Query 036594
Match_columns 214
No_of_seqs 15 out of 17
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 03:36:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036594.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036594hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05402 PqqD: Coenzyme PQQ sy 87.4 0.91 2E-05 30.3 3.5 42 139-180 27-68 (68)
2 COG0796 MurI Glutamate racemas 74.8 1.3 2.8E-05 39.7 0.8 17 151-167 184-200 (269)
3 TIGR00067 glut_race glutamate 70.0 1.8 4E-05 36.7 0.6 21 143-164 172-192 (251)
4 PRK00865 glutamate racemase; P 67.6 2 4.4E-05 36.3 0.4 24 142-166 176-199 (261)
5 TIGR03859 PQQ_PqqD coenzyme PQ 64.2 10 0.00022 27.4 3.4 42 138-180 40-81 (81)
6 PF05334 DUF719: Protein of un 61.4 2.4 5.1E-05 36.4 -0.3 14 150-163 166-179 (181)
7 TIGR02765 crypto_DASH cryptoch 55.7 12 0.00026 33.3 3.1 47 142-190 319-375 (429)
8 PF07042 TrfA: TrfA protein; 54.7 16 0.00035 32.9 3.8 45 138-183 228-272 (282)
9 PRK10674 deoxyribodipyrimidine 50.7 14 0.00031 33.9 2.8 47 141-189 311-367 (472)
10 PF11155 DUF2935: Domain of un 45.7 17 0.00036 27.5 2.1 22 153-174 102-123 (124)
11 PRK10200 putative racemase; Pr 43.1 5.9 0.00013 33.2 -0.8 13 151-163 196-208 (230)
12 COG1309 AcrR Transcriptional r 41.4 37 0.00081 23.1 3.1 33 143-175 34-68 (201)
13 PF00615 RGS: Regulator of G p 37.9 63 0.0014 21.8 3.8 37 136-172 64-103 (118)
14 PF13072 DUF3936: Protein of u 37.8 29 0.00063 23.7 2.1 20 164-183 17-37 (38)
15 TIGR00035 asp_race aspartate r 37.6 9.7 0.00021 31.3 -0.3 10 151-160 194-203 (229)
16 PF03441 FAD_binding_7: FAD bi 35.8 40 0.00087 28.9 3.1 49 140-190 112-170 (277)
17 KOG1387 Glycosyltransferase [C 34.2 36 0.00078 33.2 2.8 98 96-198 65-219 (465)
18 COG0338 Dam Site-specific DNA 33.1 58 0.0013 29.1 3.8 88 79-179 131-222 (274)
19 TIGR00591 phr2 photolyase PhrI 31.1 28 0.00061 31.4 1.5 48 139-189 335-388 (454)
20 PF13475 DUF4116: Domain of un 28.8 35 0.00076 21.1 1.3 23 145-167 2-24 (49)
21 smart00550 Zalpha Z-DNA-bindin 28.2 27 0.00059 24.3 0.7 27 164-190 37-64 (68)
22 KOG3981 Deoxyribose-phosphate 27.8 30 0.00066 32.2 1.2 38 140-177 72-125 (326)
23 smart00667 LisH Lissencephaly 26.2 58 0.0013 18.2 1.8 25 83-107 3-28 (34)
24 PF08672 APC2: Anaphase promot 25.1 63 0.0014 22.9 2.1 33 148-180 20-52 (60)
25 COG5405 HslV ATP-dependent pro 24.9 51 0.0011 28.8 1.9 41 154-194 56-98 (178)
26 cd04445 DEP_PLEK1 DEP (Disheve 24.2 86 0.0019 25.1 2.9 43 69-111 16-62 (99)
27 PF00440 TetR_N: Bacterial reg 23.8 32 0.00069 21.9 0.4 21 143-163 18-38 (47)
28 PF09639 YjcQ: YjcQ protein; 23.0 39 0.00085 24.8 0.8 30 148-180 11-41 (88)
29 TIGR03556 photolyase_8HDF deox 21.9 75 0.0016 29.3 2.5 48 140-189 315-372 (471)
30 PF02002 TFIIE_alpha: TFIIE al 21.6 62 0.0014 23.6 1.6 23 163-185 41-63 (105)
31 PF13545 HTH_Crp_2: Crp-like h 21.3 43 0.00094 22.2 0.7 35 138-180 25-59 (76)
32 PF09791 Oxidored-like: Oxidor 20.3 1.1E+02 0.0024 21.3 2.5 32 141-174 12-43 (48)
33 PF01291 LIF_OSM: LIF / OSM fa 20.1 2E+02 0.0043 24.4 4.5 43 139-182 30-87 (162)
No 1
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=87.43 E-value=0.91 Score=30.33 Aligned_cols=42 Identities=17% Similarity=0.326 Sum_probs=33.1
Q ss_pred CCCcchHHHHhhhhccCCchhhHhHHHHHHHHHHHHhchhhh
Q 036594 139 PMPVGLEAVCLKAGTHYPTLFDHFQRELRDVLQELQQKSLVQ 180 (214)
Q Consensus 139 PMP~GlEalCLKA~tHYPTLFDHFQRELRdvL~~~Q~kgli~ 180 (214)
.-|.-.+.+|.+-+.+|+.-.+.-+..+.+.|.+|.++|+|+
T Consensus 27 ~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 27 DGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp -SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT---
T ss_pred cCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcCcC
Confidence 346778999999999999999999999999999999999985
No 2
>COG0796 MurI Glutamate racemase [Cell envelope biogenesis, outer membrane]
Probab=74.77 E-value=1.3 Score=39.67 Aligned_cols=17 Identities=41% Similarity=0.546 Sum_probs=14.3
Q ss_pred hhccCCchhhHhHHHHH
Q 036594 151 AGTHYPTLFDHFQRELR 167 (214)
Q Consensus 151 A~tHYPTLFDHFQRELR 167 (214)
+|||||-|-+-||+.+-
T Consensus 184 GCTHyPll~~~i~~~~~ 200 (269)
T COG0796 184 GCTHYPLLKPEIQQVLG 200 (269)
T ss_pred eCcCcHHHHHHHHHHhC
Confidence 69999998888887765
No 3
>TIGR00067 glut_race glutamate racemase. The most closely related proteins differing in function are aspartate racemases.
Probab=69.99 E-value=1.8 Score=36.73 Aligned_cols=21 Identities=29% Similarity=0.483 Sum_probs=15.3
Q ss_pred chHHHHhhhhccCCchhhHhHH
Q 036594 143 GLEAVCLKAGTHYPTLFDHFQR 164 (214)
Q Consensus 143 GlEalCLKA~tHYPTLFDHFQR 164 (214)
|.+.+.| +|||||-|.+.|+.
T Consensus 172 ~~d~lIL-GCTh~P~l~~~i~~ 192 (251)
T TIGR00067 172 LPDTVVL-GCTHFPLLKEEIEQ 192 (251)
T ss_pred CCCEEEE-CcCChHHHHHHHHH
Confidence 3344433 79999999998875
No 4
>PRK00865 glutamate racemase; Provisional
Probab=67.59 E-value=2 Score=36.27 Aligned_cols=24 Identities=38% Similarity=0.659 Sum_probs=18.4
Q ss_pred cchHHHHhhhhccCCchhhHhHHHH
Q 036594 142 VGLEAVCLKAGTHYPTLFDHFQREL 166 (214)
Q Consensus 142 ~GlEalCLKA~tHYPTLFDHFQREL 166 (214)
.|.++++| +|||||-+++.|+..+
T Consensus 176 ~g~d~iIL-GCTh~p~l~~~i~~~~ 199 (261)
T PRK00865 176 AGIDTLVL-GCTHYPLLKPEIQQVL 199 (261)
T ss_pred CCCCEEEE-CCcCHHHHHHHHHHHc
Confidence 46666665 7999999998887644
No 5
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=64.23 E-value=10 Score=27.41 Aligned_cols=42 Identities=10% Similarity=0.194 Sum_probs=37.6
Q ss_pred CCCCcchHHHHhhhhccCCchhhHhHHHHHHHHHHHHhchhhh
Q 036594 138 IPMPVGLEAVCLKAGTHYPTLFDHFQRELRDVLQELQQKSLVQ 180 (214)
Q Consensus 138 iPMP~GlEalCLKA~tHYPTLFDHFQRELRdvL~~~Q~kgli~ 180 (214)
+.-+.-.+.+|..-+-+|+- -+.-+..+...|.+|.++|+|.
T Consensus 40 ldg~~tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~L~~~gli~ 81 (81)
T TIGR03859 40 CDGKRSLAEIIQELAQRFPA-AEEIEDDVIAFLAVARAKHWLE 81 (81)
T ss_pred ccCCCcHHHHHHHHHHHcCC-hhhHHHHHHHHHHHHHHCcCcC
Confidence 34577889999999999999 9999999999999999999873
No 6
>PF05334 DUF719: Protein of unknown function (DUF719); InterPro: IPR007998 This family consists of several eukaryotic proteins of unknown function.
Probab=61.42 E-value=2.4 Score=36.38 Aligned_cols=14 Identities=50% Similarity=0.902 Sum_probs=12.0
Q ss_pred hhhccCCchhhHhH
Q 036594 150 KAGTHYPTLFDHFQ 163 (214)
Q Consensus 150 KA~tHYPTLFDHFQ 163 (214)
|+-.||-.|||.||
T Consensus 166 k~~~hy~~LFD~yq 179 (181)
T PF05334_consen 166 KKQAHYGMLFDEYQ 179 (181)
T ss_pred hhcccHHHHHHHhc
Confidence 34589999999998
No 7
>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=55.68 E-value=12 Score=33.27 Aligned_cols=47 Identities=30% Similarity=0.389 Sum_probs=38.1
Q ss_pred cchHHHHhhhhccCCchhhHhHHHHH----------HHHHHHHhchhhhhhccchhHHH
Q 036594 142 VGLEAVCLKAGTHYPTLFDHFQRELR----------DVLQELQQKSLVQDWHETESWKL 190 (214)
Q Consensus 142 ~GlEalCLKA~tHYPTLFDHFQRELR----------dvL~~~Q~kgli~dWr~T~SWkL 190 (214)
.-+++.|. +-|||| |.|--+|||+ -++-+.-=+.|..|||.-+.|-.
T Consensus 319 ~~~~~W~~-G~TG~P-ivDAamrqL~~TG~mhnr~Rm~vAsFl~k~L~idWr~G~~~F~ 375 (429)
T TIGR02765 319 KRFEQWKT-GTTGYP-LVDANMRELNATGFMSNRGRQNVASFLVKDLGLDWRYGAEWFE 375 (429)
T ss_pred HHHHHHhC-CCCCCh-hhhHHHHHHHHhCCCCHHHHHHHHHHHHHccCCCHHHHHHHHH
Confidence 45666664 899999 8999999985 46777777799999999999843
No 8
>PF07042 TrfA: TrfA protein; InterPro: IPR010751 This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa [].
Probab=54.70 E-value=16 Score=32.86 Aligned_cols=45 Identities=20% Similarity=0.318 Sum_probs=37.3
Q ss_pred CCCCcchHHHHhhhhccCCchhhHhHHHHHHHHHHHHhchhhhhhc
Q 036594 138 IPMPVGLEAVCLKAGTHYPTLFDHFQRELRDVLQELQQKSLVQDWH 183 (214)
Q Consensus 138 iPMP~GlEalCLKA~tHYPTLFDHFQRELRdvL~~~Q~kgli~dWr 183 (214)
-|.|.-+|-+-. -|--+.+-..+|...|+.+|.+|++-|+|..|.
T Consensus 228 ~P~P~kvetl~~-lcGS~~~~l~~FR~~Lk~AL~eL~~~g~v~~~~ 272 (282)
T PF07042_consen 228 KPYPIKVETLRE-LCGSESSRLRKFRQQLKKALDELVAVGFVSSAW 272 (282)
T ss_pred CCCCccHHHHHH-HcCCCccCHHHHHHHHHHHHHHHHhcCceeEEE
Confidence 688988888754 344556678899999999999999999998764
No 9
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=50.69 E-value=14 Score=33.92 Aligned_cols=47 Identities=32% Similarity=0.518 Sum_probs=37.0
Q ss_pred CcchHHHHhhhhccCCchhhHhHHHHHH----------HHHHHHhchhhhhhccchhHH
Q 036594 141 PVGLEAVCLKAGTHYPTLFDHFQRELRD----------VLQELQQKSLVQDWHETESWK 189 (214)
Q Consensus 141 P~GlEalCLKA~tHYPTLFDHFQRELRd----------vL~~~Q~kgli~dWr~T~SWk 189 (214)
|..+|+.|. +-|+|| +.|.-+|||+. ++-..-=+.|.-|||..+.|-
T Consensus 311 ~~~~~~W~~-G~TG~P-~vDA~mrqL~~tG~mhnr~Rm~vAsfL~k~L~idWr~G~~~F 367 (472)
T PRK10674 311 PAHLQAWQQ-GKTGYP-IVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYF 367 (472)
T ss_pred HHHHHHHHc-CCCCCc-cHHHHHHHHHHHCCccHHHHHHHHHHHHcCcccCCHhHHHHH
Confidence 466788764 899999 78999999854 555555578999999998874
No 10
>PF11155 DUF2935: Domain of unknown function (DUF2935); InterPro: IPR021328 This family of proteins with unknown function appears to be restricted to Firmicutes. ; PDB: 3D19_B 3DBY_P.
Probab=45.65 E-value=17 Score=27.52 Aligned_cols=22 Identities=41% Similarity=0.585 Sum_probs=17.8
Q ss_pred ccCCchhhHhHHHHHHHHHHHH
Q 036594 153 THYPTLFDHFQRELRDVLQELQ 174 (214)
Q Consensus 153 tHYPTLFDHFQRELRdvL~~~Q 174 (214)
+=||++.||--||..--|.-++
T Consensus 102 ~l~P~l~~Hi~rEa~~yl~~L~ 123 (124)
T PF11155_consen 102 NLYPLLIDHIIREAEYYLRILN 123 (124)
T ss_dssp SS-HHHHHHHHHHHHHHHHHHH
T ss_pred ccchHHHHHHHHHHHHHHHHHc
Confidence 4699999999999988877664
No 11
>PRK10200 putative racemase; Provisional
Probab=43.13 E-value=5.9 Score=33.21 Aligned_cols=13 Identities=15% Similarity=-0.018 Sum_probs=10.7
Q ss_pred hhccCCchhhHhH
Q 036594 151 AGTHYPTLFDHFQ 163 (214)
Q Consensus 151 A~tHYPTLFDHFQ 163 (214)
+|||||-|++.+.
T Consensus 196 GCTelpll~~~~~ 208 (230)
T PRK10200 196 GCTEIGLLVPEER 208 (230)
T ss_pred CCcCHHHhCCccc
Confidence 7999999987543
No 12
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=41.41 E-value=37 Score=23.05 Aligned_cols=33 Identities=27% Similarity=0.372 Sum_probs=24.4
Q ss_pred chHHHHhhhhccCCchhhHhH--HHHHHHHHHHHh
Q 036594 143 GLEAVCLKAGTHYPTLFDHFQ--RELRDVLQELQQ 175 (214)
Q Consensus 143 GlEalCLKA~tHYPTLFDHFQ--RELRdvL~~~Q~ 175 (214)
....+|-+|-..-+|+|.||. .||-+.+.+..-
T Consensus 34 t~~~Ia~~agvs~~~~Y~~f~~K~~l~~~~~~~~~ 68 (201)
T COG1309 34 TVDEIAKAAGVSKGTLYRHFPSKEDLLLALLERAL 68 (201)
T ss_pred CHHHHHHHhCCCcchhHHHcCCHHHHHHHHHHHHH
Confidence 467899999999999999998 445544444333
No 13
>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=37.91 E-value=63 Score=21.78 Aligned_cols=37 Identities=30% Similarity=0.473 Sum_probs=29.2
Q ss_pred ccCCCCcchHHHHhhhhcc---CCchhhHhHHHHHHHHHH
Q 036594 136 NAIPMPVGLEAVCLKAGTH---YPTLFDHFQRELRDVLQE 172 (214)
Q Consensus 136 ~AiPMP~GlEalCLKA~tH---YPTLFDHFQRELRdvL~~ 172 (214)
..+.+|...-.-+.+...+ .|++||--|.++...|..
T Consensus 64 ~~l~i~~~~~~~~~~~~~~~~~~~~~f~~a~~~v~~~L~~ 103 (118)
T PF00615_consen 64 NELNIPSKIRKEVQDALENAPPSPDLFDEAQEEVYEMLEE 103 (118)
T ss_dssp TCCSSTHHHHHHHHHHHTSTSTTTTTTHHHHHHHHHHHHH
T ss_pred ccccccHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhh
Confidence 3456777777777777777 899999999999888764
No 14
>PF13072 DUF3936: Protein of unknown function (DUF3936)
Probab=37.82 E-value=29 Score=23.71 Aligned_cols=20 Identities=30% Similarity=0.644 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHhc-hhhhhhc
Q 036594 164 RELRDVLQELQQK-SLVQDWH 183 (214)
Q Consensus 164 RELRdvL~~~Q~k-gli~dWr 183 (214)
.|+|.-|..++++ +.+.||-
T Consensus 17 WeIr~~Lkey~k~~~~v~ewi 37 (38)
T PF13072_consen 17 WEIRAKLKEYGKQFGYVKEWI 37 (38)
T ss_pred HHHHHHHHHHHHhhhhHHHhc
Confidence 6999999999998 9999984
No 15
>TIGR00035 asp_race aspartate racemase.
Probab=37.62 E-value=9.7 Score=31.30 Aligned_cols=10 Identities=10% Similarity=0.195 Sum_probs=9.2
Q ss_pred hhccCCchhh
Q 036594 151 AGTHYPTLFD 160 (214)
Q Consensus 151 A~tHYPTLFD 160 (214)
+|||||.+++
T Consensus 194 gCTelpll~~ 203 (229)
T TIGR00035 194 GCTELSLILK 203 (229)
T ss_pred eCcchHhhcc
Confidence 7999999986
No 16
>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=35.84 E-value=40 Score=28.89 Aligned_cols=49 Identities=37% Similarity=0.645 Sum_probs=37.3
Q ss_pred CCcchHHHHhhhhccCCchhhHhHHHHH----------HHHHHHHhchhhhhhccchhHHH
Q 036594 140 MPVGLEAVCLKAGTHYPTLFDHFQRELR----------DVLQELQQKSLVQDWHETESWKL 190 (214)
Q Consensus 140 MP~GlEalCLKA~tHYPTLFDHFQRELR----------dvL~~~Q~kgli~dWr~T~SWkL 190 (214)
-+.-+|+.| .+-|+|| +.|.-+|||+ -++...-=+.|.-||+..+.|..
T Consensus 112 ~~~~~~~w~-~G~TG~p-~vDAamrqL~~tG~mHn~~R~~vasfl~k~l~i~W~~g~~~f~ 170 (277)
T PF03441_consen 112 NPELFEAWC-EGRTGYP-LVDAAMRQLRQTGWMHNRLRMIVASFLTKDLLIDWREGAEWFA 170 (277)
T ss_dssp THHHHHHHH-TT-SS-H-HHHHHHHHHHHHS---HHHHHHHHHHHHHTSHBHHHHHHHHHH
T ss_pred CHHHHHHHH-cCCCCCh-HHHHHHHHHHHhCcccHHHHHHHHHHHHHhccCCccccHHHHH
Confidence 346688888 8999999 6799999986 34556667788889999999973
No 17
>KOG1387 consensus Glycosyltransferase [Cell wall/membrane/envelope biogenesis]
Probab=34.22 E-value=36 Score=33.22 Aligned_cols=98 Identities=24% Similarity=0.439 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHhhhh---cchh----hhhh----hcC-----CCeeEEEeeccccccC--------------CCCcchH
Q 036594 96 QGMRAMASDFASAEIQ---GEFS----ELRQ----RMG-----PGLTFVIEAQPYLNAI--------------PMPVGLE 145 (214)
Q Consensus 96 qgM~sMAs~fAsaE~q---gd~a----~~~~----~~g-----~~L~FViqAQPYL~Ai--------------PMP~GlE 145 (214)
-+.++|-.+|+-+-+- ||+. ...+ ..+ .+.-||-+-|-||-.. -|=.|+|
T Consensus 65 ~Avr~~q~k~~n~~~viYsGD~n~t~~~IL~k~k~~F~idlDs~nI~Fi~Lk~R~lVea~~~~hfTllgQaigsmIl~~E 144 (465)
T KOG1387|consen 65 KAVRITQRKFPNNVIVIYSGDFNVTPENILNKVKNKFDIDLDSDNIFFIYLKLRYLVEASTWKHFTLLGQAIGSMILAFE 144 (465)
T ss_pred HHHHHHHHhCCCceEEEEeCCCCCCHHHHHHHHHHhcCceecccceEEEEEEeeeeeecccccceehHHHHHHHHHHHHH
Confidence 4678888888766542 5522 1111 112 7888999999887322 3678999
Q ss_pred HHHh---------------------------hhhccCCchhhHhHHHHHHHHHHHHhchhhhhhccchhHHHHHHHHhhH
Q 036594 146 AVCL---------------------------KAGTHYPTLFDHFQRELRDVLQELQQKSLVQDWHETESWKLLKELANSA 198 (214)
Q Consensus 146 alCL---------------------------KA~tHYPTLFDHFQRELRdvL~~~Q~kgli~dWr~T~SWkLLKelAnSa 198 (214)
|+|. -|.+||||+=- .+-++|++.|..| |-.|-.---|+|+--|-.++
T Consensus 145 ai~r~~Pdi~IDtMGY~fs~p~~r~l~~~~V~aYvHYP~iS~----DML~~l~qrq~s~-~l~~~KlaY~rlFa~lY~~~ 219 (465)
T KOG1387|consen 145 AIIRFPPDIFIDTMGYPFSYPIFRRLRRIPVVAYVHYPTIST----DMLKKLFQRQKSG-ILVWGKLAYWRLFALLYQSA 219 (465)
T ss_pred HHHhCCchheEecCCCcchhHHHHHHccCceEEEEecccccH----HHHHHHHhhhhcc-hhhhHHHHHHHHHHHHHHhc
Confidence 9984 25789999853 3455666677778 88899999999987765543
No 18
>COG0338 Dam Site-specific DNA methylase [DNA replication, recombination, and repair]
Probab=33.07 E-value=58 Score=29.08 Aligned_cols=88 Identities=28% Similarity=0.357 Sum_probs=57.9
Q ss_pred CCCccccchhHHHHHHHHHHHHHHHHHHHhhhh-cchhhhhhhcCCCeeEEEeeccccccCCCCcchHHHHhhh-hccCC
Q 036594 79 NPLGRRDLGKGVVRWICQGMRAMASDFASAEIQ-GEFSELRQRMGPGLTFVIEAQPYLNAIPMPVGLEAVCLKA-GTHYP 156 (214)
Q Consensus 79 DPLGrkeLGr~VV~Wl~qgM~sMAs~fAsaE~q-gd~a~~~~~~g~~L~FViqAQPYL~AiPMP~GlEalCLKA-~tHYP 156 (214)
-|.||+.-=.-. ..+-++..|..++.|++- +|+..+-..--++=.||-.-=||+. +|..+ +|+|+
T Consensus 131 vp~g~~~~~~~~---~~~~L~~~a~~l~~~~i~~~df~~v~~~a~~~~dfvY~DPPY~~----------~s~t~~f~~Y~ 197 (274)
T COG0338 131 VPFGRYKNPYFP---EEENLKLFAEKLKNATIENGDFEEVLADADSGDDFVYCDPPYLP----------LSATSNFTAYG 197 (274)
T ss_pred ccccccccCCCc---hHHHHHHHHHHHhcCeEEcCCHHHHHhhccCCCcEEEeCCCCCc----------ccccccccccc
Confidence 477776622211 122355667777777666 3555555533466689999999974 34554 69999
Q ss_pred c-hhhHhH-HHHHHHHHHHHhchhh
Q 036594 157 T-LFDHFQ-RELRDVLQELQQKSLV 179 (214)
Q Consensus 157 T-LFDHFQ-RELRdvL~~~Q~kgli 179 (214)
. .||.+| ++|.+++..|..+..|
T Consensus 198 ~~~f~~~~~~~La~~~~~l~~~~~i 222 (274)
T COG0338 198 GNGFTEDQHLRLAEVLKELEGKRGI 222 (274)
T ss_pred CCCCChHHHHHHHHHHHhccccceE
Confidence 9 888885 7899999999655443
No 19
>TIGR00591 phr2 photolyase PhrII. All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.15 E-value=28 Score=31.41 Aligned_cols=48 Identities=23% Similarity=0.261 Sum_probs=35.6
Q ss_pred CCCcchHHHHhhhhccCCchhhHhHHHHHHH------HHHHHhchhhhhhccchhHH
Q 036594 139 PMPVGLEAVCLKAGTHYPTLFDHFQRELRDV------LQELQQKSLVQDWHETESWK 189 (214)
Q Consensus 139 PMP~GlEalCLKA~tHYPTLFDHFQRELRdv------L~~~Q~kgli~dWr~T~SWk 189 (214)
+-|..+|+.| ...|||| |.|--||||+.- +.-.--|.| -||+.++-|-
T Consensus 335 ~~~~~~~~W~-~G~Tg~p-ivdA~MrqL~~TG~MHNr~RMi~aK~l-i~W~~g~~~f 388 (454)
T TIGR00591 335 EHLYSLEQLE-KSTTHDY-LWNAAQEQLVTEGKMHGFLRMYWAKKI-LEWTHSPEEA 388 (454)
T ss_pred cccCCHHHHH-hcCcCcH-hHhHHHHHHHHhCccccceeeeeeeeh-hhcCCCHHHH
Confidence 4555799998 5889999 789999999852 222222555 8999999884
No 20
>PF13475 DUF4116: Domain of unknown function (DUF4116)
Probab=28.81 E-value=35 Score=21.14 Aligned_cols=23 Identities=17% Similarity=0.128 Sum_probs=19.9
Q ss_pred HHHHhhhhccCCchhhHhHHHHH
Q 036594 145 EAVCLKAGTHYPTLFDHFQRELR 167 (214)
Q Consensus 145 EalCLKA~tHYPTLFDHFQRELR 167 (214)
+.+|++|..++|..|.|.-.+||
T Consensus 2 ~e~v~~~v~~~~~~l~~~~~~lk 24 (49)
T PF13475_consen 2 REFVLEAVKKNGYALQYASEELK 24 (49)
T ss_pred HHHHHHHHHhCCHHHHHhCHHHh
Confidence 45789999999999999888887
No 21
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=28.22 E-value=27 Score=24.31 Aligned_cols=27 Identities=37% Similarity=0.502 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhchhhhhhccc-hhHHH
Q 036594 164 RELRDVLQELQQKSLVQDWHET-ESWKL 190 (214)
Q Consensus 164 RELRdvL~~~Q~kgli~dWr~T-~SWkL 190 (214)
++.+.+|..|+++|+|..=.++ +.|.+
T Consensus 37 ~~v~r~L~~L~~~G~V~~~~~~~~~W~i 64 (68)
T smart00550 37 KEVNRVLYSLEKKGKVCKQGGTPPLWKL 64 (68)
T ss_pred HHHHHHHHHHHHCCCEEecCCCCCceEe
Confidence 5788999999999999764434 77764
No 22
>KOG3981 consensus Deoxyribose-phosphate aldolase [Nucleotide transport and metabolism]
Probab=27.83 E-value=30 Score=32.24 Aligned_cols=38 Identities=21% Similarity=0.368 Sum_probs=27.5
Q ss_pred CCcchHHHHhhhhccC-CchhhHhH---------------HHHHHHHHHHHhch
Q 036594 140 MPVGLEAVCLKAGTHY-PTLFDHFQ---------------RELRDVLQELQQKS 177 (214)
Q Consensus 140 MP~GlEalCLKA~tHY-PTLFDHFQ---------------RELRdvL~~~Q~kg 177 (214)
---..-+||+|||.-+ |.+||.|- .-+.|+-..++..+
T Consensus 72 Tasnv~rLc~rA~yP~~p~~~~~~~~~dp~ihtaaVCVYPaRv~Da~kal~~~~ 125 (326)
T KOG3981|consen 72 TASNVVRLCKRAIYPVEPQFFDKFFATDPSIHTAAVCVYPARVADAKKALASSK 125 (326)
T ss_pred cHHHHHHHHHHhcCCCCHHHHHHHhccCCccceeeEEeehHHHHHHHHHHHhcc
Confidence 3345678999999888 89999874 23566666666554
No 23
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=26.22 E-value=58 Score=18.18 Aligned_cols=25 Identities=16% Similarity=0.428 Sum_probs=19.8
Q ss_pred cccchhHHHHHHH-HHHHHHHHHHHH
Q 036594 83 RRDLGKGVVRWIC-QGMRAMASDFAS 107 (214)
Q Consensus 83 rkeLGr~VV~Wl~-qgM~sMAs~fAs 107 (214)
+.+|=+.|+++|. +|+...|..|..
T Consensus 3 ~~~l~~lI~~yL~~~g~~~ta~~l~~ 28 (34)
T smart00667 3 RSELNRLILEYLLRNGYEETAETLQK 28 (34)
T ss_pred HHHHHHHHHHHHHHcCHHHHHHHHHH
Confidence 4677788999986 899988877753
No 24
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=25.09 E-value=63 Score=22.88 Aligned_cols=33 Identities=24% Similarity=0.288 Sum_probs=23.9
Q ss_pred HhhhhccCCchhhHhHHHHHHHHHHHHhchhhh
Q 036594 148 CLKAGTHYPTLFDHFQRELRDVLQELQQKSLVQ 180 (214)
Q Consensus 148 CLKA~tHYPTLFDHFQRELRdvL~~~Q~kgli~ 180 (214)
=||-+..=|+-|+.=..||+..|..+++.|.+.
T Consensus 20 mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~ 52 (60)
T PF08672_consen 20 MLKMFPKDPGGYDISLEELQEFLDRLVEEGKLE 52 (60)
T ss_dssp HHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEE
Confidence 466666667889999999999999999999874
No 25
>COG5405 HslV ATP-dependent protease HslVU (ClpYQ), peptidase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=24.85 E-value=51 Score=28.83 Aligned_cols=41 Identities=24% Similarity=0.486 Sum_probs=28.4
Q ss_pred cCCchhhHhHHHHHHHHHHHHhc--hhhhhhccchhHHHHHHH
Q 036594 154 HYPTLFDHFQRELRDVLQELQQK--SLVQDWHETESWKLLKEL 194 (214)
Q Consensus 154 HYPTLFDHFQRELRdvL~~~Q~k--gli~dWr~T~SWkLLKel 194 (214)
|.=|||+-|.++|+.-=-+|.+. -+-.|||...--.-|.-|
T Consensus 56 DaftLfe~fe~kle~~~g~L~raavelaKdwr~Dk~lr~LEAm 98 (178)
T COG5405 56 DAFTLFERFEAKLEQYQGDLFRAAVELAKDWRTDKYLRKLEAM 98 (178)
T ss_pred hHHHHHHHHHHHHHHccCcHHHHHHHHHHhhhhhhHHHHHhhh
Confidence 45689999999998654455544 577899977665555443
No 26
>cd04445 DEP_PLEK1 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in pleckstrin 1-like proteins. Pleckstrin 1 plays a role in cell spreading and reorganization of actin cytoskeleton in platelets and leukocytes. Its activity is highly regulated by phosphorylation, mainly by protein kinase C. Pleckstrin-like proteins contain a central DEP domain, flanked by 2 PH (pleckstrin homology) domains.
Probab=24.19 E-value=86 Score=25.13 Aligned_cols=43 Identities=14% Similarity=0.237 Sum_probs=25.9
Q ss_pred hhhhhhhhcCCCCccccchhHHHHHHHHHHHHH----HHHHHHhhhh
Q 036594 69 VNVQALSQNGNPLGRRDLGKGVVRWICQGMRAM----ASDFASAEIQ 111 (214)
Q Consensus 69 i~v~~LyqnGDPLGrkeLGr~VV~Wl~qgM~sM----As~fAsaE~q 111 (214)
|....+-..+--+---=.|.+||.||-+-+..- |-.+|++=++
T Consensus 16 Ik~~~~~~~~tv~~hcftGsdVVdWLv~~~~v~~r~EAl~las~Ll~ 62 (99)
T cd04445 16 IKELNLEKDKKVFNHCFTGSCVIDWLVSNQSVRNRQEGLMLASSLLN 62 (99)
T ss_pred hhhhhHHHhhccccceecccHHHHHHHHhhcccchHHHHHHHHHHHH
Confidence 334444444544545557999999997765433 5555555444
No 27
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=23.80 E-value=32 Score=21.89 Aligned_cols=21 Identities=14% Similarity=0.404 Sum_probs=19.0
Q ss_pred chHHHHhhhhccCCchhhHhH
Q 036594 143 GLEAVCLKAGTHYPTLFDHFQ 163 (214)
Q Consensus 143 GlEalCLKA~tHYPTLFDHFQ 163 (214)
.++++|-++-..-+++|-||.
T Consensus 18 s~~~Ia~~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 18 SIRDIARRAGVSKGSFYRYFP 38 (47)
T ss_dssp SHHHHHHHHTSCHHHHHHHCS
T ss_pred CHHHHHHHHccchhhHHHHcC
Confidence 568999999999999999995
No 28
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=23.04 E-value=39 Score=24.81 Aligned_cols=30 Identities=30% Similarity=0.616 Sum_probs=20.1
Q ss_pred HhhhhccC-CchhhHhHHHHHHHHHHHHhchhhh
Q 036594 148 CLKAGTHY-PTLFDHFQRELRDVLQELQQKSLVQ 180 (214)
Q Consensus 148 CLKA~tHY-PTLFDHFQRELRdvL~~~Q~kgli~ 180 (214)
|++..+.. |.++| +.+.+.|..|++.|+|.
T Consensus 11 ~~~~~~~~~~~~~~---~~~~~il~~L~d~GyI~ 41 (88)
T PF09639_consen 11 CMKNGKEPDPDITD---SYWSDILRMLQDEGYIK 41 (88)
T ss_dssp H-S---HHHHTS-H---HHHHHHHHHHHHHTSEE
T ss_pred HHcCCCCCCcchhH---HHHHHHHHHHHHCCCcc
Confidence 66655543 54444 88999999999999995
No 29
>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=21.95 E-value=75 Score=29.33 Aligned_cols=48 Identities=27% Similarity=0.520 Sum_probs=38.7
Q ss_pred CCcchHHHHhhhhccCCchhhHhHHHH----------HHHHHHHHhchhhhhhccchhHH
Q 036594 140 MPVGLEAVCLKAGTHYPTLFDHFQREL----------RDVLQELQQKSLVQDWHETESWK 189 (214)
Q Consensus 140 MP~GlEalCLKA~tHYPTLFDHFQREL----------RdvL~~~Q~kgli~dWr~T~SWk 189 (214)
.+.-+|+.| .+.|+|| +.|.-+||| |-++-+.-=+.|.-|||.-+-|-
T Consensus 315 ~~~~~~~W~-~G~TG~P-~vDAaMrqL~~tG~mhnr~Rm~vAsfl~k~L~idWr~G~~~F 372 (471)
T TIGR03556 315 NEAHFQAWC-EGRTGYP-IVDAAMRQLNETGWMHNRCRMIVASFLTKDLIINWQWGEKYF 372 (471)
T ss_pred CHHHHHHHh-cCCCCCC-cccHHHHHHHHhCCccHHHHHHHHHHHHcccCCCHHHHHHHH
Confidence 456678777 5889999 789999998 45666766678999999988885
No 30
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=21.59 E-value=62 Score=23.60 Aligned_cols=23 Identities=26% Similarity=0.420 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHhchhhhhhccc
Q 036594 163 QRELRDVLQELQQKSLVQDWHET 185 (214)
Q Consensus 163 QRELRdvL~~~Q~kgli~dWr~T 185 (214)
..|+|.+|..|.+.|+|.-.+..
T Consensus 41 ~~~vRkiL~~L~~~~lv~~~~~~ 63 (105)
T PF02002_consen 41 PKEVRKILYKLYEDGLVSYRRRK 63 (105)
T ss_dssp HHHHHHHHHHHHHHSS-EEEEE-
T ss_pred HHHHHHHHHHHHHCCCeEEEEEE
Confidence 48999999999999999766543
No 31
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=21.28 E-value=43 Score=22.22 Aligned_cols=35 Identities=23% Similarity=0.517 Sum_probs=29.2
Q ss_pred CCCCcchHHHHhhhhccCCchhhHhHHHHHHHHHHHHhchhhh
Q 036594 138 IPMPVGLEAVCLKAGTHYPTLFDHFQRELRDVLQELQQKSLVQ 180 (214)
Q Consensus 138 iPMP~GlEalCLKA~tHYPTLFDHFQRELRdvL~~~Q~kgli~ 180 (214)
+++|.-.+.+.--+.+++.|+ -.+|..++++|+|+
T Consensus 25 ~~~~lt~~~iA~~~g~sr~tv--------~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 25 IPLPLTQEEIADMLGVSRETV--------SRILKRLKDEGIIE 59 (76)
T ss_dssp EEEESSHHHHHHHHTSCHHHH--------HHHHHHHHHTTSEE
T ss_pred EEecCCHHHHHHHHCCCHHHH--------HHHHHHHHHCCCEE
Confidence 566788899999999998774 56788899999987
No 32
>PF09791 Oxidored-like: Oxidoreductase-like protein, N-terminal; InterPro: IPR019180 This entry represents the N-terminal domain of various oxidoreductase-like proteins whose exact function is, as yet, unknown.
Probab=20.32 E-value=1.1e+02 Score=21.26 Aligned_cols=32 Identities=22% Similarity=0.471 Sum_probs=24.8
Q ss_pred CcchHHHHhhhhccCCchhhHhHHHHHHHHHHHH
Q 036594 141 PVGLEAVCLKAGTHYPTLFDHFQRELRDVLQELQ 174 (214)
Q Consensus 141 P~GlEalCLKA~tHYPTLFDHFQRELRdvL~~~Q 174 (214)
|.+-+.=|--.|. |=+||-|..||.+--.+++
T Consensus 12 P~~p~~CCgSGC~--~CVwd~Y~eel~~y~~~~~ 43 (48)
T PF09791_consen 12 PPEPDECCGSGCA--PCVWDVYAEELEEYREALA 43 (48)
T ss_pred ccCcccccccCCc--cchhHHHHHHHHHHHHHHH
Confidence 4466778888887 7999999999977655554
No 33
>PF01291 LIF_OSM: LIF / OSM family; InterPro: IPR001581 On the basis of functional and structural similarities, the small cytokines leukemia inhibitory factor (LIF) and oncostatin (OSM) can be classified into a single family [, ]. It has been said [] that LIF and OSM can be included in the IL-6 family of cytokines (IPR003573 from INTERPRO), but while all these cytokines seem to be structurally related, the sequence similarity is not high enough to allow the use of a single consensus pattern.; GO: 0005125 cytokine activity, 0006955 immune response, 0005576 extracellular region; PDB: 1LKI_A 1A7M_A 1EVS_A 1PVH_B 2Q7N_D 1EMR_A.
Probab=20.13 E-value=2e+02 Score=24.41 Aligned_cols=43 Identities=21% Similarity=0.400 Sum_probs=31.1
Q ss_pred CCCcchHHHHhhhhccCC---------------chhhHhHHHHHHHHHHHHhchhhhhh
Q 036594 139 PMPVGLEAVCLKAGTHYP---------------TLFDHFQRELRDVLQELQQKSLVQDW 182 (214)
Q Consensus 139 PMP~GlEalCLKA~tHYP---------------TLFDHFQRELRdvL~~~Q~kgli~dW 182 (214)
|-| +++.+|---.+++| |++.+++.=|.++-.++++-.-..++
T Consensus 30 ~~p-~l~~~C~~~~~~FP~~~nl~~l~r~~~L~ti~a~L~~~L~~l~~~Q~~l~~~~~~ 87 (162)
T PF01291_consen 30 PFP-DLDKLCTESPGDFPSHANLTELERLVFLYTINATLGASLHRLTRLQQDLNPPADS 87 (162)
T ss_dssp TSC-CHHHHTSTTTTTS--HCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTHHH
T ss_pred CCc-chhhHhcCCCCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHCCCcchh
Confidence 446 99999999999999 67778888887777766655444443
Done!