Query 038216
Match_columns 132
No_of_seqs 106 out of 431
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 08:46:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038216.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038216hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1668 Elongation factor 1 be 100.0 1.2E-47 2.5E-52 307.6 9.0 128 2-132 98-231 (231)
2 cd00292 EF1B Elongation factor 100.0 9.4E-36 2E-40 208.9 11.5 88 41-132 1-88 (88)
3 PRK00435 ef1B elongation facto 100.0 7E-35 1.5E-39 204.6 10.6 87 42-132 2-88 (88)
4 PF00736 EF1_GNE: EF-1 guanine 100.0 4.6E-34 1E-38 200.5 10.7 87 43-132 1-89 (89)
5 TIGR00489 aEF-1_beta translati 100.0 2.8E-32 6.1E-37 191.4 10.5 87 42-132 2-88 (88)
6 COG2092 EFB1 Translation elong 100.0 2.3E-29 5.1E-34 176.3 10.0 87 42-132 2-88 (88)
7 PF10587 EF-1_beta_acid: Eukar 98.0 7.5E-06 1.6E-10 46.5 2.7 26 13-38 1-27 (28)
8 PF03927 NapD: NapD protein; 77.3 17 0.00038 24.5 6.8 69 44-129 6-74 (79)
9 PRK10553 assembly protein for 69.0 36 0.00078 23.7 7.0 70 44-129 8-77 (87)
10 TIGR03116 cas_csf3 CRISPR-asso 41.5 10 0.00023 30.6 0.4 42 50-91 39-80 (214)
11 PRK04435 hypothetical protein; 37.7 45 0.00097 24.9 3.3 78 45-129 69-146 (147)
12 PF14790 THDPS_N: Tetrahydrodi 28.9 81 0.0018 24.8 3.5 27 61-93 2-29 (167)
13 cd04888 ACT_PheB-BS C-terminal 24.7 1.8E+02 0.0039 17.9 4.7 37 87-127 39-75 (76)
14 PF09598 Stm1_N: Stm1; InterP 24.6 25 0.00054 23.6 0.0 12 11-22 3-14 (68)
15 PRK11179 DNA-binding transcrip 21.4 3.3E+02 0.0072 19.8 6.0 66 56-127 34-102 (153)
16 PF11273 DUF3073: Protein of u 21.2 33 0.00071 23.0 0.1 19 50-68 16-34 (65)
17 COG1685 Archaeal shikimate kin 20.9 1.6E+02 0.0035 24.9 4.1 35 56-90 48-87 (278)
No 1
>KOG1668 consensus Elongation factor 1 beta/delta chain [Transcription]
Probab=100.00 E-value=1.2e-47 Score=307.64 Aligned_cols=128 Identities=65% Similarity=0.944 Sum_probs=112.0
Q ss_pred CCCCCCCCCcCCCCCCChhhH-HHHHH---HHHHHHhh-cc-ccccCcceeEEEeeeCCCcccHHHHHHHHHhhccCCeE
Q 038216 2 AAADDDNDDVDLFGEETEEDK-KAAEE---RSAAIKAS-AK-RKESGKSSVLLDIKPWNDETDMQKLEEAVRSIKMEGLH 75 (132)
Q Consensus 2 ~~~~~~ddD~Dlfg~d~ee~~-~~~~~---~~~~~~~~-~k-~k~~~Ks~vvl~VkP~d~etDl~~L~~~Vr~i~~~Gl~ 75 (132)
++..++|||+|||||++||++ ++++. |.++|+.+ ++ +.+++||+|+|+|||||++|||.+|+.+||+|+|+||.
T Consensus 98 ~ae~dddDDiDLFGsd~EEEd~eA~~~~eErla~y~~kka~k~~~iakssvlLdvkpwddeTdm~~~e~~vrsi~~~gl~ 177 (231)
T KOG1668|consen 98 AAEADDDDDVDLFGSDDEEEDEEAARIREERLAAYAAKKAKKPPPIAKSSVLLDVKPWDDETDMKELEECVRSIEMDGLV 177 (231)
T ss_pred cccccccccccccCCccccchhHHHHHHhhhhhhhhHHhccCCcccccceEEeecCCcCCCCCHHHHHHHHHHhhhccce
Confidence 455778999999999877644 45544 44445443 22 34599999999999999999999999999999999999
Q ss_pred EeeeEEeeeeeeeeeEEEEEEEeCCCCChhHHHHhhhcccccCCCceeeEeeeeecC
Q 038216 76 WGASKLVPVGYGIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEYVQSCDIVAFNKI 132 (132)
Q Consensus 76 wg~~k~~piafGlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~VqSvdI~~fnki 132 (132)
||+++++|||||||+|||+|+|+|++||+|.+++. +..+|++||||||++||||
T Consensus 178 wgasklvpvGygikKlqi~~vveddkvs~D~l~e~---i~~~e~~Vqs~di~afnki 231 (231)
T KOG1668|consen 178 WGASKLVPVGYGIKKLQIQCVVEDDKVSIDDLIEE---ITKFEDHVQSVDIAAFNKI 231 (231)
T ss_pred eccccccccccceeeEEEEEEEEcCccccchhHHH---hhhhhcceeeehhhhcccC
Confidence 99999999999999999999999999999999999 7788899999999999997
No 2
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=100.00 E-value=9.4e-36 Score=208.89 Aligned_cols=88 Identities=48% Similarity=0.783 Sum_probs=84.5
Q ss_pred cCcceeEEEeeeCCCcccHHHHHHHHHhhccCCeEEeeeEEeeeeeeeeeEEEEEEEeCCCCChhHHHHhhhcccccCCC
Q 038216 41 SGKSSVLLDIKPWNDETDMQKLEEAVRSIKMEGLHWGASKLVPVGYGIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEY 120 (132)
Q Consensus 41 ~~Ks~vvl~VkP~d~etDl~~L~~~Vr~i~~~Gl~wg~~k~~piafGlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~ 120 (132)
.+||+++|+|||||++|||++|+++||+++++||+||+++++|||||||+||++|+|+|++||||+|+++ +... ++
T Consensus 1 mak~~vvl~V~P~~~e~Dl~~l~~~Ik~~~~~gl~~~~~~~epiaFGlk~L~i~~vv~D~~~~td~lee~---i~~~-d~ 76 (88)
T cd00292 1 MAKSLVVLKVKPWDDEVDLDELEEKIRAILMDGLLWGKSKLEPIAFGLKALQIYCVVEDDEGGTDELEEA---ISEE-DG 76 (88)
T ss_pred CceEEEEEEEecCCCCcCHHHHHHHHHHhCcCCcEEEEEEEEEeeeEeeEEEEEEEEEeCCcCcHHHHHH---Hhcc-CC
Confidence 3799999999999999999999999999999999999999999999999999999999999999999999 6664 89
Q ss_pred ceeeEeeeeecC
Q 038216 121 VQSCDIVAFNKI 132 (132)
Q Consensus 121 VqSvdI~~fnki 132 (132)
||||||++||||
T Consensus 77 VqsveI~~~~ki 88 (88)
T cd00292 77 VQSVDVEAFNKL 88 (88)
T ss_pred ceEEEEEEEEeC
Confidence 999999999997
No 3
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=100.00 E-value=7e-35 Score=204.63 Aligned_cols=87 Identities=21% Similarity=0.423 Sum_probs=84.4
Q ss_pred CcceeEEEeeeCCCcccHHHHHHHHHhhccCCeEEeeeEEeeeeeeeeeEEEEEEEeCCCCChhHHHHhhhcccccCCCc
Q 038216 42 GKSSVLLDIKPWNDETDMQKLEEAVRSIKMEGLHWGASKLVPVGYGIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEYV 121 (132)
Q Consensus 42 ~Ks~vvl~VkP~d~etDl~~L~~~Vr~i~~~Gl~wg~~k~~piafGlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~V 121 (132)
+|++++|+|||||++|||++|+++||+++++||.||+++++|||||||+||++|+|+|++||||+|+++ |++|++ |
T Consensus 2 ~~v~vv~~V~P~d~e~Dl~~L~~~ik~~~~~g~~~~~~~~ePIaFGLkaL~i~~vv~D~~~~td~lee~---i~~~e~-V 77 (88)
T PRK00435 2 GDVLAVLKVMPESPEVDLDELKEKIKEVLPEGYKINGIEEEPIAFGLKALKLYVIMPDEEGGTEPVEEA---FANVEG-V 77 (88)
T ss_pred ceEEEEEEECCCCCCcCHHHHHHHHHHhCcCCcEEeEeEEEEeeccceeEEEEEEEEcCCcCcHHHHHH---HhccCC-C
Confidence 689999999999999999999999999999999999999999999999999999999999999999999 888966 9
Q ss_pred eeeEeeeeecC
Q 038216 122 QSCDIVAFNKI 132 (132)
Q Consensus 122 qSvdI~~fnki 132 (132)
||++|++||+|
T Consensus 78 qsvei~~~~r~ 88 (88)
T PRK00435 78 ESVEVEEVSRI 88 (88)
T ss_pred cEEEEEEEecC
Confidence 99999999986
No 4
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=100.00 E-value=4.6e-34 Score=200.53 Aligned_cols=87 Identities=51% Similarity=0.842 Sum_probs=80.4
Q ss_pred cceeEEEeeeCCCcccHHHHHHHH-HhhccCCeEEe-eeEEeeeeeeeeeEEEEEEEeCCCCChhHHHHhhhcccccCCC
Q 038216 43 KSSVLLDIKPWNDETDMQKLEEAV-RSIKMEGLHWG-ASKLVPVGYGIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEY 120 (132)
Q Consensus 43 Ks~vvl~VkP~d~etDl~~L~~~V-r~i~~~Gl~wg-~~k~~piafGlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~ 120 (132)
||+++|+|||||++|||++|+++| |++.++|++|| .++++|||||||+||++|+|+|++||||+|++. +..++++
T Consensus 1 ks~vv~~V~P~d~e~Dl~~l~~~Ik~~i~~~gl~w~~~~~~epIaFGlk~L~v~~vv~D~~~~~d~lee~---i~~~~e~ 77 (89)
T PF00736_consen 1 KSSVVLKVKPWDDETDLEKLEKKIKRKIPMEGLKWGEKSKEEPIAFGLKALQVSCVVEDDEGSTDDLEEA---IESFEEG 77 (89)
T ss_dssp EEEEEEEEEESSTTS-HHHHHHHHHHHS-TTTEEEEEEEEEEEECTTEEEEEEEEEECTTTCGHHHHHHH---HTTCTTT
T ss_pred CceEEEEEeeCCCcccHHHHHHHHHHhchhcceeeeeeeeeeeecccEEEEEEEEEEEcCccChHHHHHH---HHhcCCC
Confidence 689999999999999999999999 77889999999 999999999999999999999999999999999 6566799
Q ss_pred ceeeEeeeeecC
Q 038216 121 VQSCDIVAFNKI 132 (132)
Q Consensus 121 VqSvdI~~fnki 132 (132)
||||+|++||||
T Consensus 78 Vqsvei~~~~rl 89 (89)
T PF00736_consen 78 VQSVEIESFNRL 89 (89)
T ss_dssp EEEEEEEEEEE-
T ss_pred ccEEEEEEEEcC
Confidence 999999999996
No 5
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=99.98 E-value=2.8e-32 Score=191.45 Aligned_cols=87 Identities=17% Similarity=0.318 Sum_probs=84.3
Q ss_pred CcceeEEEeeeCCCcccHHHHHHHHHhhccCCeEEeeeEEeeeeeeeeeEEEEEEEeCCCCChhHHHHhhhcccccCCCc
Q 038216 42 GKSSVLLDIKPWNDETDMQKLEEAVRSIKMEGLHWGASKLVPVGYGIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEYV 121 (132)
Q Consensus 42 ~Ks~vvl~VkP~d~etDl~~L~~~Vr~i~~~Gl~wg~~k~~piafGlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~V 121 (132)
+|++++|+|||||+++||++|+++||+++++|+.|++++.+||||||++|++.|+|+|++||||+++++ +++++ +|
T Consensus 2 ~~v~~~~kV~P~s~evDle~L~~~ik~~~~~g~~~~~~~~ePiaFGLkaL~~~~vv~D~~g~td~lee~---i~~ve-~V 77 (88)
T TIGR00489 2 GDVVAKIKVMPESPDVDLEALKEKIKERIPEGVEIRKIDEEPIAFGLVAINVMVVMGDAEGGTEAAEES---LSGIE-GV 77 (88)
T ss_pred ceEEEEEEECCCCCccCHHHHHHHHHHhCcCCcEEeeeEEEeeeccceeeEEEEEEecCCcChHHHHHH---HhcCC-Cc
Confidence 689999999999999999999999999999999999999999999999999999999999999999999 88895 79
Q ss_pred eeeEeeeeecC
Q 038216 122 QSCDIVAFNKI 132 (132)
Q Consensus 122 qSvdI~~fnki 132 (132)
||++|++||+|
T Consensus 78 ~svev~~~~r~ 88 (88)
T TIGR00489 78 ESVEVTDVRLL 88 (88)
T ss_pred cEEEEEEEEcC
Confidence 99999999986
No 6
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=2.3e-29 Score=176.32 Aligned_cols=87 Identities=25% Similarity=0.413 Sum_probs=83.5
Q ss_pred CcceeEEEeeeCCCcccHHHHHHHHHhhccCCeEEeeeEEeeeeeeeeeEEEEEEEeCCCCChhHHHHhhhcccccCCCc
Q 038216 42 GKSSVLLDIKPWNDETDMQKLEEAVRSIKMEGLHWGASKLVPVGYGIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEYV 121 (132)
Q Consensus 42 ~Ks~vvl~VkP~d~etDl~~L~~~Vr~i~~~Gl~wg~~k~~piafGlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~V 121 (132)
++++++|+|||||+++||++|+++||+++|+|++|+.+..+|||||||+|++.|+|+|.+||||++++. ++.+ ++|
T Consensus 2 ~~Vlv~lkV~P~d~evdl~~L~~~ik~~l~~g~~~~~~~~epIaFGLkal~l~vvv~D~Eg~td~~ee~---l~~v-egV 77 (88)
T COG2092 2 ADVLVVLKVMPDDPEVDLEELEEKIKEKLPEGYELIKIEEEPIAFGLKALKLYVVVEDKEGGTDALEEA---LEEV-EGV 77 (88)
T ss_pred cceEEEEEecCCCCCCCHHHHHHHHHHhccccceeccceeEeeeeeeeeEEEEEEEcccccCcHHHHHH---Hhhc-cCc
Confidence 689999999999999999999999999999999999999999999999999999999999999999999 7788 469
Q ss_pred eeeEeeeeecC
Q 038216 122 QSCDIVAFNKI 132 (132)
Q Consensus 122 qSvdI~~fnki 132 (132)
||++++++++|
T Consensus 78 ~sveve~vsrl 88 (88)
T COG2092 78 ESVEVENVSRL 88 (88)
T ss_pred ceEEEEEEEeC
Confidence 99999999986
No 7
>PF10587 EF-1_beta_acid: Eukaryotic elongation factor 1 beta central acidic region; InterPro: IPR018940 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This region is found in the centre of the beta subunits of Elongation factor-1. More information about these proteins can be found at Protein of the Month: Elongation Factors [].
Probab=97.96 E-value=7.5e-06 Score=46.47 Aligned_cols=26 Identities=38% Similarity=0.601 Sum_probs=19.1
Q ss_pred CCCCCCh-hhHHHHHHHHHHHHhhccc
Q 038216 13 LFGEETE-EDKKAAEERSAAIKASAKR 38 (132)
Q Consensus 13 lfg~d~e-e~~~~~~~~~~~~~~~~k~ 38 (132)
|||||+| |++++++.|++++++++.|
T Consensus 1 LFGSddEeed~ea~r~reeRla~y~aK 27 (28)
T PF10587_consen 1 LFGSDDEEEDEEAERIREERLAAYAAK 27 (28)
T ss_pred CCCCccccccHHHHHHHHHHHHHHHcc
Confidence 8999887 6777777777776665443
No 8
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=77.29 E-value=17 Score=24.48 Aligned_cols=69 Identities=22% Similarity=0.294 Sum_probs=46.1
Q ss_pred ceeEEEeeeCCCcccHHHHHHHHHhhccCCeEEeeeEEeeeeeeeeeEEEEEEEeCCCCChhHHHHhhhcccccCCCcee
Q 038216 44 SSVLLDIKPWNDETDMQKLEEAVRSIKMEGLHWGASKLVPVGYGIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEYVQS 123 (132)
Q Consensus 44 s~vvl~VkP~d~etDl~~L~~~Vr~i~~~Gl~wg~~k~~piafGlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~VqS 123 (132)
|++++..+|. .++.+.+.+. .++|+.+...... | ++.++++.. +.+++.+.+..|+.+ ++|-|
T Consensus 6 ss~vV~~~p~----~~~~v~~~l~--~~~gvEVh~~~~~--G------KiVVtiE~~--~~~~~~~~~~~i~~l-~GVls 68 (79)
T PF03927_consen 6 SSLVVHARPE----RLEEVAEALA--AIPGVEVHAVDED--G------KIVVTIEAE--SSEEEVDLIDAINAL-PGVLS 68 (79)
T ss_dssp EEEEEEE-CC----CHHHHHHHHC--CSTTEEEEEEETT--T------EEEEEEEES--SHHHHHHHHHHHCCS-TTEEE
T ss_pred EEEEEEECch----hHHHHHHHHH--cCCCcEEEeeCCC--C------eEEEEEEeC--ChHHHHHHHHHHHcC-CCceE
Confidence 7889999994 4555555443 3468988755432 2 366777754 456677776668888 89999
Q ss_pred eEeeee
Q 038216 124 CDIVAF 129 (132)
Q Consensus 124 vdI~~f 129 (132)
+.++.-
T Consensus 69 a~lvYh 74 (79)
T PF03927_consen 69 ASLVYH 74 (79)
T ss_dssp EEESSE
T ss_pred EEEEEE
Confidence 988653
No 9
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=69.04 E-value=36 Score=23.67 Aligned_cols=70 Identities=14% Similarity=0.252 Sum_probs=44.8
Q ss_pred ceeEEEeeeCCCcccHHHHHHHHHhhccCCeEEeeeEEeeeeeeeeeEEEEEEEeCCCCChhHHHHhhhcccccCCCcee
Q 038216 44 SSVLLDIKPWNDETDMQKLEEAVRSIKMEGLHWGASKLVPVGYGIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEYVQS 123 (132)
Q Consensus 44 s~vvl~VkP~d~etDl~~L~~~Vr~i~~~Gl~wg~~k~~piafGlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~VqS 123 (132)
|++++..+|.. +..+.+.+. .++|+.+..+.-. -| ++.++++.+ +.+++.+.+..|..+ ++|-|
T Consensus 8 sSlVV~~~Pe~----~~~V~~~l~--~ipg~Evh~~d~~-~G------KiVVtiE~~--~~~~~~~~i~~I~~l-~GVls 71 (87)
T PRK10553 8 CSLVVQAKSER----ISDISTQLN--AFPGCEVAVSDAP-SG------QLIVVVEAE--DSETLLQTIESVRNV-EGVLA 71 (87)
T ss_pred eEEEEEeChHH----HHHHHHHHH--cCCCcEEEeecCC-CC------eEEEEEEeC--ChHHHHHHHHHHHcC-CCceE
Confidence 78888998875 444444443 3468887754211 01 355677754 456666666668888 89999
Q ss_pred eEeeee
Q 038216 124 CDIVAF 129 (132)
Q Consensus 124 vdI~~f 129 (132)
+.++.-
T Consensus 72 a~lVYh 77 (87)
T PRK10553 72 VSLVYH 77 (87)
T ss_pred EEEEEE
Confidence 988753
No 10
>TIGR03116 cas_csf3 CRISPR-associated protein, Csf3 family. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf3 (CRISPR/cas Subtype as in A. ferrooxidans protein 3), as it lies third closest to the repeats.
Probab=41.47 E-value=10 Score=30.61 Aligned_cols=42 Identities=19% Similarity=0.304 Sum_probs=27.7
Q ss_pred eeeCCCcccHHHHHHHHHhhccCCeEEeeeEEeeeeeeeeeE
Q 038216 50 IKPWNDETDMQKLEEAVRSIKMEGLHWGASKLVPVGYGIKKL 91 (132)
Q Consensus 50 VkP~d~etDl~~L~~~Vr~i~~~Gl~wg~~k~~piafGlkkL 91 (132)
.-||.+.-+|....-.-|.-..++-+|.+|++++|+|+=+.-
T Consensus 39 ~~p~g~~r~l~edlpl~k~e~~d~W~Wkas~l~v~~f~~~~~ 80 (214)
T TIGR03116 39 ADPWGDARDLSEDLPLGKEEEGDSWVWKASRLEVLAFLPYPK 80 (214)
T ss_pred cCcchhhhhhhcccCcccccCCCeEEEEecceeeeecCccce
Confidence 447766666654222223334578889999999999997643
No 11
>PRK04435 hypothetical protein; Provisional
Probab=37.67 E-value=45 Score=24.87 Aligned_cols=78 Identities=13% Similarity=0.209 Sum_probs=42.1
Q ss_pred eeEEEeeeCCCcccHHHHHHHHHhhccCCeEEeeeEEeeeeeeeeeEEEEEEEeCCCCChhHHHHhhhcccccCCCceee
Q 038216 45 SVLLDIKPWNDETDMQKLEEAVRSIKMEGLHWGASKLVPVGYGIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEYVQSC 124 (132)
Q Consensus 45 ~vvl~VkP~d~etDl~~L~~~Vr~i~~~Gl~wg~~k~~piafGlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~VqSv 124 (132)
.+.|.+.=.+..=-|.++-..|-....+=+..+. -.|. =|.-.+.+.+.+.+.....+.|.+. +..+ ++|.+|
T Consensus 69 ~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q--~i~~-~g~a~vs~tVevs~~~~~L~~Li~~---L~~i-~gV~~V 141 (147)
T PRK04435 69 IITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQ--SIPL-QGRANVTISIDTSSMEGDIDELLEK---LRNL-DGVEKV 141 (147)
T ss_pred EEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEE--EcCC-CCEEEEEEEEEeCChHHHHHHHHHH---HHcC-CCcEEE
Confidence 4455554334333366666666544333233221 2233 2444455555555443455666666 7778 899999
Q ss_pred Eeeee
Q 038216 125 DIVAF 129 (132)
Q Consensus 125 dI~~f 129 (132)
+|.+.
T Consensus 142 ~i~~~ 146 (147)
T PRK04435 142 ELIGM 146 (147)
T ss_pred EEEec
Confidence 99875
No 12
>PF14790 THDPS_N: Tetrahydrodipicolinate N-succinyltransferase N-terminal; PDB: 2RIJ_A 3R5A_F 3R5B_A 3R5C_B 3R5D_D.
Probab=28.85 E-value=81 Score=24.79 Aligned_cols=27 Identities=22% Similarity=0.508 Sum_probs=13.9
Q ss_pred HHHHHHHhhcc-CCeEEeeeEEeeeeeeeeeEEE
Q 038216 61 KLEEAVRSIKM-EGLHWGASKLVPVGYGIKKLQI 93 (132)
Q Consensus 61 ~L~~~Vr~i~~-~Gl~wg~~k~~piafGlkkLqi 93 (132)
+++..|..++. .|+ ..|+||||-.+..
T Consensus 2 ~Fk~~v~~iq~~~~Y------k~PlaFGIaRvd~ 29 (167)
T PF14790_consen 2 EFKNFVEEIQSSSGY------KDPLAFGIARVDR 29 (167)
T ss_dssp HHHHHHHHHHTSTT----------SEEEEEEEEE
T ss_pred hHHHHHHHHHhcccC------CCcceeeeeeeee
Confidence 34455555543 344 4799999966543
No 13
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=24.71 E-value=1.8e+02 Score=17.91 Aligned_cols=37 Identities=24% Similarity=0.358 Sum_probs=22.8
Q ss_pred eeeeEEEEEEEeCCCCChhHHHHhhhcccccCCCceeeEee
Q 038216 87 GIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEYVQSCDIV 127 (132)
Q Consensus 87 GlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~VqSvdI~ 127 (132)
|...+.+.+.+.+-....+.+... +.++ ++|++|.+.
T Consensus 39 ~~~~i~~~v~v~~~~~~l~~l~~~---L~~i-~~V~~v~~~ 75 (76)
T cd04888 39 GRANVTISIDTSTMNGDIDELLEE---LREI-DGVEKVELV 75 (76)
T ss_pred CeEEEEEEEEcCchHHHHHHHHHH---HhcC-CCeEEEEEe
Confidence 444444555455433345666666 6777 799999875
No 14
>PF09598 Stm1_N: Stm1; InterPro: IPR019084 This domain is found at the N-terminal region of the Stm1 protein. Stm1 is a G4 quadraplex and purine motif triplex nucleic acid-binding protein. It has been implicated in many biological processes including apoptosis and telomere biosynthesis. Stm1 is known to interact with CDC13 [], and is known to associate with ribosomes and nuclear telomere cap complexes []. ; PDB: 3U5G_h 3U5C_h.
Probab=24.58 E-value=25 Score=23.56 Aligned_cols=12 Identities=42% Similarity=0.872 Sum_probs=0.0
Q ss_pred cCCCCCCChhhH
Q 038216 11 VDLFGEETEEDK 22 (132)
Q Consensus 11 ~Dlfg~d~ee~~ 22 (132)
|||.|.|+|+|.
T Consensus 3 FdLLGnD~e~Dp 14 (68)
T PF09598_consen 3 FDLLGNDDEDDP 14 (68)
T ss_dssp ------------
T ss_pred hhhcCCCcccCc
Confidence 789999887665
No 15
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=21.36 E-value=3.3e+02 Score=19.84 Aligned_cols=66 Identities=15% Similarity=0.241 Sum_probs=40.7
Q ss_pred cccHHHHHHHHHhhccCCeEEe-eeEEee--eeeeeeeEEEEEEEeCCCCChhHHHHhhhcccccCCCceeeEee
Q 038216 56 ETDMQKLEEAVRSIKMEGLHWG-ASKLVP--VGYGIKKLQIMLTIVDDLVSVDNLIEEHLMAEPINEYVQSCDIV 127 (132)
Q Consensus 56 etDl~~L~~~Vr~i~~~Gl~wg-~~k~~p--iafGlkkLqi~~vVeDd~v~~D~lee~~~~i~~~ed~VqSvdI~ 127 (132)
.+.-..+..+|+...-.|+-|+ ...+-| +||.+.++ +.+.+.+. ...+.+.+. +..+ ++|..|-..
T Consensus 34 glS~~tV~~Ri~rL~~~GvI~~~~~~v~~~~lg~~~~a~-v~v~v~~~-~~~~~~~~~---l~~~-p~V~~~~~~ 102 (153)
T PRK11179 34 GVSPGTIHVRVEKMKQAGIITGTRVDVNPKQLGYDVCCF-IGIILKSA-KDYPSALAK---LESL-DEVVEAYYT 102 (153)
T ss_pred CcCHHHHHHHHHHHHHCCCeeeEEEEECHHHcCCCEEEE-EEEEEccc-ccHHHHHHH---HhCC-CCEEEEEEc
Confidence 4455677888999999999987 344444 56655542 33333322 346777777 5666 677776543
No 16
>PF11273 DUF3073: Protein of unknown function (DUF3073); InterPro: IPR021426 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=21.18 E-value=33 Score=22.98 Aligned_cols=19 Identities=21% Similarity=0.371 Sum_probs=16.6
Q ss_pred eeeCCCcccHHHHHHHHHh
Q 038216 50 IKPWNDETDMQKLEEAVRS 68 (132)
Q Consensus 50 VkP~d~etDl~~L~~~Vr~ 68 (132)
+|=.+++||+..|+..+.+
T Consensus 16 LKY~sp~tDl~~LqrEL~~ 34 (65)
T PF11273_consen 16 LKYSSPDTDLDALQRELSG 34 (65)
T ss_pred hccCCCcCCHHHHHHHHcC
Confidence 4667999999999999877
No 17
>COG1685 Archaeal shikimate kinase [Amino acid transport and metabolism / Coenzyme metabolism]
Probab=20.86 E-value=1.6e+02 Score=24.90 Aligned_cols=35 Identities=29% Similarity=0.451 Sum_probs=23.7
Q ss_pred cccHHHHHHHHHhh-----ccCCeEEeeeEEeeeeeeeee
Q 038216 56 ETDMQKLEEAVRSI-----KMEGLHWGASKLVPVGYGIKK 90 (132)
Q Consensus 56 etDl~~L~~~Vr~i-----~~~Gl~wg~~k~~piafGlkk 90 (132)
+.|..-++.++..+ ...|+..--.-..|+|+|||.
T Consensus 48 ~~d~~li~~~~~~v~e~~g~~~~~~v~v~SeiP~~~GLkS 87 (278)
T COG1685 48 EGDTRLIERCVERVREKYGIPLGVEVEVESEIPVGSGLKS 87 (278)
T ss_pred CCChHHHHHHHHHHHHHcCCCcceEEEEecCCCcccCcch
Confidence 55655566665554 234677777778899999984
Done!