Query psy12585
Match_columns 146
No_of_seqs 177 out of 1148
Neff 6.9
Searched_HMMs 46136
Date Fri Aug 16 23:05:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12585.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12585hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1471|consensus 99.9 2.6E-22 5.7E-27 163.7 6.3 86 6-91 171-260 (317)
2 PF00650 CRAL_TRIO: CRAL/TRIO 99.8 1.7E-20 3.6E-25 137.6 5.1 75 13-87 82-159 (159)
3 cd00170 SEC14 Sec14p-like lipi 99.8 6E-19 1.3E-23 127.1 6.0 74 14-87 83-157 (157)
4 smart00516 SEC14 Domain in hom 99.7 3.8E-18 8.2E-23 124.9 6.8 75 14-88 81-157 (158)
5 KOG1470|consensus 99.6 5.3E-16 1.2E-20 127.6 4.8 77 11-88 166-243 (324)
6 PF13716 CRAL_TRIO_2: Divergen 98.5 1.9E-08 4.2E-13 73.5 -0.9 75 13-88 67-144 (149)
7 KOG4406|consensus 96.4 0.0024 5.3E-08 54.7 2.7 51 25-76 161-211 (467)
8 COG0052 RpsB Ribosomal protein 58.5 19 0.00041 29.2 4.4 69 25-96 31-109 (252)
9 PF03641 Lysine_decarbox: Poss 53.0 20 0.00042 25.7 3.4 58 17-75 68-133 (133)
10 PF04378 RsmJ: Ribosomal RNA s 49.5 10 0.00023 30.5 1.6 29 31-59 206-234 (245)
11 PF10004 DUF2247: Uncharacteri 48.3 21 0.00045 26.8 3.0 36 67-104 122-157 (161)
12 COG2961 ComJ Protein involved 46.5 14 0.0003 30.3 1.9 28 31-58 237-264 (279)
13 TIGR01011 rpsB_bact ribosomal 41.2 64 0.0014 25.5 4.9 69 25-94 29-105 (225)
14 PRK05299 rpsB 30S ribosomal pr 40.9 53 0.0011 26.5 4.4 70 25-95 31-108 (258)
15 cd01425 RPS2 Ribosomal protein 32.3 1.2E+02 0.0026 23.1 5.0 69 25-94 23-99 (193)
16 PRK04020 rps2P 30S ribosomal p 30.7 75 0.0016 24.9 3.7 67 25-92 35-108 (204)
17 TIGR01012 Sa_S2_E_A ribosomal 30.3 70 0.0015 24.9 3.4 67 25-92 29-102 (196)
18 PTZ00254 40S ribosomal protein 27.1 76 0.0016 25.7 3.2 67 25-91 38-111 (249)
19 PF02771 Acyl-CoA_dh_N: Acyl-C 26.5 55 0.0012 21.7 2.0 19 75-93 45-63 (113)
20 TIGR00730 conserved hypothetic 25.0 2.1E+02 0.0045 21.7 5.2 46 29-75 125-175 (178)
21 CHL00067 rps2 ribosomal protei 24.9 2.1E+02 0.0046 22.5 5.4 69 25-95 35-112 (230)
22 PRK12311 rpsB 30S ribosomal pr 24.6 1.6E+02 0.0035 24.8 4.8 71 25-97 26-105 (326)
23 PF04838 Baculo_LEF5: Baculovi 23.5 1.4E+02 0.003 22.5 3.8 98 11-118 12-128 (159)
No 1
>KOG1471|consensus
Probab=99.86 E-value=2.6e-22 Score=163.67 Aligned_cols=86 Identities=33% Similarity=0.460 Sum_probs=77.2
Q ss_pred ccCccccC--CHHHHHHHHHh-hcchhccceeEEeCChHHHHHHHHHHHhCCchhhccee-ecCCChhhHhhhCCCCCCC
Q psy12585 6 KCGLFINA--PPGLETLVYIK-IMPMRFKCGLFINAPPGLETLVYIVKQFLPDKLQKRVF-VSSGDHTSLYEHIPRELLP 81 (146)
Q Consensus 6 ~~~~~~~~--~p~~~~~~~~q-~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k~~~rI~-~~~~~~e~L~~~i~~~~LP 81 (146)
.+.++.+. +..++++.++| +||+|++++||||+|++|+++|++++|||++++++||+ +|+++.++|+++||+++||
T Consensus 171 ~~~~~~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~~~~~~~L~k~i~~~~LP 250 (317)
T KOG1471|consen 171 SLSHLLKPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLHSKDKESLLKYIPPEVLP 250 (317)
T ss_pred cchhHHHHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecCCCchhhhhhhCCHhhCc
Confidence 45566544 44459999999 99999999999999999999999999999999999999 6767789999999999999
Q ss_pred ccCCCCCCCh
Q psy12585 82 KDYGGDDISL 91 (146)
Q Consensus 82 ~eyGG~~~~~ 91 (146)
.+|||++++.
T Consensus 251 ~~yGG~~~~~ 260 (317)
T KOG1471|consen 251 EEYGGTCGDL 260 (317)
T ss_pred cccCCCcccc
Confidence 9999999765
No 2
>PF00650 CRAL_TRIO: CRAL/TRIO domain; InterPro: IPR001251 This entry defines the C-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1OLM_E 1O6U_E 3Q8G_A 3B7Q_B 3B7Z_A ....
Probab=99.81 E-value=1.7e-20 Score=137.57 Aligned_cols=75 Identities=33% Similarity=0.417 Sum_probs=66.3
Q ss_pred CCHHHHHHHHHh-hcchhccceeEEeCChHHHHHHHHHHHhCCchhhcceeecCC-Ch-hhHhhhCCCCCCCccCCCC
Q psy12585 13 APPGLETLVYIK-IMPMRFKCGLFINAPPGLETLVYIVKQFLPDKLQKRVFVSSG-DH-TSLYEHIPRELLPKDYGGD 87 (146)
Q Consensus 13 ~~p~~~~~~~~q-~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k~~~rI~~~~~-~~-e~L~~~i~~~~LP~eyGG~ 87 (146)
.+..+.+++++| +||+|++++|+||+|++++.+|++++|||++++++||+++++ ++ ++|.++||++.||.+|||+
T Consensus 82 ~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~~l~~~i~~~~lP~~~GG~ 159 (159)
T PF00650_consen 82 ISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSGSDWKAKLKEYIDPEQLPVEYGGT 159 (159)
T ss_dssp HHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECTTCHCHHHCCCSTGGGSBGGGTSS
T ss_pred hhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECCcccHHHHHhhCCHhHCchhcCCC
Confidence 445569999999 999999999999999999999999999999999999999954 45 7899999999999999996
No 3
>cd00170 SEC14 Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.77 E-value=6e-19 Score=127.12 Aligned_cols=74 Identities=32% Similarity=0.476 Sum_probs=69.4
Q ss_pred CHHHHHHHHHh-hcchhccceeEEeCChHHHHHHHHHHHhCCchhhcceeecCCChhhHhhhCCCCCCCccCCCC
Q psy12585 14 PPGLETLVYIK-IMPMRFKCGLFINAPPGLETLVYIVKQFLPDKLQKRVFVSSGDHTSLYEHIPRELLPKDYGGD 87 (146)
Q Consensus 14 ~p~~~~~~~~q-~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k~~~rI~~~~~~~e~L~~~i~~~~LP~eyGG~ 87 (146)
+..++++..+| +||+|++.+|++|+|++++.+|+++++|+++++++||++++++.++|.+++|+++||.+|||+
T Consensus 83 ~~~k~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~L~~~i~~~~Lp~~~GG~ 157 (157)
T cd00170 83 SLLKKILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLGSDKEELLKYIDKEQLPEEYGGT 157 (157)
T ss_pred HHHHHHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEecCCHHHHHhhCChhhCcHhhCCC
Confidence 45669999999 999999999999999999999999999999999999999943389999999999999999996
No 4
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.74 E-value=3.8e-18 Score=124.91 Aligned_cols=75 Identities=29% Similarity=0.372 Sum_probs=69.8
Q ss_pred CHHHHHHHHHh-hcchhccceeEEeCChHHHHHHHHHHHhCCchhhcceeecCCC-hhhHhhhCCCCCCCccCCCCC
Q psy12585 14 PPGLETLVYIK-IMPMRFKCGLFINAPPGLETLVYIVKQFLPDKLQKRVFVSSGD-HTSLYEHIPRELLPKDYGGDD 88 (146)
Q Consensus 14 ~p~~~~~~~~q-~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k~~~rI~~~~~~-~e~L~~~i~~~~LP~eyGG~~ 88 (146)
+-.++++..+| +||+|++++||+|+|++++++|+++++|+++++++||++++++ .++|.+++|+++||++|||++
T Consensus 81 ~~lk~~~~~~~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~~~~~~~L~~~i~~~~lP~~~GG~~ 157 (158)
T smart00516 81 SVLRKILKILQDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVGNDSKEELLEYIDPEQLPEELGGTL 157 (158)
T ss_pred HHHHHHHHHHHHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeCCCCHHHHHhhCCHhhCcHhhCCCC
Confidence 34558999999 9999999999999999999999999999999999999999543 789999999999999999986
No 5
>KOG1470|consensus
Probab=99.61 E-value=5.3e-16 Score=127.59 Aligned_cols=77 Identities=26% Similarity=0.283 Sum_probs=72.6
Q ss_pred ccCCHHHHHHHHHh-hcchhccceeEEeCChHHHHHHHHHHHhCCchhhcceeecCCChhhHhhhCCCCCCCccCCCCC
Q psy12585 11 INAPPGLETLVYIK-IMPMRFKCGLFINAPPGLETLVYIVKQFLPDKLQKRVFVSSGDHTSLYEHIPRELLPKDYGGDD 88 (146)
Q Consensus 11 ~~~~p~~~~~~~~q-~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k~~~rI~~~~~~~e~L~~~i~~~~LP~eyGG~~ 88 (146)
..+++++.+++++| +||+||....++|+|++|+.+|+++||||+++|+++|.|. .+.+++.++||++.||.+|||+.
T Consensus 166 ~d~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~wkiikpflDp~t~~Kv~F~-~~~~~l~~~~d~~~l~s~~GG~~ 243 (324)
T KOG1470|consen 166 PDIKFLKELLHILQDHYPERLGKALLVNAPWIFQPFWKIIKPFLDPKTASKVKFV-EPKDDLSEYFDESQLPSLFGGKL 243 (324)
T ss_pred CCcHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHHHHHhhhccChhhhceeEEe-cChhHHHhhCCccccchhhCCCc
Confidence 35577889999999 9999999999999999999999999999999999999999 77777999999999999999977
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=98.47 E-value=1.9e-08 Score=73.52 Aligned_cols=75 Identities=16% Similarity=0.177 Sum_probs=56.2
Q ss_pred CCHHHHHHHHHh-hcchhccceeEEeCChHHHHHH-HHHHHhCCchh-hcceeecCCChhhHhhhCCCCCCCccCCCCC
Q psy12585 13 APPGLETLVYIK-IMPMRFKCGLFINAPPGLETLV-YIVKQFLPDKL-QKRVFVSSGDHTSLYEHIPRELLPKDYGGDD 88 (146)
Q Consensus 13 ~~p~~~~~~~~q-~~P~Rlk~ihiiN~P~~~~~i~-~~vkpfl~~k~-~~rI~~~~~~~e~L~~~i~~~~LP~eyGG~~ 88 (146)
++-.+++...++ .++.+++.|+|+|+.+++..++ .+.+++.+.+. ..+|.+. ++.++|.+|||++.||++.||+.
T Consensus 67 ~~~l~~~~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~-~sl~~L~~~i~~~qL~~~lp~~~ 144 (149)
T PF13716_consen 67 LSWLKQLYKLLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYV-SSLSELSKHIDPSQLPESLPGVL 144 (149)
T ss_dssp HHHHHHTTTSS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEE-SSTCGGGGTSGGGG------HHH
T ss_pred hHHHHHHHHHHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEE-CCHHHHHhhCCHHHhcccCCCEE
Confidence 344447777788 8999999999999999999999 67778889998 8999988 78999999999999999999765
No 7
>KOG4406|consensus
Probab=96.39 E-value=0.0024 Score=54.72 Aligned_cols=51 Identities=10% Similarity=0.188 Sum_probs=47.0
Q ss_pred hcchhccceeEEeCChHHHHHHHHHHHhCCchhhcceeecCCChhhHhhhCC
Q psy12585 25 IMPMRFKCGLFINAPPGLETLVYIVKQFLPDKLQKRVFVSSGDHTSLYEHIP 76 (146)
Q Consensus 25 ~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k~~~rI~~~~~~~e~L~~~i~ 76 (146)
.|---+|.+|+|.+-|+..++|+++|||++.|..+||+-. +.+++|++++.
T Consensus 161 ~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~-n~lseL~~~l~ 211 (467)
T KOG4406|consen 161 NFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYF-NSLSELFEALK 211 (467)
T ss_pred HHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEe-ehHHHHHHhhh
Confidence 7778899999999999999999999999999999999988 67899998765
No 8
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=58.51 E-value=19 Score=29.21 Aligned_cols=69 Identities=10% Similarity=0.149 Sum_probs=46.6
Q ss_pred hcchhccceeEEeCChHH---HHHHHHHHHhCCchhhcceeecCCC------hhhHhhhCCCCCCCccC-CCCCCChHHH
Q psy12585 25 IMPMRFKCGLFINAPPGL---ETLVYIVKQFLPDKLQKRVFVSSGD------HTSLYEHIPRELLPKDY-GGDDISLEEM 94 (146)
Q Consensus 25 ~~P~Rlk~ihiiN~P~~~---~~i~~~vkpfl~~k~~~rI~~~~~~------~e~L~~~i~~~~LP~ey-GG~~~~~~~l 94 (146)
-|.+| .+|||||.-... ..++++++-.... -.+|-|+|.. ..+..+....-++...| ||++.+...+
T Consensus 31 If~~R-ngihIIDL~kT~~~l~~A~~~v~~~~~~--~g~ILfVgTK~~a~~~V~~~A~r~g~~yV~~RwLgG~LTN~~ti 107 (252)
T COG0052 31 IFGER-NGIHIIDLQKTLERLREAYKFLRRIAAN--GGKILFVGTKKQAQEPVKEFAERTGAYYVNGRWLGGMLTNFKTI 107 (252)
T ss_pred ceeec-CCcEEEEHHHHHHHHHHHHHHHHHHHcC--CCEEEEEechHHHHHHHHHHHHHhCCceecCcccCccccCchhH
Confidence 58999 999999987654 4455555554422 3578888653 23344567777777777 9999887664
Q ss_pred HH
Q psy12585 95 TE 96 (146)
Q Consensus 95 ~~ 96 (146)
..
T Consensus 108 ~~ 109 (252)
T COG0052 108 RK 109 (252)
T ss_pred HH
Confidence 33
No 9
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=53.00 E-value=20 Score=25.72 Aligned_cols=58 Identities=14% Similarity=0.075 Sum_probs=41.2
Q ss_pred HHHHHHHh--hcchhcc-ceeEEeCChHHHHHHHHH-----HHhCCchhhcceeecCCChhhHhhhC
Q psy12585 17 LETLVYIK--IMPMRFK-CGLFINAPPGLETLVYIV-----KQFLPDKLQKRVFVSSGDHTSLYEHI 75 (146)
Q Consensus 17 ~~~~~~~q--~~P~Rlk-~ihiiN~P~~~~~i~~~v-----kpfl~~k~~~rI~~~~~~~e~L~~~i 75 (146)
-+++..++ .+...-+ -|.++|..-+.+-++.++ .-|+++...+.+++. ++.+++.++|
T Consensus 68 ~El~~~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~-d~~~e~~~~i 133 (133)
T PF03641_consen 68 DELFEALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFV-DDPEEALEYI 133 (133)
T ss_dssp HHHHHHHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEE-SSHHHHHHHH
T ss_pred HHHHHHHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEe-CCHHHHHhhC
Confidence 34444444 2333344 699999887888888877 468888899999998 8888887654
No 10
>PF04378 RsmJ: Ribosomal RNA small subunit methyltransferase D, RsmJ; InterPro: IPR007473 This is a bacterial protein of unknown function, possibly secreted.; PDB: 2OO3_A.
Probab=49.53 E-value=10 Score=30.50 Aligned_cols=29 Identities=24% Similarity=0.303 Sum_probs=22.4
Q ss_pred cceeEEeCChHHHHHHHHHHHhCCchhhc
Q psy12585 31 KCGLFINAPPGLETLVYIVKQFLPDKLQK 59 (146)
Q Consensus 31 k~ihiiN~P~~~~~i~~~vkpfl~~k~~~ 59 (146)
.++.|||+||.+.....-+.|+|.+.+.+
T Consensus 206 SGm~iiNPPw~l~~~l~~~l~~L~~~L~~ 234 (245)
T PF04378_consen 206 SGMLIINPPWTLDEELEEILPWLAETLAQ 234 (245)
T ss_dssp EEEEEES--TTHHHHHHHHHHHHHHHSST
T ss_pred ceEEEEcCCccHHHHHHHHHHHHHHHhCc
Confidence 57899999999999998888888766654
No 11
>PF10004 DUF2247: Uncharacterized protein conserved in bacteria (DUF2247); InterPro: IPR016630 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=48.27 E-value=21 Score=26.78 Aligned_cols=36 Identities=19% Similarity=0.540 Sum_probs=28.2
Q ss_pred ChhhHhhhCCCCCCCccCCCCCCChHHHHHHHHHHHHh
Q psy12585 67 DHTSLYEHIPRELLPKDYGGDDISLEEMTENWRKELLA 104 (146)
Q Consensus 67 ~~e~L~~~i~~~~LP~eyGG~~~~~~~l~~~w~~~l~~ 104 (146)
+++++..++|++. |.+|+... ....+...|++-|.+
T Consensus 122 dm~~Fv~Ymp~~~-P~~~~~e~-n~~~L~~~~~~yL~~ 157 (161)
T PF10004_consen 122 DMASFVRYMPPKD-PSEYSTEE-NINRLYNRWKEYLDS 157 (161)
T ss_pred HHHHHHhcCCccc-ccccchhh-hHHHHHHHHHHHHHH
Confidence 4566667889888 99998887 788888888876654
No 12
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=46.53 E-value=14 Score=30.26 Aligned_cols=28 Identities=25% Similarity=0.234 Sum_probs=24.1
Q ss_pred cceeEEeCChHHHHHHHHHHHhCCchhh
Q psy12585 31 KCGLFINAPPGLETLVYIVKQFLPDKLQ 58 (146)
Q Consensus 31 k~ihiiN~P~~~~~i~~~vkpfl~~k~~ 58 (146)
.++.|||+||.+..-+..+-|+|...+.
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~L~ 264 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTLLA 264 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHHhc
Confidence 4789999999999999999999876654
No 13
>TIGR01011 rpsB_bact ribosomal protein S2, bacterial type. TIGR01012 describes the archaeal and cytosolic forms.
Probab=41.25 E-value=64 Score=25.46 Aligned_cols=69 Identities=12% Similarity=0.059 Sum_probs=42.3
Q ss_pred hcchhccceeEEeCChHHHHHHHHHHHhCC-chhhcceeecCCCh------hhHhhhCCCCCCCccC-CCCCCChHHH
Q psy12585 25 IMPMRFKCGLFINAPPGLETLVYIVKQFLP-DKLQKRVFVSSGDH------TSLYEHIPRELLPKDY-GGDDISLEEM 94 (146)
Q Consensus 25 ~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~-~k~~~rI~~~~~~~------e~L~~~i~~~~LP~ey-GG~~~~~~~l 94 (146)
-|..| .++||||.......+-..++..-. -+-..+|-|+|.+. ++..+....-+.-..| ||++.+..++
T Consensus 29 Iyg~r-~g~~IIdL~~T~~~L~~A~~~i~~~~~~~g~iLfV~tk~~~~~~v~~~a~~~~~~yv~~rWlgG~LTN~~~i 105 (225)
T TIGR01011 29 IFGER-NGIHIIDLQKTLQLLKEAYNFVKDVAANGGKILFVGTKKQAKEIIKEEAERCGMFYVNQRWLGGMLTNFKTI 105 (225)
T ss_pred eeeee-CCeEEEcHHHHHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHHHHHHHHHHhCCcccCCeecCeeccCHHHH
Confidence 46677 899999998866554444333311 12356788886552 3333445555555555 9999887654
No 14
>PRK05299 rpsB 30S ribosomal protein S2; Provisional
Probab=40.90 E-value=53 Score=26.54 Aligned_cols=70 Identities=10% Similarity=0.048 Sum_probs=42.5
Q ss_pred hcchhccceeEEeCChHHHHHHHHHHHhCC-chhhcceeecCCCh------hhHhhhCCCCCCCccC-CCCCCChHHHH
Q psy12585 25 IMPMRFKCGLFINAPPGLETLVYIVKQFLP-DKLQKRVFVSSGDH------TSLYEHIPRELLPKDY-GGDDISLEEMT 95 (146)
Q Consensus 25 ~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~-~k~~~rI~~~~~~~------e~L~~~i~~~~LP~ey-GG~~~~~~~l~ 95 (146)
-|-.| .++||||.-.....+-..++.+-. -+-..+|-|.|.+. ++..+....-+.-..| ||++.+.....
T Consensus 31 Iyg~r-~gi~IIdL~kT~~~L~~A~~~i~~~~~~~g~iLfVgTk~~~~~~V~~~A~~~~~~yv~~rWlgG~LTN~~ti~ 108 (258)
T PRK05299 31 IFGER-NGIHIIDLQKTVPMLDEAYNFVRDVAANGGKILFVGTKKQAQEAIAEEAERCGMPYVNHRWLGGMLTNFKTIR 108 (258)
T ss_pred eeccc-CCeEEEcHHHHHHHHHHHHHHHHHHHhCCCEEEEEECcHHHHHHHHHHHHHhCCeeeCCeecCeeccCHHHHH
Confidence 46677 999999998766555444433322 13456788886552 2333344444444444 99998876543
No 15
>cd01425 RPS2 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane an
Probab=32.28 E-value=1.2e+02 Score=23.10 Aligned_cols=69 Identities=13% Similarity=0.095 Sum_probs=41.9
Q ss_pred hcchhccceeEEeCChHHHHHHHHHHHhCCch-hhcceeecCCC------hhhHhhhCCCCCCCccC-CCCCCChHHH
Q psy12585 25 IMPMRFKCGLFINAPPGLETLVYIVKQFLPDK-LQKRVFVSSGD------HTSLYEHIPRELLPKDY-GGDDISLEEM 94 (146)
Q Consensus 25 ~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k-~~~rI~~~~~~------~e~L~~~i~~~~LP~ey-GG~~~~~~~l 94 (146)
-|..| .++||||.-.....+-..++-.-.-. -..+|-|.|.+ .+...+....-.+-..| ||++......
T Consensus 23 iyg~r-~~~~Iidl~~T~~~L~~A~~~i~~i~~~~g~iLfV~t~~~~~~~v~~~a~~~~~~~i~~rw~~G~LTN~~~~ 99 (193)
T cd01425 23 IYGER-NGIHIIDLEKTLEKLRLALNFIANIAAKGGKILFVGTKPQAQRAVKKFAERTGSFYVNGRWLGGTLTNWKTI 99 (193)
T ss_pred eeccc-CCeEEEeHHHHHHHHHHHHHHHHHHHhCCCEEEEEECCHHHHHHHHHHHHHcCCeeecCeecCCcCCCHHHH
Confidence 57788 99999998876655444433331111 14678888655 13333444555555554 9999877654
No 16
>PRK04020 rps2P 30S ribosomal protein S2; Provisional
Probab=30.73 E-value=75 Score=24.87 Aligned_cols=67 Identities=12% Similarity=0.110 Sum_probs=42.0
Q ss_pred hcchhccceeEEeCChHHHHHHHHHHHhCCchhhcceeecCCCh------hhHhhhCCCCCCCccC-CCCCCChH
Q psy12585 25 IMPMRFKCGLFINAPPGLETLVYIVKQFLPDKLQKRVFVSSGDH------TSLYEHIPRELLPKDY-GGDDISLE 92 (146)
Q Consensus 25 ~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k~~~rI~~~~~~~------e~L~~~i~~~~LP~ey-GG~~~~~~ 92 (146)
-|..|-.++||||.-.....+-..++.. ......+|-|.|... ++..+.......-..| ||++.+..
T Consensus 35 Iyg~r~~gi~IIdL~kT~~~L~~A~~~i-~~~~~~~ILfVgTk~~~~~~v~k~A~~~g~~~v~~RWlgG~LTN~~ 108 (204)
T PRK04020 35 IYRVRPDGLYVLDVRKTDERIRIAAKFL-SRYEPEKILVVSSRQYGQKPVQKFAEVVGAKAITGRFIPGTLTNPS 108 (204)
T ss_pred EeeecCCCCEEEcHHHHHHHHHHHHHHH-HHhcCCeEEEEeCCHHHHHHHHHHHHHhCCeeecCccCCCcCcCcc
Confidence 5778888999999877655544433332 222467788887652 2233445555666655 99997654
No 17
>TIGR01012 Sa_S2_E_A ribosomal protein Sa(cytosolic)/S2(archaeal). TIGR01011 describes the related protein of organelles and bacteria.
Probab=30.35 E-value=70 Score=24.88 Aligned_cols=67 Identities=12% Similarity=0.045 Sum_probs=41.7
Q ss_pred hcchhccceeEEeCChHHHHHHHHHHHhCCchhhcceeecCCCh------hhHhhhCCCCCCCccC-CCCCCChH
Q psy12585 25 IMPMRFKCGLFINAPPGLETLVYIVKQFLPDKLQKRVFVSSGDH------TSLYEHIPRELLPKDY-GGDDISLE 92 (146)
Q Consensus 25 ~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k~~~rI~~~~~~~------e~L~~~i~~~~LP~ey-GG~~~~~~ 92 (146)
-|..|-.++||||.-.....+-..++..-.-. .++|-|.|... ++..+.......-..| ||++.+..
T Consensus 29 I~~~r~~gi~IIdL~kT~~~L~~A~~~i~~i~-~~~ILfVgtk~~~~~~V~~~A~~~g~~~v~~RWlgGtLTN~~ 102 (196)
T TIGR01012 29 IYKVRSDGLYVLDLRKTDERLRVAAKFLVRIE-PEDILVVSARIYGQKPVLKFAKVTGARAIAGRFTPGTFTNPM 102 (196)
T ss_pred eeeecCCCCEEEcHHHHHHHHHHHHHHHHHhh-CCeEEEEecCHHHHHHHHHHHHHhCCceECCeeCCCCCCCcc
Confidence 57778789999998776555443333332222 77888887552 3333445555555555 99997654
No 18
>PTZ00254 40S ribosomal protein SA; Provisional
Probab=27.12 E-value=76 Score=25.70 Aligned_cols=67 Identities=12% Similarity=0.023 Sum_probs=43.4
Q ss_pred hcchhccceeEEeCChHHHHHHHHHHHhCCchhhcceeecCCCh------hhHhhhCCCCCCCccC-CCCCCCh
Q psy12585 25 IMPMRFKCGLFINAPPGLETLVYIVKQFLPDKLQKRVFVSSGDH------TSLYEHIPRELLPKDY-GGDDISL 91 (146)
Q Consensus 25 ~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k~~~rI~~~~~~~------e~L~~~i~~~~LP~ey-GG~~~~~ 91 (146)
-|..|-.++||||.-.....+-...+..-.-.-..+|-|.|+.. .+..++.....+-..| ||++.+.
T Consensus 38 Iy~~r~dGi~IIdL~kT~~~L~~Aa~~i~~i~~~~~Il~Vstr~~~~~~V~k~A~~tg~~~i~~Rw~pGtlTN~ 111 (249)
T PTZ00254 38 VYKRTKEGVHIINLAKTWEKLKLAARVIAAIENPADVVVVSSRPYGQRAVLKFAQYTGASAIAGRFTPGTFTNQ 111 (249)
T ss_pred EecccCCCCEEEcHHHHHHHHHHHHHHHHHHhCCCcEEEEEcCHHHHHHHHHHHHHhCCeEECCcccCCCCCCc
Confidence 56667799999999887766655554443333466788876542 3344456666666665 8998654
No 19
>PF02771 Acyl-CoA_dh_N: Acyl-CoA dehydrogenase, N-terminal domain; InterPro: IPR006092 Mammalian Co-A dehydrogenases (1.3.99.3 from EC) are enzymes that catalyse the first step in each cycle of beta-oxidation in mitochondion. Acyl-CoA dehydrogenases [, , ] catalyze the alpha,beta-dehydrogenation of acyl-CoA thioesters to the corresponding trans 2,3-enoyl CoA-products with concommitant reduction of enzyme-bound FAD. Reoxidation of the flavin involves transfer of electrons to ETF (electron transfering flavoprotein). These enzymes are homodimers containing one molecule of FAD. The monomeric enzyme is folded into three domains of approximately equal size. The N-terminal and the C-terminal are mainly alpha-helices packed together, and the middle domain consists of two orthogonal beta-sheets. The flavin ring is buried in the crevise between two alpha-helical domains and the beta-sheet of one subunit, and the adenosine pyrophosphate moiety is stretched into the subunit junction with one formed by two C-terminal domains []. The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain, on dimerisation, the N-terminal of one molecule extends into the other dimer and lies on the surface of the molecule.; GO: 0003995 acyl-CoA dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 2WBI_B 1SIQ_A 1SIR_A 2R0N_A 2R0M_A 2DVL_A 1UKW_B 3MDD_B 1UDY_C 3MDE_B ....
Probab=26.47 E-value=55 Score=21.68 Aligned_cols=19 Identities=32% Similarity=0.517 Sum_probs=13.4
Q ss_pred CCCCCCCccCCCCCCChHH
Q psy12585 75 IPRELLPKDYGGDDISLEE 93 (146)
Q Consensus 75 i~~~~LP~eyGG~~~~~~~ 93 (146)
+-.-.+|++|||...+..+
T Consensus 45 ~~~~~~p~~~GG~~~~~~~ 63 (113)
T PF02771_consen 45 LLGLAVPEEYGGLGLSPLE 63 (113)
T ss_dssp TTSTTSCGGGTSEB-THHH
T ss_pred HhhhhccccccCcchhhhh
Confidence 4456789999998866544
No 20
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=25.03 E-value=2.1e+02 Score=21.65 Aligned_cols=46 Identities=22% Similarity=0.259 Sum_probs=35.4
Q ss_pred hccceeEEeCChHHHHHHHHHHH-----hCCchhhcceeecCCChhhHhhhC
Q psy12585 29 RFKCGLFINAPPGLETLVYIVKQ-----FLPDKLQKRVFVSSGDHTSLYEHI 75 (146)
Q Consensus 29 Rlk~ihiiN~P~~~~~i~~~vkp-----fl~~k~~~rI~~~~~~~e~L~~~i 75 (146)
.-|-|-++|..-+.+.+..+++. |++++..+.+++. .+.+++.+.+
T Consensus 125 ~~kPiil~n~~g~~~~l~~~l~~~~~~gfi~~~~~~~~~~~-d~~~e~~~~i 175 (178)
T TIGR00730 125 HQKPIILFNVNGHFDGLVEWLKYSIQEGFISESHLKLIHVV-SRPDELIEQV 175 (178)
T ss_pred CCCCEEEECCcchHHHHHHHHHHHHHCCCCCHHHcCcEEEc-CCHHHHHHHH
Confidence 34678899988788888877554 5677777888888 7888887765
No 21
>CHL00067 rps2 ribosomal protein S2
Probab=24.87 E-value=2.1e+02 Score=22.54 Aligned_cols=69 Identities=16% Similarity=0.064 Sum_probs=39.7
Q ss_pred hcchhccceeEEeCChHHHHHHHHHHHhCCch--hhcceeecCCCh------hhHhhhCCCCCCCcc-CCCCCCChHHHH
Q psy12585 25 IMPMRFKCGLFINAPPGLETLVYIVKQFLPDK--LQKRVFVSSGDH------TSLYEHIPRELLPKD-YGGDDISLEEMT 95 (146)
Q Consensus 25 ~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k--~~~rI~~~~~~~------e~L~~~i~~~~LP~e-yGG~~~~~~~l~ 95 (146)
-|..| .++||||.-.....+-... .|+..- -..+|-|.|++. +...+....-+.-.. .||++.....+.
T Consensus 35 Iyg~r-~g~~IIdl~~T~~~L~~A~-~~i~~i~~~~g~ILfV~t~~~~~~~v~~~a~~~~~~yv~~rWigG~LTN~~~i~ 112 (230)
T CHL00067 35 IYAER-NGIHIINLVQTARFLSEAC-DLVFDAASKGKKFLFVGTKKQAADLVASAAIRARCHYVNKRWLGGMLTNWSTTK 112 (230)
T ss_pred hhccc-CCcEEEcHHHHHHHHHHHH-HHHHHHHhCCCeEEEEeCcHHHHHHHHHHHHHhCCcCccCcccCCcccCHHHHH
Confidence 35555 7999999877555433322 233322 356788886552 223334444444444 499998877543
No 22
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=24.60 E-value=1.6e+02 Score=24.76 Aligned_cols=71 Identities=14% Similarity=0.159 Sum_probs=41.8
Q ss_pred hcchhccceeEEeCChHHHHHHHHHHHhCCch--hhcceeecCCCh------hhHhhhCCCCCCCccC-CCCCCChHHHH
Q psy12585 25 IMPMRFKCGLFINAPPGLETLVYIVKQFLPDK--LQKRVFVSSGDH------TSLYEHIPRELLPKDY-GGDDISLEEMT 95 (146)
Q Consensus 25 ~~P~Rlk~ihiiN~P~~~~~i~~~vkpfl~~k--~~~rI~~~~~~~------e~L~~~i~~~~LP~ey-GG~~~~~~~l~ 95 (146)
-|..|- +|||||.-.....+-..+ -|+..- -..+|-|+|.+. ++..+....-++-..| ||++.+...+.
T Consensus 26 Iyg~R~-gihIIDL~kT~~~L~~A~-~~i~~~~~~gg~iLfVgTk~~~~~~V~~~A~~~g~~yV~~RWlgG~LTN~~ti~ 103 (326)
T PRK12311 26 IFGTRN-NIHIIDLAQTVPLLHRAL-QAVSDTVAKGGRVLFVGTKRQAQDAVADAAKRSAQYFVNSRWLGGTLTNWKTIS 103 (326)
T ss_pred eecccC-CcEEEcHHHHHHHHHHHH-HHHHHHHhCCCEEEEEeCcHHHHHHHHHHHHHhCCeeeCCeecCcccCCHHHHH
Confidence 466674 999999887654433222 233322 236788887652 2233345555555554 99998887654
Q ss_pred HH
Q psy12585 96 EN 97 (146)
Q Consensus 96 ~~ 97 (146)
..
T Consensus 104 ~s 105 (326)
T PRK12311 104 GS 105 (326)
T ss_pred HH
Confidence 43
No 23
>PF04838 Baculo_LEF5: Baculoviridae late expression factor 5 ; InterPro: IPR006923 This is a family of Baculoviridae late expression factor 5, required for late and very late gene expression.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=23.53 E-value=1.4e+02 Score=22.50 Aligned_cols=98 Identities=16% Similarity=0.143 Sum_probs=62.7
Q ss_pred ccCCHHHHHHHHHh-hcchhcc--ceeEEeCChHHHHHHHHHHHhCCc--hhhcceee----------cCCC----hhhH
Q psy12585 11 INAPPGLETLVYIK-IMPMRFK--CGLFINAPPGLETLVYIVKQFLPD--KLQKRVFV----------SSGD----HTSL 71 (146)
Q Consensus 11 ~~~~p~~~~~~~~q-~~P~Rlk--~ihiiN~P~~~~~i~~~vkpfl~~--k~~~rI~~----------~~~~----~e~L 71 (146)
++-.-...++.++- .||.-+| ...++|..-.|..+|+-+ |-++. |-|+.|+. ...| +++|
T Consensus 12 R~~~~y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYv-P~~s~~~kERKQIRLs~dcI~kL~~nT~NdfKLY~El 90 (159)
T PF04838_consen 12 RRNKDYKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYV-PSVSNVEKERKQIRLSEDCIEKLFVNTINDFKLYEEL 90 (159)
T ss_pred HHhcCHHHHHHHHHhhcccccccCeeecCCCchhhhhhhhcc-CCCchHhHHHHHhhhhHHHHHHHHHhcCchHHHHHHH
Confidence 33344558899999 9999999 999999999999999876 55555 44444444 1122 5778
Q ss_pred hhhCCCCCCCccCCCCCCChHHHHHHHHHHHHhcHHHhcccCCCccC
Q psy12585 72 YEHIPRELLPKDYGGDDISLEEMTENWRKELLAHRDWFLDPTNRRSD 118 (146)
Q Consensus 72 ~~~i~~~~LP~eyGG~~~~~~~l~~~w~~~l~~~r~~~~~~~~~~~~ 118 (146)
.+.+..+.+. ...+.+ ...+++.+...|....+.-..|
T Consensus 91 f~~i~~~~~~------~~CPCe---ll~~r~~~~~~Yv~~l~~K~FD 128 (159)
T PF04838_consen 91 FDMIDDNKLK------EKCPCE---LLQQRLNEIKSYVNNLNNKNFD 128 (159)
T ss_pred HHHHHccCCC------CCCCHH---HHHHHHHHHHHHHHHhccccCC
Confidence 8887744332 223333 3455566666666644443333
Done!