Query 048544
Match_columns 153
No_of_seqs 110 out of 212
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 10:28:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048544.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048544hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4071 Uncharacterized conser 100.0 1.1E-54 2.3E-59 343.9 13.0 139 10-149 1-139 (187)
2 COG5093 Uncharacterized conser 100.0 7.8E-42 1.7E-46 265.5 10.9 141 10-150 9-150 (185)
3 PTZ00362 hypothetical protein; 100.0 2.3E-38 4.9E-43 278.6 11.1 129 21-149 282-427 (479)
4 PF05916 Sld5: GINS complex pr 99.8 2.6E-18 5.6E-23 121.7 9.4 87 53-146 1-89 (108)
5 KOG1106 Uncharacterized conser 97.8 8.9E-05 1.9E-09 59.2 7.8 100 19-120 20-119 (177)
6 COG5138 Uncharacterized conser 96.0 0.019 4.2E-07 45.0 5.6 90 19-112 9-100 (168)
7 COG1711 DNA replication initia 90.0 1.1 2.4E-05 37.2 6.3 65 77-142 1-80 (223)
8 PF03233 Cauli_AT: Aphid trans 59.2 29 0.00064 27.6 5.5 79 70-149 52-133 (163)
9 PF01090 Ribosomal_S19e: Ribos 59.2 4.6 0.0001 31.3 1.0 19 59-79 15-33 (139)
10 PF10792 DUF2605: Protein of u 56.6 31 0.00068 25.3 4.9 36 101-136 20-55 (98)
11 COG4218 MtrF Tetrahydromethano 51.2 16 0.00035 25.3 2.5 29 116-144 14-47 (73)
12 PTZ00095 40S ribosomal protein 49.5 12 0.00027 29.8 2.0 64 37-110 12-83 (169)
13 PF09472 MtrF: Tetrahydrometha 49.5 24 0.00052 23.9 3.1 26 119-144 8-38 (64)
14 COG3248 Tsx Nucleoside-binding 45.9 10 0.00022 32.3 1.0 23 26-48 101-123 (284)
15 PRK09333 30S ribosomal protein 44.6 17 0.00037 28.5 2.1 19 59-79 16-34 (150)
16 KOG3411 40S ribosomal protein 44.2 12 0.00025 29.1 1.1 22 59-82 18-39 (143)
17 PRK13275 mtrF tetrahydromethan 40.8 39 0.00084 23.1 3.1 26 119-144 8-38 (67)
18 PF15614 WHIM3: WSTF, HB1, Itc 34.4 89 0.0019 19.8 3.8 28 120-147 6-36 (46)
19 smart00545 JmjN Small domain f 34.4 22 0.00047 22.0 1.0 16 60-75 23-38 (42)
20 TIGR02507 MtrF tetrahydrometha 32.1 54 0.0012 22.3 2.7 26 119-144 8-38 (65)
21 PF11140 DUF2913: Protein of u 30.1 1.5E+02 0.0032 24.0 5.4 71 57-134 39-109 (207)
22 PF12166 DUF3595: Protein of u 27.5 50 0.0011 29.0 2.5 23 116-138 371-393 (422)
23 COG2238 RPS19A Ribosomal prote 27.3 89 0.0019 24.5 3.5 45 58-112 15-61 (147)
24 PF08542 Rep_fac_C: Replicatio 25.2 1.1E+02 0.0023 20.5 3.3 30 117-146 1-30 (89)
25 PF10835 DUF2573: Protein of u 25.1 1.3E+02 0.0029 21.3 3.7 29 110-138 47-76 (82)
26 PF01788 PsbJ: PsbJ; InterPro 23.1 34 0.00073 21.2 0.4 8 53-60 6-13 (40)
27 cd01799 Hoil1_N Ubiquitin-like 22.9 75 0.0016 21.4 2.2 36 64-99 10-45 (75)
28 COG1516 FliS Flagellin-specifi 22.8 74 0.0016 24.4 2.3 54 80-134 62-116 (132)
29 PRK15070 propanediol utilizati 22.5 66 0.0014 26.6 2.1 39 21-63 64-103 (211)
30 PF14821 Thr_synth_N: Threonin 21.4 1.3E+02 0.0029 20.4 3.2 29 101-130 48-77 (79)
31 TIGR00208 fliS flagellar biosy 21.0 50 0.0011 24.5 1.0 54 80-134 62-116 (124)
No 1
>KOG4071 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.1e-54 Score=343.86 Aligned_cols=139 Identities=52% Similarity=1.008 Sum_probs=136.9
Q ss_pred CCCChhhhhhhhcCceeEEeeCCCCCccceeccccccCCCCCcchhhHHHHHHhcccCCceEeCCCCCCHHHHHHHHHHH
Q 048544 10 SLFSPPEVEFMAEDELVEIVPNMRMDPLNFICGDFGPFYPQIPVKVPLWLAAALKKRGKCTIRPPQWMSIENLTKVLEGE 89 (153)
Q Consensus 10 ~~~~p~E~eFlae~e~i~IiP~f~~~~~~lI~g~~GPF~p~~~~~VPLWlAl~Lkk~~~C~I~pP~Wl~ve~L~~~l~~E 89 (153)
.+|+|+|++|+|++++|+|+||+++++++||+||+|||+||.|+.||||+|++||||++|+|+||.||+++.|+++++.|
T Consensus 1 ~~~~peeiefia~~eli~I~P~~S~~~l~li~~d~gp~~p~~~~rVpLWlAllLKkq~kc~Iv~P~wm~~~~L~~i~d~E 80 (187)
T KOG4071|consen 1 MAMSPEEIEFIAENELIEIIPNISMDQLHLISGDIGPFNPGVPCRVPLWLALLLKKQNKCRIVPPEWMDVDELEKIRDVE 80 (187)
T ss_pred CCCCHHHHHHHhcccceeeccCCcchhhhhhcCCCcccCCCCcceehHHHHHHHhhccCceEeCcccccHHHHHHHHHHh
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhCcCCcccCCchHHHHHHHHHhhhcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 048544 90 REDRGTFQAVPFHYIEISRLLFDHARDDIPDIYMVRSLIEDIRDVRLHKIETNLEKFSAT 149 (153)
Q Consensus 90 ~~~~~~f~~LP~~y~Eia~lLl~~a~dDi~~~~~ir~Li~DI~~iR~~Klr~gl~~~~~~ 149 (153)
+.++ .|++||+||+|+|++|+++|.|||++++++|++|+||||+|++|+|+|++.|+++
T Consensus 81 ~e~~-tfs~lp~~~~ela~lL~n~a~Ddi~~~eeiR~lV~DI~d~R~aKlr~s~~~f~~~ 139 (187)
T KOG4071|consen 81 KESE-TFSKLPFYYFELATLLLNFARDDIPDIEEIRTLVKDIRDIRLAKLRTSLDSFNRQ 139 (187)
T ss_pred hccc-ccccCChHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHHHHhHHHHhhH
Confidence 9995 9999999999999999999999999999999999999999999999999999998
No 2
>COG5093 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=7.8e-42 Score=265.53 Aligned_cols=141 Identities=32% Similarity=0.578 Sum_probs=136.8
Q ss_pred CCCChhhhhhhhcCceeEEeeCCCCCccceec-cccccCCCCCcchhhHHHHHHhcccCCceEeCCCCCCHHHHHHHHHH
Q 048544 10 SLFSPPEVEFMAEDELVEIVPNMRMDPLNFIC-GDFGPFYPQIPVKVPLWLAAALKKRGKCTIRPPQWMSIENLTKVLEG 88 (153)
Q Consensus 10 ~~~~p~E~eFlae~e~i~IiP~f~~~~~~lI~-g~~GPF~p~~~~~VPLWlAl~Lkk~~~C~I~pP~Wl~ve~L~~~l~~ 88 (153)
.+|||+|++|+|++|+|+|+|+.+++.+.|++ .+|.|+.|...+.||||+|+.|||+++|+|++|.||+.+.|+..++.
T Consensus 9 ~~fSPEEi~fia~nE~i~I~P~~t~~qlrL~~~~t~p~m~p~~~~rvpLw~ALlLKkqn~c~Iv~P~wl~~~~L~~~i~~ 88 (185)
T COG5093 9 MAFSPEEILFIAYNELIEIEPMTTIPQLRLLERATYPPMMPLDIARVPLWAALLLKKQNMCKIVLPSWLQLESLKMSIDV 88 (185)
T ss_pred hcCCHHHHHHHhcccceeeecccccchhhhhhhhcCCCCCCchhhhhHHHHHHHHHhcccccccChhHhhHHHHHhhhhH
Confidence 48999999999999999999999999999999 59999999999999999999999999999999999999999999999
Q ss_pred HhhCcCCcccCCchHHHHHHHHHhhhcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Q 048544 89 EREDRGTFQAVPFHYIEISRLLFDHARDDIPDIYMVRSLIEDIRDVRLHKIETNLEKFSATS 150 (153)
Q Consensus 89 E~~~~~~f~~LP~~y~Eia~lLl~~a~dDi~~~~~ir~Li~DI~~iR~~Klr~gl~~~~~~~ 150 (153)
|+..++.|+.|||||++.|+.||+.|.||+.+.+++|..|+||+++|++|.++|++.+++.+
T Consensus 89 e~~~~d~fSelp~~wl~lA~~Lln~~~ddvediee~r~iv~dirEiRq~K~lkGlk~lne~~ 150 (185)
T COG5093 89 EIEKADEFSELPPYWLPLATELLNENCDDVEDIEESRMIVEDIREIRQAKTLKGLKCLNEKA 150 (185)
T ss_pred HHhcccccccCCchHHHHHHHHHHhccchHhHHHHHHHHHHHHHHHHHHHHHhhHhhhhhhh
Confidence 98888999999999999999999999999999999999999999999999999999999874
No 3
>PTZ00362 hypothetical protein; Provisional
Probab=100.00 E-value=2.3e-38 Score=278.63 Aligned_cols=129 Identities=32% Similarity=0.467 Sum_probs=113.4
Q ss_pred hcCceeEEeeCCCCCcc--ceecc-ccccCCCCCcchhhHHHHHHhcccCCceEeCCCCCCHHHHHHHHHHHhhCcCCcc
Q 048544 21 AEDELVEIVPNMRMDPL--NFICG-DFGPFYPQIPVKVPLWLAAALKKRGKCTIRPPQWMSIENLTKVLEGEREDRGTFQ 97 (153)
Q Consensus 21 ae~e~i~IiP~f~~~~~--~lI~g-~~GPF~p~~~~~VPLWlAl~Lkk~~~C~I~pP~Wl~ve~L~~~l~~E~~~~~~f~ 97 (153)
|-+|+|-+--....+.+ .+|+| ++|||+||.|++||||||++||++++|+|+||.||++++|++++++|.++.+.|+
T Consensus 282 al~eLvVvKalvDip~~~L~lI~G~digpfkag~~~~VPLWLAi~LKq~~KC~IvpP~Wm~ie~Lk~I~eeE~~~~~~Ft 361 (479)
T PTZ00362 282 ALDELVVVKALVDIPYIDLSEIEGFDFKEMKSGERQWLPIYIAKELSHFGLVTVEFPFWFYIKNLKNIYEREFEDQNELT 361 (479)
T ss_pred HhcceEEEEEecCCCCCcceeeeccccCCcCCCCeeEEeeeehhhhcccCceEEeCcccccHHHHHHHHHHHhhCccccc
Confidence 55677766544444432 37999 9999999999999999999999999999999999999999999999955568999
Q ss_pred cCCc-hHHHHHHHHHhh-------hcCCCcC------HHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Q 048544 98 AVPF-HYIEISRLLFDH-------ARDDIPD------IYMVRSLIEDIRDVRLHKIETNLEKFSAT 149 (153)
Q Consensus 98 ~LP~-~y~Eia~lLl~~-------a~dDi~~------~~~ir~Li~DI~~iR~~Klr~gl~~~~~~ 149 (153)
+||+ ||+|||++||++ |+||+++ +++||++|+|||++|++|+|+|++.++++
T Consensus 362 ~LP~p~y~EIa~lLl~~~~F~~~~a~edi~~~d~~~~~~kVR~LIeDIrd~R~~KIr~~Le~~~~~ 427 (479)
T PTZ00362 362 DLPSPYFFEISSMFLENNIFKKVTPIETIGQRTVYKYISKVAGLVEDIRYKRLKKIMNHLENQDVH 427 (479)
T ss_pred cCCchhHHHHHHHHHhcccccccCChhhcccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 9996 999999999999 6677665 69999999999999999999999999874
No 4
>PF05916 Sld5: GINS complex protein; InterPro: IPR021151 DNA replication in eukaryotes results from a highly coordinated interaction between proteins, often as part of protein complexes, and the DNA template. One of the key early steps leading to DNA replication is formation of the pre- replication complex, or pre-RC. The pre-RC is formed by the sequential binding of the origin recognition complex (ORC), Cdc6 and Cdt1 proteins, and the MCM complex. Activation of the pre-RC into the initiation complex (IC) is achieved via the action of S-phase kinases, eventually leading to the loading of the replication machinery. Recently, a novel replication complex, GINS (for Go, Ichi, Nii, and San; five, one, two, and three in Japanese), has been identified [, ]. The precise function of GINS is not known. However, genetic and two-hybrid interactions indicate that it mediates the loading of the enzymatic replication machinery at a step after the action of the S-phase kinases []. Furthermore, GINS may be a part of the replication machinery itself, since it is found associated with replicating DNA [, ]. Electron microscopy of GINS shows that it forms a ring-like structure [], reminiscent of the structure of PCNA [], the DNA polymerase delta replication clamp.This observation, coupled with the observed interactions for GINS, indicates that the complex may represent the replication clamp for DNA polymerase epsilon []. The GINS complex is essential for initiation of DNA replication in Xenopus egg extracts []. This 100 kDa stable complex includes Sld5, Psf1, Psf2, and Psf3. Homologues of these components are found also in other eukaryotes. ; PDB: 2EHO_L 2E9X_G 2Q9Q_H 3ANW_B.
Probab=99.77 E-value=2.6e-18 Score=121.71 Aligned_cols=87 Identities=32% Similarity=0.587 Sum_probs=77.6
Q ss_pred chhhHHHHHHhcccCCceEeCCCCCCHHHHHHHHHHHhhCc--CCcccCCchHHHHHHHHHhhhcCCCcCHHHHHHHHHH
Q 048544 53 VKVPLWLAAALKKRGKCTIRPPQWMSIENLTKVLEGEREDR--GTFQAVPFHYIEISRLLFDHARDDIPDIYMVRSLIED 130 (153)
Q Consensus 53 ~~VPLWlAl~Lkk~~~C~I~pP~Wl~ve~L~~~l~~E~~~~--~~f~~LP~~y~Eia~lLl~~a~dDi~~~~~ir~Li~D 130 (153)
++||+|+|..|++++.|+|++|+|++++.++.+..+|+.+. ..|++||+||++.+.+|++.+ +.++.++.+
T Consensus 1 v~lP~w~a~~L~~~~~~~i~~p~~~~~~~~~~l~~e~~~~~~~~~l~~l~~~f~~~~~~l~~~~-------~~ik~~l~~ 73 (108)
T PF05916_consen 1 VELPLWLAKELKKRNLVEIQPPDWFSIEYLNALEAEEKNNSNKVDLSKLPPYFYELGEMLLELL-------ERIKRLLRD 73 (108)
T ss_dssp EEEEHHHHHHHHHTTSEEEE-TCCHCHHHHHHHHHHHCCCS-HCSCCTSSTTHHHHHHHHHHHH-------HHHHHHHHH
T ss_pred CcCCcchHHHHHHcCCeeecCcHhhhHHHHHHHHhhhccccchhhhhcCChHHHHHHHHHHHHH-------HHHHHHHHH
Confidence 57999999999999999999999999999666666665543 489999999999999999999 789999999
Q ss_pred HHHHHHHHHHHHHHHh
Q 048544 131 IRDVRLHKIETNLEKF 146 (153)
Q Consensus 131 I~~iR~~Klr~gl~~~ 146 (153)
++..|..||+++....
T Consensus 74 ~~~~R~~KI~~~~~~~ 89 (108)
T PF05916_consen 74 YLRIRLKKILSLAWHL 89 (108)
T ss_dssp HHHHHHHHHHHHHCHH
T ss_pred HHHHHHHHHHHHHHHh
Confidence 9999999999998777
No 5
>KOG1106 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.83 E-value=8.9e-05 Score=59.23 Aligned_cols=100 Identities=17% Similarity=0.252 Sum_probs=76.8
Q ss_pred hhhcCceeEEeeCCCCCccceeccccccCCCCCcchhhHHHHHHhcccCCceEeCCCCCCHHHHHHHHHHHhhCcCCccc
Q 048544 19 FMAEDELVEIVPNMRMDPLNFICGDFGPFYPQIPVKVPLWLAAALKKRGKCTIRPPQWMSIENLTKVLEGEREDRGTFQA 98 (153)
Q Consensus 19 Flae~e~i~IiP~f~~~~~~lI~g~~GPF~p~~~~~VPLWlAl~Lkk~~~C~I~pP~Wl~ve~L~~~l~~E~~~~~~f~~ 98 (153)
-+|..+.|...=..++..+-+++..--+..+|..+++|+|||-.|+-.+-..|.+|+-++.. .++.++.+-+. -.+..
T Consensus 20 Ila~~~ki~ct~e~~i~~lgfl~~~~~~~~~g~kVelP~wl~~~L~~~~~~si~lP~~fs~~-~rn~i~Adp~~-vdL~s 97 (177)
T KOG1106|consen 20 ILASGEKIPCTFETKIPNLGFLQAPPRELPAGRKVELPYWLAEELAINQFVSILLPDIFSEK-VRNVIKADPNK-VDLRS 97 (177)
T ss_pred HHhcCCcccceeeecCCCCCccCCCcccCCCCCcccchHHHHHHHhhccceeecCchHHHHH-HHHHHhcCcce-eeccc
Confidence 36677776655555666666666555566788999999999999999999999999998765 55666666554 36788
Q ss_pred CCchHHHHHHHHHhhhcCCCcC
Q 048544 99 VPFHYIEISRLLFDHARDDIPD 120 (153)
Q Consensus 99 LP~~y~Eia~lLl~~a~dDi~~ 120 (153)
+-+||++.+..|+-.-+++-.+
T Consensus 98 ~~phFY~fg~kl~~l~s~~~l~ 119 (177)
T KOG1106|consen 98 LCPHFYEFGMKLLPLDSGENLG 119 (177)
T ss_pred cccHHHHHHHHHhhcccCcchh
Confidence 8999999999999887765543
No 6
>COG5138 Uncharacterized conserved protein [Function unknown]
Probab=95.97 E-value=0.019 Score=44.99 Aligned_cols=90 Identities=13% Similarity=0.162 Sum_probs=62.6
Q ss_pred hhhcCceeEEeeCCCCCccceeccccccCCCCCcchhhHHHHHHhcccCCceEeCCCCCCHHHHHHHHHHHhhCc--CCc
Q 048544 19 FMAEDELVEIVPNMRMDPLNFICGDFGPFYPQIPVKVPLWLAAALKKRGKCTIRPPQWMSIENLTKVLEGEREDR--GTF 96 (153)
Q Consensus 19 Flae~e~i~IiP~f~~~~~~lI~g~~GPF~p~~~~~VPLWlAl~Lkk~~~C~I~pP~Wl~ve~L~~~l~~E~~~~--~~f 96 (153)
-++++..|...=..+++.+-+++..=-|.--|.++++|+|||-.|-...-..+.+|+.++-.-+.++. .++ -.+
T Consensus 9 iL~~~s~ipctf~~~IpglG~l~~~gr~~p~n~kvelP~wLa~~Lainsfv~~l~p~~fs~~v~naik----a~P~tvdl 84 (168)
T COG5138 9 ILLGESRIPCTFKHKIPGLGFLGPRGRILPENRKVELPYWLASFLAINSFVCELGPGFFSESVLNAIK----AKPSTVDL 84 (168)
T ss_pred HhcCCCccceeeEeecCCcccCCCCCcccCCCCeeechHHHHHHHHHhhhHHhcCcchHHHHHHHHHh----cCCceeeh
Confidence 46777777666667777777766444466677999999999999998867778999998866555543 333 234
Q ss_pred ccCCchHHHHHHHHHh
Q 048544 97 QAVPFHYIEISRLLFD 112 (153)
Q Consensus 97 ~~LP~~y~Eia~lLl~ 112 (153)
-.+-.|||-.|...+-
T Consensus 85 rsI~~hff~lA~K~~m 100 (168)
T COG5138 85 RSICPHFFYLAEKYAM 100 (168)
T ss_pred hhcchHHHHHHHHHHH
Confidence 4666677777654433
No 7
>COG1711 DNA replication initiation complex subunit, GINS family [Replication, recombination, and repair]
Probab=89.97 E-value=1.1 Score=37.18 Aligned_cols=65 Identities=26% Similarity=0.299 Sum_probs=46.2
Q ss_pred CCHHHHHHHHHHHhhCcCCcccCCchHHHHHHHHHh----hh-----cCCCcC------HHHHHHHHHHHHHHHHHHHHH
Q 048544 77 MSIENLTKVLEGEREDRGTFQAVPFHYIEISRLLFD----HA-----RDDIPD------IYMVRSLIEDIRDVRLHKIET 141 (153)
Q Consensus 77 l~ve~L~~~l~~E~~~~~~f~~LP~~y~Eia~lLl~----~a-----~dDi~~------~~~ir~Li~DI~~iR~~Klr~ 141 (153)
|.++.|++++..|+.. +.++.++..|++-.+-.++ .+ ++|+.. .+.+.+..+-|.++|..|+.+
T Consensus 1 m~i~eLR~~~~kErS~-~~L~~Id~dFY~~v~~~I~eLe~~~~~~~~~~D~e~~~~~~~~et~~~~~r~ifqrR~~Kiv~ 79 (223)
T COG1711 1 MDIEELRRALYKERSQ-DGLTEIDEDFYRDVRSFIKELEDEAGRAEEARDIEKYLLTDRIETAKSDARSIFQRRYGKIVS 79 (223)
T ss_pred CCHHHHHHHHHHHhhh-hhhhhcCHHHHHHHHHHHHHHHHHhhccccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6789999999999987 7899999755555444443 22 234433 236667778888889999875
Q ss_pred H
Q 048544 142 N 142 (153)
Q Consensus 142 g 142 (153)
.
T Consensus 80 ~ 80 (223)
T COG1711 80 R 80 (223)
T ss_pred H
Confidence 4
No 8
>PF03233 Cauli_AT: Aphid transmission protein; InterPro: IPR004917 This protein is found in various caulimoviruses. It codes for an 18 kDa protein (PII), which is dispensable for infection but which is required for aphid transmission of the virus []. This protein interacts with the PIII protein []. ; GO: 0019089 transmission of virus
Probab=59.22 E-value=29 Score=27.60 Aligned_cols=79 Identities=19% Similarity=0.395 Sum_probs=51.9
Q ss_pred eEeCCCCCCHHHHHHHHHHHhhCcCCcc--cCCc-hHHHHHHHHHhhhcCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 048544 70 TIRPPQWMSIENLTKVLEGEREDRGTFQ--AVPF-HYIEISRLLFDHARDDIPDIYMVRSLIEDIRDVRLHKIETNLEKF 146 (153)
Q Consensus 70 ~I~pP~Wl~ve~L~~~l~~E~~~~~~f~--~LP~-~y~Eia~lLl~~a~dDi~~~~~ir~Li~DI~~iR~~Klr~gl~~~ 146 (153)
.|+.=-||.+-+|...+-.|+...++++ +.|| -|+--+.-.|....+|.......-..++++-. |..||....+.+
T Consensus 52 ~i~~r~~l~~~kl~sylGleKD~Se~~S~~K~Pf~~~~k~~~~ifkegg~d~~k~~~~l~~L~e~sn-ki~kLe~~~k~L 130 (163)
T PF03233_consen 52 EIVGRNWLKLSKLLSYLGLEKDPSEGLSKSKSPFESFFKDLSKIFKEGGGDKQKQLKLLPTLEEISN-KIRKLETEVKKL 130 (163)
T ss_pred HHHHHHHHHHHHHHHHhccccCCccccccCCCcHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHH-HHHHHHHHHHhH
Confidence 4666689999999999999988666554 6775 56676777777777776654222223334444 666666655555
Q ss_pred hcc
Q 048544 147 SAT 149 (153)
Q Consensus 147 ~~~ 149 (153)
..+
T Consensus 131 ~d~ 133 (163)
T PF03233_consen 131 KDN 133 (163)
T ss_pred hhh
Confidence 443
No 9
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 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 family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=59.21 E-value=4.6 Score=31.29 Aligned_cols=19 Identities=63% Similarity=1.111 Sum_probs=14.6
Q ss_pred HHHHhcccCCceEeCCCCCCH
Q 048544 59 LAAALKKRGKCTIRPPQWMSI 79 (153)
Q Consensus 59 lAl~Lkk~~~C~I~pP~Wl~v 79 (153)
+|-+||+.++ |.+|+|.++
T Consensus 15 ~A~~LK~~gk--i~~P~w~d~ 33 (139)
T PF01090_consen 15 LAEFLKKSGK--IEPPEWADI 33 (139)
T ss_dssp HHHHHTCSST--S--TSCGGG
T ss_pred HHHHHHHcCC--cCCcchHHH
Confidence 7899999977 899999765
No 10
>PF10792 DUF2605: Protein of unknown function (DUF2605); InterPro: IPR019728 This entry represents a protein conserved in Cyanobacteria. The function is not known.
Probab=56.61 E-value=31 Score=25.27 Aligned_cols=36 Identities=14% Similarity=0.131 Sum_probs=28.6
Q ss_pred chHHHHHHHHHhhhcCCCcCHHHHHHHHHHHHHHHH
Q 048544 101 FHYIEISRLLFDHARDDIPDIYMVRSLIEDIRDVRL 136 (153)
Q Consensus 101 ~~y~Eia~lLl~~a~dDi~~~~~ir~Li~DI~~iR~ 136 (153)
.|||+.|+-||+.+++++-+.++=..|+.-+.+.+.
T Consensus 20 ~yWF~Rs~~LLe~e~~~fls~~eQ~~Ll~Rv~qaq~ 55 (98)
T PF10792_consen 20 QYWFSRSRELLETEPISFLSPEEQSDLLERVKQAQQ 55 (98)
T ss_pred HHHHHHHHHHHhcCCcccCCHHHHHHHHHHHHHHHH
Confidence 399999999999999999887766666666555543
No 11
>COG4218 MtrF Tetrahydromethanopterin S-methyltransferase, subunit F [Coenzyme metabolism]
Probab=51.20 E-value=16 Score=25.30 Aligned_cols=29 Identities=24% Similarity=0.397 Sum_probs=23.5
Q ss_pred CCCcCHHHHHHHHHHHHHH-----HHHHHHHHHH
Q 048544 116 DDIPDIYMVRSLIEDIRDV-----RLHKIETNLE 144 (153)
Q Consensus 116 dDi~~~~~ir~Li~DI~~i-----R~~Klr~gl~ 144 (153)
-..||.+.|.+.|+||+.. |-+||-.|+.
T Consensus 14 snkpn~~~id~yVediryr~qligRd~rL~sGl~ 47 (73)
T COG4218 14 SNKPNTDRIDTYVEDIRYRSQLIGRDARLYSGLN 47 (73)
T ss_pred cCCCChhHHHHHHHHHHHHHHhhcccchhhhhhh
Confidence 3567889999999999997 7778777764
No 12
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=49.53 E-value=12 Score=29.84 Aligned_cols=64 Identities=22% Similarity=0.264 Sum_probs=37.0
Q ss_pred cceeccccccCCCCC-cchhhHH-----HHHHhcccCCceEeCCCCCCHHHHHHHHHHHhhCcCCcccC-C-chHHHHHH
Q 048544 37 LNFICGDFGPFYPQI-PVKVPLW-----LAAALKKRGKCTIRPPQWMSIENLTKVLEGEREDRGTFQAV-P-FHYIEISR 108 (153)
Q Consensus 37 ~~lI~g~~GPF~p~~-~~~VPLW-----lAl~Lkk~~~C~I~pP~Wl~ve~L~~~l~~E~~~~~~f~~L-P-~~y~Eia~ 108 (153)
+..|++..|=.+++. --.||-+ +|-+||+.++ |.+|+|.++- +.-... +..|. | |+|.-.|.
T Consensus 12 ~~~~~~~~~~~~~~~tvkDVpa~~fI~~~A~~LK~~gk--i~~P~W~d~v--KTg~~K------ElaP~d~DW~YiRaAS 81 (169)
T PTZ00095 12 IKRIGKPVPYRRKNATLKDVSPWRFIKAFAQHFKLEGK--IFVPKCTEIV--KTSHGR------ELAPQNPDWYYIRCAA 81 (169)
T ss_pred HHHhcCCCCcccCCCceeeCCHHHHHHHHHHHHHHcCC--CCCCcchhhh--cccccc------cCCCCCccHHHHHHHH
Confidence 445555554335553 2456765 6888998777 9999996543 322222 23333 2 56666666
Q ss_pred HH
Q 048544 109 LL 110 (153)
Q Consensus 109 lL 110 (153)
++
T Consensus 82 il 83 (169)
T PTZ00095 82 VL 83 (169)
T ss_pred HH
Confidence 54
No 13
>PF09472 MtrF: Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF); InterPro: IPR013347 Many archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This domain is mostly found in MtrF, where it covers the entire length of the protein. This polypeptide is one of eight subunits of the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase complex found in methanogenic archaea. This is a membrane-associated enzyme complex that uses methyl-transfer reactions to drive a sodium-ion pump []. MtrF itself is involved in the transfer of the methyl group from N5-methyltetrahydromethanopterin to coenzyme M. Subsequently, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase. In some organisms this domain is found at the C-terminal region of what appears to be a fusion of the MtrA and MtrF proteins [, ]. The function of these proteins is unknown, though it is likely that they are involved in C1 metabolism.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016020 membrane
Probab=49.48 E-value=24 Score=23.90 Aligned_cols=26 Identities=31% Similarity=0.540 Sum_probs=22.1
Q ss_pred cCHHHHHHHHHHHHHH-----HHHHHHHHHH
Q 048544 119 PDIYMVRSLIEDIRDV-----RLHKIETNLE 144 (153)
Q Consensus 119 ~~~~~ir~Li~DI~~i-----R~~Klr~gl~ 144 (153)
|+...|..+++||+.. |-.|+-+|+.
T Consensus 8 P~m~~I~~~vedi~Yk~qLiaR~~kL~SGv~ 38 (64)
T PF09472_consen 8 PNMGAIDKMVEDIRYKAQLIARDQKLESGVM 38 (64)
T ss_pred CCHHHHHHHHHHHHHHHHHhhhcchhHHHHh
Confidence 5567899999999987 8899998875
No 14
>COG3248 Tsx Nucleoside-binding outer membrane protein [Cell envelope biogenesis, outer membrane]
Probab=45.94 E-value=10 Score=32.27 Aligned_cols=23 Identities=35% Similarity=0.491 Sum_probs=19.2
Q ss_pred eEEeeCCCCCccceeccccccCC
Q 048544 26 VEIVPNMRMDPLNFICGDFGPFY 48 (153)
Q Consensus 26 i~IiP~f~~~~~~lI~g~~GPF~ 48 (153)
.+|.|||+.+++.=..-+||||+
T Consensus 101 mei~PR~S~dklTgaDlSFGPvk 123 (284)
T COG3248 101 MEIEPRFSIDKLTGADLSFGPVK 123 (284)
T ss_pred EEeccceeeccccccccccccce
Confidence 68999999999876666788876
No 15
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=44.61 E-value=17 Score=28.49 Aligned_cols=19 Identities=42% Similarity=0.889 Sum_probs=15.5
Q ss_pred HHHHhcccCCceEeCCCCCCH
Q 048544 59 LAAALKKRGKCTIRPPQWMSI 79 (153)
Q Consensus 59 lAl~Lkk~~~C~I~pP~Wl~v 79 (153)
+|-.||+.++ |.+|+|.++
T Consensus 16 ~A~~LK~~~k--i~~P~W~~~ 34 (150)
T PRK09333 16 LAEYLKNVDE--IKPPEWAAF 34 (150)
T ss_pred HHHHHHhcCC--cCCCcchhh
Confidence 6889997777 899999654
No 16
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=44.22 E-value=12 Score=29.09 Aligned_cols=22 Identities=41% Similarity=0.767 Sum_probs=18.3
Q ss_pred HHHHhcccCCceEeCCCCCCHHHH
Q 048544 59 LAAALKKRGKCTIRPPQWMSIENL 82 (153)
Q Consensus 59 lAl~Lkk~~~C~I~pP~Wl~ve~L 82 (153)
+|..||+.++ +.+|.|.++=.+
T Consensus 18 ~asfLK~sgk--v~vp~~~DivKt 39 (143)
T KOG3411|consen 18 YASFLKRSGK--VEVPQWVDIVKT 39 (143)
T ss_pred HHHHHHhcCC--ccCcchhhhhhc
Confidence 7889999998 789999876544
No 17
>PRK13275 mtrF tetrahydromethanopterin S-methyltransferase subunit F; Provisional
Probab=40.81 E-value=39 Score=23.12 Aligned_cols=26 Identities=31% Similarity=0.569 Sum_probs=22.3
Q ss_pred cCHHHHHHHHHHHHHH-----HHHHHHHHHH
Q 048544 119 PDIYMVRSLIEDIRDV-----RLHKIETNLE 144 (153)
Q Consensus 119 ~~~~~ir~Li~DI~~i-----R~~Klr~gl~ 144 (153)
|+...|..+++||+.. |-.||-+|+.
T Consensus 8 P~m~~I~~~ve~i~Yk~qLiaR~~kL~SGv~ 38 (67)
T PRK13275 8 PNMSAIDNVVEDIRYKAQLIARNQKLESGVI 38 (67)
T ss_pred CChHHHHHHHHHHHHHHHHHhhcchhhHHhh
Confidence 5667899999999987 8899988875
No 18
>PF15614 WHIM3: WSTF, HB1, Itc1p, MBD9 motif 3
Probab=34.43 E-value=89 Score=19.81 Aligned_cols=28 Identities=25% Similarity=0.350 Sum_probs=21.5
Q ss_pred CHHHHHHHHH---HHHHHHHHHHHHHHHHhh
Q 048544 120 DIYMVRSLIE---DIRDVRLHKIETNLEKFS 147 (153)
Q Consensus 120 ~~~~ir~Li~---DI~~iR~~Klr~gl~~~~ 147 (153)
+++++..|++ |-+-+|..||++.++...
T Consensus 6 ~~e~ld~L~~aL~~prG~RE~~L~~~L~~~~ 36 (46)
T PF15614_consen 6 DPEELDELLKALENPRGKRESKLKKELDKHR 36 (46)
T ss_pred CHHHHHHHHHHHcCcccHhHHHHHHHHHHHh
Confidence 4566777776 558899999999988764
No 19
>smart00545 JmjN Small domain found in the jumonji family of transcription factors. To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).
Probab=34.39 E-value=22 Score=22.00 Aligned_cols=16 Identities=31% Similarity=0.725 Sum_probs=12.7
Q ss_pred HHHhcccCCceEeCCC
Q 048544 60 AAALKKRGKCTIRPPQ 75 (153)
Q Consensus 60 Al~Lkk~~~C~I~pP~ 75 (153)
.-.-++-|.|+|+||.
T Consensus 23 ~~~~~~yGi~KIvPP~ 38 (42)
T smart00545 23 RPQAEKYGICKVVPPK 38 (42)
T ss_pred HHHHhhCCEEEEECCC
Confidence 3446788999999995
No 20
>TIGR02507 MtrF tetrahydromethanopterin S-methyltransferase, F subunit. coenzyme M methyltransferase in methanogenic archaea. This methyltranferase is membrane-associated enzyme complex that uses methy-transfer reaction to drive sodium-ion pump. Archaea domain, have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=32.13 E-value=54 Score=22.31 Aligned_cols=26 Identities=31% Similarity=0.451 Sum_probs=21.8
Q ss_pred cCHHHHHHHHHHHHHH-----HHHHHHHHHH
Q 048544 119 PDIYMVRSLIEDIRDV-----RLHKIETNLE 144 (153)
Q Consensus 119 ~~~~~ir~Li~DI~~i-----R~~Klr~gl~ 144 (153)
|+...|..+++||+.. |..||-+|+.
T Consensus 8 P~m~~I~~~ve~i~YK~qLiaR~~kL~SGv~ 38 (65)
T TIGR02507 8 PDIESIKSLVEAIDYRVQLITRDIGLASGVQ 38 (65)
T ss_pred CcHHHHHHHHHHHHHHHHHHhhccchhhhhh
Confidence 5667899999999987 8888888865
No 21
>PF11140 DUF2913: Protein of unknown function (DUF2913); InterPro: IPR021316 This family of proteins with unknown function appear to be restricted to Gammaproteobacteria.
Probab=30.12 E-value=1.5e+02 Score=23.95 Aligned_cols=71 Identities=20% Similarity=0.306 Sum_probs=50.1
Q ss_pred HHHHHHhcccCCceEeCCCCCCHHHHHHHHHHHhhCcCCcccCCchHHHHHHHHHhhhcCCCcCHHHHHHHHHHHHHH
Q 048544 57 LWLAAALKKRGKCTIRPPQWMSIENLTKVLEGEREDRGTFQAVPFHYIEISRLLFDHARDDIPDIYMVRSLIEDIRDV 134 (153)
Q Consensus 57 LWlAl~Lkk~~~C~I~pP~Wl~ve~L~~~l~~E~~~~~~f~~LP~~y~Eia~lLl~~a~dDi~~~~~ir~Li~DI~~i 134 (153)
=||+-.+|+++-=+.+ .+.|+.++.+=+.. ..-..|+..+-+|.+..-........+...+..+++.+.+.
T Consensus 39 ~WL~~alK~krF~k~v------~~dlk~ll~~gRs~-g~~a~L~~~L~~i~~~~~~~~~~~~~~~~~l~~~l~~L~~~ 109 (207)
T PF11140_consen 39 RWLKPALKQKRFSKLV------KKDLKWLLQQGRSK-GKNADLEQKLEYIWRLYSSGELSKQSDLFRLTAFLELLEEM 109 (207)
T ss_pred HHHHHHHcCcccchhH------HHHHHHHHHhCCCC-CCcccHHHHHHHHHHHHhcccccccCCHHHHHHHHHHHHHc
Confidence 4999999999987777 66899988888754 34578888888888765322223334456777777777653
No 22
>PF12166 DUF3595: Protein of unknown function (DUF3595); InterPro: IPR021999 This family of proteins is functionally uncharacterised.This family of proteins is found in eukaryotes. Proteins in this family are typically between 578 and 2525 amino acids in length.
Probab=27.54 E-value=50 Score=29.01 Aligned_cols=23 Identities=22% Similarity=0.283 Sum_probs=21.4
Q ss_pred CCCcCHHHHHHHHHHHHHHHHHH
Q 048544 116 DDIPDIYMVRSLIEDIRDVRLHK 138 (153)
Q Consensus 116 dDi~~~~~ir~Li~DI~~iR~~K 138 (153)
||+|++|.+-.|.+||.=+|..+
T Consensus 371 eelp~~d~ll~lc~dI~~aRe~g 393 (422)
T PF12166_consen 371 EELPNPDRLLKLCQDIYLAREEG 393 (422)
T ss_pred cCCCChHHHHHHHHHHHHHHhcC
Confidence 99999999999999999999754
No 23
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=27.26 E-value=89 Score=24.48 Aligned_cols=45 Identities=24% Similarity=0.497 Sum_probs=28.1
Q ss_pred HHHHHhcccCCceEeCCCCCCHHHHHHHHHHHhhCcCCcccCC--chHHHHHHHHHh
Q 048544 58 WLAAALKKRGKCTIRPPQWMSIENLTKVLEGEREDRGTFQAVP--FHYIEISRLLFD 112 (153)
Q Consensus 58 WlAl~Lkk~~~C~I~pP~Wl~ve~L~~~l~~E~~~~~~f~~LP--~~y~Eia~lLl~ 112 (153)
-+|-.||..+ +|.||+|-. ..+.=-..| ..|.. |+|.--|.+|=+
T Consensus 15 ~lA~~LK~~~--kv~pP~wa~--~vKTG~~kE------~~P~~~DWwY~RaASilRk 61 (147)
T COG2238 15 ALASYLKETG--KVKPPEWAD--IVKTGVHKE------RPPEQEDWWYVRAASILRK 61 (147)
T ss_pred HHHHHHHhcC--CcCChhhhh--hhhcccccc------CCCCCCchHHHHHHHHHHH
Confidence 5788999998 699999944 333322233 23333 567766766543
No 24
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=25.15 E-value=1.1e+02 Score=20.49 Aligned_cols=30 Identities=13% Similarity=0.264 Sum_probs=17.3
Q ss_pred CCcCHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 048544 117 DIPDIYMVRSLIEDIRDVRLHKIETNLEKF 146 (153)
Q Consensus 117 Di~~~~~ir~Li~DI~~iR~~Klr~gl~~~ 146 (153)
|.|.++.++.+++.+..-...+++..+..+
T Consensus 1 ~~p~~~~i~~i~~~~~~~~~~~~~~~~~~l 30 (89)
T PF08542_consen 1 DWPPPEVIEEILESCLNGDFKEARKKLYEL 30 (89)
T ss_dssp TS--HHHHHHHHHHHHHTCHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 345556666666666666666666665554
No 25
>PF10835 DUF2573: Protein of unknown function (DUF2573); InterPro: IPR020393 This entry contains proteins with no known function.
Probab=25.10 E-value=1.3e+02 Score=21.28 Aligned_cols=29 Identities=24% Similarity=0.416 Sum_probs=23.0
Q ss_pred HHhhhcCCCcCH-HHHHHHHHHHHHHHHHH
Q 048544 110 LFDHARDDIPDI-YMVRSLIEDIRDVRLHK 138 (153)
Q Consensus 110 Ll~~a~dDi~~~-~~ir~Li~DI~~iR~~K 138 (153)
|-.|..+..|++ ++||.+|++|++.-.++
T Consensus 47 L~kHWN~~~PeaK~~ik~li~~Ik~lNe~~ 76 (82)
T PF10835_consen 47 LAKHWNGTYPEAKEEIKELIEEIKQLNEAH 76 (82)
T ss_pred HHHhhcccCchHHHHHHHHHHHHHHHHHHH
Confidence 566777888886 79999999999875543
No 26
>PF01788 PsbJ: PsbJ; InterPro: IPR002682 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbJ found in PSII. PsbJ is one of the most hydrophobic proteins in the thylakoid membrane, and is located in a gene cluster with PsbE, PsbF and PsbL (PsbEFJL). Both PsbJ and PsbL (IPR003372 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbJ cause the light-harvesting antenna to remain detached from the PSII dimers []. In addition, both PsbJ and PsbL are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_J 3ARC_J 3A0B_J 3KZI_J 2AXT_J 3PRQ_J 4FBY_b 3BZ2_J 1S5L_j 3PRR_J ....
Probab=23.15 E-value=34 Score=21.18 Aligned_cols=8 Identities=50% Similarity=1.348 Sum_probs=5.1
Q ss_pred chhhHHHH
Q 048544 53 VKVPLWLA 60 (153)
Q Consensus 53 ~~VPLWlA 60 (153)
-++|||+.
T Consensus 6 GRIPLWlV 13 (40)
T PF01788_consen 6 GRIPLWLV 13 (40)
T ss_dssp TSS-HHHH
T ss_pred CcccchHH
Confidence 36899984
No 27
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=22.92 E-value=75 Score=21.43 Aligned_cols=36 Identities=8% Similarity=-0.122 Sum_probs=26.4
Q ss_pred cccCCceEeCCCCCCHHHHHHHHHHHhhCcCCcccC
Q 048544 64 KKRGKCTIRPPQWMSIENLTKVLEGEREDRGTFQAV 99 (153)
Q Consensus 64 kk~~~C~I~pP~Wl~ve~L~~~l~~E~~~~~~f~~L 99 (153)
...+...+..+...+|+.|++.++....-+...+.|
T Consensus 10 ~~~~t~~l~v~~~~TV~~lK~kI~~~~gip~~~QrL 45 (75)
T cd01799 10 SHTVTIWLTVRPDMTVAQLKDKVFLDYGFPPAVQRW 45 (75)
T ss_pred cCCCeEEEEECCCCcHHHHHHHHHHHHCcCHHHEEE
Confidence 445667788889999999999998776554444455
No 28
>COG1516 FliS Flagellin-specific chaperone FliS [Cell motility and secretion / Intracellular trafficking and secretion / Posttranslational modification, protein turnover, chaperones]
Probab=22.77 E-value=74 Score=24.45 Aligned_cols=54 Identities=22% Similarity=0.298 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhhCcCCcccCCchHHHHHH-HHHhhhcCCCcCHHHHHHHHHHHHHH
Q 048544 80 ENLTKVLEGEREDRGTFQAVPFHYIEISR-LLFDHARDDIPDIYMVRSLIEDIRDV 134 (153)
Q Consensus 80 e~L~~~l~~E~~~~~~f~~LP~~y~Eia~-lLl~~a~dDi~~~~~ir~Li~DI~~i 134 (153)
..|...|+.|+-. +--..|---|--+.+ ++-.+...|....++|..+++++++.
T Consensus 62 ~eL~~~Ld~E~Gg-eia~nL~~LY~y~~~rL~~ANl~nd~~~i~eV~~ll~~l~ea 116 (132)
T COG1516 62 TELRASLDYEKGG-EIAQNLDALYDYMVRRLVQANLKNDASKIDEVIGLLRELREA 116 (132)
T ss_pred HHHHHhcCHhhcc-hHHHHHHHHHHHHHHHHHHHHhccCHHHHHHHHHHHHHHHHH
Confidence 4677777777643 223444432333344 44445678888899999999999886
No 29
>PRK15070 propanediol utilization phosphotransacylase; Provisional
Probab=22.54 E-value=66 Score=26.64 Aligned_cols=39 Identities=26% Similarity=0.399 Sum_probs=29.2
Q ss_pred hcCceeEEe-eCCCCCccceeccccccCCCCCcchhhHHHHHHh
Q 048544 21 AEDELVEIV-PNMRMDPLNFICGDFGPFYPQIPVKVPLWLAAAL 63 (153)
Q Consensus 21 ae~e~i~Ii-P~f~~~~~~lI~g~~GPF~p~~~~~VPLWlAl~L 63 (153)
|-+|.|+|+ |+-.++++..+ ||.|+...++|-.==|..|
T Consensus 64 A~~E~Vtl~GPKG~i~~VriL----GP~R~~tQVEiS~TDa~~L 103 (211)
T PRK15070 64 AAEETVTLVGPKGVIENVRIL----GPLRKKTQVEISRTDAFKL 103 (211)
T ss_pred hhceEEEEEcCCccccCeEEe----CCCCCCceEEEEehhhHhh
Confidence 445566766 99999999887 9999998888765554444
No 30
>PF14821 Thr_synth_N: Threonine synthase N terminus; PDB: 3V7N_A 1VB3_A 1KL7_A.
Probab=21.44 E-value=1.3e+02 Score=20.43 Aligned_cols=29 Identities=28% Similarity=0.513 Sum_probs=20.8
Q ss_pred chHHHHHHHHHhhhc-CCCcCHHHHHHHHHH
Q 048544 101 FHYIEISRLLFDHAR-DDIPDIYMVRSLIED 130 (153)
Q Consensus 101 ~~y~Eia~lLl~~a~-dDi~~~~~ir~Li~D 130 (153)
..|-|+|..+++.-- +|+++ ++++.+|++
T Consensus 48 ~sy~elA~~il~~f~~~di~~-~~L~~ii~~ 77 (79)
T PF14821_consen 48 LSYAELAFEILSPFLGDDIPE-EELKEIIEK 77 (79)
T ss_dssp S-HHHHHHHHHHHHCCCCS-H-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHccCCCH-HHHHHHHHH
Confidence 368999999998765 88875 677777764
No 31
>TIGR00208 fliS flagellar biosynthetic protein FliS. The function of this protein in flagellar biosynthesis is unknown, but appears to be regulatory. The member of this family in Vibrio parahaemolyticus is designated FlaJ (creating a synonym for FliS) and was shown essential for flagellin biosynthesis.
Probab=20.96 E-value=50 Score=24.53 Aligned_cols=54 Identities=20% Similarity=0.286 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhhCcCCcccCCchHHHHHHHHHh-hhcCCCcCHHHHHHHHHHHHHH
Q 048544 80 ENLTKVLEGEREDRGTFQAVPFHYIEISRLLFD-HARDDIPDIYMVRSLIEDIRDV 134 (153)
Q Consensus 80 e~L~~~l~~E~~~~~~f~~LP~~y~Eia~lLl~-~a~dDi~~~~~ir~Li~DI~~i 134 (153)
..|...|+.|+.. +--..|-.-|--+.+.|.+ +...|....++++.++++|++.
T Consensus 62 ~eL~~~Ld~e~gg-eiA~nL~~LY~y~~~~L~~An~~~d~~~l~ev~~~l~~Lr~a 116 (124)
T TIGR00208 62 QELNFTLDREKNI-ELSASLGALYDYMYRRLVQANIKNDTSKLAEVEGYVRDFRDA 116 (124)
T ss_pred HHHHhhcCCccch-HHHHHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHH
Confidence 4455555555432 1223444333333444433 3457777789999999999875
Done!