Query psy423
Match_columns 255
No_of_seqs 45 out of 47
Neff 2.0
Searched_HMMs 46136
Date Fri Aug 16 20:08:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy423.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/423hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03615 GCM: GCM motif protei 100.0 6.7E-99 1E-103 623.6 8.1 143 88-230 1-143 (143)
2 PF04997 RNA_pol_Rpb1_1: RNA p 77.0 0.59 1.3E-05 38.7 -0.7 28 171-202 56-88 (337)
3 cd05750 Ig_Pro_neuregulin Immu 51.1 13 0.00028 24.7 2.0 24 183-206 2-26 (75)
4 PF06906 DUF1272: Protein of u 44.6 17 0.00038 27.3 2.0 36 136-185 20-55 (57)
5 PF07202 Tcp10_C: T-complex pr 37.5 26 0.00056 30.5 2.2 52 55-107 103-154 (179)
6 PF01927 Mut7-C: Mut7-C RNAse 35.6 37 0.0008 27.5 2.7 43 168-214 90-140 (147)
7 PRK15340 transcriptional regul 32.8 50 0.0011 29.4 3.3 45 123-168 5-59 (216)
8 PF03561 Allantoicase: Allanto 31.9 34 0.00074 29.0 2.0 61 62-139 2-64 (152)
9 PF00837 T4_deiodinase: Iodoth 30.4 18 0.00038 33.1 0.1 25 49-73 197-222 (237)
10 PF07636 PSRT: PSRT; InterPro 27.6 21 0.00047 24.3 0.1 23 209-231 2-24 (32)
11 PF11006 DUF2845: Protein of u 27.5 20 0.00043 27.0 -0.1 28 44-71 56-87 (87)
12 PF02591 DUF164: Putative zinc 26.8 52 0.0011 22.8 1.9 30 149-180 26-55 (56)
13 PF14828 Amnionless: Amnionles 26.8 52 0.0011 31.9 2.5 58 118-190 171-228 (437)
14 PF14939 DCAF15_WD40: DDB1-and 26.4 41 0.0009 30.5 1.7 30 76-105 71-114 (211)
15 cd04970 Ig6_Contactin_like Six 25.5 66 0.0014 22.4 2.3 30 183-213 4-36 (85)
16 cd05853 Ig6_Contactin-4 Sixth 25.2 40 0.00087 25.2 1.2 31 183-213 4-36 (85)
17 PRK14873 primosome assembly pr 25.0 45 0.00097 33.9 1.9 51 171-232 394-453 (665)
18 cd02980 TRX_Fd_family Thioredo 24.0 1.6E+02 0.0034 20.3 3.9 53 138-199 3-56 (77)
19 PF10571 UPF0547: Uncharacteri 22.6 51 0.0011 20.8 1.1 20 170-192 1-22 (26)
20 PF08746 zf-RING-like: RING-li 22.3 27 0.00059 23.7 -0.2 20 168-188 10-29 (43)
21 TIGR02386 rpoC_TIGR DNA-direct 21.3 52 0.0011 36.0 1.6 44 167-214 62-130 (1140)
No 1
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=100.00 E-value=6.7e-99 Score=623.63 Aligned_cols=143 Identities=77% Similarity=1.417 Sum_probs=90.7
Q ss_pred ccccccccCCCceeEEecCCcHHHHhcccccccccCCCcccceeecccceEEEecCCcccCCCCeeeechhhhHHHHhhh
Q psy423 88 EFNSWQEWADGHCRFVYPASSEEAKRHASGWAMRNTNNHNVHILKKSCLGVLVCSRRCVLPSGDSVHLRPAICDKARKKQ 167 (255)
Q Consensus 88 ~~D~F~EWpDG~vr~iY~~~~~~ArrH~SGWAMRNTNNHN~~ILKKSCLGVlvCS~~C~lp~G~ki~LRPAICDKAR~KQ 167 (255)
+||+|+||||||||+||++++++||||+||||||||||||++|||||||||||||++|++|+|.+|+||||||||||+||
T Consensus 1 ~~D~f~eW~dG~~r~iy~~~~~~ArrH~SgWAMRnTnNHn~~ilKKsCLGVl~Cs~~C~~~~g~~i~lRPAicdkAR~KQ 80 (143)
T PF03615_consen 1 EFDEFNEWPDGHVRRIYSASDKEARRHLSGWAMRNTNNHNVRILKKSCLGVLVCSQDCALPNGEKIHLRPAICDKARKKQ 80 (143)
T ss_dssp ------SS--SS-EE--BTT-HHHHTT--SS-EEEE--S-TT-EEEEE--EEEETT----SSS---EE---SSHHHHHHH
T ss_pred CCcccccCCCCcEEEEecccCHhHhhhcccceeecCCCCcceeeeeeeeeEEEeCCCccCCCCCEEEechHHhHHHHHHh
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCcceeeeeccCCCCCccceEEEEeCCEEEEeecccCCCCCCCCcchHHHHHhh
Q psy423 168 TGKPCPNRKCTGRLEIMPCRGHCGYPVTHFWRHTDYGIFFQAKGVHDHLRPEAKSTSEARRSL 230 (255)
Q Consensus 168 qgK~CPN~~C~G~Lel~pCRGH~GYPVThFWRh~g~aIfFQaKG~HDHpRPe~K~~~EaRrs~ 230 (255)
|+|+|||++|+|+|+++||||||||||||||||+|++|||||||+|||||||+|+++||||++
T Consensus 81 q~k~Cpn~~C~g~L~~~pCrGh~GYPVThFWr~~~~~IfFQaKG~HDHpRPe~K~~~earr~~ 143 (143)
T PF03615_consen 81 QGKPCPNRNCKGRLELIPCRGHCGYPVTHFWRHDGNAIFFQAKGVHDHPRPEAKSEAEARRSL 143 (143)
T ss_dssp HHSB-SS--S--BEEEE---TBTTB--EEEEEE-SSBEEEEEE----S-----HHHHHHHHS-
T ss_pred cCCCCCccccCCceeEEeccCcCCCceeEEEecCCCEEEEEcccccCCCCCCccchhhHhhcC
Confidence 999999999999999999999999999999999999999999999999999999999999985
No 2
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....
Probab=77.00 E-value=0.59 Score=38.67 Aligned_cols=28 Identities=32% Similarity=0.559 Sum_probs=22.3
Q ss_pred CCCCCCCCcceeeeeccCCCCC-----ccceEEEEeC
Q psy423 171 PCPNRKCTGRLEIMPCRGHCGY-----PVTHFWRHTD 202 (255)
Q Consensus 171 ~CPN~~C~G~Lel~pCRGH~GY-----PVThFWRh~g 202 (255)
.|+. |...... |.||-|| ||+|.|..+.
T Consensus 56 ~C~t--C~~~~~~--CpGHfGhI~L~~PV~h~~f~~~ 88 (337)
T PF04997_consen 56 ICST--CGLNYTE--CPGHFGHIELALPVYHPGFFKE 88 (337)
T ss_dssp TSSS--SSSSSSS--CCCSEEEEEEEEEEETCCCHHH
T ss_pred cccc--ccccccc--cCCceeEEEeCHHHHhhccccc
Confidence 8888 8854333 9999997 9999998654
No 3
>cd05750 Ig_Pro_neuregulin Immunoglobulin (Ig)-like domain in neuregulins (NRGs). Ig_Pro_neuregulin: immunoglobulin (Ig)-like domain in neuregulins (NRGs). NRGs are signaling molecules, which participate in cell-cell interactions in the nervous system, breast, heart, and other organ systems, and are implicated in the pathology of diseases including schizophrenia, multiple sclerosis, and breast cancer. There are four members of the neuregulin gene family (NRG1, -2, -3, and -4). The NRG-1 protein, binds to and activates the tyrosine kinases receptors ErbB3 and ErbB4, initiating signaling cascades. The other NRGs proteins bind one or the other or both of these ErbBs. NRG-1 has multiple functions; for example, in the brain it regulates various processes such as radial glia formation and neuronal migration, dendritic development, and expression of neurotransmitters receptors; in the peripheral nervous system NRG-1 regulates processes such as target cell differentiation, and Schwann cell surv
Probab=51.15 E-value=13 Score=24.72 Aligned_cols=24 Identities=17% Similarity=0.540 Sum_probs=19.0
Q ss_pred eeeccCCCCCc-cceEEEEeCCEEE
Q psy423 183 IMPCRGHCGYP-VTHFWRHTDYGIF 206 (255)
Q Consensus 183 l~pCRGH~GYP-VThFWRh~g~aIf 206 (255)
.+.|...+|+| .+-.|+++|..|-
T Consensus 2 ~l~C~~~g~~P~p~~~W~k~g~~l~ 26 (75)
T cd05750 2 VLKCEATSEYPSLRFKWFKDGKELN 26 (75)
T ss_pred EEEEEccCCCCCceEEEEcCCeecc
Confidence 47899998777 6789999887664
No 4
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=44.62 E-value=17 Score=27.33 Aligned_cols=36 Identities=31% Similarity=0.727 Sum_probs=26.2
Q ss_pred ceEEEecCCcccCCCCeeeechhhhHHHHhhhcCCCCCCCCCCcceeeee
Q psy423 136 LGVLVCSRRCVLPSGDSVHLRPAICDKARKKQTGKPCPNRKCTGRLEIMP 185 (255)
Q Consensus 136 LGVlvCS~~C~lp~G~ki~LRPAICDKAR~KQqgK~CPN~~C~G~Lel~p 185 (255)
....+||-.|+. |..--+.-....||| |.|-|.-.|
T Consensus 20 ~~A~ICSfECTF------------C~~C~e~~l~~~CPN--CgGelv~RP 55 (57)
T PF06906_consen 20 PEAYICSFECTF------------CADCAETMLNGVCPN--CGGELVRRP 55 (57)
T ss_pred CcceEEeEeCcc------------cHHHHHHHhcCcCcC--CCCccccCC
Confidence 346788888887 455455555789999 999887655
No 5
>PF07202 Tcp10_C: T-complex protein 10 C-terminus; InterPro: IPR009852 Proteins in this entry include T-complex 10, involved in spermatogenesis in mice, and centromere protein J, which not only inhibits microtubule nucleation from the centrosome, but also depolymerises taxol-stabilised microtubules [, ]. These proteins share an approximately 180 residue C-terminal region which contains unsual G repreats [].
Probab=37.53 E-value=26 Score=30.46 Aligned_cols=52 Identities=25% Similarity=0.592 Sum_probs=39.2
Q ss_pred hhhhhcccccccccccccceeeecCCCceeeecccccccccCCCceeEEecCC
Q psy423 55 ERLILEDGKVVNMSTLGHAQMVIHPGNRVLLVTEFNSWQEWADGHCRFVYPAS 107 (255)
Q Consensus 55 ~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~V~~~D~F~EWpDG~vr~iY~~~ 107 (255)
|..++.||.++-...-|...+...-|.+-+.-.+|- -.|+|||-++-+|..-
T Consensus 103 e~~~fpDGT~~~~~~nG~k~i~~pnGq~ei~t~~~k-rreyPDGTvk~vy~dG 154 (179)
T PF07202_consen 103 EETVFPDGTIVTIDPNGDKTITFPNGQKEIHTADFK-RREYPDGTVKTVYPDG 154 (179)
T ss_pred EEEECCCceEEEEeCCCcEEEEeCCCcEEEEccccE-EEEcCCCCEEEEecCC
Confidence 566788999988888888777766677655444433 4699999999999853
No 6
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=35.64 E-value=37 Score=27.53 Aligned_cols=43 Identities=26% Similarity=0.488 Sum_probs=27.7
Q ss_pred cCCCCCCCCCCcceeeeeccCC-------CCCccceEEEEeC-CEEEEeecccCC
Q psy423 168 TGKPCPNRKCTGRLEIMPCRGH-------CGYPVTHFWRHTD-YGIFFQAKGVHD 214 (255)
Q Consensus 168 qgK~CPN~~C~G~Lel~pCRGH-------~GYPVThFWRh~g-~aIfFQaKG~HD 214 (255)
.-..|+- |||.|+.++..-= -=.....||+=.+ +-|||+ |+|-
T Consensus 90 ~~sRC~~--CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~--GsH~ 140 (147)
T PF01927_consen 90 IFSRCPK--CNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE--GSHW 140 (147)
T ss_pred CCCccCC--CCcEeeechhhccccccCccccccCCeEEECCCCCCEecc--cccH
Confidence 3467888 8888888776511 1123456999444 688985 6663
No 7
>PRK15340 transcriptional regulator InvF; Provisional
Probab=32.82 E-value=50 Score=29.42 Aligned_cols=45 Identities=29% Similarity=0.449 Sum_probs=32.9
Q ss_pred CCCcccceeecccceEEEecCCcccCCCCeeeech----------hhhHHHHhhhc
Q psy423 123 TNNHNVHILKKSCLGVLVCSRRCVLPSGDSVHLRP----------AICDKARKKQT 168 (255)
Q Consensus 123 TNNHN~~ILKKSCLGVlvCS~~C~lp~G~ki~LRP----------AICDKAR~KQq 168 (255)
+||||..+.=.+= |+++|-+.|..++-..+.+.| |+.|+|+.+.+
T Consensus 5 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~la~id~~~~~~~ 59 (216)
T PRK15340 5 ESRHNENCLIQEG-ALLFCEQAVVAPVSGDLVFRPLKIEVLSKLLAFIDGAGLVDT 59 (216)
T ss_pred ecCCCceEEeeCC-eEEEeccccccccCCceEEEeccHHHHHHHHHHHHHhccccc
Confidence 3556665444433 999999999998888888776 78898866443
No 8
>PF03561 Allantoicase: Allantoicase repeat; InterPro: IPR015908 Allantoicase (also known as allantoate amidinohydrolase) is involved in purine degradation, facilitating the utilization of purines as secondary nitrogen sources under nitrogen-limiting conditions. While purine degradation converges to uric acid in all vertebrates, its further degradation varies from species to species. Uric acid is excreted by birds, reptiles, and some mammals that do not have a functional uricase gene, whereas other mammals produce allantoin. Amphibians and microorganisms produce ammonia and carbon dioxide using the uricolytic pathway. Allantoicase performs the second step in this pathway catalyzing the conversion of allantoate into ureidoglycolate and urea. allantoate + H(2)0 = (S)-ureidoglycolate + urea The structure of allantoicase is best described as being composed of two repeats (the allantoicase repeats: AR1 and AR2), which are connected by a flexible linker. The crystal structure, resolved at 2.4A resolution, reveals that AR1 has a very similar fold to AR2, both repeats being jelly-roll motifs, composed of four-stranded and five-stranded antiparallel beta-sheets []. Each jelly-roll motif has two conserved surface patches that probably constitute the active site []. The mammalian proteins matched by this entry are thought to be non-functional as mammals do not appear to possess allantoicase activity [].; GO: 0004037 allantoicase activity; PDB: 1O59_A 1SG3_A.
Probab=31.90 E-value=34 Score=29.03 Aligned_cols=61 Identities=28% Similarity=0.430 Sum_probs=32.8
Q ss_pred cccccccc--cccceeeecCCCceeeecccccccccCCCceeEEecCCcHHHHhcccccccccCCCcccceeecccceEE
Q psy423 62 GKVVNMST--LGHAQMVIHPGNRVLLVTEFNSWQEWADGHCRFVYPASSEEAKRHASGWAMRNTNNHNVHILKKSCLGVL 139 (255)
Q Consensus 62 ~~~~~~~~--~~~~~~~~~~~~r~~~V~~~D~F~EWpDG~vr~iY~~~~~~ArrH~SGWAMRNTNNHN~~ILKKSCLGVl 139 (255)
|+||..|. .||+.-+|-||.-+.+-.+||.+-.|-||.-.+ |+ ++..|++-|+|=..-|++
T Consensus 2 g~vv~~SD~~f~~~~nll~p~~~~~~~~~f~~~g~~~DGWETr----------Rr-------r~~g~DW~IikLg~~G~I 64 (152)
T PF03561_consen 2 GRVVACSDEFFAPAENLLKPGRPVFKPGKFDENGKMMDGWETR----------RR-------RDPGHDWAIIKLGAPGVI 64 (152)
T ss_dssp -EEEEES--SCC-GGGCC-SSS-S----------SGGCSEE------------SS--------STT-EEEEEE-SSSCEE
T ss_pred CEEEEEcccccccHHHhcCCCCCcccccccccccccccceeec----------cc-------cCCCCCEEEEECCCCCEE
Confidence 67777664 689998899999999999999999999998543 32 336789999998777765
No 9
>PF00837 T4_deiodinase: Iodothyronine deiodinase; InterPro: IPR000643 Iodothyronine deiodinase (1.97.1.10 from EC) (DI) [] is the vertebrate enzyme responsible for the deiodination of the prohormone thyroxine (T4 or 3,5,3',5'-tetraiodothyronine) into the biologically active hormone T3 (3,5,3'-triiodothyronine) and of T3 into the inactive metabolite T2 (3,3'-diiodothyronine). All known DI are proteins of about 250 residues that contain a selenocysteine at their active site. Three types of DI are known, type II is essential for providing the brain with the appropriate levels of T3 during the critical period of development, and type III is essential for the regulation of thyroid hormone inactivation during embryological development.; GO: 0004800 thyroxine 5'-deiodinase activity, 0055114 oxidation-reduction process
Probab=30.44 E-value=18 Score=33.14 Aligned_cols=25 Identities=48% Similarity=0.739 Sum_probs=20.5
Q ss_pred hhccchhhh-hhcccccccccccccc
Q psy423 49 TFERLPERL-ILEDGKVVNMSTLGHA 73 (255)
Q Consensus 49 ~~~~~~~~~-~~~~~~~~~~~~~~~~ 73 (255)
.|.-+|||| |++||||++....|.-
T Consensus 197 ~YgA~PeRlyIi~~gkv~Y~Gg~GP~ 222 (237)
T PF00837_consen 197 AYGALPERLYIIQDGKVVYKGGPGPF 222 (237)
T ss_pred HhCCCcceEEEEECCEEEEeCCCCCC
Confidence 467789997 6899999998887753
No 10
>PF07636 PSRT: PSRT; InterPro: IPR011504 This motif is found at the N terminus of several short hypothetical proteins in Rhodopirellula baltica and the predicted Arylsulphatase B (3.1.6.12 from EC) Q7UX97 from SWISSPROT.
Probab=27.63 E-value=21 Score=24.30 Aligned_cols=23 Identities=39% Similarity=0.491 Sum_probs=19.6
Q ss_pred ecccCCCCCCCCcchHHHHHhhc
Q psy423 209 AKGVHDHLRPEAKSTSEARRSLG 231 (255)
Q Consensus 209 aKG~HDHpRPe~K~~~EaRrs~~ 231 (255)
+-+.|.|-||....+.|.|||..
T Consensus 2 gn~~~~haRpsPSRTpeRrrS~s 24 (32)
T PF07636_consen 2 GNTRHFHARPSPSRTPERRRSTS 24 (32)
T ss_pred CccccccccCCCCCCcccccccC
Confidence 34689999999999999999864
No 11
>PF11006 DUF2845: Protein of unknown function (DUF2845); InterPro: IPR021268 This bacterial family of proteins has no known function.
Probab=27.47 E-value=20 Score=26.99 Aligned_cols=28 Identities=32% Similarity=0.477 Sum_probs=18.8
Q ss_pred cchhhhhccch----hhhhhcccccccccccc
Q psy423 44 RFELLTFERLP----ERLILEDGKVVNMSTLG 71 (255)
Q Consensus 44 ~~~~~~~~~~~----~~~~~~~~~~~~~~~~~ 71 (255)
.+|..+|..=| -.|++|||||+-+.+.|
T Consensus 56 ~vE~W~Yn~Gp~~~~~~l~f~~Gkl~~I~~~~ 87 (87)
T PF11006_consen 56 PVEEWTYNFGPNGFMQILTFENGKLVRIESGG 87 (87)
T ss_pred eeeEEEEeCCCCCcEEEEEEECCEEEEEEeCc
Confidence 45666665434 34678999999877654
No 12
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=26.76 E-value=52 Score=22.76 Aligned_cols=30 Identities=33% Similarity=0.488 Sum_probs=24.1
Q ss_pred CCCeeeechhhhHHHHhhhcCCCCCCCCCCcc
Q psy423 149 SGDSVHLRPAICDKARKKQTGKPCPNRKCTGR 180 (255)
Q Consensus 149 ~G~ki~LRPAICDKAR~KQqgK~CPN~~C~G~ 180 (255)
.|=.+.|.|....+.++...--.||| |.-.
T Consensus 26 ~gC~~~l~~~~~~~i~~~~~i~~Cp~--CgRi 55 (56)
T PF02591_consen 26 SGCHMELPPQELNEIRKGDEIVFCPN--CGRI 55 (56)
T ss_pred CCCCEEcCHHHHHHHHcCCCeEECcC--CCcc
Confidence 44556699999999988878889999 8644
No 13
>PF14828 Amnionless: Amnionless
Probab=26.76 E-value=52 Score=31.93 Aligned_cols=58 Identities=19% Similarity=0.444 Sum_probs=37.6
Q ss_pred cccccCCCcccceeecccceEEEecCCcccCCCCeeeechhhhHHHHhhhcCCCCCCCCCCcceeeeeccCCC
Q psy423 118 WAMRNTNNHNVHILKKSCLGVLVCSRRCVLPSGDSVHLRPAICDKARKKQTGKPCPNRKCTGRLEIMPCRGHC 190 (255)
Q Consensus 118 WAMRNTNNHN~~ILKKSCLGVlvCS~~C~lp~G~ki~LRPAICDKAR~KQqgK~CPN~~C~G~Lel~pCRGH~ 190 (255)
+-|+=.|.....|-...|--.- +|.-.+. .+.+.||...++ .||.+.|..+|.- -|||
T Consensus 171 g~~~F~g~~~~~v~~~~C~d~~----gC~C~n~---~~l~~ICs~v~~-----~C~~~~C~~pl~P---~GhC 228 (437)
T PF14828_consen 171 GQLQFHGPGSLRVTPYRCSDPS----GCPCGND---EVLEWICSNVLQ-----RCPKPHCRSPLRP---EGHC 228 (437)
T ss_pred hhheecCCceEEEecccccccc----cCccCcc---cchhhhhHHhhC-----cCCCCccCCCCCC---CCCc
Confidence 3355556677777777654333 3443332 378899999987 7888888887754 4664
No 14
>PF14939 DCAF15_WD40: DDB1-and CUL4-substrate receptor 15, WD repeat
Probab=26.40 E-value=41 Score=30.50 Aligned_cols=30 Identities=17% Similarity=0.297 Sum_probs=21.2
Q ss_pred eecCCCceeeeccccccc-------------ccC-CCceeEEec
Q psy423 76 VIHPGNRVLLVTEFNSWQ-------------EWA-DGHCRFVYP 105 (255)
Q Consensus 76 ~~~~~~r~~~V~~~D~F~-------------EWp-DG~vr~iY~ 105 (255)
...||.++++|.+---|. ||+ |...=.||.
T Consensus 71 ~F~p~~~l~~v~~v~LF~d~~I~~~l~i~vcqW~~D~~~lvV~G 114 (211)
T PF14939_consen 71 NFNPHQKLRKVFSVRLFGDEEIDSDLYITVCQWPSDSQKLVVHG 114 (211)
T ss_pred EecCCCeEEEEEEEeccCCccccceeEEEEEEcCCCCcEEEEEc
Confidence 456899988877654443 688 666667777
No 15
>cd04970 Ig6_Contactin_like Sixth Ig domain of contactin. Ig6_Contactin_like: Sixth Ig domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III(FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 week
Probab=25.54 E-value=66 Score=22.43 Aligned_cols=30 Identities=27% Similarity=0.522 Sum_probs=21.5
Q ss_pred eeeccCCCCCcc---ceEEEEeCCEEEEeecccC
Q psy423 183 IMPCRGHCGYPV---THFWRHTDYGIFFQAKGVH 213 (255)
Q Consensus 183 l~pCRGH~GYPV---ThFWRh~g~aIfFQaKG~H 213 (255)
.+.|.. .|+|- |-+|.++|..|.++..+.+
T Consensus 4 ~L~C~~-~g~P~p~i~~~W~~~g~~i~~~~~~~~ 36 (85)
T cd04970 4 TLQCHA-SHDPTLDLTFTWSFNGVPIDFDKDGGH 36 (85)
T ss_pred EEEEEE-ecCCCCCeEEEEEECCeEeeccCCCcc
Confidence 467887 57763 6799999988877655433
No 16
>cd05853 Ig6_Contactin-4 Sixth Ig domain of contactin-4. Ig6_Contactin-4: sixth Ig domain of the neural cell adhesion molecule contactin-4. Contactins are neural cell adhesion molecules, and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The different contactins show different expression patterns in the central nervous system. Highest expresson of contactin-4 is in testes, thyroid, small intestine, uterus and brain. Contactin-4 plays a role in the response of neuroblastoma cells to differentiating agents, such as retinoids. The contactin 4 gene is associated with cerebellar degeneration in spinocerebellar ataxia type 16.
Probab=25.17 E-value=40 Score=25.23 Aligned_cols=31 Identities=26% Similarity=0.529 Sum_probs=23.3
Q ss_pred eeeccCCC--CCccceEEEEeCCEEEEeecccC
Q psy423 183 IMPCRGHC--GYPVTHFWRHTDYGIFFQAKGVH 213 (255)
Q Consensus 183 l~pCRGH~--GYPVThFWRh~g~aIfFQaKG~H 213 (255)
.+.|..=. --|+|=+|.++|.-|.|+..|.|
T Consensus 4 ~l~C~v~~d~~l~~~~~W~~dg~~i~~~~~~~~ 36 (85)
T cd05853 4 VLPCQVSHDHSLDIVFTWSFNGHLIDFQKDGDH 36 (85)
T ss_pred EEEEEeccCCCCCcEEEEEECCEECcccCCCcc
Confidence 45677532 45788899999999998877765
No 17
>PRK14873 primosome assembly protein PriA; Provisional
Probab=25.05 E-value=45 Score=33.91 Aligned_cols=51 Identities=27% Similarity=0.573 Sum_probs=32.9
Q ss_pred CCCCCCCCcceee------eeccCCCCCccceEEEE--eCC-EEEEeecccCCCCCCCCcchHHHHHhhcC
Q psy423 171 PCPNRKCTGRLEI------MPCRGHCGYPVTHFWRH--TDY-GIFFQAKGVHDHLRPEAKSTSEARRSLGA 232 (255)
Q Consensus 171 ~CPN~~C~G~Lel------~pCRGH~GYPVThFWRh--~g~-aIfFQaKG~HDHpRPe~K~~~EaRrs~~~ 232 (255)
.||+ |+++|.. +-|. ||||.. ..|+= =|. .+-...-|+ .|.+.|..+.+..
T Consensus 394 ~C~~--C~~~L~~h~~~~~l~Ch-~CG~~~-~p~~Cp~Cgs~~l~~~g~Gt-------er~eeeL~~~FP~ 453 (665)
T PRK14873 394 RCRH--CTGPLGLPSAGGTPRCR-WCGRAA-PDWRCPRCGSDRLRAVVVGA-------RRTAEELGRAFPG 453 (665)
T ss_pred ECCC--CCCceeEecCCCeeECC-CCcCCC-cCccCCCCcCCcceeeeccH-------HHHHHHHHHHCCC
Confidence 5999 9999986 4587 999976 47772 122 233333332 2677777777763
No 18
>cd02980 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers.
Probab=23.96 E-value=1.6e+02 Score=20.30 Aligned_cols=53 Identities=23% Similarity=0.397 Sum_probs=30.6
Q ss_pred EEEecC-CcccCCCCeeeechhhhHHHHhhhcCCCCCCCCCCcceeeeeccCCCCCccceEEE
Q psy423 138 VLVCSR-RCVLPSGDSVHLRPAICDKARKKQTGKPCPNRKCTGRLEIMPCRGHCGYPVTHFWR 199 (255)
Q Consensus 138 VlvCS~-~C~lp~G~ki~LRPAICDKAR~KQqgK~CPN~~C~G~Lel~pCRGH~GYPVThFWR 199 (255)
|+||.. .|....|.. |.-++.+++..+.. .. .-.++-..|.|.|.+..+-...
T Consensus 3 I~VC~~~~C~~~G~~~--l~~~l~~~~~~~~~----~~---~v~v~~~~Clg~C~~~P~v~i~ 56 (77)
T cd02980 3 ILVCTGTACGLRGAEE--LLEALEKELGIRGG----DG---RVTVERVGCLGACGLAPVVVVY 56 (77)
T ss_pred EEEccCCCcccCCHHH--HHHHHHHHHhhhcC----CC---eEEEEEcCCcCcccCCCEEEEe
Confidence 789977 688754433 33455555544322 00 1255666899999886554444
No 19
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=22.63 E-value=51 Score=20.79 Aligned_cols=20 Identities=45% Similarity=1.107 Sum_probs=12.8
Q ss_pred CCCCCCCCCc--ceeeeeccCCCCC
Q psy423 170 KPCPNRKCTG--RLEIMPCRGHCGY 192 (255)
Q Consensus 170 K~CPN~~C~G--~Lel~pCRGH~GY 192 (255)
|.||+ |.. ++...-| -||||
T Consensus 1 K~CP~--C~~~V~~~~~~C-p~CG~ 22 (26)
T PF10571_consen 1 KTCPE--CGAEVPESAKFC-PHCGY 22 (26)
T ss_pred CcCCC--CcCCchhhcCcC-CCCCC
Confidence 56888 875 5555666 36776
No 20
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=22.26 E-value=27 Score=23.72 Aligned_cols=20 Identities=40% Similarity=0.780 Sum_probs=10.2
Q ss_pred cCCCCCCCCCCcceeeeeccC
Q psy423 168 TGKPCPNRKCTGRLEIMPCRG 188 (255)
Q Consensus 168 qgK~CPN~~C~G~Lel~pCRG 188 (255)
||..|+|++|+.+| |..|--
T Consensus 10 ~G~~C~~~~C~~r~-H~~C~~ 29 (43)
T PF08746_consen 10 QGQRCSNRDCNVRL-HDDCFK 29 (43)
T ss_dssp SSEE-SS--S--EE--HHHHH
T ss_pred eeccCCCCccCchH-HHHHHH
Confidence 67889999999984 556654
No 21
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=21.30 E-value=52 Score=36.03 Aligned_cols=44 Identities=27% Similarity=0.566 Sum_probs=31.8
Q ss_pred hcCCCCCCCCCCcceeeeecc---CCCCC-----ccceEEEEeC-----------------CEEEEeecccCC
Q psy423 167 QTGKPCPNRKCTGRLEIMPCR---GHCGY-----PVTHFWRHTD-----------------YGIFFQAKGVHD 214 (255)
Q Consensus 167 QqgK~CPN~~C~G~Lel~pCR---GH~GY-----PVThFWRh~g-----------------~aIfFQaKG~HD 214 (255)
..+..|.. |.. |+..|+ +|-|| ||+|.|...+ ..|||.++=+=|
T Consensus 62 ~~~~~C~~--Cgv--e~t~~~vrr~rmGhI~La~Pv~Hiwy~k~~ps~~~~ll~~~~k~le~v~y~~~~~v~~ 130 (1140)
T TIGR02386 62 YKGVVCER--CGV--EVTESKVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLD 130 (1140)
T ss_pred cCCcCCCC--CCC--CcccchhhhhcccceeecCCceeehhcCCCchHHHHHhCCCHHHhhheeeccceEEeC
Confidence 44788888 854 445676 77776 9999999886 478888754433
Done!