Query 029846
Match_columns 186
No_of_seqs 164 out of 323
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 04:35:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029846.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029846hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2768 Translation initiation 100.0 3.6E-34 7.7E-39 244.1 6.4 125 51-179 17-141 (231)
2 PRK03988 translation initiatio 99.8 2.2E-20 4.8E-25 149.8 6.7 60 115-179 4-63 (138)
3 TIGR00311 aIF-2beta translatio 99.8 3.6E-19 7.9E-24 142.0 6.2 58 117-179 1-58 (133)
4 PRK12336 translation initiatio 99.8 9E-19 1.9E-23 147.0 6.5 58 116-178 1-58 (201)
5 COG1601 GCD7 Translation initi 99.5 5.9E-15 1.3E-19 120.4 4.0 61 113-178 3-64 (151)
6 PF01873 eIF-5_eIF-2B: Domain 99.5 1.2E-14 2.7E-19 114.9 5.1 49 131-179 4-53 (125)
7 smart00653 eIF2B_5 domain pres 99.4 1.3E-13 2.7E-18 107.1 4.5 39 141-179 2-40 (110)
8 COG1163 DRG Predicted GTPase [ 84.9 0.78 1.7E-05 42.7 2.9 50 113-173 272-326 (365)
9 KOG2767 Translation initiation 78.7 1.3 2.9E-05 41.5 2.0 21 155-175 31-51 (400)
10 COG4936 PocR Predicted sensor 59.2 7.5 0.00016 32.7 2.2 53 119-181 9-61 (169)
11 PF10114 PocR: Sensory domain 42.2 26 0.00056 27.5 2.8 33 150-182 28-60 (173)
12 PF14527 LAGLIDADG_WhiA: WhiA 40.2 41 0.00089 25.1 3.5 44 117-171 29-72 (93)
13 smart00497 IENR1 Intron encode 38.0 84 0.0018 19.9 4.3 23 159-181 16-38 (53)
14 KOG2768 Translation initiation 36.1 13 0.00029 32.8 0.3 21 14-34 20-40 (231)
15 PF13921 Myb_DNA-bind_6: Myb-l 32.7 38 0.00082 22.3 2.0 18 162-179 19-37 (60)
16 PF09271 LAG1-DNAbind: LAG1, D 31.9 29 0.00063 28.2 1.6 19 138-156 15-33 (140)
17 PRK11200 grxA glutaredoxin 1; 31.8 47 0.001 23.2 2.5 24 146-172 58-81 (85)
18 KOG1486 GTP-binding protein DR 30.6 47 0.001 30.8 2.9 52 113-173 271-325 (364)
19 PF00249 Myb_DNA-binding: Myb- 30.3 49 0.0011 21.1 2.2 18 162-179 23-42 (48)
20 PF13936 HTH_38: Helix-turn-he 29.0 47 0.001 21.3 2.0 18 162-179 22-39 (44)
21 PF04908 SH3BGR: SH3-binding, 28.4 1.1E+02 0.0024 23.3 4.2 39 127-169 47-86 (99)
22 cd05781 DNA_polB_B3_exo DEDDy 27.9 44 0.00095 27.5 2.0 17 119-135 49-65 (188)
23 PF01359 Transposase_1: Transp 27.3 77 0.0017 23.2 3.0 21 118-138 59-79 (81)
24 PF02682 AHS1: Allophanate hyd 25.8 1.1E+02 0.0025 25.7 4.2 60 116-181 61-120 (202)
25 cd02685 MIT_C MIT_C; domain fo 25.8 27 0.00058 28.9 0.4 53 114-180 3-55 (148)
26 PF04545 Sigma70_r4: Sigma-70, 24.9 83 0.0018 20.0 2.6 21 162-182 22-42 (50)
27 TIGR02190 GlrX-dom Glutaredoxi 22.0 1E+02 0.0022 21.3 2.7 22 146-170 57-78 (79)
28 smart00717 SANT SANT SWI3, AD 21.0 97 0.0021 18.3 2.2 20 161-180 22-42 (49)
No 1
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.6e-34 Score=244.06 Aligned_cols=125 Identities=51% Similarity=0.725 Sum_probs=95.2
Q ss_pred ccccCccccccccccccCCCCcccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCchHHHHHHHHHHHHH
Q 029846 51 SVSEGLESTFTGLKKKKKKPVESSLLNDEIGDAGDDLDGHVGEDDEADGSGGPRQRYPWEGSDRDYEYEELLGRVFNILR 130 (186)
Q Consensus 51 ~~~~~~~~~f~~~KKKKKK~~~~~~~~~e~~~~~e~~~~~~~~~~~~~gi~~~~~~~~w~~~~~~y~YeeLL~R~f~~L~ 130 (186)
.+++.++..+.++||||||++..+.++++...+++..+....++.++ ++. ++.++|.|++++|+|+|||.|+|++||
T Consensus 17 ~~~~~l~~~~~~kKKKKkk~k~~s~~ee~~~~~~e~~~e~~~~~~e~-~~~--~~~~~~~g~e~dy~Y~ElL~rvf~ilr 93 (231)
T KOG2768|consen 17 EASERLDFLSLKKKKKKKKSKSLSALEEEDVNAGEFADEDKDPDKEV-RQN--QQGVSWVGSEPDYTYYELLSRVFNILR 93 (231)
T ss_pred chhhcccccccccccccCCCCchhhhHHHHHhccchhhhccChhhcc-ccc--cccccccccCCCccHHHHHHHHHHHHH
Confidence 34556666666667766666655555554444444332221222211 133 334999999999999999999999999
Q ss_pred hcCCCCcccccceecCCCeEEEeCCceeEeechHHHHHHhCCCHHHHhh
Q 029846 131 ENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLHASAARS 179 (186)
Q Consensus 131 e~NPela~~~~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rdp~hv~~ 179 (186)
+|||+++|++++|+|+||||+|+| |||+|.||+|||++|||+|+||=+
T Consensus 94 eknpe~aGe~~k~v~~PPqvlReg-kkT~f~Nf~Dick~mhR~pdHv~~ 141 (231)
T KOG2768|consen 94 EKNPELAGEKRKFVMKPPQVLREG-KKTVFVNFADICKTMHRSPDHVMQ 141 (231)
T ss_pred hcCchhcccccceeeCCHHHHhhc-cceeeeeHHHHHHHhccChHHHHH
Confidence 999999999999999999999999 779999999999999999999854
No 2
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=99.81 E-value=2.2e-20 Score=149.81 Aligned_cols=60 Identities=30% Similarity=0.474 Sum_probs=56.1
Q ss_pred CchHHHHHHHHHHHHHhcCCCCcccccceecCCCeEEEeCCceeEeechHHHHHHhCCCHHHHhh
Q 029846 115 DYEYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLHASAARS 179 (186)
Q Consensus 115 ~y~YeeLL~R~f~~L~e~NPela~~~~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rdp~hv~~ 179 (186)
+|+|++||+|||++| |+..++..||.||+|+|.++|+| |+|.||.+||+.|||+|+||-.
T Consensus 4 ~~~Y~~lL~R~~~~l----p~~~~~~~R~~~p~~~v~~eG~k-Tvi~Nf~~I~~~L~R~~~hv~k 63 (138)
T PRK03988 4 YYDYEELLDRAYEKL----PEKVFKESRFEVPKPDVRIEGNR-TIIRNFKEIADRLNRDPKHVAK 63 (138)
T ss_pred ccCHHHHHHHHHHHC----ccccCCCcceeCCCCeEEEEcCc-EEEecHHHHHHHHCCCHHHHHH
Confidence 689999999999999 88888889999999999999965 9999999999999999999863
No 3
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=99.77 E-value=3.6e-19 Score=142.04 Aligned_cols=58 Identities=24% Similarity=0.406 Sum_probs=53.9
Q ss_pred hHHHHHHHHHHHHHhcCCCCcccccceecCCCeEEEeCCceeEeechHHHHHHhCCCHHHHhh
Q 029846 117 EYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLHASAARS 179 (186)
Q Consensus 117 ~YeeLL~R~f~~L~e~NPela~~~~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rdp~hv~~ 179 (186)
+|++||+|||+.| |+..++..||.||+|+|.++|+| |+|.||.+||++|||+|+||-.
T Consensus 1 ~Y~~lL~R~~~~l----~~~~~~~~R~~mP~~~v~~eG~k-Tvi~Nf~~Ia~~L~R~~~~v~k 58 (133)
T TIGR00311 1 DYEKLLERAIDQL----PDEVFETKRFEVPKAYIVIEGNR-TIIQNFREVAKALNRDEQHLLK 58 (133)
T ss_pred CHHHHHHHHHHHC----ccccCCCccccCCCceEEEEcCc-EEEecHHHHHHHHCCCHHHHHH
Confidence 5999999999999 88777788999999999999965 9999999999999999999863
No 4
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=99.76 E-value=9e-19 Score=147.04 Aligned_cols=58 Identities=28% Similarity=0.506 Sum_probs=55.1
Q ss_pred chHHHHHHHHHHHHHhcCCCCcccccceecCCCeEEEeCCceeEeechHHHHHHhCCCHHHHh
Q 029846 116 YEYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLHASAAR 178 (186)
Q Consensus 116 y~YeeLL~R~f~~L~e~NPela~~~~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rdp~hv~ 178 (186)
|+|++||+|+|+.| |++.++..||.||+|||.++| +||+|.||.+||+.|||+|+||-
T Consensus 1 ~~Y~~lL~r~~~~l----~~~~~~~~R~~~p~~~v~~eG-~kT~i~N~~~i~~~l~R~~~~~~ 58 (201)
T PRK12336 1 MDYESLLDRAMEVL----PEPTKSGERFSIPEPKIFIEG-KTTILTNFGEIADALNRDPDHLM 58 (201)
T ss_pred CCHHHHHHHHHHHC----CcccCCccceecCCceEEEEc-CcEEEecHHHHHHHHCCCHHHHH
Confidence 68999999999999 998888899999999999999 56999999999999999999986
No 5
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=99.53 E-value=5.9e-15 Score=120.38 Aligned_cols=61 Identities=30% Similarity=0.479 Sum_probs=54.7
Q ss_pred CCCchHHHHHHHHHHHHHhcCCCCccccc-ceecCCCeEEEeCCceeEeechHHHHHHhCCCHHHHh
Q 029846 113 DRDYEYEELLGRVFNILRENNPELAGDRR-RTVMRPPQVLREGTKKTVFVNFMDLCKTYVLHASAAR 178 (186)
Q Consensus 113 ~~~y~YeeLL~R~f~~L~e~NPela~~~~-Rf~ippPqV~reGtKKTif~NF~eIck~L~Rdp~hv~ 178 (186)
...|.|++||+|+|..| |+..+... ||.||+|.|.++|++ ||+.||.+||+.|||||+|+-
T Consensus 3 ~~~~~yeelLeR~~~~l----P~~~~~~~~R~~ip~~~i~~~g~~-Ti~~Nf~dia~~l~rDp~h~~ 64 (151)
T COG1601 3 EMEDDYEELLERAYSEL----PEKEVKNDERFRIPEPEINREGNR-TIIRNFGDIAEALNRDPEHLV 64 (151)
T ss_pred hhhhhHHHHHHHHHHhC----CccccccccceecCCcceecccch-hHHHhHHHHHHHhcCCHHHHH
Confidence 34678999999999666 99888766 999999999999977 999999999999999999864
No 6
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=99.52 E-value=1.2e-14 Score=114.85 Aligned_cols=49 Identities=47% Similarity=0.672 Sum_probs=41.1
Q ss_pred hcCCC-CcccccceecCCCeEEEeCCceeEeechHHHHHHhCCCHHHHhh
Q 029846 131 ENNPE-LAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLHASAARS 179 (186)
Q Consensus 131 e~NPe-la~~~~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rdp~hv~~ 179 (186)
++||+ ..++..||.||+|+|.++|++||+|.||.+||++|||+|+||-.
T Consensus 4 ~~np~~~~~~~~R~kmP~~~v~~eG~~KTvi~Nf~dI~~~L~R~p~~~~k 53 (125)
T PF01873_consen 4 EKNPERSNSDKFRYKMPPPQVKIEGKKKTVIVNFVDICKALNRDPEHVLK 53 (125)
T ss_dssp CSSTTTSCSSSSS-CCCT--EEEETSTEEEETTHHHHHHHHTSSHHHHHH
T ss_pred HhCcCcccCCCcceecCCCeEEEEccceeeeecHHHHHHHHCCCHHHHHH
Confidence 57899 45666799999999999998889999999999999999999864
No 7
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=99.43 E-value=1.3e-13 Score=107.11 Aligned_cols=39 Identities=46% Similarity=0.595 Sum_probs=36.5
Q ss_pred cceecCCCeEEEeCCceeEeechHHHHHHhCCCHHHHhh
Q 029846 141 RRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLHASAARS 179 (186)
Q Consensus 141 ~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rdp~hv~~ 179 (186)
.||.||+|+|.++|++||+|.||.+||++|||+|+||-.
T Consensus 2 ~R~~~p~~~v~~eG~~kTvi~Nf~~I~~~L~R~p~hv~k 40 (110)
T smart00653 2 YRFKMPPPQVLREGKGKTVIVNFADIAKALNRPPDHVLK 40 (110)
T ss_pred CccccCCCeEEEEcCCeEEEEcHHHHHHHHCCCHHHHHH
Confidence 489999999999998779999999999999999999863
No 8
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=84.93 E-value=0.78 Score=42.71 Aligned_cols=50 Identities=22% Similarity=0.460 Sum_probs=37.8
Q ss_pred CCCchHHHHHHHHHHHHHhcCCCCc-----ccccceecCCCeEEEeCCceeEeechHHHHHHhCCC
Q 029846 113 DRDYEYEELLGRVFNILRENNPELA-----GDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLH 173 (186)
Q Consensus 113 ~~~y~YeeLL~R~f~~L~e~NPela-----~~~~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rd 173 (186)
.++++-++|++++|..| .+. ........++|-|+|.|+. .+|+|.+|||+
T Consensus 272 ~~~~nld~L~e~i~~~L-----~liRVYtK~~g~~pd~~~PlIlr~GsT------V~Dvc~~IH~~ 326 (365)
T COG1163 272 KKGINLDELKERIWDVL-----GLIRVYTKPPGEEPDFDEPLILRRGST------VGDVCRKIHRD 326 (365)
T ss_pred ccCCCHHHHHHHHHHhh-----CeEEEEecCCCCCCCCCCCeEEeCCCc------HHHHHHHHHHH
Confidence 44667899999999998 221 0112334579999999966 89999999996
No 9
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=78.66 E-value=1.3 Score=41.47 Aligned_cols=21 Identities=29% Similarity=0.298 Sum_probs=18.8
Q ss_pred CceeEeechHHHHHHhCCCHH
Q 029846 155 TKKTVFVNFMDLCKTYVLHAS 175 (186)
Q Consensus 155 tKKTif~NF~eIck~L~Rdp~ 175 (186)
.-||+|.|..+|++.|+|.|-
T Consensus 31 GIKTvIvNm~eIakAL~RPp~ 51 (400)
T KOG2767|consen 31 GIKTVIVNMVEIAKALGRPPL 51 (400)
T ss_pred CeeeeeecHHHHHHHhCCCCC
Confidence 356999999999999999985
No 10
>COG4936 PocR Predicted sensor domain [Signal transduction mechanisms / Transcription]
Probab=59.23 E-value=7.5 Score=32.68 Aligned_cols=53 Identities=17% Similarity=0.303 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHhcCCCCcccccceecCCCeEEEeCCceeEeechHHHHHHhCCCHHHHhhhh
Q 029846 119 EELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLHASAARSCH 181 (186)
Q Consensus 119 eeLL~R~f~~L~e~NPela~~~~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rdp~hv~~~~ 181 (186)
..||+.+.+-. ....| +....|-+.|+--|-..||...|..|+-.|+|=+.|.
T Consensus 9 ~~ll~k~~d~F--------s~at~--lA~VvVdihG~evs~l~NftpfCqlirs~pk~~~rC~ 61 (169)
T COG4936 9 IGLLQKFQDNF--------SEATR--LAAVVVDIHGKEVSKLSNFTPFCQLIRSTPKGEKRCA 61 (169)
T ss_pred HHHHHHHHHHH--------HHhhc--eeEEEEecCCceecchhcccHHHHHHHhCcchhhHHH
Confidence 57888877655 22223 5567888999988999999999999999999988885
No 11
>PF10114 PocR: Sensory domain found in PocR; InterPro: IPR018771 This entry is thought to act as a sensory domain in histidine kinases catalysing the reaction: ATP + protein L-histidine = ADP + protein N- phospho-L-histidine.
Probab=42.16 E-value=26 Score=27.52 Aligned_cols=33 Identities=24% Similarity=0.373 Sum_probs=27.2
Q ss_pred EEEeCCceeEeechHHHHHHhCCCHHHHhhhhh
Q 029846 150 VLREGTKKTVFVNFMDLCKTYVLHASAARSCHD 182 (186)
Q Consensus 150 V~reGtKKTif~NF~eIck~L~Rdp~hv~~~~~ 182 (186)
+-..|+--|...||..+|..++..|...+.|..
T Consensus 28 ~d~~G~~l~~~~~~~~fC~~~~~~~~~~~~C~~ 60 (173)
T PF10114_consen 28 VDPDGNPLTQPSNFCPFCKLIRSSPEGRERCRE 60 (173)
T ss_pred EeCCCCEEeeCCCchhhhhHHhcCCcccccCHH
Confidence 445687777899999999999989988888854
No 12
>PF14527 LAGLIDADG_WhiA: WhiA LAGLIDADG-like domain; PDB: 3HYI_A 3HYJ_D.
Probab=40.20 E-value=41 Score=25.09 Aligned_cols=44 Identities=9% Similarity=0.091 Sum_probs=31.1
Q ss_pred hHHHHHHHHHHHHHhcCCCCcccccceecCCCeEEEeCCceeEeechHHHHHHhC
Q 029846 117 EYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTYV 171 (186)
Q Consensus 117 ~YeeLL~R~f~~L~e~NPela~~~~Rf~ippPqV~reGtKKTif~NF~eIck~L~ 171 (186)
.|+++.+++..+|+ +|-+++-.+.|-++-...+.+..+|++.|.
T Consensus 29 ~~~e~a~~l~~lL~-----------~~~i~~k~~~r~~~~~vYlK~~e~I~dfL~ 72 (93)
T PF14527_consen 29 NDEEFAEQLKELLN-----------KFGINAKIIKRKNKYVVYLKDSEQISDFLK 72 (93)
T ss_dssp S-HHHHHHHHHHHH-----------HH----EEEEESSEEEEEE--HHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----------HcCCCceeeeecCceEEEEcCHHHHHHHHH
Confidence 57899999999992 556777788888887889999999999875
No 13
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=38.02 E-value=84 Score=19.87 Aligned_cols=23 Identities=13% Similarity=0.091 Sum_probs=20.8
Q ss_pred EeechHHHHHHhCCCHHHHhhhh
Q 029846 159 VFVNFMDLCKTYVLHASAARSCH 181 (186)
Q Consensus 159 if~NF~eIck~L~Rdp~hv~~~~ 181 (186)
.|..+.+.|+.|+-+..+|..|-
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~ 38 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYL 38 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHH
Confidence 59999999999999999998774
No 14
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=36.11 E-value=13 Score=32.81 Aligned_cols=21 Identities=38% Similarity=0.278 Sum_probs=14.4
Q ss_pred hccCCCCCcccccccccccCC
Q 029846 14 AELAPFDPTKKKKKKKVVIQD 34 (186)
Q Consensus 14 ~~l~~fd~~KKKKKKK~~~~d 34 (186)
..|..|++.|||||||.....
T Consensus 20 ~~l~~~~~~kKKKKkk~k~~s 40 (231)
T KOG2768|consen 20 ERLDFLSLKKKKKKKKSKSLS 40 (231)
T ss_pred hcccccccccccccCCCCchh
Confidence 456778887777777766543
No 15
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=32.71 E-value=38 Score=22.30 Aligned_cols=18 Identities=6% Similarity=0.180 Sum_probs=14.1
Q ss_pred chHHHHHHhC-CCHHHHhh
Q 029846 162 NFMDLCKTYV-LHASAARS 179 (186)
Q Consensus 162 NF~eIck~L~-Rdp~hv~~ 179 (186)
|+..|+..|+ |.|..|+.
T Consensus 19 ~W~~Ia~~l~~Rt~~~~~~ 37 (60)
T PF13921_consen 19 DWKKIAEHLGNRTPKQCRN 37 (60)
T ss_dssp -HHHHHHHSTTS-HHHHHH
T ss_pred CHHHHHHHHCcCCHHHHHH
Confidence 7999999999 99987764
No 16
>PF09271 LAG1-DNAbind: LAG1, DNA binding; InterPro: IPR015351 This domain is found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. It adopts a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding []. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2FO1_A 3IAG_C 3BRG_C 3NBN_A 2F8X_C 3V79_C.
Probab=31.86 E-value=29 Score=28.19 Aligned_cols=19 Identities=32% Similarity=0.571 Sum_probs=10.1
Q ss_pred ccccceecCCCeEEEeCCc
Q 029846 138 GDRRRTVMRPPQVLREGTK 156 (186)
Q Consensus 138 ~~~~Rf~ippPqV~reGtK 156 (186)
|..+||--|||.|...|+-
T Consensus 15 G~EKRF~CPPP~v~L~G~~ 33 (140)
T PF09271_consen 15 GNEKRFFCPPPCVYLSGPG 33 (140)
T ss_dssp TT-----SS--EEEEESTH
T ss_pred cccccccCCCCeEEEECCC
Confidence 5668999999999999954
No 17
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=31.82 E-value=47 Score=23.21 Aligned_cols=24 Identities=13% Similarity=0.054 Sum_probs=20.2
Q ss_pred CCCeEEEeCCceeEeechHHHHHHhCC
Q 029846 146 RPPQVLREGTKKTVFVNFMDLCKTYVL 172 (186)
Q Consensus 146 ppPqV~reGtKKTif~NF~eIck~L~R 172 (186)
-.|+|+..| ..+-+|.+|...++.
T Consensus 58 ~vP~ifi~g---~~igg~~~~~~~~~~ 81 (85)
T PRK11200 58 TVPQIFVDQ---KHIGGCTDFEAYVKE 81 (85)
T ss_pred cCCEEEECC---EEEcCHHHHHHHHHH
Confidence 468999999 679999999988764
No 18
>KOG1486 consensus GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms]
Probab=30.65 E-value=47 Score=30.76 Aligned_cols=52 Identities=25% Similarity=0.417 Sum_probs=36.1
Q ss_pred CCCchHHHHHHHHHHHHHhcCCCCcccc---cceecCCCeEEEeCCceeEeechHHHHHHhCCC
Q 029846 113 DRDYEYEELLGRVFNILRENNPELAGDR---RRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLH 173 (186)
Q Consensus 113 ~~~y~YeeLL~R~f~~L~e~NPela~~~---~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rd 173 (186)
++..+.+.||+|++..| |--..-++ .+-..-.|-|+|-|.. ..++|.++||+
T Consensus 271 ~m~lnld~lle~iWe~l---~L~rvYtKk~g~~Pdfdd~~vlr~g~t------ve~~C~~iHr~ 325 (364)
T KOG1486|consen 271 NMKLNLDRLLERIWEEL---NLVRVYTKKKGQRPDFDDPLVLRKGST------VEDVCHRIHRT 325 (364)
T ss_pred ccccCHHHHHHHHHHHh---ceEEEEecCCCCCCCCCCceEEeCCCc------HHHHHHHHHHH
Confidence 44556788999999888 22211122 2333447899999976 89999999996
No 19
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=30.33 E-value=49 Score=21.08 Aligned_cols=18 Identities=28% Similarity=0.335 Sum_probs=16.2
Q ss_pred chHHHHHHhC--CCHHHHhh
Q 029846 162 NFMDLCKTYV--LHASAARS 179 (186)
Q Consensus 162 NF~eIck~L~--Rdp~hv~~ 179 (186)
||..|+..|. |.+..+++
T Consensus 23 ~W~~Ia~~~~~~Rt~~qc~~ 42 (48)
T PF00249_consen 23 NWKKIAKRMPGGRTAKQCRS 42 (48)
T ss_dssp HHHHHHHHHSSSSTHHHHHH
T ss_pred HHHHHHHHcCCCCCHHHHHH
Confidence 8999999998 99988875
No 20
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=29.05 E-value=47 Score=21.28 Aligned_cols=18 Identities=11% Similarity=0.102 Sum_probs=13.3
Q ss_pred chHHHHHHhCCCHHHHhh
Q 029846 162 NFMDLCKTYVLHASAARS 179 (186)
Q Consensus 162 NF~eIck~L~Rdp~hv~~ 179 (186)
.+.+||+.|+|++.-|..
T Consensus 22 s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 22 SIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp -HHHHHHHTT--HHHHHH
T ss_pred CHHHHHHHHCcCcHHHHH
Confidence 488999999999998864
No 21
>PF04908 SH3BGR: SH3-binding, glutamic acid-rich protein; InterPro: IPR006993 This family of proteins, which contains SH3BGRL3, is functionally uncharacterised. SH3BGRL3 is a highly conserved small protein, which is widely expressed and shows a significant similarity to glutaredoxin 1 (GRX1) of Escherichia coli which is predicted to belong to the thioredoxin superfamily. However, SH3BGRL3 lacks both conserved cysteine residues, which characterise the enzymatic active site of GRX. This structural feature raises the possibility that SH3BGRL3 and its homologues could function as endogenous modulators of GRX activity []. ; PDB: 1SJ6_A 1U6T_A 1WRY_A 1T1V_B 1J0F_A 2CT6_A.
Probab=28.38 E-value=1.1e+02 Score=23.34 Aligned_cols=39 Identities=23% Similarity=0.367 Sum_probs=22.5
Q ss_pred HHHHhcC-CCCcccccceecCCCeEEEeCCceeEeechHHHHHH
Q 029846 127 NILRENN-PELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKT 169 (186)
Q Consensus 127 ~~L~e~N-Pela~~~~Rf~ippPqV~reGtKKTif~NF~eIck~ 169 (186)
+.||++. |.......+. ..||||+..| ..+-+|.++-..
T Consensus 47 ~~mr~~~g~~~~~~~~~~-~lpPqiF~~~---~Y~Gdye~f~ea 86 (99)
T PF04908_consen 47 QWMRENAGPEEKDPGNGK-PLPPQIFNGD---EYCGDYEDFEEA 86 (99)
T ss_dssp HHHHHHT--CCCS-TSTT---S-EEEETT---EEEEEHHHHHHH
T ss_pred HHHHHhccccccCCCCCC-CCCCEEEeCC---EEEeeHHHHHHH
Confidence 3556666 5543333332 3578999999 788888887544
No 22
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=27.88 E-value=44 Score=27.51 Aligned_cols=17 Identities=12% Similarity=0.513 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHhcCCC
Q 029846 119 EELLGRVFNILRENNPE 135 (186)
Q Consensus 119 eeLL~R~f~~L~e~NPe 135 (186)
.+||.++++.+++.+|+
T Consensus 49 ~~lL~~F~~~i~~~dPd 65 (188)
T cd05781 49 RKIIREFVKYVKEYDPD 65 (188)
T ss_pred HHHHHHHHHHHHHcCCC
Confidence 69999999999999999
No 23
>PF01359 Transposase_1: Transposase (partial DDE domain); InterPro: IPR001888 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the mariner transposase []. More information about these proteins can be found at Protein of the Month: Transposase [].; PDB: 3HOT_B 3HOS_A 3K9K_B 3F2K_B 3K9J_B 2F7T_A.
Probab=27.26 E-value=77 Score=23.20 Aligned_cols=21 Identities=38% Similarity=0.623 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHhcCCCCcc
Q 029846 118 YEELLGRVFNILRENNPELAG 138 (186)
Q Consensus 118 YeeLL~R~f~~L~e~NPela~ 138 (186)
|-..|+++++.|+++.|.+..
T Consensus 59 Y~~ql~~l~~~l~~krp~~~~ 79 (81)
T PF01359_consen 59 YCQQLDKLKQALREKRPELVN 79 (81)
T ss_dssp HHHHHHHHHHHHHHHTCCCCT
T ss_pred HHHHHHHHHHHHHHhChHhhc
Confidence 889999999999999999864
No 24
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=25.79 E-value=1.1e+02 Score=25.74 Aligned_cols=60 Identities=13% Similarity=0.108 Sum_probs=41.9
Q ss_pred chHHHHHHHHHHHHHhcCCCCcccccceecCCCeEEEeCCceeEeechHHHHHHhCCCHHHHhhhh
Q 029846 116 YEYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLHASAARSCH 181 (186)
Q Consensus 116 y~YeeLL~R~f~~L~e~NPela~~~~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rdp~hv~~~~ 181 (186)
.+|..|+.++-+++....+......+.++|| |...|.- =.|...+|+..+-+++.|-++|
T Consensus 61 ~~~~~l~~~l~~~~~~~~~~~~~~~r~~~iP---V~Y~~~~---g~DL~~vA~~~gls~~evi~~H 120 (202)
T PF02682_consen 61 IDRAALRAALEELLASPQPSEKPPSRLIEIP---VCYDGEF---GPDLEEVAEHNGLSVEEVIRLH 120 (202)
T ss_dssp SHHHHHHHHHHHHHCCCCSSCCCCEEEEEEE---EEESTTT---HTTHHHHHHHHTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHhhhhccccccCCCceEEEE---EEECCCC---CCCHHHHHHHhCcCHHHHHHHH
Confidence 3689999999988855333333344456655 5666422 2399999999999999999988
No 25
>cd02685 MIT_C MIT_C; domain found C-terminal to MIT (contained within Microtubule Interacting and Trafficking molecules) domains, as well as in some bacterial proteins. The function of this domain is unknown.
Probab=25.76 E-value=27 Score=28.92 Aligned_cols=53 Identities=15% Similarity=0.336 Sum_probs=34.7
Q ss_pred CCchHHHHHHHHHHHHHhcCCCCcccccceecCCCeEEEeCCceeEeechHHHHHHhCCCHHHHhhh
Q 029846 114 RDYEYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTYVLHASAARSC 180 (186)
Q Consensus 114 ~~y~YeeLL~R~f~~L~e~NPela~~~~Rf~ippPqV~reGtKKTif~NF~eIck~L~Rdp~hv~~~ 180 (186)
++|+|+.|+.+-++ +- .....|-.|.|..- -=+.||+++|+.+-+.+..+...
T Consensus 3 ~G~sYd~LFg~Yl~-------d~---~~~I~ieDPYir~~----hQi~Nl~~F~El~vk~~~~~~~i 55 (148)
T cd02685 3 TGFSYDRLFGPYLD-------DG---VTEITVEDPYIRNF----HQIRNFLRFCELVVKPPCELKYI 55 (148)
T ss_pred CcccHHHHHHHHHh-------CC---ceEEEEeCccccch----HHHHHHHHHHHHHhcCccceEEE
Confidence 46889999888654 11 12445677776432 44789999999988755554443
No 26
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=24.89 E-value=83 Score=20.00 Aligned_cols=21 Identities=10% Similarity=0.178 Sum_probs=18.7
Q ss_pred chHHHHHHhCCCHHHHhhhhh
Q 029846 162 NFMDLCKTYVLHASAARSCHD 182 (186)
Q Consensus 162 NF~eIck~L~Rdp~hv~~~~~ 182 (186)
.+.+|+..|+-....|+..+.
T Consensus 22 t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 22 TLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp SHHHHHHHHTSCHHHHHHHHH
T ss_pred CHHHHHHHHCCcHHHHHHHHH
Confidence 489999999999999998764
No 27
>TIGR02190 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain.
Probab=21.99 E-value=1e+02 Score=21.34 Aligned_cols=22 Identities=23% Similarity=0.194 Sum_probs=18.5
Q ss_pred CCCeEEEeCCceeEeechHHHHHHh
Q 029846 146 RPPQVLREGTKKTVFVNFMDLCKTY 170 (186)
Q Consensus 146 ppPqV~reGtKKTif~NF~eIck~L 170 (186)
--|+|+..| ..|..|.+|+..|
T Consensus 57 ~vP~i~i~g---~~igG~~~l~~~l 78 (79)
T TIGR02190 57 TVPQVFIGG---KLIGGSDELEAYL 78 (79)
T ss_pred CcCeEEECC---EEEcCHHHHHHHh
Confidence 468999888 5799999999876
No 28
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=20.99 E-value=97 Score=18.26 Aligned_cols=20 Identities=20% Similarity=0.192 Sum_probs=16.2
Q ss_pred echHHHHHHhC-CCHHHHhhh
Q 029846 161 VNFMDLCKTYV-LHASAARSC 180 (186)
Q Consensus 161 ~NF~eIck~L~-Rdp~hv~~~ 180 (186)
.||..|+..|. |.+..++..
T Consensus 22 ~~w~~Ia~~~~~rt~~~~~~~ 42 (49)
T smart00717 22 NNWEKIAKELPGRTAEQCRER 42 (49)
T ss_pred CCHHHHHHHcCCCCHHHHHHH
Confidence 57999999998 888877654
Done!