Query 003369
Match_columns 825
No_of_seqs 226 out of 467
Neff 3.2
Searched_HMMs 46136
Date Thu Mar 28 22:12:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003369.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003369hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06507 Auxin_resp: Auxin res 100.0 5.7E-36 1.2E-40 263.6 7.9 83 94-177 1-83 (83)
2 KOG0644 Uncharacterized conser 99.6 1.1E-15 2.5E-20 175.1 6.4 149 46-203 874-1045(1113)
3 PF02362 B3: B3 DNA binding do 99.2 5E-11 1.1E-15 103.8 6.0 65 5-69 33-99 (100)
4 KOG3598 Thyroid hormone recept 80.0 1.7 3.8E-05 55.5 4.0 15 36-50 1723-1737(2220)
5 KOG3598 Thyroid hormone recept 76.2 3.5 7.5E-05 53.0 5.1 8 188-195 1858-1865(2220)
6 PRK10737 FKBP-type peptidyl-pr 65.1 14 0.0003 38.5 5.9 103 46-162 3-114 (196)
7 PF03754 DUF313: Domain of unk 63.9 6.5 0.00014 37.8 3.0 37 7-43 75-114 (114)
8 KOG3207 Beta-tubulin folding c 51.9 17 0.00037 42.5 4.2 43 133-189 3-45 (505)
9 smart00743 Agenet Tudor-like d 49.2 23 0.00051 29.1 3.6 28 132-162 2-29 (61)
10 PF05641 Agenet: Agenet domain 49.2 31 0.00068 29.6 4.5 42 133-184 1-42 (68)
11 smart00333 TUDOR Tudor domain. 35.6 52 0.0011 26.4 3.6 53 132-201 2-54 (57)
12 PF10844 DUF2577: Protein of u 33.9 60 0.0013 30.2 4.1 27 40-66 71-97 (100)
13 PF11515 Cul7: Mouse developme 33.5 50 0.0011 30.5 3.5 72 120-202 6-77 (78)
14 COG1047 SlpA FKBP-type peptidy 33.0 2.1E+02 0.0045 29.8 8.2 105 45-162 2-115 (174)
15 PF14478 DUF4430: Domain of un 27.6 30 0.00065 29.6 1.0 21 35-55 39-68 (68)
16 PF01878 EVE: EVE domain; Int 27.2 56 0.0012 31.2 2.9 38 31-68 19-63 (143)
17 PF12852 Cupin_6: Cupin 27.1 66 0.0014 31.6 3.4 53 9-61 17-74 (186)
18 PF13163 DUF3999: Protein of u 26.4 2.1E+02 0.0045 32.9 7.6 138 5-182 36-196 (429)
19 PF04014 Antitoxin-MazE: Antid 26.2 55 0.0012 26.2 2.2 27 40-66 15-41 (47)
20 PF06003 SMN: Survival motor n 23.4 74 0.0016 34.4 3.2 57 131-202 67-123 (264)
21 TIGR01439 lp_hng_hel_AbrB loop 23.1 68 0.0015 24.4 2.2 26 39-64 14-39 (43)
22 PF13437 HlyD_3: HlyD family s 22.3 92 0.002 27.6 3.1 29 132-162 49-78 (105)
23 PF02513 Spin-Ssty: Spin/Ssty 22.0 1.3E+02 0.0029 25.8 3.7 31 135-165 1-31 (50)
24 PF08206 OB_RNB: Ribonuclease 21.8 1.3E+02 0.0027 25.3 3.7 51 100-160 8-58 (58)
25 PF04225 OapA: Opacity-associa 21.0 73 0.0016 28.9 2.2 18 45-62 42-59 (85)
26 cd04451 S1_IF1 S1_IF1: Transla 20.8 3.7E+02 0.0079 22.7 6.3 13 45-57 40-52 (64)
No 1
>PF06507 Auxin_resp: Auxin response factor; InterPro: IPR010525 This pattern represents a conserved region of auxin-responsive transcription factors. The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins (IPR003311 from INTERPRO) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression []. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains (IPR011525 from INTERPRO) found in both Aux/IAA and ARF proteins. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0009725 response to hormone stimulus, 0005634 nucleus
Probab=100.00 E-value=5.7e-36 Score=263.64 Aligned_cols=83 Identities=67% Similarity=1.128 Sum_probs=81.7
Q ss_pred HHHHHhcCCceEEEEcCCCCCCccccchHHHHHhhhhcCccccceeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCc
Q 003369 94 AAHAAANNSPFTVFYNPRASPSEFVVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQW 173 (825)
Q Consensus 94 AahaAatgspFtV~Y~PRas~sEFVVp~~kY~kAm~~~~ws~GMRFRM~FEtEDss~rry~GTItgVsd~DPvrWP~S~W 173 (825)
|+|||++|++|+|+||||++++|||||++||++||+ ++|++||||||.||+||+++++|+|||+||+|+||+|||+|+|
T Consensus 1 A~~aa~~~~~F~V~Y~PRa~~sEFVV~~~k~~~al~-~~~~~GmRfkM~fE~eds~~~~~~GtI~~v~~~dp~~w~~S~W 79 (83)
T PF06507_consen 1 AAHAAATGSPFEVFYYPRASPSEFVVPASKYDKALN-HPWSVGMRFKMRFETEDSSERRWQGTIVGVSDLDPIRWPGSKW 79 (83)
T ss_pred ChhHhhcCCeEEEEECCCCCCcceEEEHHHHHHHhc-CCCCCCcEEEEEeccCCCccceeeeEEeEeeccCCCCCCCCCc
Confidence 689999999999999999999999999999999999 9999999999999999999999999999999999999999999
Q ss_pred ccee
Q 003369 174 RNLQ 177 (825)
Q Consensus 174 R~Lk 177 (825)
||||
T Consensus 80 R~Lq 83 (83)
T PF06507_consen 80 RMLQ 83 (83)
T ss_pred ccCc
Confidence 9997
No 2
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=99.58 E-value=1.1e-15 Score=175.06 Aligned_cols=149 Identities=22% Similarity=0.384 Sum_probs=124.5
Q ss_pred cCCCCeEEEEEcCCCcEEEEEEeccCCCCCC---------------------CCcccCCCCcCcchhHHHHHHHhcCCce
Q 003369 46 LFAGDSVLFIRDEKQQLLLGIRRANRQPANL---------------------SSSVLSSDSMHIGILAAAAHAAANNSPF 104 (825)
Q Consensus 46 L~AGDsVVF~R~e~geL~vGIRRA~R~~~~~---------------------~ssvlSsdsM~~GvLAaAahaAatgspF 104 (825)
...||.|+|+|.++.+++-.+|+.++.-.+. +.+.-+.=.|.+.++..|.|+ -+..|
T Consensus 874 pQmgDEViyfrQghqeyl~~~~~n~~~~~~~~p~~~~~v~~~kv~kl~~~~y~~~~~s~c~m~l~~idp~s~~--~~k~F 951 (1113)
T KOG0644|consen 874 PQMGDEVIYFRQGHQEYLEAVRLNNIELNNKEPWNKMAVEICKVEKLVYITYPGSGDSCCKMKLAVIDPASKL--MDKSF 951 (1113)
T ss_pred ccccceeehhhhhhHHHHhhhhhccccccccCcccccchhhheeeeeeeeeccCCCcchheeeeeeecchhhh--hhccc
Confidence 4579999999999999998888876632221 122223335888899888754 45789
Q ss_pred EEEEcCCCCCCccccchHHHHHhhhhcCccccceeeeeee--ccCCCcceeeEEEEEeecCCCCCCCCCCccceeeeccc
Q 003369 105 TVFYNPRASPSEFVVPLAKYYKAVHSNQISLGMRFRMMFE--TEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDE 182 (825)
Q Consensus 105 tV~Y~PRas~sEFVVp~~kY~kAm~~~~ws~GMRFRM~FE--tEDss~rry~GTItgVsd~DPvrWP~S~WR~LkV~WDE 182 (825)
.+.|....+.+||+|.+..|++|+. ++|..+++||..|. +||. .+||.|+|.++.+..| .+|+|+|+|+.|+||.
T Consensus 952 ~ltlpdlv~fpDFlV~rsrYd~AiQ-rnW~~~d~crvwwrda~~e~-g~WWeG~ils~~pksp-~fpdSpwery~v~~~~ 1028 (1113)
T KOG0644|consen 952 KLTLPDLVTFPDFLVERSRYDAAIQ-RNWTCRDKCRVWWRDAGEED-GAWWEGRILSVKPKSP-DFPDSPWERYIVRYDN 1028 (1113)
T ss_pred eeecccccCcchhhhhhhhHHHHHh-hccccccceeEEEccCCCcC-CceeeeeeeeccCCCC-CCCCCcceeEEEEecC
Confidence 9999999999999999999999999 99999999999994 4454 4999999999999888 9999999999999999
Q ss_pred cCCCCCCCccccccccccCCC
Q 003369 183 STAGEKRNRVSIWEIEPVTAP 203 (825)
Q Consensus 183 ~~~~~~~eRVSPWEIEPv~~p 203 (825)
.+ .+.-||||.|++..-
T Consensus 1029 ~e----~~~~spwe~~~i~de 1045 (1113)
T KOG0644|consen 1029 TE----TELHSPWEMEPIPDE 1045 (1113)
T ss_pred Cc----ccccCccccCCCccc
Confidence 97 468899999999753
No 3
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.15 E-value=5e-11 Score=103.76 Aligned_cols=65 Identities=29% Similarity=0.450 Sum_probs=53.2
Q ss_pred ccEEEEeecCCCeeEeeEEEcCCCcccccccccceeecCCCcCCCCeEEEEEcC--CCcEEEEEEec
Q 003369 5 AQELMARDLHDNIWTFRHIYRGQPKRHLLTTGWSLFVSGKRLFAGDSVLFIRDE--KQQLLLGIRRA 69 (825)
Q Consensus 5 ~QeLvarDlhGk~W~FRhiYRG~PkRhlLTtGWS~FVk~KrL~AGDsVVF~R~e--~geL~vGIRRA 69 (825)
..++.++|..|++|.+++.|++.+.+++|+.||..||++++|.+||.|+|...+ ..++.|.|.|+
T Consensus 33 ~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~GD~~~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 33 SREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKEGDVCVFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp -CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--TT-EEEEEE-SSSCE-EEEEEE--
T ss_pred CeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCCCCEEEEEEecCCCceEEEEEEEC
Confidence 458999999999999999999999999999999999999999999999999865 45669999886
No 4
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=79.96 E-value=1.7 Score=55.51 Aligned_cols=15 Identities=33% Similarity=0.521 Sum_probs=9.9
Q ss_pred ccceeecCCCcCCCC
Q 003369 36 GWSLFVSGKRLFAGD 50 (825)
Q Consensus 36 GWS~FVk~KrL~AGD 50 (825)
-|-.|--.|.++.|-
T Consensus 1723 pwdlFEg~k~~apls 1737 (2220)
T KOG3598|consen 1723 PWDLFEGTKHLAPLS 1737 (2220)
T ss_pred cchhhccCCCCCCcc
Confidence 477777777775554
No 5
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=76.19 E-value=3.5 Score=53.02 Aligned_cols=8 Identities=25% Similarity=-0.001 Sum_probs=3.8
Q ss_pred CCCccccc
Q 003369 188 KRNRVSIW 195 (825)
Q Consensus 188 ~~eRVSPW 195 (825)
+..|-+-|
T Consensus 1858 hhp~~~~~ 1865 (2220)
T KOG3598|consen 1858 HHPRASDA 1865 (2220)
T ss_pred cCCCchhh
Confidence 34455555
No 6
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=65.14 E-value=14 Score=38.49 Aligned_cols=103 Identities=20% Similarity=0.212 Sum_probs=60.7
Q ss_pred cCCCCeEEE---EEcCCCcEEEEEEeccCCCCCCCCcccCCCCcCcchhHHHHHHHhcCCceEEEEcCCCC------CCc
Q 003369 46 LFAGDSVLF---IRDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAAAHAAANNSPFTVFYNPRAS------PSE 116 (825)
Q Consensus 46 L~AGDsVVF---~R~e~geL~vGIRRA~R~~~~~~ssvlSsdsM~~GvLAaAahaAatgspFtV~Y~PRas------~sE 116 (825)
+..|+.|.+ +|.++|+++-.-+ . ..|-..+--...-+-.|.+|..-...|..|+|..-|-.. -.-
T Consensus 3 I~~~~vV~l~Y~l~~~dG~v~dst~-~-----~~Pl~~~~G~g~lipglE~aL~G~~~Gd~~~v~l~peeAyGe~d~~lV 76 (196)
T PRK10737 3 VAKDLVVSLAYQVRTEDGVLVDESP-V-----SAPLDYLHGHGSLISGLETALEGHEVGDKFDVAVGANDAYGQYDENLV 76 (196)
T ss_pred cCCCCEEEEEEEEEeCCCCEEEecC-C-----CCCeEEEeCCCcchHHHHHHHcCCCCCCEEEEEEChHHhcCCCChHHE
Confidence 445666655 3566777644322 1 112222222223334566666667788889998655432 234
Q ss_pred cccchHHHHHhhhhcCccccceeeeeeeccCCCcceeeEEEEEeec
Q 003369 117 FVVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISD 162 (825)
Q Consensus 117 FVVp~~kY~kAm~~~~ws~GMRFRM~FEtEDss~rry~GTItgVsd 162 (825)
+.||++.|... ....+||||.+ ++++. .+.++|+.|.+
T Consensus 77 ~~vpr~~F~~~---~~l~~G~~~~~--~~~~G---~~~~~V~ev~~ 114 (196)
T PRK10737 77 QRVPKDVFMGV---DELQVGMRFLA--ETDQG---PVPVEITAVED 114 (196)
T ss_pred EEecHHHCCCc---cCCCCCCEEEE--eCCCC---cEEEEEEEEcC
Confidence 57888877422 24789999886 55543 36889999975
No 7
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=63.94 E-value=6.5 Score=37.82 Aligned_cols=37 Identities=24% Similarity=0.409 Sum_probs=31.3
Q ss_pred EEEEeecCCCeeEeeEEEcCC---CcccccccccceeecC
Q 003369 7 ELMARDLHDNIWTFRHIYRGQ---PKRHLLTTGWSLFVSG 43 (825)
Q Consensus 7 eLvarDlhGk~W~FRhiYRG~---PkRhlLTtGWS~FVk~ 43 (825)
++.+.|-.++.|.-+.-.|.. .-.|+|++||..+|++
T Consensus 75 ~V~lvdp~~~~~~m~lkkW~mg~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 75 EVILVDPSLRKWTMRLKKWNMGNGTSNYVLNSGWNKVVED 114 (114)
T ss_pred eEEEECCcCcEEEEEEEEecccCCceEEEEEcChHhhccC
Confidence 467889999999999889855 5679999999999863
No 8
>KOG3207 consensus Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones]
Probab=51.95 E-value=17 Score=42.51 Aligned_cols=43 Identities=30% Similarity=0.726 Sum_probs=30.7
Q ss_pred ccccceeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCccceeeeccccCCCCCC
Q 003369 133 ISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKR 189 (825)
Q Consensus 133 ws~GMRFRM~FEtEDss~rry~GTItgVsd~DPvrWP~S~WR~LkV~WDE~~~~~~~ 189 (825)
..+|.|+|.-+|- ++.||.|+|.|. ++ +| +-|.||.+.-|.+.
T Consensus 3 ~~IG~RvkI~~~~---~Tvr~iG~V~g~--------~~-~w--~GvEWDd~~RGKH~ 45 (505)
T KOG3207|consen 3 MEIGTRVKIGGEI---ATVRYIGEVEGN--------NS-KW--YGVEWDDPVRGKHD 45 (505)
T ss_pred eeccceEEEcCEE---EEEEEEEEEcCC--------CC-cc--eeeEecCCCccccC
Confidence 4689999987662 356777776654 44 45 78999999977654
No 9
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=49.25 E-value=23 Score=29.15 Aligned_cols=28 Identities=11% Similarity=0.190 Sum_probs=23.7
Q ss_pred CccccceeeeeeeccCCCcceeeEEEEEeec
Q 003369 132 QISLGMRFRMMFETEESGTRRYMGTITGISD 162 (825)
Q Consensus 132 ~ws~GMRFRM~FEtEDss~rry~GTItgVsd 162 (825)
.|++|+++...|+. ...||.|+|+.+..
T Consensus 2 ~~~~G~~Ve~~~~~---~~~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKE---EDSWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECC---CCEEEEEEEEEECC
Confidence 58899999999963 36999999999964
No 10
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=49.19 E-value=31 Score=29.63 Aligned_cols=42 Identities=12% Similarity=0.121 Sum_probs=27.3
Q ss_pred ccccceeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCccceeeeccccC
Q 003369 133 ISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDEST 184 (825)
Q Consensus 133 ws~GMRFRM~FEtEDss~rry~GTItgVsd~DPvrWP~S~WR~LkV~WDE~~ 184 (825)
|+.|+++...-+.+.....||.|||+.....+ .+.|+.+.-.
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~----------~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD----------KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-----------EEEEEETT-S
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc----------EEEEEECCcc
Confidence 56899999987666666899999999997532 6778886544
No 11
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=35.57 E-value=52 Score=26.37 Aligned_cols=53 Identities=11% Similarity=0.214 Sum_probs=37.7
Q ss_pred CccccceeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCccceeeeccccCCCCCCCccccccccccC
Q 003369 132 QISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKRNRVSIWEIEPVT 201 (825)
Q Consensus 132 ~ws~GMRFRM~FEtEDss~rry~GTItgVsd~DPvrWP~S~WR~LkV~WDE~~~~~~~eRVSPWEIEPv~ 201 (825)
.|.+|..+...| .+ ..||.|+|+++.. + ..+.|.-++-+. .+.|...+|-++.
T Consensus 2 ~~~~G~~~~a~~-~d---~~wyra~I~~~~~-------~---~~~~V~f~D~G~---~~~v~~~~l~~l~ 54 (57)
T smart00333 2 TFKVGDKVAARW-ED---GEWYRARIIKVDG-------E---QLYEVFFIDYGN---EEVVPPSDLRPLP 54 (57)
T ss_pred CCCCCCEEEEEe-CC---CCEEEEEEEEECC-------C---CEEEEEEECCCc---cEEEeHHHeecCC
Confidence 578999999988 32 6999999999964 1 456788877442 2466666666553
No 12
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=33.93 E-value=60 Score=30.17 Aligned_cols=27 Identities=26% Similarity=0.314 Sum_probs=23.0
Q ss_pred eecCCCcCCCCeEEEEEcCCCcEEEEE
Q 003369 40 FVSGKRLFAGDSVLFIRDEKQQLLLGI 66 (825)
Q Consensus 40 FVk~KrL~AGDsVVF~R~e~geL~vGI 66 (825)
|.-...|++||.|+-+|.++|+.|+=+
T Consensus 71 i~~~~~Lk~GD~V~ll~~~~gQ~yiVl 97 (100)
T PF10844_consen 71 ITFTDGLKVGDKVLLLRVQGGQKYIVL 97 (100)
T ss_pred EEEecCCcCCCEEEEEEecCCCEEEEE
Confidence 777889999999999998888776644
No 13
>PF11515 Cul7: Mouse development and cellular proliferation protein Cullin-7; InterPro: IPR021097 The CPH domain is found in the Cullin-7, PARC and HERC2 proteins, which are all components of known or predicted E3-ubiquitin ligases. The CPH domain is a protein-protein interaction module that binds the teramerisation domain of the tumour suppressor protein p53 []. Structurally it forms a beta-barrel fold similar to the SH3, Tudor and KOW and domains. Unlike the SH3 and Tudor domains, which bind to small peptides, the CPH domain appears to bind to an extended surface on p53.; PDB: 2JUF_A 2JNG_A.
Probab=33.54 E-value=50 Score=30.48 Aligned_cols=72 Identities=24% Similarity=0.249 Sum_probs=36.1
Q ss_pred chHHHHHhhhhcCccccceeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCccceeeeccccCCCCCCCccccccccc
Q 003369 120 PLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKRNRVSIWEIEP 199 (825)
Q Consensus 120 p~~kY~kAm~~~~ws~GMRFRM~FEtEDss~rry~GTItgVsd~DPvrWP~S~WR~LkV~WDE~~~~~~~eRVSPWEIEP 199 (825)
..+.|..=++ -++.+||++||.=.-||-. ..=.|+|..++. |- -| =-+++|.|...+. .-.|--=.||.
T Consensus 6 s~d~Ya~YVr-~~i~~GM~VRc~~~yeeV~-~GD~G~V~k~~~-dg--~~---~lnvqv~W~~~G~---tyWV~~~~vEi 74 (78)
T PF11515_consen 6 SNDDYAEYVR-DNIQPGMRVRCCRDYEEVR-AGDEGEVFKQDR-DG--LH---DLNVQVDWQSKGR---TYWVHWHHVEI 74 (78)
T ss_dssp SSHHHHHHHH-HH--TT-EEEESS-BTTB--TT-EEE-EEEE--TT--SS---E--EEEEETTTTE---EEEEEGGGEEE
T ss_pred chhHHHHHHH-HhCCCCcEEEEeccccccc-ccccceeEeecc-CC--CC---CcceEEEeeecCc---eEEEEEEEEEE
Confidence 3456666666 7899999999974444333 223677776654 21 11 2357899987652 23455556666
Q ss_pred cCC
Q 003369 200 VTA 202 (825)
Q Consensus 200 v~~ 202 (825)
++.
T Consensus 75 ig~ 77 (78)
T PF11515_consen 75 IGF 77 (78)
T ss_dssp ---
T ss_pred ecC
Confidence 643
No 14
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=32.97 E-value=2.1e+02 Score=29.85 Aligned_cols=105 Identities=19% Similarity=0.255 Sum_probs=63.7
Q ss_pred CcCCCCeEEE---EEcCCCcEEEEEEeccCCCCCCCCcccCCCCcCcchhHHHHHHHhcCCceEEEEcCCCCCCcc----
Q 003369 45 RLFAGDSVLF---IRDEKQQLLLGIRRANRQPANLSSSVLSSDSMHIGILAAAAHAAANNSPFTVFYNPRASPSEF---- 117 (825)
Q Consensus 45 rL~AGDsVVF---~R~e~geL~vGIRRA~R~~~~~~ssvlSsdsM~~GvLAaAahaAatgspFtV~Y~PRas~sEF---- 117 (825)
++..||.|.. +|.++|+++---+- ...|..++--+..-+.-|.+|.....-|..|+|.--|-..-.||
T Consensus 2 ~i~k~~~V~i~Y~~~~~dg~v~Dtt~e-----~~~P~~~i~G~g~li~glE~al~g~~~Ge~~~V~IpPE~AfGe~~~~l 76 (174)
T COG1047 2 KIEKGDVVSLHYTLKVEDGEVVDTTDE-----NYGPLTFIVGAGQLIPGLEEALLGKEVGEEFTVEIPPEDAFGEYDPDL 76 (174)
T ss_pred cccCCCEEEEEEEEEecCCcEEEcccc-----cCCCeEEEecCCCcchhHHHHHhCCCCCceeEEEeCchHhcCCCChHH
Confidence 4456676665 25555654422111 01122233333334445777888888899999998887644444
Q ss_pred --ccchHHHHHhhhhcCccccceeeeeeeccCCCcceeeEEEEEeec
Q 003369 118 --VVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGISD 162 (825)
Q Consensus 118 --VVp~~kY~kAm~~~~ws~GMRFRM~FEtEDss~rry~GTItgVsd 162 (825)
.||+++|... ....+||+|.+ ++++ .-.-|+|+.|..
T Consensus 77 vq~vp~~~F~~~---~~~~vGm~~~~--~~~~---~~~~~~V~~V~~ 115 (174)
T COG1047 77 VQRVPRDEFQGV---GELEVGMEVEA--EGGD---GEIPGVVTEVSG 115 (174)
T ss_pred eEEecHHHhCcC---CCCCCCcEEEE--cCCC---ceeeEEEEEEcC
Confidence 4677776432 15789998875 6554 456899999974
No 15
>PF14478 DUF4430: Domain of unknown function (DUF4430); PDB: 3U7Z_B 2BB5_A.
Probab=27.59 E-value=30 Score=29.62 Aligned_cols=21 Identities=29% Similarity=0.741 Sum_probs=13.5
Q ss_pred cccceeecCC---------CcCCCCeEEEE
Q 003369 35 TGWSLFVSGK---------RLFAGDSVLFI 55 (825)
Q Consensus 35 tGWS~FVk~K---------rL~AGDsVVF~ 55 (825)
+||.-+|+.+ +|++||.|+|.
T Consensus 39 ~~W~~~vNG~~~~~ga~~~~l~~GD~i~~~ 68 (68)
T PF14478_consen 39 SYWMYYVNGESANVGAGSYKLKDGDKITWY 68 (68)
T ss_dssp EEEEEEETTEE-SS-CCC-B--TTEEEEE-
T ss_pred ceeEEEECCEEhhcCcceeEeCCCCEEEeC
Confidence 4666666554 89999999983
No 16
>PF01878 EVE: EVE domain; InterPro: IPR002740 The EVE domain is part of the wider PUA domain superfamily. The function of this domain is not known but, given the structural similarities to PUA, is likely to involve RNA binding []. ; PDB: 2G2X_B 2AR1_A 3EOP_A 2EVE_A 2HD9_A 2ZBN_A 1WMM_A 2P5D_A 2GBS_A 1ZCE_A.
Probab=27.19 E-value=56 Score=31.21 Aligned_cols=38 Identities=29% Similarity=0.417 Sum_probs=24.2
Q ss_pred cccccccceeec------CCCcCCCCeEEEEEcC-CCcEEEEEEe
Q 003369 31 HLLTTGWSLFVS------GKRLFAGDSVLFIRDE-KQQLLLGIRR 68 (825)
Q Consensus 31 hlLTtGWS~FVk------~KrL~AGDsVVF~R~e-~geL~vGIRR 68 (825)
|.-+.-|..|.. -|+++.||.|+|++.. ++.-++|+=|
T Consensus 19 ~~~~~~~~gv~~~~~~~~l~~mk~GD~vifY~s~~~~~~ivai~~ 63 (143)
T PF01878_consen 19 HWGVTVWDGVRNYQARKNLKRMKPGDKVIFYHSGCKERGIVAIGE 63 (143)
T ss_dssp HHSEEECHTEEEHHHHHHHHC--TT-EEEEEETSSSS-EEEEEEE
T ss_pred ccceEEEcCEeehhhhhhhhcCCCCCEEEEEEcCCCCCEEEEEEE
Confidence 344556666655 2489999999999988 6777888744
No 17
>PF12852 Cupin_6: Cupin
Probab=27.07 E-value=66 Score=31.64 Aligned_cols=53 Identities=26% Similarity=0.286 Sum_probs=35.6
Q ss_pred EEeecCCCeeEeeEEEcCCCcccccccc--cceeec---CCCcCCCCeEEEEEcCCCc
Q 003369 9 MARDLHDNIWTFRHIYRGQPKRHLLTTG--WSLFVS---GKRLFAGDSVLFIRDEKQQ 61 (825)
Q Consensus 9 varDlhGk~W~FRhiYRG~PkRhlLTtG--WS~FVk---~KrL~AGDsVVF~R~e~ge 61 (825)
..+-.-+-.|.|++-......=|+++.| |..+-. .-.|.+||.|+|-|+....
T Consensus 17 ~~~~~~~~~W~~~~~~~~~~~fh~V~~G~~~l~~~~~~~~~~L~~GDivllp~g~~H~ 74 (186)
T PF12852_consen 17 FFRCELCGPWGLRFPGSPGASFHVVLRGSCWLRVPGGGEPIRLEAGDIVLLPRGTAHV 74 (186)
T ss_pred EEEEEEeCCcEEeccCCCceEEEEEECCeEEEEEcCCCCeEEecCCCEEEEcCCCCeE
Confidence 3344456678888655544677888877 666433 2389999999988765433
No 18
>PF13163 DUF3999: Protein of unknown function (DUF3999)
Probab=26.36 E-value=2.1e+02 Score=32.93 Aligned_cols=138 Identities=14% Similarity=0.221 Sum_probs=79.9
Q ss_pred ccEEEEeecCCCeeEeeEEEcCCC-----cccccccccce-eecCCCcCCCCe-EEEEEcCCCcEEEEEEeccCCCCCCC
Q 003369 5 AQELMARDLHDNIWTFRHIYRGQP-----KRHLLTTGWSL-FVSGKRLFAGDS-VLFIRDEKQQLLLGIRRANRQPANLS 77 (825)
Q Consensus 5 ~QeLvarDlhGk~W~FRhiYRG~P-----kRhlLTtGWS~-FVk~KrL~AGDs-VVF~R~e~geL~vGIRRA~R~~~~~~ 77 (825)
-++|.+-|-.|..=-|.-+....+ .++-| =|=. .++++. ..||. +.+.|+.+|.+ |-||++........
T Consensus 36 L~DvrVfn~~G~~vP~al~~~~~~~~~~~~~~~~--~~fpl~~~~~~-~~~~~~~~v~~~~~G~~-ve~~~~~~~~~~~~ 111 (429)
T PF13163_consen 36 LGDVRVFNAAGEPVPYALLPPRAPAAQAPTRQPV--PWFPLPASADA-ARGDPQLRVERDADGAL-VEVRPASGAAPADG 111 (429)
T ss_pred ccceEEECCCCCCCceeecccccccCCCCceeee--eeeecCCcccc-ccCCccEEEEECCCCcE-EEecccCCCCcccc
Confidence 467788888888776664443221 11111 1222 244545 66774 77888999998 88888776422110
Q ss_pred CcccCCCCcCcchhHHHHHHHhcCCceEEEEcCCCCCCccccchHHHHH---hhhhcCc-ccccee--eeeeeccCCCcc
Q 003369 78 SSVLSSDSMHIGILAAAAHAAANNSPFTVFYNPRASPSEFVVPLAKYYK---AVHSNQI-SLGMRF--RMMFETEESGTR 151 (825)
Q Consensus 78 ssvlSsdsM~~GvLAaAahaAatgspFtV~Y~PRas~sEFVVp~~kY~k---Am~~~~w-s~GMRF--RM~FEtEDss~r 151 (825)
. ...|+|.++..++ ++. ..| .....+ |...|+-|.-..
T Consensus 112 ~-----------------------------------~~~~Lld~s~~~~~l~~L~-L~w~~~~~~~~~~v~VeaSdDl~~ 155 (429)
T PF13163_consen 112 Q-----------------------------------ARGWLLDLSALKEPLDALR-LDWPQSNFNWQARVSVEASDDLQH 155 (429)
T ss_pred c-----------------------------------ccEEEEECcccccchhheE-EEeecCCCCceEEEEEEEecCccc
Confidence 0 0133444443333 333 466 333444 555666666556
Q ss_pred ee----eEEEEEeecCC------CCCCCCCCccceeeeccc
Q 003369 152 RY----MGTITGISDLD------PVRWKNSQWRNLQVGWDE 182 (825)
Q Consensus 152 ry----~GTItgVsd~D------PvrWP~S~WR~LkV~WDE 182 (825)
|+ .|+|..+..-+ -+..|+...|.|+|.|++
T Consensus 156 W~~l~~~~~l~~L~~~~~~l~~~~I~L~~~~~rYLRl~~~~ 196 (429)
T PF13163_consen 156 WRPLAGDAQLMDLSNGGQRLVQDRIELPGSNARYLRLTWND 196 (429)
T ss_pred ceEccCCceEEEeccCCcceeeeeEccCCCCCceEEEEeCC
Confidence 64 57777776322 356789999999999965
No 19
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=26.17 E-value=55 Score=26.24 Aligned_cols=27 Identities=15% Similarity=0.139 Sum_probs=21.3
Q ss_pred eecCCCcCCCCeEEEEEcCCCcEEEEE
Q 003369 40 FVSGKRLFAGDSVLFIRDEKQQLLLGI 66 (825)
Q Consensus 40 FVk~KrL~AGDsVVF~R~e~geL~vGI 66 (825)
|...-+|.+||.|.|.-.++|++.+--
T Consensus 15 ~~~~l~l~~Gd~v~i~~~~~g~i~i~p 41 (47)
T PF04014_consen 15 IREKLGLKPGDEVEIEVEGDGKIVIRP 41 (47)
T ss_dssp HHHHTTSSTTTEEEEEEETTSEEEEEE
T ss_pred HHHHcCCCCCCEEEEEEeCCCEEEEEE
Confidence 344558999999999999988776654
No 20
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=23.44 E-value=74 Score=34.39 Aligned_cols=57 Identities=16% Similarity=0.301 Sum_probs=33.8
Q ss_pred cCccccceeeeeeeccCCCcceeeEEEEEeecCCCCCCCCCCccceeeeccccCCCCCCCccccccccccCC
Q 003369 131 NQISLGMRFRMMFETEESGTRRYMGTITGISDLDPVRWKNSQWRNLQVGWDESTAGEKRNRVSIWEIEPVTA 202 (825)
Q Consensus 131 ~~ws~GMRFRM~FEtEDss~rry~GTItgVsd~DPvrWP~S~WR~LkV~WDE~~~~~~~eRVSPWEIEPv~~ 202 (825)
..|.+|++.+-.|..+ ..+|-+||++|..-+- .+.|..++=+ +.+.|..=+|.+...
T Consensus 67 ~~WkvGd~C~A~~s~D---g~~Y~A~I~~i~~~~~---------~~~V~f~gYg---n~e~v~l~dL~~~~~ 123 (264)
T PF06003_consen 67 KKWKVGDKCMAVYSED---GQYYPATIESIDEEDG---------TCVVVFTGYG---NEEEVNLSDLKPSEG 123 (264)
T ss_dssp T---TT-EEEEE-TTT---SSEEEEEEEEEETTTT---------EEEEEETTTT---EEEEEEGGGEEETT-
T ss_pred cCCCCCCEEEEEECCC---CCEEEEEEEEEcCCCC---------EEEEEEcccC---CeEeeehhhhccccc
Confidence 6999999999998543 4789999999975221 2347776643 235566666665543
No 21
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=23.08 E-value=68 Score=24.39 Aligned_cols=26 Identities=27% Similarity=0.300 Sum_probs=20.3
Q ss_pred eeecCCCcCCCCeEEEEEcCCCcEEE
Q 003369 39 LFVSGKRLFAGDSVLFIRDEKQQLLL 64 (825)
Q Consensus 39 ~FVk~KrL~AGDsVVF~R~e~geL~v 64 (825)
.|.+.-++..||.|.+.+.++|+|.+
T Consensus 14 ~~r~~l~~~~gd~~~i~~~~~~~l~l 39 (43)
T TIGR01439 14 EIREKLGLKEGDRLEVIRVEDGEIIL 39 (43)
T ss_pred HHHHHcCcCCCCEEEEEEeCCCEEEE
Confidence 35566688999999999887777654
No 22
>PF13437 HlyD_3: HlyD family secretion protein
Probab=22.33 E-value=92 Score=27.64 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=23.6
Q ss_pred Ccc-ccceeeeeeeccCCCcceeeEEEEEeec
Q 003369 132 QIS-LGMRFRMMFETEESGTRRYMGTITGISD 162 (825)
Q Consensus 132 ~ws-~GMRFRM~FEtEDss~rry~GTItgVsd 162 (825)
.+. .|+++++.+. +.....|.|+|+.|+.
T Consensus 49 ~i~~~g~~v~v~~~--~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 49 RIKDPGQKVTVRLD--PGPEKTIEGKVSSISP 78 (105)
T ss_pred ceEeCCCEEEEEEC--CCCCcEEEEEEEEEeC
Confidence 665 9999999988 3335589999999986
No 23
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=22.03 E-value=1.3e+02 Score=25.75 Aligned_cols=31 Identities=16% Similarity=0.358 Sum_probs=23.8
Q ss_pred ccceeeeeeeccCCCcceeeEEEEEeecCCC
Q 003369 135 LGMRFRMMFETEESGTRRYMGTITGISDLDP 165 (825)
Q Consensus 135 ~GMRFRM~FEtEDss~rry~GTItgVsd~DP 165 (825)
+|-|+.-.||.++.+...|.|+|..--+..|
T Consensus 1 vGk~Veh~~~~g~g~~s~w~G~Vl~Qvp~~p 31 (50)
T PF02513_consen 1 VGKRVEHTWEDGDGPKSKWKGMVLHQVPAKP 31 (50)
T ss_dssp TT-EEEEEECTSTS-EEEEEEEEEEE-TTST
T ss_pred CCceEEEEEccCCCcccEEEEEEEEEeecCC
Confidence 5889999999988888888999999877654
No 24
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=21.77 E-value=1.3e+02 Score=25.32 Aligned_cols=51 Identities=14% Similarity=0.229 Sum_probs=33.1
Q ss_pred cCCceEEEEcCCCCCCccccchHHHHHhhhhcCccccceeeeeeeccCCCcceeeEEEEEe
Q 003369 100 NNSPFTVFYNPRASPSEFVVPLAKYYKAVHSNQISLGMRFRMMFETEESGTRRYMGTITGI 160 (825)
Q Consensus 100 tgspFtV~Y~PRas~sEFVVp~~kY~kAm~~~~ws~GMRFRM~FEtEDss~rry~GTItgV 160 (825)
.|--|-+... ...|.+||......|+. |++++..... .+..++..|.|+.|
T Consensus 8 ~GfGFv~~~~---~~~DifIp~~~l~~A~~------gD~V~v~i~~-~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 8 KGFGFVIPDD---GGEDIFIPPRNLNGAMD------GDKVLVRITP-PSRGKRPEGEVVEV 58 (58)
T ss_dssp SS-EEEEECT----TEEEEE-HHHHTTS-T------T-EEEEEEEE-SSSEEEEEEEEEE-
T ss_pred CCCEEEEECC---CCCCEEECHHHHCCCCC------CCEEEEEEec-CCCCCCCCEEEEeC
Confidence 4445555433 46689999988877776 8999987766 55567789999875
No 25
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=20.96 E-value=73 Score=28.94 Aligned_cols=18 Identities=44% Similarity=0.577 Sum_probs=12.2
Q ss_pred CcCCCCeEEEEEcCCCcE
Q 003369 45 RLFAGDSVLFIRDEKQQL 62 (825)
Q Consensus 45 rL~AGDsVVF~R~e~geL 62 (825)
+|++||+|.|..+++|+|
T Consensus 42 ~L~pGq~l~f~~d~~g~L 59 (85)
T PF04225_consen 42 RLKPGQTLEFQLDEDGQL 59 (85)
T ss_dssp G--TT-EEEEEE-TTS-E
T ss_pred hCCCCCEEEEEECCCCCE
Confidence 799999999999999986
No 26
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=20.79 E-value=3.7e+02 Score=22.73 Aligned_cols=13 Identities=31% Similarity=0.460 Sum_probs=10.8
Q ss_pred CcCCCCeEEEEEc
Q 003369 45 RLFAGDSVLFIRD 57 (825)
Q Consensus 45 rL~AGDsVVF~R~ 57 (825)
++.+||.|.|-..
T Consensus 40 ~~~vGD~V~~~~~ 52 (64)
T cd04451 40 RILPGDRVKVELS 52 (64)
T ss_pred ccCCCCEEEEEEe
Confidence 4899999999854
Done!