Query 030771
Match_columns 171
No_of_seqs 147 out of 977
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 04:19:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030771.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030771hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00469 60S ribosomal subunit 100.0 1.6E-51 3.4E-56 337.5 17.1 144 1-144 1-144 (187)
2 PTZ00195 60S ribosomal protein 100.0 7.3E-51 1.6E-55 335.5 17.0 144 1-144 1-152 (198)
3 COG1727 RPL18A Ribosomal prote 100.0 1.5E-42 3.2E-47 267.6 14.8 121 15-139 2-122 (122)
4 KOG1714 60s ribosomal protein 100.0 4E-42 8.6E-47 279.8 13.2 142 1-143 1-144 (188)
5 PRK04005 50S ribosomal protein 100.0 8.5E-35 1.8E-39 222.3 13.5 111 25-139 1-111 (111)
6 PF00828 Ribosomal_L18e: Ribos 99.7 1.5E-18 3.2E-23 133.5 4.7 80 41-122 31-129 (129)
7 PRK05592 rplO 50S ribosomal pr 99.7 8.2E-18 1.8E-22 133.6 3.0 77 40-121 53-145 (146)
8 TIGR01071 rplO_bact ribosomal 99.7 1.6E-17 3.5E-22 131.3 2.9 78 40-119 52-144 (145)
9 COG0200 RplO Ribosomal protein 99.6 2.7E-15 5.8E-20 120.4 5.6 81 40-122 54-151 (152)
10 PRK06419 rpl15p 50S ribosomal 99.5 1.3E-14 2.9E-19 115.5 5.0 75 48-124 55-147 (148)
11 PTZ00160 60S ribosomal protein 99.3 1.5E-11 3.3E-16 98.3 7.1 71 50-122 55-146 (147)
12 KOG0846 Mitochondrial/chloropl 98.5 3.3E-07 7.1E-12 79.3 6.3 80 40-121 72-174 (274)
13 KOG1742 60s ribosomal protein 97.5 0.00026 5.7E-09 56.7 5.6 67 55-121 64-145 (147)
14 cd00118 LysM Lysin domain, fou 61.2 4.7 0.0001 22.8 1.0 26 121-146 21-46 (46)
15 PF01476 LysM: LysM domain; I 38.8 4.3 9.3E-05 24.6 -1.7 27 120-146 18-44 (44)
16 cd03565 VHS_Tom1 VHS domain fa 37.5 30 0.00066 27.1 2.5 35 21-55 50-85 (141)
17 cd03567 VHS_GGA VHS domain fam 35.6 30 0.00064 27.3 2.2 40 16-55 44-84 (139)
18 PF05573 NosL: NosL; InterPro 34.8 40 0.00087 26.4 2.8 32 97-128 116-147 (149)
19 cd03568 VHS_STAM VHS domain fa 33.3 29 0.00063 27.3 1.8 40 16-55 43-83 (144)
20 PF13209 DUF4017: Protein of u 30.5 32 0.00069 23.8 1.4 25 130-154 24-53 (60)
21 COG1888 Uncharacterized protei 29.6 58 0.0013 24.7 2.7 32 96-127 52-84 (97)
22 PRK05192 tRNA uridine 5-carbox 27.8 23 0.0005 34.6 0.4 29 127-155 257-285 (618)
23 cd03569 VHS_Hrs_Vps27p VHS dom 27.3 58 0.0013 25.5 2.6 40 16-55 47-87 (142)
24 smart00288 VHS Domain present 26.4 65 0.0014 24.7 2.7 40 16-55 43-83 (133)
25 PF08734 GYD: GYD domain; Int 24.7 62 0.0013 23.5 2.1 16 106-121 23-38 (91)
26 KOG2678 Predicted membrane pro 22.3 62 0.0013 28.3 2.0 26 142-170 215-240 (244)
27 PF11973 NQRA_SLBB: NQRA C-ter 22.2 72 0.0016 21.2 1.9 22 122-143 23-44 (51)
28 PF02680 DUF211: Uncharacteriz 22.1 51 0.0011 24.9 1.3 32 95-126 49-81 (95)
29 cd03561 VHS VHS domain family; 21.9 1E+02 0.0022 23.5 2.9 39 16-54 43-82 (133)
30 TIGR01997 sufA_proteo FeS asse 21.2 1.9E+02 0.004 21.2 4.2 33 102-144 3-35 (107)
31 PF09158 MotCF: Bacteriophage 21.0 1.8E+02 0.0039 22.4 4.0 32 83-120 46-77 (103)
32 TIGR00136 gidA glucose-inhibit 20.6 36 0.00078 33.3 0.2 27 129-155 257-283 (617)
33 KOG0829 60S ribosomal protein 20.4 53 0.0012 27.2 1.1 37 107-143 42-81 (169)
No 1
>PTZ00469 60S ribosomal subunit protein L18; Provisional
Probab=100.00 E-value=1.6e-51 Score=337.51 Aligned_cols=144 Identities=57% Similarity=0.832 Sum_probs=139.9
Q ss_pred CceeeccCCccccCCCCCCCCCCHHHHHHHHHHHHhhhccCChHHHHHHHhhhcCCCCCCccchHHHHhhhccCCCcEEE
Q 030771 1 MGIDLVAGGKSKKSKRTAPKSDDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKPPLSLSRLINFMKGKEDKIAV 80 (171)
Q Consensus 1 mg~~~~~~~~~~~~~rk~~~stN~~L~~Li~~lk~~ar~t~~pl~rrI~KRlf~~r~~~~~VNLs~L~~~~~~~e~k~vv 80 (171)
||||+.+++++++++|++|+||||||++||++|+++||+|++|||++|++||++|+++++|||||+|++++++.|++++|
T Consensus 1 mgid~~~~~~~~k~~r~~~~stN~yL~~Lik~yk~larrt~a~fwk~Va~RL~~srrnr~pVnLSkI~r~~~~ke~~~~V 80 (187)
T PTZ00469 1 MGIALKNVGRIKKHGRKNLVSKNPYLRLLVKLYRFLARRTNANFNKIIAKRLIMPKRFRPPLSLSKLHRHMASYPDDVAV 80 (187)
T ss_pred CceecccCccccCCCccCCCCCCHHHHHHHHHHHHHHHhhCChHHHHHHHHHhcccccCCceeHHHHHHHhccCCCCEEE
Confidence 99999966899999999999999999999999999999999999999999999999999999999999999666899999
Q ss_pred EEeeecCCceeecccCeEEEEEecCHHHHHHHHHhCCEEEeHHHHHHhCCCCCcEEEeecCCCc
Q 030771 81 VVGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGECLTFDQLALRAPLGQNTVCVFNANYC 144 (171)
Q Consensus 81 v~~KVLg~G~lt~v~kl~V~A~kfS~sAreKIekAGGkv~~ldqL~~~~P~G~~v~ll~g~~~~ 144 (171)
+||||||||+|.|||+++|||++||++|+++|++|||+|++||||+++||+|+||+||+||+-+
T Consensus 81 VvGkVl~dgrl~~vpkvtVaAL~fS~~Ar~kI~~AGGe~lT~dqLa~~~P~G~nv~Ll~g~r~~ 144 (187)
T PTZ00469 81 VVGSITDDKRLYDCKKLKVCALRFTETARKRILDAGGECLTFDQLALKYPTGQKCILLRGPTKA 144 (187)
T ss_pred EEeeEccCccccccCceEEEEEecCHHHHHHHHHhCCEEEeHHHHHHHCCCCCceEEEECCCch
Confidence 9999999999999999999999999999999999999999999999999999999999999764
No 2
>PTZ00195 60S ribosomal protein L18; Provisional
Probab=100.00 E-value=7.3e-51 Score=335.49 Aligned_cols=144 Identities=50% Similarity=0.772 Sum_probs=138.3
Q ss_pred CceeeccCCccccCCCCCCCCCCHHHHHHHHHHHHhhhccCChHHHHHHHhhhcCCCCCCccchHHHHhhhcc-------
Q 030771 1 MGIDLVAGGKSKKSKRTAPKSDDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKPPLSLSRLINFMKG------- 73 (171)
Q Consensus 1 mg~~~~~~~~~~~~~rk~~~stN~~L~~Li~~lk~~ar~t~~pl~rrI~KRlf~~r~~~~~VNLs~L~~~~~~------- 73 (171)
|||||.+++++++++|++|+||||||++||++|+++||+|++|||+.|++|||+|+++++|||||+|++++++
T Consensus 1 mgid~~~~~~~~~~~r~~pkstN~yL~lLVklyrflaRrt~a~fnk~VakRL~~sr~nRppVsLSrI~r~~k~~d~~~~~ 80 (198)
T PTZ00195 1 MGVDLTGISKKSRVVRHHTYSTNPYIKLLIKLYKFLAKRTSSGFNKVVYQRLIKSRSNRAPISLSRIAVVMKRKAVFTAK 80 (198)
T ss_pred CceecccccccccccccCCCCCCHHHHHHHHHHHHHHHhhCCHHHHHHHHHHhcccccCCceeHHHHHHHHhcccccccc
Confidence 9999996699999999999999999999999999999999999999999999999999999999999999962
Q ss_pred -CCCcEEEEEeeecCCceeecccCeEEEEEecCHHHHHHHHHhCCEEEeHHHHHHhCCCCCcEEEeecCCCc
Q 030771 74 -KEDKIAVVVGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGECLTFDQLALRAPLGQNTVCVFNANYC 144 (171)
Q Consensus 74 -~e~k~vvv~~KVLg~G~lt~v~kl~V~A~kfS~sAreKIekAGGkv~~ldqL~~~~P~G~~v~ll~g~~~~ 144 (171)
.+++++|++|||||||+|.+|||++|||++||++|+++|++|||+|++||||+++||+|+||+||+||+-+
T Consensus 81 ~~~~k~~VVvGkVtdd~rl~~vPkvtVaALrfS~tAr~rI~kAGGe~lT~dQLa~~~PkG~ntvLlrg~r~~ 152 (198)
T PTZ00195 81 GKKAPIAVVVGDVLDDVRMARIPAMRVCALRFSKSARQSIVAAGGECLTFDQLAMIAPTGKNTYLLRGRKSG 152 (198)
T ss_pred CCCCcEEEEEeeEcCCccccccCceEEEEEecCHHHHHHHHHhCCEEEeHHHHHHHCCCCCCeEEEECCCch
Confidence 35679999999999999999999999999999999999999999999999999999999999999999864
No 3
>COG1727 RPL18A Ribosomal protein L18E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-42 Score=267.62 Aligned_cols=121 Identities=35% Similarity=0.540 Sum_probs=117.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhhccCChHHHHHHHhhhcCCCCCCccchHHHHhhhccCCCcEEEEEeeecCCceeecc
Q 030771 15 KRTAPKSDDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKPPLSLSRLINFMKGKEDKIAVVVGTVTDDIRAYEV 94 (171)
Q Consensus 15 ~rk~~~stN~~L~~Li~~lk~~ar~t~~pl~rrI~KRlf~~r~~~~~VNLs~L~~~~~~~e~k~vvv~~KVLg~G~lt~v 94 (171)
.|+.|+|||+||+.||++|+++||++++|+|++|++||++|+++|++||+|+|+++.+ ++|++||||||||+|.+.
T Consensus 2 ~~~~t~~tN~~L~~Li~~l~~~ar~~~a~iwk~vaerL~~prr~ra~VnlsKI~r~ak--~~d~vvVpGkVLg~g~l~-- 77 (122)
T COG1727 2 SMKKTGSTNVYLRKLIRFLRKAARRSSAPIWKDVAERLEKPRRNRAEVNVSKINRYAK--EGDTVVVPGKVLGDGKLD-- 77 (122)
T ss_pred CcCCCCCCCHHHHHHHHHHHHHHhhcCCHHHHHHHHHHhcccccCCceeHHHHHhhcC--CCCEEEEeeeEecCcccc--
Confidence 3788999999999999999999999999999999999999999999999999999988 899999999999999999
Q ss_pred cCeEEEEEecCHHHHHHHHHhCCEEEeHHHHHHhCCCCCcEEEee
Q 030771 95 PALKVTALRFTETARARIEKAGGECLTFDQLALRAPLGQNTVCVF 139 (171)
Q Consensus 95 ~kl~V~A~kfS~sAreKIekAGGkv~~ldqL~~~~P~G~~v~ll~ 139 (171)
|+++|.|++||++|++||++|||+|+++|||+++||+|+||+|++
T Consensus 78 ~kVtVaAl~FS~~A~~KI~~aGGe~~tl~el~e~nPkGs~vri~~ 122 (122)
T COG1727 78 KKVTVAALRFSKTAREKIEEAGGECLTLEELAERNPKGSNVRIMR 122 (122)
T ss_pred cceEEEEEecCHHHHHHHHHcCCeEeeHHHHHHHCCCCCCeEeeC
Confidence 999999999999999999999999999999999999999999984
No 4
>KOG1714 consensus 60s ribosomal protein L18 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4e-42 Score=279.77 Aligned_cols=142 Identities=68% Similarity=1.000 Sum_probs=137.9
Q ss_pred CceeeccCCccccCCCCCCCCCCHHHHHHHHHHHHhhhccCChHHHHHHHhhhcCCCCCCccchHHHHhhhc--cCCCcE
Q 030771 1 MGIDLVAGGKSKKSKRTAPKSDDIYLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKPPLSLSRLINFMK--GKEDKI 78 (171)
Q Consensus 1 mg~~~~~~~~~~~~~rk~~~stN~~L~~Li~~lk~~ar~t~~pl~rrI~KRlf~~r~~~~~VNLs~L~~~~~--~~e~k~ 78 (171)
||+||.| +++++..|++|+|.|+||++|+++|+++||+|++.||+.|.|||||++.+++|++|++|.+.++ +.|+++
T Consensus 1 mg~di~~-~~~~k~~RtePkS~dvYLrllvkly~flarrT~s~fn~vvLKrLfmSk~nrpPlsls~iir~~k~~~~enKt 79 (188)
T KOG1714|consen 1 MGIDILH-NKSRKVRRTEPKSQDVYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSKTNRPPLSLSRIIRKMKLPGQENKT 79 (188)
T ss_pred CCccccC-CccccccccCCCCccHHHHHHHHHHHHHHHhcccHHHHHHHHHHhhhcccCCCcCHHHHHHHhhccCccCce
Confidence 9999877 9999999999999999999999999999999999999999999999999999999999999986 347889
Q ss_pred EEEEeeecCCceeecccCeEEEEEecCHHHHHHHHHhCCEEEeHHHHHHhCCCCCcEEEeecCCC
Q 030771 79 AVVVGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGECLTFDQLALRAPLGQNTVCVFNANY 143 (171)
Q Consensus 79 vvv~~KVLg~G~lt~v~kl~V~A~kfS~sAreKIekAGGkv~~ldqL~~~~P~G~~v~ll~g~~~ 143 (171)
+|++|+|+||.++.||||++|+|+.||++|+++|++|||+|.+|||||+.+|+|+|++|++||+.
T Consensus 80 aVVVgTvtdD~rv~~vPkl~v~al~~t~~ar~rI~kagg~i~TlDQLal~sP~g~~TvLlsgp~~ 144 (188)
T KOG1714|consen 80 AVVVGTVTDDLRVQEVPKLKVAALRFTKGARARILKAGGEILTLDQLALDSPKGCNTVLLSGPKK 144 (188)
T ss_pred EEEEeeecccceeeecccceeeeeecccchhhhhhccCceEEeeHHhcccCCCCCceEEeeCCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999986
No 5
>PRK04005 50S ribosomal protein L18e; Provisional
Probab=100.00 E-value=8.5e-35 Score=222.26 Aligned_cols=111 Identities=29% Similarity=0.408 Sum_probs=105.2
Q ss_pred HHHHHHHHHHHhhhccCChHHHHHHHhhhcCCCCCCccchHHHHhhhccCCCcEEEEEeeecCCceeecccCeEEEEEec
Q 030771 25 YLKLLVKLYRFLVRRTDSNFNKVILKRLFMSKVNKPPLSLSRLINFMKGKEDKIAVVVGTVTDDIRAYEVPALKVTALRF 104 (171)
Q Consensus 25 ~L~~Li~~lk~~ar~t~~pl~rrI~KRlf~~r~~~~~VNLs~L~~~~~~~e~k~vvv~~KVLg~G~lt~v~kl~V~A~kf 104 (171)
++++|+++|+++||++++|||+++|+|+++|+++|++|||++|+++.. +++++.+++||||+|+++ ++++|+|++|
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~v~~rl~~~r~~y~vVNL~~L~~~~~--~~~vv~~~~KVLg~G~l~--k~l~V~a~~~ 76 (111)
T PRK04005 1 RLRKLIRDLKKASRENGAPIWKDVAERLEKPRRRRAEVNLSKINRYAK--EGDTVVVPGKVLGSGKLD--HKVTVAALSF 76 (111)
T ss_pred CHHHHHHHHHHHHhhhCCcHHHHHHHHHhCCCCccceEEHHHHHhhcc--CCCEEEEeeEEEcCceEc--CCEEEEEeec
Confidence 478999999999999999999999999999999999999999998764 456777899999999999 9999999999
Q ss_pred CHHHHHHHHHhCCEEEeHHHHHHhCCCCCcEEEee
Q 030771 105 TETARARIEKAGGECLTFDQLALRAPLGQNTVCVF 139 (171)
Q Consensus 105 S~sAreKIekAGGkv~~ldqL~~~~P~G~~v~ll~ 139 (171)
|++|+++||+|||++++++||+++||+|+||+||+
T Consensus 77 Sk~A~ekIe~aGG~v~~~~~l~~~~p~g~~~~l~~ 111 (111)
T PRK04005 77 SETAKEKIEEAGGKALTIEELVEENPKGSNVRIMR 111 (111)
T ss_pred CHHHHHHHHHcCCEEEEHHHHHHHCCCCCCeEEeC
Confidence 99999999999999999999999999999999984
No 6
>PF00828 Ribosomal_L18e: Ribosomal protein L18e/L15; InterPro: IPR021131 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents both L15 and L18e ribosomal proteins, which share a common structure consisting mainly of parallel beta sheets (beta-alpha-beta units) with a core of three turns of irregular (beta-beta-alpha)n superhelix [, ].; PDB: 3O58_Y 1S1I_V 3O5H_Y 3IZS_O 3IZR_R 2OTL_L 1M1K_M 3G6E_L 1VQ9_L 1YIT_L ....
Probab=99.74 E-value=1.5e-18 Score=133.49 Aligned_cols=80 Identities=31% Similarity=0.463 Sum_probs=67.5
Q ss_pred CChHHHHHHHhhhcC------CCCCCccchHHHHhhhccC-------CCcEEEE------EeeecCCceeecccCeEEEE
Q 030771 41 DSNFNKVILKRLFMS------KVNKPPLSLSRLINFMKGK-------EDKIAVV------VGTVTDDIRAYEVPALKVTA 101 (171)
Q Consensus 41 ~~pl~rrI~KRlf~~------r~~~~~VNLs~L~~~~~~~-------e~k~vvv------~~KVLg~G~lt~v~kl~V~A 101 (171)
..|+|+++|||+|.+ +.++++|||++|+++++.. +.+++++ ..||||+|+++ ++++|+|
T Consensus 31 q~pl~rr~pK~Gf~~~~~~~~~~~~~~vnL~~L~~~i~~~~~~~~~~~~~~~~~~~~~~~~~KvLg~G~l~--~~l~I~a 108 (129)
T PF00828_consen 31 QMPLYRRLPKRGFNNPHLRKNRREYPPVNLSKLQELIEKLKIDGTEIDGKILVDAGLIKGYVKVLGKGELT--KPLTIKA 108 (129)
T ss_dssp HSHHHHHSSSSSHHHCCHCSGTCCCEEEEHHHHHHHTTTSSSSSCECTTSEEEECCEESSEEEEESSSSSS--SSEEEEE
T ss_pred ccccccccCcccccccccccCcceeEeeeHHHHHHHHHhccccccccCCceeeeccccccceeeeccCCcc--cceEEEE
Confidence 468899999998886 3589999999999876521 3455544 35999999999 9999999
Q ss_pred EecCHHHHHHHHHhCCEEEeH
Q 030771 102 LRFTETARARIEKAGGECLTF 122 (171)
Q Consensus 102 ~kfS~sAreKIekAGGkv~~l 122 (171)
++||++|+|+||+|||+|++|
T Consensus 109 ~~~S~~A~ekIe~aGG~v~~~ 129 (129)
T PF00828_consen 109 HRFSKSAKEKIEAAGGEVVTF 129 (129)
T ss_dssp SEETHHHHHHHHHTSEEEEEH
T ss_pred EecCHHHHHHHHHcCCEEEeC
Confidence 999999999999999999986
No 7
>PRK05592 rplO 50S ribosomal protein L15; Reviewed
Probab=99.69 E-value=8.2e-18 Score=133.63 Aligned_cols=77 Identities=22% Similarity=0.255 Sum_probs=66.7
Q ss_pred cCChHHHHHHHhhhcC--CCCCCccchHHHHhhhccCCCcEE---------E-----EEeeecCCceeecccCeEEEEEe
Q 030771 40 TDSNFNKVILKRLFMS--KVNKPPLSLSRLINFMKGKEDKIA---------V-----VVGTVTDDIRAYEVPALKVTALR 103 (171)
Q Consensus 40 t~~pl~rrI~KRlf~~--r~~~~~VNLs~L~~~~~~~e~k~v---------v-----v~~KVLg~G~lt~v~kl~V~A~k 103 (171)
-..|||+|+|||+|.| +++|.+|||++|+++.+ ++.+ + .++||||+|+++ .+++|.|++
T Consensus 53 GQ~Pl~rrlPk~Gf~~~~~~~y~~VNL~~L~~~~~---~~~I~~~~L~~~gli~~~~~~vKvLg~G~l~--~~i~I~a~~ 127 (146)
T PRK05592 53 GQMPLYRRLPKRGFTNIFRKEYAVVNLGDLNKFEE---GTEVTLEALKAAGLIRKNIKGVKVLGNGELT--KKLTVKAHK 127 (146)
T ss_pred CCCceEEEcccCCcCCCCcceEEEEeHHHhhccCC---CCeECHHHHHHCCcccCCCcceEEEecCccc--cCEEEEEEc
Confidence 5689999999999998 68899999999997532 2222 1 279999999999 999999999
Q ss_pred cCHHHHHHHHHhCCEEEe
Q 030771 104 FTETARARIEKAGGECLT 121 (171)
Q Consensus 104 fS~sAreKIekAGGkv~~ 121 (171)
||++|+|+||+|||+|..
T Consensus 128 ~S~sA~e~IE~aGG~v~~ 145 (146)
T PRK05592 128 FSKSAKEAIEAAGGKVEE 145 (146)
T ss_pred cCHHHHHHHHHcCCEEEe
Confidence 999999999999999864
No 8
>TIGR01071 rplO_bact ribosomal protein L15, bacterial/organelle.
Probab=99.67 E-value=1.6e-17 Score=131.34 Aligned_cols=78 Identities=26% Similarity=0.317 Sum_probs=65.5
Q ss_pred cCChHHHHHHHhhhcC---CCCCCccchHHHHhhhccCC--------CcEEE----EEeeecCCceeecccCeEEEEEec
Q 030771 40 TDSNFNKVILKRLFMS---KVNKPPLSLSRLINFMKGKE--------DKIAV----VVGTVTDDIRAYEVPALKVTALRF 104 (171)
Q Consensus 40 t~~pl~rrI~KRlf~~---r~~~~~VNLs~L~~~~~~~e--------~k~vv----v~~KVLg~G~lt~v~kl~V~A~kf 104 (171)
-..|||+|+|||+|++ +.+|.+|||++|++++++.+ +.-++ .++||||+|+++ .+++|.|++|
T Consensus 52 GQ~Pl~rrlPK~GF~~~~~~~~~~~VNL~~L~~~~~~g~~i~~~~L~~~gli~~~~~~vKvLg~G~l~--~~l~I~a~~~ 129 (145)
T TIGR01071 52 GQMPLYRRLPKRGFSNKRFKKEYAEVNLGKLAKLFPNGEVVTLETLKEKGLITKKIKFVKVLGNGKLT--KPLTVKAHRV 129 (145)
T ss_pred CCCceEEECCCCCCCCcccCcceeEEEHHHHhhhhhcCCEecHHHHhhCccCcCCCCceEEeCCCCcC--cCEEEEEEEE
Confidence 4689999999999997 37899999999998754210 00011 258999999999 9999999999
Q ss_pred CHHHHHHHHHhCCEE
Q 030771 105 TETARARIEKAGGEC 119 (171)
Q Consensus 105 S~sAreKIekAGGkv 119 (171)
|++|+++||+|||+|
T Consensus 130 S~sA~ekIE~aGG~v 144 (145)
T TIGR01071 130 SKSAKAAIEAAGGSV 144 (145)
T ss_pred CHHHHHHHHHcCCEE
Confidence 999999999999998
No 9
>COG0200 RplO Ribosomal protein L15 [Translation, ribosomal structure and biogenesis]
Probab=99.57 E-value=2.7e-15 Score=120.39 Aligned_cols=81 Identities=19% Similarity=0.215 Sum_probs=65.4
Q ss_pred cCChHHHHHHHhhhcC-C--C-CCCccchHHHHhhhccC---------CCcEEE---EEeeecCCceeecccCeEEEEE-
Q 030771 40 TDSNFNKVILKRLFMS-K--V-NKPPLSLSRLINFMKGK---------EDKIAV---VVGTVTDDIRAYEVPALKVTAL- 102 (171)
Q Consensus 40 t~~pl~rrI~KRlf~~-r--~-~~~~VNLs~L~~~~~~~---------e~k~vv---v~~KVLg~G~lt~v~kl~V~A~- 102 (171)
-.+|+|+++|||+|++ . . .|.+||+++|++++++. +.+++. ..+||||+|+|+ +++.+.+.
T Consensus 54 gq~Pl~rrlpK~GF~~~~~~~~~~~~vn~~~l~~~~~~~~~v~~~~l~~~~~i~~~~~~vKvLg~G~l~--~~~~~~v~a 131 (152)
T COG0200 54 GQMPLYRRLPKRGFTNSKFKKVEYAVVNLGKLAELLPEGEEVTLASLKAAGVIRKLKDLVKVLGNGKLT--KAVPVKVKA 131 (152)
T ss_pred CCcchhhhcCCCCCccccccccceeEEEHHHhhhhccccccccHHHHhhCCeEeccccccEEeccCeec--cceeEEEEe
Confidence 4689999999999996 2 3 67999999999888421 233432 259999999999 66666655
Q ss_pred ecCHHHHHHHHHhCCEEEeH
Q 030771 103 RFTETARARIEKAGGECLTF 122 (171)
Q Consensus 103 kfS~sAreKIekAGGkv~~l 122 (171)
+||++|+|+||+|||+|+.+
T Consensus 132 ~~S~~A~ekIe~aGG~v~~~ 151 (152)
T COG0200 132 KASKSAIEKIEAAGGKVELI 151 (152)
T ss_pred eeCHHHHHHHHHcCCEEEec
Confidence 99999999999999999764
No 10
>PRK06419 rpl15p 50S ribosomal protein L15P; Reviewed
Probab=99.51 E-value=1.3e-14 Score=115.51 Aligned_cols=75 Identities=28% Similarity=0.315 Sum_probs=61.7
Q ss_pred HHHhhhcC--C--CCCCccchHHHHhhhc----c----CCC-cEEEE-----EeeecCCceeecccCeEEEEEecCHHHH
Q 030771 48 ILKRLFMS--K--VNKPPLSLSRLINFMK----G----KED-KIAVV-----VGTVTDDIRAYEVPALKVTALRFTETAR 109 (171)
Q Consensus 48 I~KRlf~~--r--~~~~~VNLs~L~~~~~----~----~e~-k~vvv-----~~KVLg~G~lt~v~kl~V~A~kfS~sAr 109 (171)
+||++|++ + .++++|||++|+++.+ . .++ ..+++ +.||||+|+++ .+++|.|..||++|+
T Consensus 55 fpK~GF~~~~~~~~~~~~INL~~L~~l~~~l~~~g~i~~~~~~~vid~~~~g~~KVLG~G~l~--~pl~Vka~~fS~~A~ 132 (148)
T PRK06419 55 YGKHGFKRPPKLIKEVSTINVGELDELADLLKAEGKAEEEDGKIVVDLTELGYDKVLGGGKVT--RPLVIKADAFSEKAI 132 (148)
T ss_pred CCCCCccCCCcCcceeeeEEHHHHHHhHHHHHHCCcccccCCcceeeeccCCceEEeCCCccC--cCEEEEEeccCHHHH
Confidence 68999998 2 5799999999998762 1 122 22332 68999999999 899999999999999
Q ss_pred HHHHHhCCEEEeHHH
Q 030771 110 ARIEKAGGECLTFDQ 124 (171)
Q Consensus 110 eKIekAGGkv~~ldq 124 (171)
||||+|||+|+.++|
T Consensus 133 ekIe~aGG~v~l~~~ 147 (148)
T PRK06419 133 EKIEAAGGEVVLSEE 147 (148)
T ss_pred HHHHHcCCEEEEeec
Confidence 999999999988765
No 11
>PTZ00160 60S ribosomal protein L27a; Provisional
Probab=99.25 E-value=1.5e-11 Score=98.30 Aligned_cols=71 Identities=21% Similarity=0.265 Sum_probs=54.7
Q ss_pred HhhhcC----CCCC--CccchHHHHhhhcc--------CCC-cEEEE-----EeeecCCcee-ecccCeEEEEEecCHHH
Q 030771 50 KRLFMS----KVNK--PPLSLSRLINFMKG--------KED-KIAVV-----VGTVTDDIRA-YEVPALKVTALRFTETA 108 (171)
Q Consensus 50 KRlf~~----r~~~--~~VNLs~L~~~~~~--------~e~-k~vvv-----~~KVLg~G~l-t~v~kl~V~A~kfS~sA 108 (171)
|.+|+. +.++ ++|||++|++.... .++ ..+++ ..||||+|+| + ++++|.|..||++|
T Consensus 55 K~Gfr~~~~~~~~~~~~~INl~~L~~lv~~~~~~~~a~~~~~~~vIDl~~~g~~KVLG~G~l~~--~~v~Vka~~~Sk~A 132 (147)
T PTZ00160 55 KVGMRHFHLKKNKYYCPTINVDKLWSLVPEETRYKYAKKGDKAPVIDVTKAGYFKVLGKGHLPK--QPVIVKARYFSKKA 132 (147)
T ss_pred CCCccCCccccccccCceeEHHHHHHHhHHHHHHhhhhccCCceEEEeeccCceEEecCCeEcC--ccEEEEEeecCHHH
Confidence 566653 2344 89999999877542 122 23333 4899999999 6 79999999999999
Q ss_pred HHHHHHhCCEEEeH
Q 030771 109 RARIEKAGGECLTF 122 (171)
Q Consensus 109 reKIekAGGkv~~l 122 (171)
++|||+|||+|+.+
T Consensus 133 ~ekIe~aGG~v~l~ 146 (147)
T PTZ00160 133 EKKIKAVGGACVLT 146 (147)
T ss_pred HHHHHHcCCEEEEc
Confidence 99999999999754
No 12
>KOG0846 consensus Mitochondrial/chloroplast ribosomal protein L15/L10 [Translation, ribosomal structure and biogenesis]
Probab=98.46 E-value=3.3e-07 Score=79.33 Aligned_cols=80 Identities=25% Similarity=0.233 Sum_probs=64.0
Q ss_pred cCChHHHHHHHhhhcC--CCCCCccchHHHHhhhccC---CCcEE----------E--------EEeeecCCceeecccC
Q 030771 40 TDSNFNKVILKRLFMS--KVNKPPLSLSRLINFMKGK---EDKIA----------V--------VVGTVTDDIRAYEVPA 96 (171)
Q Consensus 40 t~~pl~rrI~KRlf~~--r~~~~~VNLs~L~~~~~~~---e~k~v----------v--------v~~KVLg~G~lt~v~k 96 (171)
-+-|||+++|+++|.+ ++++.|++|.+|+++++.+ ..+.+ + +..+..|-+++. -+
T Consensus 72 GqtP~yrr~Pk~~~~~~~~r~~~pl~L~rlq~lID~grid~~q~Idm~tL~~~g~i~p~~~eyGv~L~~~G~d~~~--~~ 149 (274)
T KOG0846|consen 72 GQTPLYRRFPKFGFGNGGRRQYLPLSLGRLQKLIDTGRIDPSQPIDMKTLKDSGLINPKGREYGVQLTADGADEFK--AK 149 (274)
T ss_pred CCchhHHhcccccccccccccCCcccHHHHHHHHHhcCCCccCceeHHHHHhccCCCccccccCceeeccCCcccc--ce
Confidence 3579999999999998 7999999999999888732 11111 0 134556667788 89
Q ss_pred eEEEEEecCHHHHHHHHHhCCEEEe
Q 030771 97 LKVTALRFTETARARIEKAGGECLT 121 (171)
Q Consensus 97 l~V~A~kfS~sAreKIekAGGkv~~ 121 (171)
++|.|-++|..|.++||+|||+|-+
T Consensus 150 i~iEvs~aS~~AiaaIEkaGG~vtt 174 (274)
T KOG0846|consen 150 INIEVSRASVQAIAAIEKAGGSVTT 174 (274)
T ss_pred EEEEehhhhHHHHHHHHhcCCeEEE
Confidence 9999999999999999999998865
No 13
>KOG1742 consensus 60s ribosomal protein L15/L27 [Translation, ribosomal structure and biogenesis]
Probab=97.46 E-value=0.00026 Score=56.71 Aligned_cols=67 Identities=25% Similarity=0.335 Sum_probs=51.3
Q ss_pred CCCCCCccchHHHHhhhcc---------CCC--cEE-EE---EeeecCCceeecccCeEEEEEecCHHHHHHHHHhCCEE
Q 030771 55 SKVNKPPLSLSRLINFMKG---------KED--KIA-VV---VGTVTDDIRAYEVPALKVTALRFTETARARIEKAGGEC 119 (171)
Q Consensus 55 ~r~~~~~VNLs~L~~~~~~---------~e~--k~v-vv---~~KVLg~G~lt~v~kl~V~A~kfS~sAreKIekAGGkv 119 (171)
+....++|||++|-.+... ..+ .++ |+ +.||||.|.+.|=.++.|.|-.||+.|.|+|.++||.+
T Consensus 64 n~~~~P~vnldkLWtlv~~~~~~~~~~~k~g~aPvidv~~~Gy~kvlGkgklp~~~PvIVKak~~s~~AeekIk~~gg~~ 143 (147)
T KOG1742|consen 64 NQSFCPTVNLDKLWTLVREQTRVKAAKNKTGAAPVIDVVQSGYYKVLGKGKLPEETPVIVKAKYFSRRAEEKIKKAGGAV 143 (147)
T ss_pred ccCcCCcccHHHHHHhhhHHHHHHHhccCCCCCceeeeeecceeEeeccccCCCCCcEEEeccccCccchHHHHhcCcee
Confidence 4566899999999544421 111 122 11 57999999998668999999999999999999999988
Q ss_pred Ee
Q 030771 120 LT 121 (171)
Q Consensus 120 ~~ 121 (171)
+.
T Consensus 144 ~~ 145 (147)
T KOG1742|consen 144 VL 145 (147)
T ss_pred ee
Confidence 64
No 14
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=61.19 E-value=4.7 Score=22.78 Aligned_cols=26 Identities=12% Similarity=0.137 Sum_probs=20.6
Q ss_pred eHHHHHHhCCCCCcEEEeecCCCchh
Q 030771 121 TFDQLALRAPLGQNTVCVFNANYCLP 146 (171)
Q Consensus 121 ~ldqL~~~~P~G~~v~ll~g~~~~~~ 146 (171)
..+++++.||......+-.|..+|+|
T Consensus 21 ~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 21 SVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred CHHHHHHHcCCCCccccCCCCEEecC
Confidence 47899999997555567789999987
No 15
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=38.85 E-value=4.3 Score=24.61 Aligned_cols=27 Identities=19% Similarity=0.305 Sum_probs=21.2
Q ss_pred EeHHHHHHhCCCCCcEEEeecCCCchh
Q 030771 120 LTFDQLALRAPLGQNTVCVFNANYCLP 146 (171)
Q Consensus 120 ~~ldqL~~~~P~G~~v~ll~g~~~~~~ 146 (171)
.+.++|.+-||.-..-.|..|...|+|
T Consensus 18 ~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 18 ISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp S-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred hhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 358899999987666568889988887
No 16
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=37.53 E-value=30 Score=27.05 Aligned_cols=35 Identities=11% Similarity=0.235 Sum_probs=28.8
Q ss_pred CCCHHHHH-HHHHHHHhhhccCChHHHHHHHhhhcC
Q 030771 21 SDDIYLKL-LVKLYRFLVRRTDSNFNKVILKRLFMS 55 (171)
Q Consensus 21 stN~~L~~-Li~~lk~~ar~t~~pl~rrI~KRlf~~ 55 (171)
++||..+. -+.++....+++|.+|+..|+.|-|.+
T Consensus 50 ~~n~~v~l~aL~LLe~~vkNCG~~fh~eiask~Fl~ 85 (141)
T cd03565 50 NKNHKEVMLTLTVLETCVKNCGHRFHVLVAKKDFIK 85 (141)
T ss_pred CCCHHHHHHHHHHHHHHHHHccHHHHHHHHHHHhhh
Confidence 46776544 578889999999999999999988875
No 17
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=35.62 E-value=30 Score=27.26 Aligned_cols=40 Identities=13% Similarity=0.110 Sum_probs=30.7
Q ss_pred CCCCCCCCHHHHHH-HHHHHHhhhccCChHHHHHHHhhhcC
Q 030771 16 RTAPKSDDIYLKLL-VKLYRFLVRRTDSNFNKVILKRLFMS 55 (171)
Q Consensus 16 rk~~~stN~~L~~L-i~~lk~~ar~t~~pl~rrI~KRlf~~ 55 (171)
+|+..+.||..+.+ +.++....+++|.+|+..|+.+-|.+
T Consensus 44 ~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas~~Fl~ 84 (139)
T cd03567 44 AHKIQSPQEKEALQALTVLEACMKNCGERFHSEVGKFRFLN 84 (139)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHHhHHHHH
Confidence 45566778765544 45778889999999999999988765
No 18
>PF05573 NosL: NosL; InterPro: IPR008719 NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallocentre assembly []. This entry also contains HTH-type transcriptional repressors, including YcnK. YcnK may act as a negative transcriptional regulator of YcnJ in the presence of copper and may use copper as a corepressor. The gene, ycnK, is significantly induced under copper-limiting conditions.; PDB: 2HQ3_A 2HPU_A.
Probab=34.84 E-value=40 Score=26.41 Aligned_cols=32 Identities=31% Similarity=0.423 Sum_probs=21.8
Q ss_pred eEEEEEecCHHHHHHHHHhCCEEEeHHHHHHh
Q 030771 97 LKVTALRFTETARARIEKAGGECLTFDQLALR 128 (171)
Q Consensus 97 l~V~A~kfS~sAreKIekAGGkv~~ldqL~~~ 128 (171)
-.+.|++=-+.|++=..+.||++++++|+-++
T Consensus 116 ~~~~aF~~~~~A~~F~~~~GG~v~~f~ev~~~ 147 (149)
T PF05573_consen 116 PDLIAFASKEDAEAFAKEHGGKVLTFDEVTED 147 (149)
T ss_dssp --EEEES-HHHHHHHHHHTEEEEEEGGG--HH
T ss_pred CcccccCCHHHHHHHHHHcCCEEeeHHHCCHh
Confidence 34556666667788889999999999998653
No 19
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=33.29 E-value=29 Score=27.32 Aligned_cols=40 Identities=15% Similarity=0.186 Sum_probs=32.0
Q ss_pred CCCCCCCCHHHHHH-HHHHHHhhhccCChHHHHHHHhhhcC
Q 030771 16 RTAPKSDDIYLKLL-VKLYRFLVRRTDSNFNKVILKRLFMS 55 (171)
Q Consensus 16 rk~~~stN~~L~~L-i~~lk~~ar~t~~pl~rrI~KRlf~~ 55 (171)
+|+..+.||..+.+ +.++....+++|.+|+..|+.|-|.+
T Consensus 43 ~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evask~Fl~ 83 (144)
T cd03568 43 MKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVASRDFTQ 83 (144)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHH
Confidence 45566778877665 56778889999999999999988875
No 20
>PF13209 DUF4017: Protein of unknown function (DUF4017)
Probab=30.46 E-value=32 Score=23.84 Aligned_cols=25 Identities=40% Similarity=0.708 Sum_probs=18.4
Q ss_pred CCCCcE---EEeecCCCchhHHHH--HHhh
Q 030771 130 PLGQNT---VCVFNANYCLPIMLL--IITF 154 (171)
Q Consensus 130 P~G~~v---~ll~g~~~~~~~~~~--~~~~ 154 (171)
.+|.|+ +++.|.-|.+||++. +|||
T Consensus 24 SegYN~vgWKlfvGQ~YAiPif~i~aiitF 53 (60)
T PF13209_consen 24 SEGYNTVGWKLFVGQAYAIPIFIITAIITF 53 (60)
T ss_pred ccCccccchhheecchhHhHHHHHHHHHhh
Confidence 356665 789999999999764 4554
No 21
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.63 E-value=58 Score=24.73 Aligned_cols=32 Identities=16% Similarity=0.362 Sum_probs=23.4
Q ss_pred CeEEEEEecC-HHHHHHHHHhCCEEEeHHHHHH
Q 030771 96 ALKVTALRFT-ETARARIEKAGGECLTFDQLAL 127 (171)
Q Consensus 96 kl~V~A~kfS-~sAreKIekAGGkv~~ldqL~~ 127 (171)
+++|....+. ..-++.||+.||.+.++||.+.
T Consensus 52 ~itIeG~~ldydei~~~iE~~Gg~IHSiDevva 84 (97)
T COG1888 52 KITIEGTNLDYDEIEEVIEELGGAIHSIDEVVA 84 (97)
T ss_pred EEEEEcCCCCHHHHHHHHHHcCCeeeehhhhhh
Confidence 3444443332 4578899999999999999874
No 22
>PRK05192 tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA; Validated
Probab=27.82 E-value=23 Score=34.59 Aligned_cols=29 Identities=28% Similarity=0.442 Sum_probs=19.3
Q ss_pred HhCCCCCcEEEeecCCCchhHHHHHHhhh
Q 030771 127 LRAPLGQNTVCVFNANYCLPIMLLIITFA 155 (171)
Q Consensus 127 ~~~P~G~~v~ll~g~~~~~~~~~~~~~~~ 155 (171)
..+|--++..--.|||||.||=-=+.-|+
T Consensus 257 ~~s~~~~g~i~~~gpRYCpsiE~k~~rf~ 285 (618)
T PRK05192 257 HRSPMYSGVIEGVGPRYCPSIEDKIVRFA 285 (618)
T ss_pred ccccCcCcccCCCCCCCCCCHHHHhhhcC
Confidence 33555555555579999999866555554
No 23
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=27.29 E-value=58 Score=25.47 Aligned_cols=40 Identities=20% Similarity=0.310 Sum_probs=30.7
Q ss_pred CCCCCCCCHHHHHH-HHHHHHhhhccCChHHHHHHHhhhcC
Q 030771 16 RTAPKSDDIYLKLL-VKLYRFLVRRTDSNFNKVILKRLFMS 55 (171)
Q Consensus 16 rk~~~stN~~L~~L-i~~lk~~ar~t~~pl~rrI~KRlf~~ 55 (171)
||+..+.||..+.+ +.++....+++|.+|+..++.+-|.+
T Consensus 47 ~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~~fl~ 87 (142)
T cd03569 47 KKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASREFMD 87 (142)
T ss_pred HHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHH
Confidence 45556677766554 46777789999999999999988876
No 24
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=26.44 E-value=65 Score=24.69 Aligned_cols=40 Identities=18% Similarity=0.306 Sum_probs=31.1
Q ss_pred CCCCCCCCHHHHHH-HHHHHHhhhccCChHHHHHHHhhhcC
Q 030771 16 RTAPKSDDIYLKLL-VKLYRFLVRRTDSNFNKVILKRLFMS 55 (171)
Q Consensus 16 rk~~~stN~~L~~L-i~~lk~~ar~t~~pl~rrI~KRlf~~ 55 (171)
||+..+.||..+.+ +.++....++++.+|+..++.+-|..
T Consensus 43 ~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~s~~fl~ 83 (133)
T smart00288 43 KKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKEFLN 83 (133)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHH
Confidence 55666777776654 56777789999999999999987775
No 25
>PF08734 GYD: GYD domain; InterPro: IPR014845 These proteins of unknown function are usually less than 100 amino acids in length. They may belong to the dimeric alpha/beta barrel superfamily.
Probab=24.67 E-value=62 Score=23.46 Aligned_cols=16 Identities=44% Similarity=0.574 Sum_probs=13.3
Q ss_pred HHHHHHHHHhCCEEEe
Q 030771 106 ETARARIEKAGGECLT 121 (171)
Q Consensus 106 ~sAreKIekAGGkv~~ 121 (171)
+.+++.+|++||++..
T Consensus 23 ~a~~~~~e~~Gg~l~~ 38 (91)
T PF08734_consen 23 EAVRALIEALGGKLKS 38 (91)
T ss_pred HHHHHHHHHcCCEEEE
Confidence 5688899999999863
No 26
>KOG2678 consensus Predicted membrane protein [Function unknown]
Probab=22.34 E-value=62 Score=28.28 Aligned_cols=26 Identities=23% Similarity=0.646 Sum_probs=20.4
Q ss_pred CCchhHHHHHHhhhcchhhHHHhhhhhhc
Q 030771 142 NYCLPIMLLIITFAADFTWLCIILTMQVM 170 (171)
Q Consensus 142 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 170 (171)
.||+-+|++|+.| |.+...||.||.|
T Consensus 215 s~wf~~~miI~v~---~sFVsMiliiqif 240 (244)
T KOG2678|consen 215 SYWFYITMIIFVI---LSFVSMILIIQIF 240 (244)
T ss_pred hHHHHHHHHHHHH---HHHHHHHHHHHHh
Confidence 7899999988876 4566777788876
No 27
>PF11973 NQRA_SLBB: NQRA C-terminal domain; InterPro: IPR022615 This domain is found in bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration []. The function of this domain has not been characterised.; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=22.25 E-value=72 Score=21.18 Aligned_cols=22 Identities=9% Similarity=-0.017 Sum_probs=19.4
Q ss_pred HHHHHHhCCCCCcEEEeecCCC
Q 030771 122 FDQLALRAPLGQNTVCVFNANY 143 (171)
Q Consensus 122 ldqL~~~~P~G~~v~ll~g~~~ 143 (171)
+++|...+-+.+++++|+|+..
T Consensus 23 i~~l~~g~~~~~~~RiIsG~vL 44 (51)
T PF11973_consen 23 ISDLLAGNLKEDNVRIISGSVL 44 (51)
T ss_pred HHHHhCcccCCCCcEEEEcCCC
Confidence 7899999988889999999854
No 28
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=22.13 E-value=51 Score=24.94 Aligned_cols=32 Identities=16% Similarity=0.324 Sum_probs=23.0
Q ss_pred cCeEEEEEecC-HHHHHHHHHhCCEEEeHHHHH
Q 030771 95 PALKVTALRFT-ETARARIEKAGGECLTFDQLA 126 (171)
Q Consensus 95 ~kl~V~A~kfS-~sAreKIekAGGkv~~ldqL~ 126 (171)
-+++|....+. ..-++.||..||.+.++||.+
T Consensus 49 lkitiEG~~id~d~i~~~Ie~~Gg~IHSIDeVv 81 (95)
T PF02680_consen 49 LKITIEGDDIDFDEIKEAIEELGGVIHSIDEVV 81 (95)
T ss_dssp EEEEEEESSE-HHHHHHHHHHTT-EEEEEEEEE
T ss_pred EEEEEEeCCCCHHHHHHHHHHcCCeEEeeeeee
Confidence 45666666554 456789999999999999863
No 29
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=21.94 E-value=1e+02 Score=23.48 Aligned_cols=39 Identities=23% Similarity=0.395 Sum_probs=28.0
Q ss_pred CCCCCCCCHHHHHH-HHHHHHhhhccCChHHHHHHHhhhc
Q 030771 16 RTAPKSDDIYLKLL-VKLYRFLVRRTDSNFNKVILKRLFM 54 (171)
Q Consensus 16 rk~~~stN~~L~~L-i~~lk~~ar~t~~pl~rrI~KRlf~ 54 (171)
||+.++.||..+.+ +.++....++++.+|+..++.+-|.
T Consensus 43 ~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~fl 82 (133)
T cd03561 43 RKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVADKEFL 82 (133)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhhHHHH
Confidence 44555667766554 5677778999999999888885544
No 30
>TIGR01997 sufA_proteo FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria.
Probab=21.23 E-value=1.9e+02 Score=21.23 Aligned_cols=33 Identities=18% Similarity=0.288 Sum_probs=22.4
Q ss_pred EecCHHHHHHHHHhCCEEEeHHHHHHhCCCCCcEEEeecCCCc
Q 030771 102 LRFTETARARIEKAGGECLTFDQLALRAPLGQNTVCVFNANYC 144 (171)
Q Consensus 102 ~kfS~sAreKIekAGGkv~~ldqL~~~~P~G~~v~ll~g~~~~ 144 (171)
..+|+.|.++|. +++++.|++..++|--.+.-|
T Consensus 3 i~iT~~A~~~i~----------~l~~~~~~~~~lRi~v~~~GC 35 (107)
T TIGR01997 3 ITLTDAAAIHIR----------ELVAKRPEAVGIRLGVKKTGC 35 (107)
T ss_pred EEECHHHHHHHH----------HHHhcCCCCcEEEEEEECCCC
Confidence 568999999887 455556655677876544444
No 31
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=20.97 E-value=1.8e+02 Score=22.37 Aligned_cols=32 Identities=9% Similarity=0.068 Sum_probs=23.2
Q ss_pred eeecCCceeecccCeEEEEEecCHHHHHHHHHhCCEEE
Q 030771 83 GTVTDDIRAYEVPALKVTALRFTETARARIEKAGGECL 120 (171)
Q Consensus 83 ~KVLg~G~lt~v~kl~V~A~kfS~sAreKIekAGGkv~ 120 (171)
--|+.+|.+. |.+.+.|+...++.+..|-++-
T Consensus 46 fEi~n~G~~R------I~gYk~se~~~~~f~slG~~~K 77 (103)
T PF09158_consen 46 FEIRNKGEFR------IFGYKMSEEIIKKFTSLGMEVK 77 (103)
T ss_dssp EEEETTSEEE------EEEES--HHHHHHHHHTT-EEE
T ss_pred EEEecCCcEE------EEEEcCCHHHHHHHHhcCcEEE
Confidence 4566666655 9999999999999999987763
No 32
>TIGR00136 gidA glucose-inhibited division protein A. GidA, the longer of two forms of GidA-related proteins, appears to be present in all complete eubacterial genomes so far, as well as Saccharomyces cerevisiae. A subset of these organisms have a closely related protein. GidA is absent in the Archaea. It appears to act with MnmE, in an alpha2/beta2 heterotetramer, in the 5-carboxymethylaminomethyl modification of uridine 34 in certain tRNAs. The shorter, related protein, previously called gid or gidA(S), is now called TrmFO (see model TIGR00137).
Probab=20.63 E-value=36 Score=33.27 Aligned_cols=27 Identities=22% Similarity=0.390 Sum_probs=17.1
Q ss_pred CCCCCcEEEeecCCCchhHHHHHHhhh
Q 030771 129 APLGQNTVCVFNANYCLPIMLLIITFA 155 (171)
Q Consensus 129 ~P~G~~v~ll~g~~~~~~~~~~~~~~~ 155 (171)
+|--++..-=.|||||.||=-=+..|.
T Consensus 257 s~~~~g~i~~~GpRYCpsIe~k~~~f~ 283 (617)
T TIGR00136 257 SPMYSGVIEGNGPRYCPSIEDKVVRFA 283 (617)
T ss_pred ccccCcccCCCCCCCCCCHHHHHhhcC
Confidence 343344322359999999977666665
No 33
>KOG0829 consensus 60S ribosomal protein L18A [Translation, ribosomal structure and biogenesis]
Probab=20.43 E-value=53 Score=27.16 Aligned_cols=37 Identities=16% Similarity=0.353 Sum_probs=28.9
Q ss_pred HHHHHHHHhCCEEEeHHHHHHhCCC---CCcEEEeecCCC
Q 030771 107 TARARIEKAGGECLTFDQLALRAPL---GQNTVCVFNANY 143 (171)
Q Consensus 107 sAreKIekAGGkv~~ldqL~~~~P~---G~~v~ll~g~~~ 143 (171)
+-..|+.++.|+++.+.|+.+.+|+ .-|+-|--.+|.
T Consensus 42 ~~l~KvKks~Geiv~i~qi~E~~p~~vkNfGIwlrYdSRs 81 (169)
T KOG0829|consen 42 SKLKKVKKSSGEIVAINQIFEKSPLKVKNFGIWLRYDSRS 81 (169)
T ss_pred HHHHHHhhcCceEEEeceecCCCCceeeeeEEEEEEccCC
Confidence 3567999999999999999999995 455666555544
Done!