Query 044191
Match_columns 87
No_of_seqs 104 out of 196
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 12:17:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044191.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044191hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09341 Pcc1: Transcription f 99.9 1.3E-27 2.9E-32 148.5 7.0 75 5-80 2-76 (76)
2 PRK14887 KEOPS complex Pcc1-li 99.9 4.2E-24 9E-29 136.7 10.4 78 2-80 2-80 (84)
3 COG2892 Uncharacterized protei 99.6 5.3E-15 1.1E-19 94.3 8.9 74 8-81 5-79 (82)
4 PRK14888 KEOPS complex Pcc1-li 97.4 0.00092 2E-08 40.2 6.2 55 23-82 2-56 (59)
5 PF04468 PSP1: PSP1 C-terminal 66.9 15 0.00033 23.0 4.3 47 16-62 24-70 (88)
6 PF05372 Delta_lysin: Delta ly 55.4 24 0.00052 17.7 2.9 19 64-82 6-24 (25)
7 PF12759 HTH_Tnp_IS1: InsA C-t 48.4 10 0.00022 21.8 1.0 18 55-72 26-43 (46)
8 PF02120 Flg_hook: Flagellar h 44.5 67 0.0014 19.0 4.8 25 35-59 25-49 (85)
9 PF13893 RRM_5: RNA recognitio 43.8 18 0.00039 19.8 1.6 19 8-26 23-41 (56)
10 KOG0131 Splicing factor 3b, su 42.2 15 0.00033 27.1 1.3 61 11-83 56-122 (203)
11 PF09840 DUF2067: Uncharacteri 41.6 1.3E+02 0.0029 21.6 7.7 63 9-76 1-63 (190)
12 PF09764 Nt_Gln_amidase: N-ter 38.9 32 0.0007 24.9 2.6 32 11-44 82-113 (184)
13 PF11774 Lsr2: Lsr2 ; InterPr 35.5 73 0.0016 21.0 3.7 38 33-70 16-53 (110)
14 PRK11700 hypothetical protein; 34.8 64 0.0014 23.6 3.6 33 8-41 115-147 (187)
15 KOG4208 Nucleolar RNA-binding 34.0 29 0.00063 25.9 1.7 16 11-26 97-112 (214)
16 PF00076 RRM_1: RNA recognitio 33.0 33 0.00072 18.7 1.6 20 8-27 41-60 (70)
17 PRK15091 ABC transporter outer 30.7 67 0.0015 24.3 3.3 33 51-83 58-90 (251)
18 PF03670 UPF0184: Uncharacteri 30.0 79 0.0017 20.2 3.0 20 61-80 28-47 (83)
19 PF10934 DUF2634: Protein of u 29.6 1.2E+02 0.0027 19.7 4.1 40 15-56 67-107 (112)
20 PF04333 VacJ: VacJ like lipop 29.2 73 0.0016 23.2 3.1 31 52-82 35-65 (200)
21 smart00361 RRM_1 RNA recogniti 26.6 54 0.0012 18.9 1.8 20 8-27 39-58 (70)
22 COG1774 Uncharacterized homolo 24.3 3.3E+02 0.0071 20.8 6.3 55 10-64 75-129 (265)
23 PF02538 Hydantoinase_B: Hydan 23.1 81 0.0018 25.8 2.7 43 33-76 251-293 (527)
24 PRK12651 putative monovalent c 23.0 2.6E+02 0.0056 19.1 5.0 52 19-70 73-151 (158)
25 PF09432 THP2: Tho complex sub 21.7 76 0.0017 22.0 2.0 22 53-74 50-71 (132)
26 PF05036 SPOR: Sporulation rel 21.7 48 0.001 18.7 0.8 17 11-27 49-65 (76)
27 PF07045 DUF1330: Protein of u 21.1 1.1E+02 0.0024 17.6 2.4 23 2-25 36-58 (65)
28 cd07268 Glo_EDI_BRP_like_4 Thi 20.8 55 0.0012 23.1 1.1 35 8-42 77-111 (149)
29 PRK08965 putative monovalent c 20.7 96 0.0021 21.4 2.3 25 19-43 77-101 (162)
No 1
>PF09341 Pcc1: Transcription factor Pcc1; InterPro: IPR015419 Pcc1 is a proposed transcription factor involved in the expression of genes regulated by alpha-factor and galactose; component of the EKC/KEOPS protein complex with Kae1, Gon7, Bud32, and Cgi121; related to human cancer-testis antigens [].; PDB: 2BNR_C 2P5W_C 3KLA_C 2F54_C 2P5E_C 2F53_C 3ENO_E 3ENC_B.
Probab=99.95 E-value=1.3e-27 Score=148.49 Aligned_cols=75 Identities=43% Similarity=0.667 Sum_probs=68.2
Q ss_pred ceeEEEEeCCChhHHHHHHhhcccCcccCccceEEEEEEECCEEEEEEEeccCchHHHHHHHHHHHHHHHHHHHHh
Q 044191 5 PCNDFEVDYESNENASIVYAALAIDKELQPDKVKRQISVIDGKLLVHFEAVEARFPRALFSAFVDVLTLETKTIEQ 80 (87)
Q Consensus 5 ~~~~L~VpF~s~~~A~ia~~sL~vD~e~~p~~v~r~l~v~g~~L~v~~~a~d~r~LRvsvnsfld~l~Lv~~tm~~ 80 (87)
.+ +++|||+|+++|++|+++|+||++++|+.++++++++|+.|.|+|+|.|.|+||+|+|||||+|+|+++||+|
T Consensus 2 ~~-~l~i~f~s~~~A~ii~~sL~~d~e~~~~~~~~~~~~~~~~L~i~~~A~d~~~LRasvns~l~~l~l~~~~i~e 76 (76)
T PF09341_consen 2 SF-TLEIPFESEEKAEIIYRSLKPDKELKPSRVKRELSVDGNKLVITIEAEDLRSLRASVNSFLDLLKLAEETIEE 76 (76)
T ss_dssp -E-EEEEE-SSHHHHHHHHHHHHHHHH-SS-SSEEEEEEESSEEEEEEEESSHHHHHHHHHHHHHHHHHHCHHH--
T ss_pred EE-EEEEEeCCHHHHHHHHHHhCCCCCCCCCcEEEEEEEeCCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 45 9999999999999999999999999999999999999999999999999999999999999999999999986
No 2
>PRK14887 KEOPS complex Pcc1-like subunit; Provisional
Probab=99.91 E-value=4.2e-24 Score=136.71 Aligned_cols=78 Identities=17% Similarity=0.357 Sum_probs=75.3
Q ss_pred CccceeEEEEeCCChhHHHHHHhhcccCcccCc-cceEEEEEEECCEEEEEEEeccCchHHHHHHHHHHHHHHHHHHHHh
Q 044191 2 WFFPCNDFEVDYESNENASIVYAALAIDKELQP-DKVKRQISVIDGKLLVHFEAVEARFPRALFSAFVDVLTLETKTIEQ 80 (87)
Q Consensus 2 ~~~~~~~L~VpF~s~~~A~ia~~sL~vD~e~~p-~~v~r~l~v~g~~L~v~~~a~d~r~LRvsvnsfld~l~Lv~~tm~~ 80 (87)
+++.+ .+++||+|+++|+++|+||.||++.+| ++++.+++++|+.|.|+|+|.|.+.||+|+|||++|++++.++++-
T Consensus 2 ~~~~~-~lei~f~s~~~A~iiy~sl~~E~~~~~~~rs~~~~~~~~~~l~i~i~A~D~~~LRAslNs~lr~i~va~e~~~~ 80 (84)
T PRK14887 2 RMHKF-TLEFEFETEERARIIYRSVLPEHGDSQGERSKADLSLDGNTIVITIEAEDLSALRASLNSWLRLIKVAEEVLEL 80 (84)
T ss_pred CCceE-EEEEEECCHHHHHHHHHHhCcCcccCCcCceEEEEEEeCCEEEEEEEECcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67888 999999999999999999999999999 7899999999999999999999999999999999999999999874
No 3
>COG2892 Uncharacterized protein conserved in archaea [Function unknown]
Probab=99.61 E-value=5.3e-15 Score=94.31 Aligned_cols=74 Identities=14% Similarity=0.336 Sum_probs=67.8
Q ss_pred EEEEeCCChhHHHHHHhhcccCcccCc-cceEEEEEEECCEEEEEEEeccCchHHHHHHHHHHHHHHHHHHHHhh
Q 044191 8 DFEVDYESNENASIVYAALAIDKELQP-DKVKRQISVIDGKLLVHFEAVEARFPRALFSAFVDVLTLETKTIEQF 81 (87)
Q Consensus 8 ~L~VpF~s~~~A~ia~~sL~vD~e~~p-~~v~r~l~v~g~~L~v~~~a~d~r~LRvsvnsfld~l~Lv~~tm~~f 81 (87)
.+.+.|+|++.|+++|+++.||+-..| .+.+..+..+|+.+.+++.|.|...||+++||||+|++++++.++--
T Consensus 5 ~~viE~~see~AevIY~sv~~E~~~~~~~rSrv~l~~~~~rI~l~I~A~D~s~lRaa~nS~lRlI~~a~~vi~i~ 79 (82)
T COG2892 5 EIVIEFPSEEVAEVIYRSVLPEHVEVPSRRSRVKLERDGNRIVLEIRAEDSSALRAAINSYLRLIKVAQEVIEIS 79 (82)
T ss_pred EEEEEcCcHHHHHHHHHHhhHHHhccccccceeEEEecCCEEEEEEEecchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999999999996665 56788999999999999999999999999999999999999998743
No 4
>PRK14888 KEOPS complex Pcc1-like subunit; Provisional
Probab=97.40 E-value=0.00092 Score=40.16 Aligned_cols=55 Identities=16% Similarity=0.094 Sum_probs=48.1
Q ss_pred HhhcccCcccCccceEEEEEEECCEEEEEEEeccCchHHHHHHHHHHHHHHHHHHHHhhC
Q 044191 23 YAALAIDKELQPDKVKRQISVIDGKLLVHFEAVEARFPRALFSAFVDVLTLETKTIEQFG 82 (87)
Q Consensus 23 ~~sL~vD~e~~p~~v~r~l~v~g~~L~v~~~a~d~r~LRvsvnsfld~l~Lv~~tm~~f~ 82 (87)
+++|.||-.- ..+-.++|+.+..++++.+.+.|+.++--|+.+++++-++++.-.
T Consensus 2 ~~AL~pDN~~-----~~~t~~~~~~v~~~i~~~~igsl~~TvDD~l~nl~vae~v~~~~~ 56 (59)
T PRK14888 2 AKALEPDNLD-----IMETEVDGDTVVYTIESEKIGTLLNTVDDYLMNLKVAEKVIEALS 56 (59)
T ss_pred ccccCCCCcc-----cEEEEEcCCEEEEEEEeCcHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 5678888764 466678899999999999999999999999999999999998754
No 5
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=66.93 E-value=15 Score=23.02 Aligned_cols=47 Identities=19% Similarity=0.055 Sum_probs=36.9
Q ss_pred hhHHHHHHhhcccCcccCccceEEEEEEECCEEEEEEEeccCchHHH
Q 044191 16 NENASIVYAALAIDKELQPDKVKRQISVIDGKLLVHFEAVEARFPRA 62 (87)
Q Consensus 16 ~~~A~ia~~sL~vD~e~~p~~v~r~l~v~g~~L~v~~~a~d~r~LRv 62 (87)
++.|-..|+-+.-+..+.=.-+..+++.+|+.+.+-|.|++---+|.
T Consensus 24 e~~al~~c~~~~~~~~L~m~lvd~e~~~D~~k~~fyy~a~~rvDFR~ 70 (88)
T PF04468_consen 24 EEEALKFCRELVKELGLPMKLVDVEYQFDGSKLTFYYTAESRVDFRE 70 (88)
T ss_pred HHHHHHHHHHHHHHcCCCeEEEEEEEEcCCCEEEEEEEeCCcCcHHH
Confidence 35677778888878887667789999999999999999976544443
No 6
>PF05372 Delta_lysin: Delta lysin family; InterPro: IPR008034 Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted by Staphylococcus aureus. It is thought that delta-toxin forms an amphipathic helix upon binding to lipid bilayers []. The precise mode of action of delta-lysis is unclear.; GO: 0019836 hemolysis by symbiont of host erythrocytes, 0005576 extracellular region; PDB: 2KAM_A 2DTB_A 1DTC_A.
Probab=55.38 E-value=24 Score=17.73 Aligned_cols=19 Identities=26% Similarity=0.427 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHhhC
Q 044191 64 FSAFVDVLTLETKTIEQFG 82 (87)
Q Consensus 64 vnsfld~l~Lv~~tm~~f~ 82 (87)
++..-|.++++++|.+.|-
T Consensus 6 isTIgdfvKlI~~TV~KF~ 24 (25)
T PF05372_consen 6 ISTIGDFVKLIIETVKKFT 24 (25)
T ss_dssp HHHHHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHHHHHhc
Confidence 5566788999999999884
No 7
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=48.37 E-value=10 Score=21.83 Aligned_cols=18 Identities=17% Similarity=0.185 Sum_probs=16.0
Q ss_pred ccCchHHHHHHHHHHHHH
Q 044191 55 VEARFPRALFSAFVDVLT 72 (87)
Q Consensus 55 ~d~r~LRvsvnsfld~l~ 72 (87)
..+|.|++|+|..+..||
T Consensus 26 dtaRvL~I~~nTVlrtLK 43 (46)
T PF12759_consen 26 DTARVLKISINTVLRTLK 43 (46)
T ss_pred hhHhHhcchHHHHHHHHh
Confidence 678999999999988876
No 8
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=44.49 E-value=67 Score=19.01 Aligned_cols=25 Identities=24% Similarity=0.369 Sum_probs=18.5
Q ss_pred cceEEEEEEECCEEEEEEEeccCch
Q 044191 35 DKVKRQISVIDGKLLVHFEAVEARF 59 (87)
Q Consensus 35 ~~v~r~l~v~g~~L~v~~~a~d~r~ 59 (87)
..+...+.+.|+.+.|+|.+.....
T Consensus 25 G~v~v~l~~~~~~l~v~~~~~~~~~ 49 (85)
T PF02120_consen 25 GSVEVKLRLQGGNLSVQFTAENPET 49 (85)
T ss_dssp --EEEEEEEETTEEEEEEE--SSHH
T ss_pred CcEEEEEEEeCCEEEEEEEECCHHH
Confidence 5689999999999999999976643
No 9
>PF13893 RRM_5: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); PDB: 2PE8_A 2PEH_A 2D9O_A 1A9N_D 2DIT_A 3S6E_A 2LQ5_A 1SJQ_A 2AD9_A 1X4D_A ....
Probab=43.79 E-value=18 Score=19.82 Aligned_cols=19 Identities=26% Similarity=0.177 Sum_probs=17.0
Q ss_pred EEEEeCCChhHHHHHHhhc
Q 044191 8 DFEVDYESNENASIVYAAL 26 (87)
Q Consensus 8 ~L~VpF~s~~~A~ia~~sL 26 (87)
..-|.|.+.++|+.|.+.|
T Consensus 23 ~a~V~f~~~~~A~~a~~~l 41 (56)
T PF13893_consen 23 FAFVEFASVEDAQKAIEQL 41 (56)
T ss_dssp EEEEEESSHHHHHHHHHHH
T ss_pred EEEEEECCHHHHHHHHHHh
Confidence 4568899999999999988
No 10
>KOG0131 consensus Splicing factor 3b, subunit 4 [RNA processing and modification]
Probab=42.15 E-value=15 Score=27.06 Aligned_cols=61 Identities=18% Similarity=0.259 Sum_probs=43.0
Q ss_pred EeCCChhHHHHHHhhcccCcccCccceEEEEEEECCEEEEEEEeccCchHHHHHHHHHHHH------HHHHHHHHhhCC
Q 044191 11 VDYESNENASIVYAALAIDKELQPDKVKRQISVIDGKLLVHFEAVEARFPRALFSAFVDVL------TLETKTIEQFGQ 83 (87)
Q Consensus 11 VpF~s~~~A~ia~~sL~vD~e~~p~~v~r~l~v~g~~L~v~~~a~d~r~LRvsvnsfld~l------~Lv~~tm~~f~~ 83 (87)
+.|.++++|+.|++.|.- +++=|.-|.|.-.+..-..++++-|-|+-+| ++...|...||+
T Consensus 56 ~Ef~~eedadYAikiln~------------VkLYgrpIrv~kas~~~~nl~vganlfvgNLd~~vDe~~L~dtFsafG~ 122 (203)
T KOG0131|consen 56 AEFRTEEDADYAIKILNM------------VKLYGRPIRVNKASAHQKNLDVGANLFVGNLDPEVDEKLLYDTFSAFGV 122 (203)
T ss_pred EEEechhhhHHHHHHHHH------------HHhcCceeEEEecccccccccccccccccccCcchhHHHHHHHHHhccc
Confidence 679999999999998862 2233455666666666677777777777666 455666667764
No 11
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=41.64 E-value=1.3e+02 Score=21.63 Aligned_cols=63 Identities=10% Similarity=0.167 Sum_probs=45.6
Q ss_pred EEEeCCChhHHHHHHhhcccCcccCccceEEEEEEECCEEEEEEEeccCchHHHHHHHHHHHHHHHHH
Q 044191 9 FEVDYESNENASIVYAALAIDKELQPDKVKRQISVIDGKLLVHFEAVEARFPRALFSAFVDVLTLETK 76 (87)
Q Consensus 9 L~VpF~s~~~A~ia~~sL~vD~e~~p~~v~r~l~v~g~~L~v~~~a~d~r~LRvsvnsfld~l~Lv~~ 76 (87)
+++-|++.++++=.++-|+ +..+. ...++.+.||.|.|+..+.+. .+|-+....-+-...+-.
T Consensus 1 i~~~~~~~~E~~~fle~l~--~~~~~--~~~~v~~k~n~l~I~i~G~~~-eike~~~~Ik~~~~~vr~ 63 (190)
T PF09840_consen 1 ISFKFRDDEECEEFLERLS--KMVKS--IYIYVEVKGNSLKIEIQGYEK-EIKEAIRRIKELVRRVRS 63 (190)
T ss_pred CeEEcCChHHHHHHHHHHH--hhccC--cEEEEEEeCCEEEEEEecChH-HHHHHHHHHHHHHHHHHH
Confidence 3577899999999999883 22333 345788899999999999887 777776655554444433
No 12
>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=38.94 E-value=32 Score=24.91 Aligned_cols=32 Identities=19% Similarity=0.373 Sum_probs=20.6
Q ss_pred EeCCChhHHHHHHhhcccCcccCccceEEEEEEE
Q 044191 11 VDYESNENASIVYAALAIDKELQPDKVKRQISVI 44 (87)
Q Consensus 11 VpF~s~~~A~ia~~sL~vD~e~~p~~v~r~l~v~ 44 (87)
+|||+ .-.+.+.+++.+|..+.+. .+|.|.|-
T Consensus 82 Lpfp~-~~~~Y~~~tf~~~~~l~~~-~~r~FRVV 113 (184)
T PF09764_consen 82 LPFPC-PFDEYVEETFRPDMQLPPE-YRRKFRVV 113 (184)
T ss_dssp S-SSE-EHHHHHHHTT--STTS-GG-G--EEEEE
T ss_pred CCCCc-CHHHHHHHhcCCcccCCcc-ceeEEEEE
Confidence 68998 4568899999999888665 78888874
No 13
>PF11774 Lsr2: Lsr2 ; InterPro: IPR024412 This entry represents Lsr2, which is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homologue of the H-NS-like proteins []. H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression [, ].; PDB: 4E1R_B 4E1P_B 2KNG_A.
Probab=35.45 E-value=73 Score=20.99 Aligned_cols=38 Identities=8% Similarity=0.085 Sum_probs=31.7
Q ss_pred CccceEEEEEEECCEEEEEEEeccCchHHHHHHHHHHH
Q 044191 33 QPDKVKRQISVIDGKLLVHFEAVEARFPRALFSAFVDV 70 (87)
Q Consensus 33 ~p~~v~r~l~v~g~~L~v~~~a~d~r~LRvsvnsfld~ 70 (87)
.+..-..+|.++|..-.|..++..+..||.++.-|++.
T Consensus 16 ~~a~etv~F~ldG~~YeIDLs~~na~~lr~~l~~yi~~ 53 (110)
T PF11774_consen 16 SEADETVRFGLDGVDYEIDLSAENAAKLRDALAPYIAA 53 (110)
T ss_dssp SB-SEEEEEEETTEEEEEEE-HHHHHHHHHHHHHHHHH
T ss_pred CccceEEEEEECCeEEEEECCHHHHHHHHHHHHHHHHH
Confidence 34446889999999999999999999999999988763
No 14
>PRK11700 hypothetical protein; Provisional
Probab=34.76 E-value=64 Score=23.56 Aligned_cols=33 Identities=18% Similarity=0.143 Sum_probs=17.5
Q ss_pred EEEEeCCChhHHHHHHhhcccCcccCccceEEEE
Q 044191 8 DFEVDYESNENASIVYAALAIDKELQPDKVKRQI 41 (87)
Q Consensus 8 ~L~VpF~s~~~A~ia~~sL~vD~e~~p~~v~r~l 41 (87)
.+.+|+.- +...-..++|.+|..+.+..++..+
T Consensus 115 ElVlp~~~-~t~~~~~~all~~~~l~~~gikvK~ 147 (187)
T PRK11700 115 ELVLPGDP-ETLDARALALLSDEGLSLPGIKVKT 147 (187)
T ss_pred EEEecCCc-chHHHHHHHhccccccccCCcEEEe
Confidence 33344433 2344455566777666666566554
No 15
>KOG4208 consensus Nucleolar RNA-binding protein NIFK [General function prediction only]
Probab=33.98 E-value=29 Score=25.86 Aligned_cols=16 Identities=38% Similarity=0.565 Sum_probs=14.6
Q ss_pred EeCCChhHHHHHHhhc
Q 044191 11 VDYESNENASIVYAAL 26 (87)
Q Consensus 11 VpF~s~~~A~ia~~sL 26 (87)
|.|+|++-|+||..+.
T Consensus 97 VEFEs~eVA~IaAETM 112 (214)
T KOG4208|consen 97 VEFESEEVAKIAAETM 112 (214)
T ss_pred EEeccHHHHHHHHHHh
Confidence 8999999999998875
No 16
>PF00076 RRM_1: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); InterPro: IPR000504 Many eukaryotic proteins containing one or more copies of a putative RNA-binding domain of about 90 amino acids are known to bind single-stranded RNAs [, , ]. The largest group of single strand RNA-binding proteins is the eukaryotic RNA recognition motif (RRM) family that contains an eight amino acid RNP-1 consensus sequence [, ]. RRM proteins have a variety of RNA binding preferences and functions, and include heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing (SR, U2AF, Sxl), protein components of small nuclear ribonucleoproteins (U1 and U2 snRNPs), and proteins that regulate RNA stability and translation (PABP, La, Hu) [, , ]. The RRM in heterodimeric splicing factor U2 snRNP auxiliary factor (U2AF) appears to have two RRM-like domains with specialised features for protein recognition []. The motif also appears in a few single stranded DNA binding proteins. The typical RRM consists of four anti-parallel beta-strands and two alpha-helices arranged in a beta-alpha-beta-beta-alpha-beta fold with side chains that stack with RNA bases. Specificity of RNA binding is determined by multiple contacts with surrounding amino acids. A third helix is present during RNA binding in some cases []. The RRM is reviewed in a number of publications [, , ].; GO: 0003676 nucleic acid binding; PDB: 2RNE_A 2DGO_A 2DO4_A 1YTY_B 2VOO_B 2VOP_A 2VON_B 1ZH5_B 2VOD_A 1S79_A ....
Probab=33.03 E-value=33 Score=18.71 Aligned_cols=20 Identities=30% Similarity=0.318 Sum_probs=16.6
Q ss_pred EEEEeCCChhHHHHHHhhcc
Q 044191 8 DFEVDYESNENASIVYAALA 27 (87)
Q Consensus 8 ~L~VpF~s~~~A~ia~~sL~ 27 (87)
.--|-|.++++|+.|.+.+.
T Consensus 41 ~a~V~F~~~~~a~~a~~~l~ 60 (70)
T PF00076_consen 41 YAFVEFESEEDAEKALEELN 60 (70)
T ss_dssp EEEEEESSHHHHHHHHHHHT
T ss_pred eEEEEEcCHHHHHHHHHHcC
Confidence 34588999999999998764
No 17
>PRK15091 ABC transporter outer membrane lipoprotein; Provisional
Probab=30.72 E-value=67 Score=24.28 Aligned_cols=33 Identities=18% Similarity=0.156 Sum_probs=28.1
Q ss_pred EEEeccCchHHHHHHHHHHHHHHHHHHHHhhCC
Q 044191 51 HFEAVEARFPRALFSAFVDVLTLETKTIEQFGQ 83 (87)
Q Consensus 51 ~~~a~d~r~LRvsvnsfld~l~Lv~~tm~~f~~ 83 (87)
-|......-.|.+|++|++||.-....++.+-+
T Consensus 58 gY~~v~P~~vr~gv~Nff~NL~~P~~~vN~lLQ 90 (251)
T PRK15091 58 AWRDYVPQPARNGLSNFTGNLEEPASMVNYFLQ 90 (251)
T ss_pred hhchhCChHHHHHHHHHHHHHhhHHHHHHHHhc
Confidence 467788999999999999999999888876543
No 18
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=29.95 E-value=79 Score=20.22 Aligned_cols=20 Identities=25% Similarity=0.275 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 044191 61 RALFSAFVDVLTLETKTIEQ 80 (87)
Q Consensus 61 Rvsvnsfld~l~Lv~~tm~~ 80 (87)
-.+|||.||.|.-++..+++
T Consensus 28 ~~~ins~LD~Lns~LD~LE~ 47 (83)
T PF03670_consen 28 YAAINSMLDQLNSCLDHLEQ 47 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999988875
No 19
>PF10934 DUF2634: Protein of unknown function (DUF2634); InterPro: IPR020288 This entry is represented by the Bacteriophage EJ-1, Orf60. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Bacteriophage EJ-1, Orf60 function has not been characterised. It has been shown to be simialr to XkdS (P54331 from SWISSPROT), which is encoded on a phage-like element (prophage) of PSBX found in Bacillus subtilis.
Probab=29.62 E-value=1.2e+02 Score=19.69 Aligned_cols=40 Identities=20% Similarity=0.184 Sum_probs=29.6
Q ss_pred ChhHHHHHHhhcccCcccCccce-EEEEEEECCEEEEEEEecc
Q 044191 15 SNENASIVYAALAIDKELQPDKV-KRQISVIDGKLLVHFEAVE 56 (87)
Q Consensus 15 s~~~A~ia~~sL~vD~e~~p~~v-~r~l~v~g~~L~v~~~a~d 56 (87)
..+.-..+..+|.+|+.... | .-+++.+|+.|.|+|...+
T Consensus 67 ~sEi~r~I~EaL~~d~rI~~--V~~f~f~~~~~~l~v~f~V~t 107 (112)
T PF10934_consen 67 ESEIEREIEEALLQDPRITS--VENFSFEWEGDSLYVSFTVTT 107 (112)
T ss_pred HHHHHHHHHHHHhcCCCcce--EEEEEEEEECCEEEEEEEEEE
Confidence 34445678899999997653 3 4467888999999998754
No 20
>PF04333 VacJ: VacJ like lipoprotein; InterPro: IPR007428 Lipoproteins in Gram-negative microbes also act as structural stabilisers, forming non-covalent bonds with peptidoglycan on the outer membrane of the cell []. Following completion of the genomes of several Gram-negative prokaryotes, a putative lipoprotein, VacJ, has been discovered in the raw sequence open reading frames. Biochemical analysis of the Shigella flexneri VacJ protein revealed it to be essential for virulence, promoting spread of bacterial cells through the intercellular space of tissues []. Upon expression in the facultative intracellular microbe, host cells form membranous protrusions containing the pathogen, allowing it to move to the cytoplasm of the next target cell. As homologues of this lipoprotein have largely been found in obligate or facultative intracellular microbial genomes, it appears to be specific for that particular lifestyle []. ; GO: 0016020 membrane
Probab=29.17 E-value=73 Score=23.18 Aligned_cols=31 Identities=16% Similarity=0.137 Sum_probs=25.5
Q ss_pred EEeccCchHHHHHHHHHHHHHHHHHHHHhhC
Q 044191 52 FEAVEARFPRALFSAFVDVLTLETKTIEQFG 82 (87)
Q Consensus 52 ~~a~d~r~LRvsvnsfld~l~Lv~~tm~~f~ 82 (87)
|...-..-.|.+|++|++||.-....++.+-
T Consensus 35 Y~~v~P~pvr~gv~Nf~~NL~~P~~~vN~lL 65 (200)
T PF04333_consen 35 YRKVVPDPVRTGVSNFFSNLREPVRFVNNLL 65 (200)
T ss_pred cchhCCHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 4556677899999999999999888877653
No 21
>smart00361 RRM_1 RNA recognition motif.
Probab=26.63 E-value=54 Score=18.94 Aligned_cols=20 Identities=20% Similarity=0.366 Sum_probs=16.5
Q ss_pred EEEEeCCChhHHHHHHhhcc
Q 044191 8 DFEVDYESNENASIVYAALA 27 (87)
Q Consensus 8 ~L~VpF~s~~~A~ia~~sL~ 27 (87)
-.-|-|.++++|.-|++.|.
T Consensus 39 ~~fV~f~~~~dA~~A~~~l~ 58 (70)
T smart00361 39 NVYITFERSEDAARAIVDLN 58 (70)
T ss_pred EEEEEECCHHHHHHHHHHhC
Confidence 35688999999999998653
No 22
>COG1774 Uncharacterized homolog of PSP1 [Function unknown]
Probab=24.35 E-value=3.3e+02 Score=20.83 Aligned_cols=55 Identities=18% Similarity=0.181 Sum_probs=47.0
Q ss_pred EEeCCChhHHHHHHhhcccCcccCccceEEEEEEECCEEEEEEEeccCchHHHHH
Q 044191 10 EVDYESNENASIVYAALAIDKELQPDKVKRQISVIDGKLLVHFEAVEARFPRALF 64 (87)
Q Consensus 10 ~VpF~s~~~A~ia~~sL~vD~e~~p~~v~r~l~v~g~~L~v~~~a~d~r~LRvsv 64 (87)
..-|.+++.|...|..--.++.+--.-+..+|+++.|.+++-|+|...--.|.-+
T Consensus 75 ~~~~~~~~~a~~~~~~k~~e~~Ldm~lv~~~~~~d~n~~v~~~ta~grvDfr~lv 129 (265)
T COG1774 75 NLNFASAKKAFTICIVKFEEHRLDMKLVDVEITLDNNKYVFLFTARGRVDFRELV 129 (265)
T ss_pred hhhhccHHHHHHHHHHHHHhCCcceEEEEEEeeccCccEEEEeccccchhHHHHH
Confidence 4568899999999999999999988889999999999999999998755555544
No 23
>PF02538 Hydantoinase_B: Hydantoinase B/oxoprolinase; InterPro: IPR003692 An appreciable fraction of the sulphur present in mammals occurs in the form of glutathione. The synthesis of glutathione and its utilization take place by the reactions of the gamma-glutamyl cycle, which include those catalysed by gamma-glutamylcysteine and glutathione synthetases, gamma-glutamyl transpeptidase, cysteinylglycinase, gamma-glutamyl cyclotransferease, and 5-oxoprolinase []. This family includes N-methylhydantoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase 3.5.2.9 from EC which catalyses the formation of L-glutamate from 5-oxo-L-proline. These enzymes are part of the oxoprolinase family and are related to hydantoinase_A.; GO: 0003824 catalytic activity
Probab=23.10 E-value=81 Score=25.84 Aligned_cols=43 Identities=16% Similarity=0.206 Sum_probs=33.2
Q ss_pred CccceEEEEEEECCEEEEEEEeccCchHHHHHHHHHHHHHHHHH
Q 044191 33 QPDKVKRQISVIDGKLLVHFEAVEARFPRALFSAFVDVLTLETK 76 (87)
Q Consensus 33 ~p~~v~r~l~v~g~~L~v~~~a~d~r~LRvsvnsfld~l~Lv~~ 76 (87)
.+-.++.+++++|..|.+.|+.++.- .+.++|+-+-...-.+.
T Consensus 251 ~~i~i~v~vtv~gd~l~~DfsGt~pq-~~~~iN~~~~~t~~~~~ 293 (527)
T PF02538_consen 251 EPIKIKVTVTVKGDELTVDFSGTSPQ-VPGPINCPLASTRAAVY 293 (527)
T ss_pred cEEEEEEEEEECCCEEEEEcCCCCcc-cCCCcccCHHHHHHHHH
Confidence 34568888899999999999998665 68888887766554444
No 24
>PRK12651 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=23.01 E-value=2.6e+02 Score=19.13 Aligned_cols=52 Identities=13% Similarity=0.103 Sum_probs=34.8
Q ss_pred HHHHHhhcccCcccCccceEEEEEEE------------------------C--CEEEEEEE-eccCchHHHHHHHHHHH
Q 044191 19 ASIVYAALAIDKELQPDKVKRQISVI------------------------D--GKLLVHFE-AVEARFPRALFSAFVDV 70 (87)
Q Consensus 19 A~ia~~sL~vD~e~~p~~v~r~l~v~------------------------g--~~L~v~~~-a~d~r~LRvsvnsfld~ 70 (87)
.++|+.++.+.+.++|..++..+.+. + +.|.||.- +.|....|..+.+-++.
T Consensus 73 ~~Va~~vl~p~~~~~p~iv~v~~~~~~~~~~~~la~~ITLtPGTl~vdv~~~~~~l~VH~l~~~~~~~~~~~i~~~~E~ 151 (158)
T PRK12651 73 IDVAKIVLKPKLNIEPGIVAVPTDLKTDWEITLLANLITLTPGTLTLDVSDDRKKLYIHAIDVKDKEEEIREIKDSFEK 151 (158)
T ss_pred HHHHHHHcCCCCCCCCeEEEEeccCCCHHHHHHHHHHHcCCCCeEEEEEeCCCCEEEEEEeeCCCHHHHHHHHHHHHHH
Confidence 56788888888888887666644432 2 34777654 46667788888775554
No 25
>PF09432 THP2: Tho complex subunit THP2; InterPro: IPR018557 The THO complex plays a role in coupling transcription elongation to mRNA export. It is composed of subunits THP2, HPR1, THO2 and MFT1 [].
Probab=21.73 E-value=76 Score=22.00 Aligned_cols=22 Identities=18% Similarity=0.357 Sum_probs=19.7
Q ss_pred EeccCchHHHHHHHHHHHHHHH
Q 044191 53 EAVEARFPRALFSAFVDVLTLE 74 (87)
Q Consensus 53 ~a~d~r~LRvsvnsfld~l~Lv 74 (87)
.+.|.+.||.-+..|||.+|+-
T Consensus 50 ~~~d~~~lr~~L~~YLD~IKm~ 71 (132)
T PF09432_consen 50 PSTDTEELRAQLDRYLDDIKME 71 (132)
T ss_pred CCccHHHHHHHHHHHHHHHHHH
Confidence 6788999999999999999863
No 26
>PF05036 SPOR: Sporulation related domain; InterPro: IPR007730 This 70 residue domain is composed of two 35 residue repeats that are found in bacterial proteins involved in sporulation and cell division, such as FtsN, CwlM and RlpA. This repeat might be involved in binding peptidoglycan. FtsN is an essential cell division protein with a simple bitopic topology: a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. The repeats lie at the periplasmic C terminus, which has an RNP-like fold []. FtsN localises to the septum ring complex. The CwlM protein is a cell wall hydrolase, where the C-terminal region, including the repeats, determines substrate specificity []. RlpA is a rare lipoprotein A protein that may be important for cell division. Its N-terminal cysteine may be attached to thioglyceride and N-fatty acyl residues [].; PDB: 1X60_A 1UTA_A.
Probab=21.66 E-value=48 Score=18.67 Aligned_cols=17 Identities=24% Similarity=0.253 Sum_probs=15.6
Q ss_pred EeCCChhHHHHHHhhcc
Q 044191 11 VDYESNENASIVYAALA 27 (87)
Q Consensus 11 VpF~s~~~A~ia~~sL~ 27 (87)
=||+|.++|+-+++.|.
T Consensus 49 G~f~~~~~A~~~~~~l~ 65 (76)
T PF05036_consen 49 GPFSSREEAEAALRKLK 65 (76)
T ss_dssp CCECTCCHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHh
Confidence 49999999999999887
No 27
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=21.08 E-value=1.1e+02 Score=17.63 Aligned_cols=23 Identities=22% Similarity=0.276 Sum_probs=17.0
Q ss_pred CccceeEEEEeCCChhHHHHHHhh
Q 044191 2 WFFPCNDFEVDYESNENASIVYAA 25 (87)
Q Consensus 2 ~~~~~~~L~VpF~s~~~A~ia~~s 25 (87)
|+... .+-|.|||.+.|.=-+++
T Consensus 36 ~~~~~-~viieFPs~~aa~~~~~s 58 (65)
T PF07045_consen 36 WDPDR-VVIIEFPSMEAAKAWYNS 58 (65)
T ss_dssp -SSSE-EEEEEESSHHHHHHHHCS
T ss_pred CCCCe-EEEEECCCHHHHHHHHCC
Confidence 55556 788999999998766553
No 28
>cd07268 Glo_EDI_BRP_like_4 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=20.77 E-value=55 Score=23.08 Aligned_cols=35 Identities=14% Similarity=0.120 Sum_probs=15.2
Q ss_pred EEEEeCCChhHHHHHHhhcccCcccCccceEEEEE
Q 044191 8 DFEVDYESNENASIVYAALAIDKELQPDKVKRQIS 42 (87)
Q Consensus 8 ~L~VpF~s~~~A~ia~~sL~vD~e~~p~~v~r~l~ 42 (87)
.+.+|+.-...-+-+...|.-...+.+..++..++
T Consensus 77 E~Vlp~~~~~~~~~~~~ll~~~~~~~~~gikvK~S 111 (149)
T cd07268 77 EIVIPSPPQESIELRAPLLLKSPPLLNAGLKVKFS 111 (149)
T ss_pred EEEecCCcchHHHHHHHhhhcccccccCCcEEEec
Confidence 34444444433334443333324444444555553
No 29
>PRK08965 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=20.75 E-value=96 Score=21.42 Aligned_cols=25 Identities=12% Similarity=0.191 Sum_probs=19.3
Q ss_pred HHHHHhhcccCcccCccceEEEEEE
Q 044191 19 ASIVYAALAIDKELQPDKVKRQISV 43 (87)
Q Consensus 19 A~ia~~sL~vD~e~~p~~v~r~l~v 43 (87)
.++|+.++.|+..++|..++..+++
T Consensus 77 ~~Va~~vl~p~~~i~P~iv~vp~~~ 101 (162)
T PRK08965 77 IQVAWLILRPGPRPRPGFVAVPLRL 101 (162)
T ss_pred HHHHHHHcCCCCCCCCeEEEEeecC
Confidence 4688899999888888877765544
Done!