Query 031182
Match_columns 164
No_of_seqs 132 out of 182
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 10:24:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031182.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031182hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1043 Ca2+-binding transmemb 99.9 3.4E-28 7.3E-33 222.8 5.5 147 11-163 307-456 (499)
2 PF07766 LETM1: LETM1-like pro 99.7 9E-18 1.9E-22 142.4 3.3 83 11-99 185-268 (268)
3 KOG4263 Putative receptor CCR1 96.9 0.001 2.2E-08 58.5 4.4 55 44-99 230-285 (299)
4 PF02037 SAP: SAP domain; Int 96.6 0.0036 7.8E-08 38.7 3.9 34 49-83 2-35 (35)
5 smart00513 SAP Putative DNA-bi 96.4 0.0073 1.6E-07 37.0 4.1 34 49-83 2-35 (35)
6 TIGR00578 ku70 ATP-dependent D 62.9 10 0.00022 36.1 4.1 38 46-84 547-584 (584)
7 smart00540 LEM in nuclear memb 62.0 8.7 0.00019 25.3 2.5 34 47-81 2-39 (44)
8 PF07498 Rho_N: Rho terminatio 53.0 26 0.00056 22.3 3.6 31 48-79 2-34 (43)
9 PF06840 DUF1241: Protein of u 47.1 12 0.00026 30.6 1.6 18 110-127 97-114 (154)
10 PF10281 Ish1: Putative stress 44.6 61 0.0013 19.9 4.2 32 49-81 2-36 (38)
11 PF07766 LETM1: LETM1-like pro 41.3 41 0.00088 28.9 4.0 50 35-85 153-204 (268)
12 PF00605 IRF: Interferon regul 40.5 14 0.00031 28.2 1.1 57 8-67 28-88 (109)
13 PF13297 Telomere_Sde2_2: Telo 39.3 81 0.0018 22.3 4.6 35 45-80 9-43 (60)
14 PF01031 Dynamin_M: Dynamin ce 36.3 29 0.00063 29.4 2.4 55 33-87 151-211 (295)
15 PF14223 UBN2: gag-polypeptide 34.2 87 0.0019 22.6 4.3 59 103-162 59-118 (119)
16 PF03683 UPF0175: Uncharacteri 29.5 1.2E+02 0.0025 21.3 4.2 32 48-80 43-74 (76)
17 PF06971 Put_DNA-bind_N: Putat 24.8 84 0.0018 21.0 2.6 30 43-80 21-50 (50)
18 PF10309 DUF2414: Protein of u 22.7 34 0.00074 24.0 0.4 22 41-62 6-27 (62)
19 PF12627 PolyA_pol_RNAbd: Prob 22.1 1.5E+02 0.0032 19.2 3.4 31 54-84 6-36 (64)
20 PF11300 DUF3102: Protein of u 22.1 59 0.0013 25.8 1.7 17 46-62 113-129 (130)
21 PRK11436 biofilm-dependent mod 21.9 81 0.0018 22.7 2.2 44 44-89 4-50 (71)
22 KOG0571 Asparagine synthase (g 21.7 48 0.001 32.0 1.3 55 7-61 389-468 (543)
23 PF00193 Xlink: Extracellular 20.4 89 0.0019 23.0 2.2 40 45-86 6-47 (92)
No 1
>KOG1043 consensus Ca2+-binding transmembrane protein LETM1/MRS7 [Function unknown]
Probab=99.94 E-value=3.4e-28 Score=222.79 Aligned_cols=147 Identities=24% Similarity=0.237 Sum_probs=136.2
Q ss_pred cccccCCccchhhhccccccccccchhhhhhhhhhhh-hhcCCHHHHHHHHHHhcCCcc-CCChhHHHHHHHHHhhcccC
Q 031182 11 KVRFLNNNFQPACCTWSRPYFCSFKNWILKYGKYSEC-EAALSKALITELLKEHYTIDA-VANFDSLCHGLHDWLDLSLN 88 (164)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~y~EG-vdsLS~~ELq~AC~ssRGmr~-~vs~e~Lr~qL~qWLdL~L~ 88 (164)
.-+||+||.++|=++.+.+++-.+|.=|.. || |++||..||+.||++ ||||+ +|++++|++||.+|+|||++
T Consensus 307 l~~~Gt~~~lr~~lr~kik~ik~dD~~I~~-----eg~v~~ls~~el~~aC~~-rgmra~gv~~e~l~~ql~~wldlsl~ 380 (499)
T KOG1043|consen 307 LNSFGTDKLLRYQLRKKIKEIKKDDKHIAT-----EGAVESLSLLELQIACRE-RGMRALGVSEERLREQLRVWLDLSLD 380 (499)
T ss_pred ccccCchHHHHHHHHHHHHHhcccccchhh-----hhhhhHhhHHHHHHHHHh-hhcchhccchhhhhHHHHHHHhhhcc
Confidence 358999999999999999999999876655 99 999999999999996 99998 59999999999999999999
Q ss_pred CCCChHHHHHHhhhhcCCCCChHHhHHHHHhc-CChhhHhhhhcccccCCccccchhhhHHHhHhhhhhhHhhhhc
Q 031182 89 HTVPSSLLILSRAFYASGEASPEKAGQATLSF-LPDKIVDTVGVTTLPLEDSVLGSRRKLEFLEMQEEPIKVFDTT 163 (164)
Q Consensus 89 ~~IPssLLiLSrAf~~~~~~s~~daLkatLSS-LPDevv~ea~v~v~e~E~~~~d~K~KLevLkeQEElIkeE~e~ 163 (164)
++|||+||+|||+|++++.....+++.++|+. +||.+....+..+.+.+++.++++.|++.|++||+.|.+|.++
T Consensus 381 ~~vps~lL~Lsr~~~~~~~~~~~~s~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kl~~l~~~e~~~~~e~ee 456 (499)
T KOG1043|consen 381 KKVPSVLLLLSRTFSLGQNSKAPSSSSGKLQIAAPDDLEKLEKLKKEESELGAVDRKKKLELLREGEEIISEEEEE 456 (499)
T ss_pred ccCchHHHHHhhhhhhhhcccCCchhhhHhhhhccccHHHhcccccccccccccchHHHHHhhhccccccchhhhc
Confidence 99999999999999999887778888888885 9999999988888888888999999999999999999999875
No 2
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=99.69 E-value=9e-18 Score=142.43 Aligned_cols=83 Identities=25% Similarity=0.255 Sum_probs=66.4
Q ss_pred cccccCCccchhhhccccccccccchhhhhhhhhhhhhhcCCHHHHHHHHHHhcCCcc-CCChhHHHHHHHHHhhcccCC
Q 031182 11 KVRFLNNNFQPACCTWSRPYFCSFKNWILKYGKYSECEAALSKALITELLKEHYTIDA-VANFDSLCHGLHDWLDLSLNH 89 (164)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~y~EGvdsLS~~ELq~AC~ssRGmr~-~vs~e~Lr~qL~qWLdL~L~~ 89 (164)
--||+.++++++.++....++..+|.=|.+ |||++||.+||+.||.+ |||++ ++|+++||++|.+||+||++.
T Consensus 185 l~~~~~~~~lr~rL~~~~~~l~~dD~~i~~-----eGv~~Ls~~EL~~Ac~~-RGl~~~~~s~~~lr~~L~~WL~ls~~~ 258 (268)
T PF07766_consen 185 LTPFGPSSLLRRRLRKRLRYLKQDDRLIKR-----EGVDSLSEEELQDACYE-RGLRSTGLSEEELREWLKQWLQLSSNK 258 (268)
T ss_dssp ----SSHHHHHHHHHHHHHHHHHHHHHHHH-----H-GGGS-HHHHHHHHHH-TT---TT--HHHHHHHHHHHHHHHHTS
T ss_pred cCcCCchHHHHHHHHHHHHHHHHHHHHHHH-----hccccCCHHHHHHHHHH-hCCCcCCCCHHHHHHHHHHHHHHHccC
Confidence 458999999999999999999999988888 99999999999999996 99997 599999999999999999999
Q ss_pred CCChHHHHHH
Q 031182 90 TVPSSLLILS 99 (164)
Q Consensus 90 ~IPssLLiLS 99 (164)
++|+++|+||
T Consensus 259 ~~p~~lLlL~ 268 (268)
T PF07766_consen 259 KVPSSLLLLH 268 (268)
T ss_dssp ---HHHHHHH
T ss_pred CCCchhhccC
Confidence 9999999997
No 3
>KOG4263 consensus Putative receptor CCR1 [Signal transduction mechanisms]
Probab=96.95 E-value=0.001 Score=58.52 Aligned_cols=55 Identities=13% Similarity=0.120 Sum_probs=45.6
Q ss_pred hhhhhhcCCHHHHHHHHHHhcCCccC-CChhHHHHHHHHHhhcccCCCCChHHHHHH
Q 031182 44 YSECEAALSKALITELLKEHYTIDAV-ANFDSLCHGLHDWLDLSLNHTVPSSLLILS 99 (164)
Q Consensus 44 y~EGvdsLS~~ELq~AC~ssRGmr~~-vs~e~Lr~qL~qWLdL~L~~~IPssLLiLS 99 (164)
.-+||++|+..||..||=- ||+..+ .++++||+.|.+|+..+-.=+-|--.|++-
T Consensus 230 ~~~gi~~lt~~~l~~~CYl-Rgln~~~~~~~~mr~wLr~wvkiS~Slk~~~~slllh 285 (299)
T KOG4263|consen 230 AKLGIGQLTAQELKSACYL-RGLNSTHIGEDRMRTWLREWVKISCSLKEAELSLLLH 285 (299)
T ss_pred HHhccccCCHHHHHHHhhh-ccCCCCccChHHHHHHHHHHHhhhhcccccchhhhhh
Confidence 4499999999999999997 999986 899999999999999887544444444443
No 4
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=96.62 E-value=0.0036 Score=38.69 Aligned_cols=34 Identities=26% Similarity=0.289 Sum_probs=30.3
Q ss_pred hcCCHHHHHHHHHHhcCCccCCChhHHHHHHHHHh
Q 031182 49 AALSKALITELLKEHYTIDAVANFDSLCHGLHDWL 83 (164)
Q Consensus 49 dsLS~~ELq~AC~ssRGmr~~vs~e~Lr~qL~qWL 83 (164)
.+|+++||++.|++ ||+.+..+.++|.+-|.+|+
T Consensus 2 ~~l~v~eLk~~l~~-~gL~~~G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 2 SKLTVAELKEELKE-RGLSTSGKKAELIERLKEHL 35 (35)
T ss_dssp TTSHHHHHHHHHHH-TTS-STSSHHHHHHHHHHHH
T ss_pred CcCcHHHHHHHHHH-CCCCCCCCHHHHHHHHHHhC
Confidence 57899999999996 99999999999999999885
No 5
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=96.37 E-value=0.0073 Score=36.97 Aligned_cols=34 Identities=21% Similarity=0.199 Sum_probs=30.9
Q ss_pred hcCCHHHHHHHHHHhcCCccCCChhHHHHHHHHHh
Q 031182 49 AALSKALITELLKEHYTIDAVANFDSLCHGLHDWL 83 (164)
Q Consensus 49 dsLS~~ELq~AC~ssRGmr~~vs~e~Lr~qL~qWL 83 (164)
.+|+.+||++.|++ +|+.+..+.++|.+-+.+|+
T Consensus 2 ~~l~~~~Lk~~l~~-~gl~~~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 2 AKLKVSELKDELKK-RGLSTSGTKAELVDRLLEAL 35 (35)
T ss_pred CcCcHHHHHHHHHH-cCCCCCCCHHHHHHHHHHhC
Confidence 57999999999996 99999889999999998875
No 6
>TIGR00578 ku70 ATP-dependent DNA helicase ii, 70 kDa subunit (ku70). Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast.
Probab=62.88 E-value=10 Score=36.15 Aligned_cols=38 Identities=11% Similarity=0.243 Sum_probs=34.1
Q ss_pred hhhhcCCHHHHHHHHHHhcCCccCCChhHHHHHHHHHhh
Q 031182 46 ECEAALSKALITELLKEHYTIDAVANFDSLCHGLHDWLD 84 (164)
Q Consensus 46 EGvdsLS~~ELq~AC~ssRGmr~~vs~e~Lr~qL~qWLd 84 (164)
.++..||+++|+..|++ .|+++....++|-+.+.+|++
T Consensus 547 ~~l~kltv~~Lk~~l~~-~g~~~~~kKadLi~~i~~~~~ 584 (584)
T TIGR00578 547 GTLGKLTVSVLKDFCRA-YGLRSGSKKQELLDALTKHFK 584 (584)
T ss_pred CChhhccHHHHHHHHHH-cCCCccccHHHHHHHHHHHhC
Confidence 56788999999999996 999987889999999999974
No 7
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=62.03 E-value=8.7 Score=25.29 Aligned_cols=34 Identities=21% Similarity=0.113 Sum_probs=25.3
Q ss_pred hhhcCCHHHHHHHHHHhcCCccC-C---ChhHHHHHHHH
Q 031182 47 CEAALSKALITELLKEHYTIDAV-A---NFDSLCHGLHD 81 (164)
Q Consensus 47 GvdsLS~~ELq~AC~ssRGmr~~-v---s~e~Lr~qL~q 81 (164)
.+++||..||+.-|.+ -|+..+ + |..-+...|..
T Consensus 2 d~~~LSd~eL~~~L~~-~G~~~gPIt~sTR~vy~kkL~~ 39 (44)
T smart00540 2 DVDRLSDAELRAELKQ-YGLPPGPITDTTRKLYEKKLRK 39 (44)
T ss_pred chhHcCHHHHHHHHHH-cCCCCCCcCcchHHHHHHHHHH
Confidence 4789999999999996 999964 4 44445555544
No 8
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=53.03 E-value=26 Score=22.29 Aligned_cols=31 Identities=16% Similarity=0.233 Sum_probs=22.1
Q ss_pred hhcCCHHHHHHHHHHhcCCccC--CChhHHHHHH
Q 031182 48 EAALSKALITELLKEHYTIDAV--ANFDSLCHGL 79 (164)
Q Consensus 48 vdsLS~~ELq~AC~ssRGmr~~--vs~e~Lr~qL 79 (164)
..++|..||+.-|.+ .||... ...++|-..+
T Consensus 2 L~~~~~~eL~~iAk~-lgI~~~~~~~K~eLI~~I 34 (43)
T PF07498_consen 2 LKSMTLSELREIAKE-LGIEGYSKMRKQELIFAI 34 (43)
T ss_dssp HHCS-HHHHHHHHHC-TT-TTGCCS-HHHHHHHH
T ss_pred cccCCHHHHHHHHHH-cCCCCCCcCCHHHHHHHH
Confidence 468999999999996 999853 6777776554
No 9
>PF06840 DUF1241: Protein of unknown function (DUF1241); InterPro: IPR009652 This family consists of several programmed cell death 10 protein (PDCD10 or TFAR15) sequences. The function of this family is unknown.; PDB: 3L8I_A 3RQG_B 3RQE_B 3L8J_A 3RQF_B 3AJM_B.
Probab=47.05 E-value=12 Score=30.58 Aligned_cols=18 Identities=39% Similarity=0.455 Sum_probs=15.4
Q ss_pred hHHhHHHHHhcCChhhHh
Q 031182 110 PEKAGQATLSFLPDKIVD 127 (164)
Q Consensus 110 ~~daLkatLSSLPDevv~ 127 (164)
-..+||.+||.|||++-+
T Consensus 97 ~A~~LK~iLSrIPdei~d 114 (154)
T PF06840_consen 97 RATALKRILSRIPDEISD 114 (154)
T ss_dssp HHHHHHHHHHTHHHHTTS
T ss_pred HHHHHHHHHhcCcHhhcc
Confidence 357899999999998765
No 10
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=44.60 E-value=61 Score=19.87 Aligned_cols=32 Identities=22% Similarity=0.114 Sum_probs=25.8
Q ss_pred hcCCHHHHHHHHHHhcCCccC--C-ChhHHHHHHHH
Q 031182 49 AALSKALITELLKEHYTIDAV--A-NFDSLCHGLHD 81 (164)
Q Consensus 49 dsLS~~ELq~AC~ssRGmr~~--v-s~e~Lr~qL~q 81 (164)
++-|.++|++-+.+ .||... . +.++|.+.++.
T Consensus 2 dtWs~~~L~~wL~~-~gi~~~~~~~~rd~Ll~~~k~ 36 (38)
T PF10281_consen 2 DTWSDSDLKSWLKS-HGIPVPKSAKTRDELLKLAKK 36 (38)
T ss_pred CCCCHHHHHHHHHH-cCCCCCCCCCCHHHHHHHHHH
Confidence 56789999999996 999964 4 78888877653
No 11
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=41.27 E-value=41 Score=28.91 Aligned_cols=50 Identities=12% Similarity=0.110 Sum_probs=34.0
Q ss_pred chhhhhhhhhhh--hhhcCCHHHHHHHHHHhcCCccCCChhHHHHHHHHHhhc
Q 031182 35 KNWILKYGKYSE--CEAALSKALITELLKEHYTIDAVANFDSLCHGLHDWLDL 85 (164)
Q Consensus 35 ~~~i~~~~~y~E--GvdsLS~~ELq~AC~ssRGmr~~vs~e~Lr~qL~qWLdL 85 (164)
+..+....+|.+ ++++||.+.|...|+. -||....+..-+|.+|..++..
T Consensus 153 ~eil~~~~lF~d~~~Ld~Lsr~~L~~L~r~-~~l~~~~~~~~lr~rL~~~~~~ 204 (268)
T PF07766_consen 153 EEILKVAKLFKDELTLDNLSRPHLRALCRL-LGLTPFGPSSLLRRRLRKRLRY 204 (268)
T ss_dssp HHHHHHHTTS-HHHHHHHS-HHHHHHHHHH-TT----SSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCcccccCCHHHHHHHHHH-hccCcCCchHHHHHHHHHHHHH
Confidence 334444455444 8999999999999995 9998888888899999887653
No 12
>PF00605 IRF: Interferon regulatory factor transcription factor; InterPro: IPR001346 Viral infections induce the expression of type I interferons (IFN-alpha and IFN-beta) genes. The induction is due to the transcriptional activation of the IFN genes. Interferon regulatory factor I (IRF-1) is one of the transcription factors responsible for that activation. IRF-1 binds to an upstream regulatory cis element, known as the interferon consensus sequence (ICS), which is found in the promoters of type I IFN and IFN-inducible MHC class I genes. Interferon regulatory factor 2 (IRF-2) is a protein that also interacts with the ICS, but that does not function as an activator; rather, it suppresses the function of IRF-1 under certain circumstances []. These proteins share a highly conserved N-terminal domain of about 100 amino acid residues which is involved in DNA-binding and which contain five conserved tryptophans. This domain is known as a 'tryptophan pentad repeat' or a 'tryptophan cluster' and is also present in: Interferon consensus sequence binding protein (ICSBP) [], a transcription factor expressed predominantly in lymphoid tissues and induced by IFN-gamma that also binds to the ICS. Transcriptional regulator ISGF3 gamma subunit []. ISGF3 is responsible for the initial stimulation of interferon-alpha-responsive genes. It recognises and binds to the interferon-stimulated response element (ISRE) within the regulatory sequences of target genes. Interferon regulatory factor 3 (IRF-3). Interferon regulatory factor 4 (IRF-4) which binds to the interferon- stimulated response element (ISRE) of the MHC class I promoter. Interferon regulatory factor 5 (IRF-5). Interferon regulatory factor 6 (IRF-6). Interferon regulatory factor 7 (IRF-7). Gamma Herpesviruses vIRF-1, -2 and -3, proteins with homology to the cellular transcription factors of the IRF family []. Neither vIRF-1 nor vIRF-2 bind to DNA with the same specificity as cellular IRFs, indicating that if vIRFs are DNA-binding proteins, their binding has a pattern distinct from that of the cellular IRFs. Whether vIRF-3 can bind DNA with the same specificity as cellular IRFs is not known. The IRF tryptophan pentad repeat DNA-binding domain has an alpha/beta architecture comprising a cluster of three alpha-helices (alpha1-alpha3) flanked on one side by a mixed four-stranded beta-sheet (beta1-beta4). It forms a helix-turn-helix motif that binds to ISRE consensus sequences found in target promoters. Three of the tryptophan residues contact DNA by recognising a GAAA sequence []. This entry represents the IRF tryptophan pentad repeat DNA-binding domain.; GO: 0000975 regulatory region DNA binding; PDB: 2IRF_H 1IRF_A 1IRG_A 2DLL_A 3QU3_C 2PI0_D 2O6G_G 1T2K_A 2O61_A 3QU6_C ....
Probab=40.54 E-value=14 Score=28.21 Aligned_cols=57 Identities=16% Similarity=0.167 Sum_probs=43.3
Q ss_pred ccccccccCCccchhhhccccccccccchhhhhhhhhhhhhhcCCHHH----HHHHHHHhcCCc
Q 031182 8 LAFKVRFLNNNFQPACCTWSRPYFCSFKNWILKYGKYSECEAALSKAL----ITELLKEHYTID 67 (164)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~y~EGvdsLS~~E----Lq~AC~ssRGmr 67 (164)
--|++|.-...-+.++. -.-..=|+-|-..+|+|-+|++..+... ++.|-.+++++.
T Consensus 28 t~FrIPWkH~~r~~~~~---~~D~~iFkaWA~~~Gk~~~g~~~~dp~~wKtnfRcALnk~~~~~ 88 (109)
T PF00605_consen 28 TIFRIPWKHAGRQDWDQ---EEDAKIFKAWAVHRGKYRPGIDKPDPSTWKTNFRCALNKSPDFE 88 (109)
T ss_dssp SEEEEETTSTTSTTSSH---CGGGHHHHHHHHHTTSS-CTTCSSHHHHHHHHHHHHHHHSTTEE
T ss_pred CEEEeeCccCCCCCccc---cchHHHHHHHHHHhcccCCCCCCCCHHHHHHHHHHHHhCCCCeE
Confidence 35888887777666653 2345669999999999999999999888 777877767765
No 13
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=39.25 E-value=81 Score=22.27 Aligned_cols=35 Identities=14% Similarity=0.093 Sum_probs=27.0
Q ss_pred hhhhhcCCHHHHHHHHHHhcCCccCCChhHHHHHHH
Q 031182 45 SECEAALSKALITELLKEHYTIDAVANFDSLCHGLH 80 (164)
Q Consensus 45 ~EGvdsLS~~ELq~AC~ssRGmr~~vs~e~Lr~qL~ 80 (164)
.|-+++|..+-|.+|-++ ||++.+.|..+=-+.|.
T Consensus 9 a~eLe~lGldrLK~~L~a-~GLKcGGTl~ERA~RLf 43 (60)
T PF13297_consen 9 AEELEALGLDRLKSALMA-LGLKCGGTLQERAARLF 43 (60)
T ss_pred HHHHHHhCHHHHHHHHHH-cCCccCCCHHHHHHHHH
Confidence 367788999999999995 99998876665444443
No 14
>PF01031 Dynamin_M: Dynamin central region; InterPro: IPR000375 Dynamin is a microtubule-associated force-producing protein of 100 Kd which is involved in the production of microtubule bundles. At the N terminus of dynamin is a GTPase domain (see IPR001401 from INTERPRO), and at the C terminus is a PH domain (see IPR001849 from INTERPRO). Between these two domains lies a central region of unknown function, which this entry represents.; GO: 0005525 GTP binding; PDB: 3ZVR_A 2AKA_B 2X2F_D 2X2E_D 3SNH_A 3ZYS_D 3ZYC_D 1JWY_B 1JX2_B 3SZR_A ....
Probab=36.29 E-value=29 Score=29.41 Aligned_cols=55 Identities=13% Similarity=0.141 Sum_probs=35.9
Q ss_pred ccchhhhhhhhhhhhhhcCCHHHHHHHHHHhcCCcc-C-CChhH----HHHHHHHHhhccc
Q 031182 33 SFKNWILKYGKYSECEAALSKALITELLKEHYTIDA-V-ANFDS----LCHGLHDWLDLSL 87 (164)
Q Consensus 33 ~~~~~i~~~~~y~EGvdsLS~~ELq~AC~ssRGmr~-~-vs~e~----Lr~qL~qWLdL~L 87 (164)
-|..|....--.....+.++..|+..+.+.+||... + ++..- +++++..|-+-++
T Consensus 151 ~f~~~~~~~~~~~~~~~~~~~~eI~~~i~~~~G~elp~f~p~~afe~Li~~~i~~l~~Pa~ 211 (295)
T PF01031_consen 151 IFNEWFDKFLEKIDPFEDLSDEEIRTAIRNSRGRELPGFVPESAFESLIRKQIEKLEEPAL 211 (295)
T ss_dssp HHHHHHHHHHHHTSHHHHHHHHHHHHHHHH--S-SSS-SCCHHHHHHHHHHHHHTTHHHHH
T ss_pred HHHhhhhhhhhhhccccchhHHHHHHHHHhhcccccccchhHHHHHHHHHHHHHHHHhHHH
Confidence 366676654444455777899999999998899995 3 56555 5778877765443
No 15
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=34.20 E-value=87 Score=22.62 Aligned_cols=59 Identities=17% Similarity=0.048 Sum_probs=36.9
Q ss_pred hcCCCCChHHhHHHHHhcCChhhHhhhhcccccCCc-cccchhhhHHHhHhhhhhhHhhhh
Q 031182 103 YASGEASPEKAGQATLSFLPDKIVDTVGVTTLPLED-SVLGSRRKLEFLEMQEEPIKVFDT 162 (164)
Q Consensus 103 ~~~~~~s~~daLkatLSSLPDevv~ea~v~v~e~E~-~~~d~K~KLevLkeQEElIkeE~e 162 (164)
.++...+-.+.+...|.+||+..-..+.+ +....+ ...+...=+..|...|..++.+++
T Consensus 59 ~~g~~i~d~~~v~~iL~~Lp~~y~~~~~~-i~~~~~~~~~t~~el~~~L~~~E~~~~~~~~ 118 (119)
T PF14223_consen 59 AIGKPISDEDLVSKILRSLPPSYDTFVTA-IRNSKDLPKMTLEELISRLLAEEMRLKSKEE 118 (119)
T ss_pred hcCCcccchhHHHHHHhcCCchhHHHHHH-HHhcCCCCcCCHHHHHHHHHHHHHHHHHccC
Confidence 45556777889999999999665543332 111111 112456666777888888777654
No 16
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=29.55 E-value=1.2e+02 Score=21.31 Aligned_cols=32 Identities=31% Similarity=0.229 Sum_probs=27.2
Q ss_pred hhcCCHHHHHHHHHHhcCCccCCChhHHHHHHH
Q 031182 48 EAALSKALITELLKEHYTIDAVANFDSLCHGLH 80 (164)
Q Consensus 48 vdsLS~~ELq~AC~ssRGmr~~vs~e~Lr~qL~ 80 (164)
+-.+|..+....+.. |||-...+++++.+.+.
T Consensus 43 lag~s~~eF~~~L~~-~gI~~~~~~eel~~dle 74 (76)
T PF03683_consen 43 LAGMSRWEFLELLKE-RGIPINYDEEELEEDLE 74 (76)
T ss_pred HhCCCHHHHHHHHHH-CCCCCCCCHHHHHHHHH
Confidence 456799999999996 99995589999998875
No 17
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=24.78 E-value=84 Score=20.97 Aligned_cols=30 Identities=17% Similarity=0.056 Sum_probs=21.4
Q ss_pred hhhhhhhcCCHHHHHHHHHHhcCCccCCChhHHHHHHH
Q 031182 43 KYSECEAALSKALITELLKEHYTIDAVANFDSLCHGLH 80 (164)
Q Consensus 43 ~y~EGvdsLS~~ELq~AC~ssRGmr~~vs~e~Lr~qL~ 80 (164)
+-.+|++..|..||-+++. +++.+.|..|+
T Consensus 21 l~~~G~~~vSS~~La~~~g--------i~~~qVRKDlS 50 (50)
T PF06971_consen 21 LKEEGVERVSSQELAEALG--------ITPAQVRKDLS 50 (50)
T ss_dssp HHHTT-SEE-HHHHHHHHT--------S-HHHHHHHHH
T ss_pred HHHcCCeeECHHHHHHHHC--------CCHHHhcccCC
Confidence 3458999999999988876 58888888764
No 18
>PF10309 DUF2414: Protein of unknown function (DUF2414); InterPro: IPR019416 This entry contains proteins that have no known function.
Probab=22.66 E-value=34 Score=23.95 Aligned_cols=22 Identities=18% Similarity=0.004 Sum_probs=18.6
Q ss_pred hhhhhhhhhcCCHHHHHHHHHH
Q 031182 41 YGKYSECEAALSKALITELLKE 62 (164)
Q Consensus 41 ~~~y~EGvdsLS~~ELq~AC~s 62 (164)
..++.-|||+||+.++..-..+
T Consensus 6 eavhirGvd~lsT~dI~~y~~~ 27 (62)
T PF10309_consen 6 EAVHIRGVDELSTDDIKAYFSE 27 (62)
T ss_pred ceEEEEcCCCCCHHHHHHHHHH
Confidence 4467789999999999988876
No 19
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=22.10 E-value=1.5e+02 Score=19.18 Aligned_cols=31 Identities=16% Similarity=0.142 Sum_probs=21.6
Q ss_pred HHHHHHHHHhcCCccCCChhHHHHHHHHHhh
Q 031182 54 ALITELLKEHYTIDAVANFDSLCHGLHDWLD 84 (164)
Q Consensus 54 ~ELq~AC~ssRGmr~~vs~e~Lr~qL~qWLd 84 (164)
++...||+.....-..+|.+|+++.+..-|.
T Consensus 6 ~~t~~ai~~~~~~L~~is~ERi~~El~kil~ 36 (64)
T PF12627_consen 6 PETEEAIKENAELLSKISKERIREELEKILS 36 (64)
T ss_dssp HHHHHHHHHHGGGGGGS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHhcCCHHHHHHHHHHHHc
Confidence 5667788764443346999999999988654
No 20
>PF11300 DUF3102: Protein of unknown function (DUF3102); InterPro: IPR021451 This entry is represented by Streptococcus phage 7201, Orf2. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.08 E-value=59 Score=25.82 Aligned_cols=17 Identities=12% Similarity=0.126 Sum_probs=14.9
Q ss_pred hhhhcCCHHHHHHHHHH
Q 031182 46 ECEAALSKALITELLKE 62 (164)
Q Consensus 46 EGvdsLS~~ELq~AC~s 62 (164)
-.|++||.-||++|.++
T Consensus 113 ~dv~~Mt~REL~~avke 129 (130)
T PF11300_consen 113 NDVERMTVRELQQAVKE 129 (130)
T ss_pred hhhccccHHHHHHHHhc
Confidence 45889999999999886
No 21
>PRK11436 biofilm-dependent modulation protein; Provisional
Probab=21.88 E-value=81 Score=22.69 Aligned_cols=44 Identities=18% Similarity=0.328 Sum_probs=34.1
Q ss_pred hhhhhhcCCHHHHHHHHHHhcCCcc--C-CChhHHHHHHHHHhhcccCC
Q 031182 44 YSECEAALSKALITELLKEHYTIDA--V-ANFDSLCHGLHDWLDLSLNH 89 (164)
Q Consensus 44 y~EGvdsLS~~ELq~AC~ssRGmr~--~-vs~e~Lr~qL~qWLdL~L~~ 89 (164)
||-.-.+--.++|-.|.. .|+|+ + |+++++--.|..|.+-.=|+
T Consensus 4 yy~ant~~aqp~lv~aie--qglraehgavteddilmeltkwvea~dnd 50 (71)
T PRK11436 4 YYQAENSTAEPALVNAIE--QGLRAEHGVVTEDDILMELTKWVEASDND 50 (71)
T ss_pred eecCcccccCHHHHHHHH--HHhhhhcCCcchhHHHHHHHHHHHhcccc
Confidence 344445556788999988 69996 3 89999999999999877655
No 22
>KOG0571 consensus Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism]
Probab=21.71 E-value=48 Score=31.97 Aligned_cols=55 Identities=20% Similarity=0.193 Sum_probs=36.0
Q ss_pred cccccccccCCccchhhhcc----ccc---------cccc--c--------chhhhhhhh--hhhhhhcCCHHHHHHHHH
Q 031182 7 ELAFKVRFLNNNFQPACCTW----SRP---------YFCS--F--------KNWILKYGK--YSECEAALSKALITELLK 61 (164)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~----~~~---------~~~~--~--------~~~i~~~~~--y~EGvdsLS~~ELq~AC~ 61 (164)
-|-..|||+...|..+|.+- |++ |++| | -.||+|||+ +++||..=-..=|+.-|.
T Consensus 389 GlE~RVPFLDk~F~~~~~sldPe~K~~k~~~~r~eK~vlrsafd~~~~pyLP~eilwrqkeqfsdgVgySwid~L~d~~e 468 (543)
T KOG0571|consen 389 GLEARVPFLDKRFLELAMSLDPEEKMIKPKEGRIEKYVLRSAFDTTEKPYLPDEILWRQKEQFSDGVGYSWIDGLKDHAE 468 (543)
T ss_pred ceeeecccccHHHHHHHhcCChhHhcCCcchhhHHHHHHHhhcCCcCCCcChHHHHHHHHhhhccccchHHHHHHHHHHH
Confidence 45678999999999999752 221 1221 2 249999999 888887544444444443
No 23
>PF00193 Xlink: Extracellular link domain; InterPro: IPR000538 The link domain [] is a hyaluronan(HA)-binding region found in proteins of vertebrates that are involved in the assembly of extracellular matrix, cell adhesion, and migration. The structure has been shown [] to consist of two alpha helices and two antiparallel beta sheets arranged around a large hydrophobic core similar to that of C-type lectin. This domain contains four conserved cysteines involved in two disulphide bonds. The link domain has also been termed HABM [] (HA binding module) and PTR [] (proteoglycan tandem repeat). Proteins with such a domain include the proteoglycans aggrecan, brevican, neurocan and versican, which are expressed in the CNS; the cartilage link protein (LP), a proteoglycan that together with HA and aggrecan forms multimolecular aggregates; Tumour necrosis factor-inducible protein TSG-6, which may be involved in cell-cell and cell-matrix interactions during inflammation and tumourgenesis; and CD44 antigen, the main cell surface receptor for HA.; GO: 0005540 hyaluronic acid binding, 0007155 cell adhesion; PDB: 1O7B_T 2PF5_C 1O7C_T 2JCQ_A 2JCR_A 2JCP_A 1UUH_B 1POZ_A 2I83_A.
Probab=20.35 E-value=89 Score=23.03 Aligned_cols=40 Identities=10% Similarity=0.028 Sum_probs=26.1
Q ss_pred hhhhh--cCCHHHHHHHHHHhcCCccCCChhHHHHHHHHHhhcc
Q 031182 45 SECEA--ALSKALITELLKEHYTIDAVANFDSLCHGLHDWLDLS 86 (164)
Q Consensus 45 ~EGvd--sLS~~ELq~AC~ssRGmr~~vs~e~Lr~qL~qWLdL~ 86 (164)
+++-+ .|+-.|=++||++ .|.+ ..|.++|..--+..+|.+
T Consensus 6 ~~~~~~y~l~f~eA~~~C~~-~ga~-LAs~~qL~~A~~~G~~~C 47 (92)
T PF00193_consen 6 LESPNRYKLTFTEAQQACRA-LGAR-LASPEQLEAAWKAGFETC 47 (92)
T ss_dssp EEETTSSSB-HHHHHHHHHH-TTCB-E--HHHHHHHHHTT---S
T ss_pred ecCCCcCcCcHHHHHHHHHH-cCCe-eCCHHHHHHHHHhhhhHh
Confidence 44555 7899999999996 7653 378999988877777665
Done!