~~e~---s~ENl~Fw~a~e--~~k~~~~~~~~~~~a~~Iy~~yi~~ 115 (125)
..+..||.+|+ |.|-+.|..+-- +++........-...++++..||..
T Consensus 175 ~eik~~la~e~~~Ps~Efvkffaa~v~~g~~t~~~~~kFt~ivk~~~~qFi~D 227 (365)
T COG4748 175 KEIKAYLAKETNNPSVEFVKFFAAKVYTGFKTTSVDEKFTDIVKNAFSQFIND 227 (365)
T ss_pred HHHHHHHHHhccCCCHHHHHHHHHHHhccceeeeHHHHHHHHHHHHHHHHHHH
Confidence 56788888876 889999988754 5665555556677888899999864
No 53
>PF14615 Rsa3: Ribosome-assembly protein 3
Probab=20.16 E-value=1.2e+02 Score=17.39 Aligned_cols=41 Identities=12% Similarity=0.217 Sum_probs=29.1
Q ss_pred HHHHHHhhChhHHHHHhhcCCCCchhhhhHHhhhcccHHHH
Q psy1257 30 VIRRLKKDYPEEWKILLEKWDPKGEYTRKFQEKFGDTYKLF 70 (125)
Q Consensus 30 vi~~l~~~~P~~W~~l~~k~dP~~~~v~kw~~s~~~g~~~F 70 (125)
-++.+.+.+-++.+.++...|=+...+.-...++..|...|
T Consensus 6 yl~~~t~efgdDLd~lR~~~dF~~~sl~~Li~aL~~G~~~F 46 (47)
T PF14615_consen 6 YLQRLTDEFGDDLDELRKAPDFTDKSLPLLIDALQQGTDMF 46 (47)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHHhccccc
Confidence 35566777888888888777767677766666666666554
No 54
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=20.14 E-value=45 Score=27.86 Aligned_cols=18 Identities=33% Similarity=0.818 Sum_probs=15.9
Q ss_pred hhcCCCCchhhhhHHhhh
Q psy1257 46 LEKWDPKGEYTRKFQEKF 63 (125)
Q Consensus 46 ~~k~dP~~~~v~kw~~s~ 63 (125)
..+|||+|+|+++|.-.+
T Consensus 410 ~~k~Dp~G~yIr~w~PeL 427 (471)
T TIGR03556 410 AQKFDPEAEYIRRWLPEL 427 (471)
T ss_pred HHHhCCCCchHHHhCHhh
Confidence 358999999999998887
Done!