Query psy1865
Match_columns 152
No_of_seqs 115 out of 524
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 18:18:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1865.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1865hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1521|consensus 100.0 1.2E-50 2.5E-55 339.1 13.0 137 15-151 133-273 (338)
2 cd07032 RNAP_I_II_AC40 AC40 su 100.0 1.7E-45 3.6E-50 310.1 15.8 137 8-144 81-218 (291)
3 KOG1522|consensus 100.0 2.5E-34 5.4E-39 235.9 6.7 124 7-145 87-215 (285)
4 cd07031 RNAP_II_RPB3 RPB3 subu 100.0 7.4E-31 1.6E-35 218.6 12.9 103 8-125 84-192 (265)
5 PRK00783 DNA-directed RNA poly 99.9 1.5E-27 3.3E-32 197.2 10.5 108 9-145 84-191 (263)
6 cd07030 RNAP_D D subunit of Ar 99.9 2.8E-27 6.1E-32 195.3 11.2 108 9-145 84-191 (259)
7 smart00662 RPOLD RNA polymeras 99.9 8.6E-26 1.9E-30 183.8 7.9 111 7-143 70-180 (224)
8 cd07028 RNAP_RPB3_like RPB3 su 99.9 2.3E-25 4.9E-30 180.6 9.0 91 7-115 84-174 (212)
9 PF01000 RNA_pol_A_bac: RNA po 99.7 3.2E-18 7E-23 125.2 7.1 70 8-104 43-112 (112)
10 COG0202 RpoA DNA-directed RNA 99.7 5.5E-17 1.2E-21 138.6 6.0 127 8-138 101-227 (317)
11 PRK14979 DNA-directed RNA poly 99.6 5E-16 1.1E-20 124.9 7.9 76 14-119 77-152 (195)
12 cd06928 RNAP_alpha_NTD N-termi 99.1 4.5E-10 9.7E-15 91.3 8.8 76 12-115 81-173 (215)
13 PRK05182 DNA-directed RNA poly 99.0 8.1E-10 1.8E-14 94.3 7.5 73 15-115 93-181 (310)
14 TIGR02027 rpoA DNA-directed RN 98.7 9.8E-08 2.1E-12 81.1 8.5 62 44-115 86-164 (297)
15 CHL00013 rpoA RNA polymerase a 96.5 0.016 3.5E-07 50.2 8.4 61 44-115 106-180 (327)
16 PRK15449 ferredoxin-like prote 81.3 1.7 3.7E-05 31.4 2.9 39 109-147 14-55 (95)
17 COG2440 FixX Ferredoxin-like p 79.2 1.3 2.9E-05 32.3 1.8 37 114-150 24-62 (99)
18 COG0202 RpoA DNA-directed RNA 57.4 25 0.00054 30.4 5.2 48 68-115 114-178 (317)
19 PF04775 Bile_Hydr_Trans: Acyl 45.7 41 0.00089 24.9 4.2 41 74-119 6-46 (126)
20 PF04225 OapA: Opacity-associa 42.0 7.9 0.00017 27.0 -0.2 19 74-92 37-55 (85)
21 KOG1101|consensus 36.0 9.8 0.00021 29.5 -0.5 11 98-108 72-82 (147)
22 PF11604 CusF_Ec: Copper bindi 35.6 34 0.00073 22.8 2.2 26 70-95 33-58 (70)
23 PF01835 A2M_N: MG2 domain; I 35.4 38 0.00082 23.1 2.5 18 80-97 11-28 (99)
24 smart00110 C1Q Complement comp 30.6 1.1E+02 0.0024 22.8 4.5 20 73-92 93-112 (135)
25 PF07679 I-set: Immunoglobulin 28.6 97 0.0021 19.9 3.5 26 78-104 10-35 (90)
26 COG3592 Uncharacterized conser 28.5 45 0.00097 23.1 1.8 22 122-143 51-72 (74)
27 cd02198 YjgH_like YjgH belongs 27.4 57 0.0012 23.1 2.3 26 69-94 85-111 (111)
28 cd04473 S1_RecJ_like S1_RecJ_l 27.2 97 0.0021 20.4 3.3 27 78-106 51-77 (77)
29 cd05735 Ig8_DSCAM Eight immuno 26.4 92 0.002 20.9 3.2 20 83-103 1-20 (88)
30 TIGR03610 RutC pyrimidine util 26.2 79 0.0017 23.2 3.0 27 69-95 101-127 (127)
31 PRK10665 nitrogen regulatory p 25.8 1.3E+02 0.0028 22.0 4.0 45 88-132 28-74 (112)
32 PF13099 DUF3944: Domain of un 25.1 20 0.00043 21.5 -0.4 24 111-134 1-24 (35)
33 cd05724 Ig2_Robo Second immuno 24.8 87 0.0019 20.1 2.7 25 79-103 7-31 (86)
34 TIGR00004 endoribonuclease L-P 24.6 63 0.0014 23.2 2.2 26 69-94 99-124 (124)
35 PF00386 C1q: C1q domain; Int 22.9 97 0.0021 22.1 2.9 25 72-96 87-111 (127)
36 PRK11401 putative endoribonucl 22.7 88 0.0019 22.8 2.7 27 69-95 102-128 (129)
37 PF05187 ETF_QO: Electron tran 21.9 52 0.0011 24.3 1.3 15 131-145 95-109 (110)
38 CHL00030 rpl23 ribosomal prote 20.3 70 0.0015 22.8 1.6 16 73-88 72-87 (93)
No 1
>KOG1521|consensus
Probab=100.00 E-value=1.2e-50 Score=339.13 Aligned_cols=137 Identities=54% Similarity=0.910 Sum_probs=133.7
Q ss_pred CeEEEEEEEEecCCCCC-ccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEe
Q psy1865 15 DTLQFQLKIKCTKSASF-SHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAV 93 (152)
Q Consensus 15 csV~f~L~V~c~~~~~~-~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~ 93 (152)
+|++|+|+|+|++++.+ ++++||..||.|+.|||+|++|.|+|.|.+.|.+..++|+++||+|+||||||+|+|+|||+
T Consensus 133 ntlvF~L~VkC~~n~~a~~~~sdpk~Ly~ns~vyS~~~~w~P~g~Q~~~f~e~~i~~~~~DILiAkLrPGQEI~le~hav 212 (338)
T KOG1521|consen 133 NTLVFKLNVKCTKNPNAKKDSSDPKELYNNSEVYSRDLTWKPKGYQAEIFAENPIRPVHDDILIAKLRPGQEIELEAHAV 212 (338)
T ss_pred ceEEEEEEeeccCCCCcccCCCChhHhccCcEEecCcceeccccchhhhcccCCccccCcceEEEecCCCCEeeeeeeee
Confidence 99999999999999999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEeccCCC---ceee
Q psy1865 94 KSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKKPN---AGVV 151 (152)
Q Consensus 94 kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~~~---a~v~ 151 (152)
|||||+||||||||||+||++|.|.|+.++.||+|++|++|||+|||+|+++++ |+|+
T Consensus 213 kGIGkdHAKfSPVaTAsYRLlP~I~l~~ei~ge~A~~lqkcfs~gVi~iee~~~kk~A~Va 273 (338)
T KOG1521|consen 213 KGIGKDHAKFSPVATASYRLLPTIVLLAEIEGEDAERLQKCFSPGVIDIEEMGGKKRAYVA 273 (338)
T ss_pred cccCcccccccCcccceeeccceeEecCcccchhHHHHHhhCCCCeEeeecCCCceEEEec
Confidence 999999999999999999999999999999999999999999999999999876 7664
No 2
>cd07032 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subun
Probab=100.00 E-value=1.7e-45 Score=310.13 Aligned_cols=137 Identities=55% Similarity=0.964 Sum_probs=131.4
Q ss_pred CCCCCCCCeEEEEEEEEecCCCCC-ccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEE
Q psy1865 8 KYEPCEQDTLQFQLKIKCTKSASF-SHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEI 86 (152)
Q Consensus 8 ~~~~c~~csV~f~L~V~c~~~~~~-~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I 86 (152)
++++|++|||+|+|+|+|++++.. +++++|.++|.+..|||+||+|.|.|.|...+.++++.|++++|+|+||++||+|
T Consensus 81 ~~~~~~~~~v~f~L~v~c~~~~~~~~~~~~~~~~~~~~~VyS~dl~~~p~g~q~~~~~~~~v~~v~~dI~I~kL~~gQ~l 160 (291)
T cd07032 81 DDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHKVYSGDLKWVPIGSQEKRFADNPIRPVHPDILIAKLRPGQEI 160 (291)
T ss_pred ccCCCCCcEEEEEEEEEccCCcccccccccccccccccEEECCCCEecCCCccccccCCCCcEEeCCCcEEEEECCCCEE
Confidence 578999999999999999988777 8888999999999999999999999999888889999999999999999999999
Q ss_pred EEEEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEecc
Q psy1865 87 DVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEK 144 (152)
Q Consensus 87 ~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~ 144 (152)
+|+|+|+||+||+||||||||+|+|||+|+|+|++++.++++++|+++||+|||++++
T Consensus 161 ~le~~a~kG~Gk~HAKwsPv~ta~yr~~P~I~i~~~~~~~~~~~~~~~cP~~Vf~i~~ 218 (291)
T cd07032 161 DLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPITGEDAEKLQKCFPPGVIDIEE 218 (291)
T ss_pred EEEEEEEcCcccccceecCceeEEEEecceEEEcCcCCHHHHHHHHhhCCCccEEecc
Confidence 9999999999999999999999999999999999999999999999999999999975
No 3
>KOG1522|consensus
Probab=100.00 E-value=2.5e-34 Score=235.92 Aligned_cols=124 Identities=27% Similarity=0.407 Sum_probs=96.5
Q ss_pred cCCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeE-----EeecCCCCCCCCCCCCcccCCCceEEEcC
Q psy1865 7 LKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQ-----WVPIGSQGDMYKSSDVGPIHDDILIAKLR 81 (152)
Q Consensus 7 ~~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~-----~~p~~~q~~~~~~~~~~p~~~~I~I~KL~ 81 (152)
+|+++|++|||.|+|+++|+.+++ .+|||+||. ..|+.+... ......+-+++|+|+|||
T Consensus 87 ~C~~~C~eCSVef~L~~kc~~d~T-------------~~VtsrDL~s~~~~v~pv~~~~~--~~~~~~~e~~gilI~KLR 151 (285)
T KOG1522|consen 87 ECDEFCPECSVEFTLDVKCTDDQT-------------RDVTSRDLVSLDPTVTPVDSNRG--SEIDDDSESKGILIVKLR 151 (285)
T ss_pred chhccCCcceEEEEEeeeecccce-------------eeeehHhhhccCCcccccccCCC--CccccccccCCcEEEEee
Confidence 489999999999999999998865 466666666 345543211 111123447899999999
Q ss_pred CCCEEEEEEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEeccC
Q psy1865 82 PGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKK 145 (152)
Q Consensus 82 ~GQ~I~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~ 145 (152)
+||+|+|+|+|+|||||+||||||+|++.|+|+|.+.+++.+..++...+.+--+...+++++.
T Consensus 152 kgQELkLra~akKGigKeHAKWsPta~V~FeYDPdn~lrhT~y~~e~~~~~Ewp~sk~~e~~~~ 215 (285)
T KOG1522|consen 152 KGQELKLRAIAKKGIGKEHAKWSPTAAVAFEYDPDNKLRHTLYWFEEDDLIEWPKSKNSELEED 215 (285)
T ss_pred cCCceeeeeeecccccccccccCCcceEEEEECccHhhhccCCCccccchhhCCcccccCCCCC
Confidence 9999999999999999999999999999999999999998877655544444445566777665
No 4
>cd07031 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=99.97 E-value=7.4e-31 Score=218.58 Aligned_cols=103 Identities=28% Similarity=0.420 Sum_probs=85.9
Q ss_pred CCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCc------ccCCCceEEEcC
Q psy1865 8 KYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVG------PIHDDILIAKLR 81 (152)
Q Consensus 8 ~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~------p~~~~I~I~KL~ 81 (152)
+++.|+.|++.|+|+|+|+++. ...|||+||+|.|.+.|... ...+. +++++|+|+||+
T Consensus 84 ~~~~~~~~~v~~~L~v~~~~~~-------------~~~V~s~Dl~~~~~~~~~~~--~~pi~~~~~~~~~~~~i~I~kL~ 148 (265)
T cd07031 84 CDEFCDKCSVELTLDVKCTGDQ-------------TREVTSRDLVSSGPKVNDVV--PVPIRNDSEDNGEEDGILIVKLR 148 (265)
T ss_pred ccCCCCCCeEEEEEEEEeccCC-------------CceEEHHHcccccccccccC--CcccccccccccCCCCeEEEEEC
Confidence 4567999999999999998753 26899999999876554421 11111 346899999999
Q ss_pred CCCEEEEEEEEeecCCcceeeeccceeEEeEeeeeeEEccccCh
Q psy1865 82 PGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEG 125 (152)
Q Consensus 82 ~GQ~I~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~ 125 (152)
|||+|+|+|+|+||+||+||||||||+|+|||+|+|+|+++..+
T Consensus 149 ~gq~i~le~~a~kG~Gk~HAKwsPv~~~~y~~~p~i~i~~~~~~ 192 (265)
T cd07031 149 KGQELKLRCIAKKGIGKEHAKWSPTAAVTFEYDPDNALRHTDYW 192 (265)
T ss_pred CCCEEEEEEEEECCEeccCCEeccceEEEEEEccceEEcccccc
Confidence 99999999999999999999999999999999999999976544
No 5
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=99.95 E-value=1.5e-27 Score=197.21 Aligned_cols=108 Identities=23% Similarity=0.501 Sum_probs=95.2
Q ss_pred CCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEE
Q psy1865 9 YEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDV 88 (152)
Q Consensus 9 ~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l 88 (152)
+++|++|++.|+|+++.+ ..|||+||++ .++.+.|++++|+|++|++||+|+|
T Consensus 84 ~~~~~~~~~~~~l~~~~~-----------------~~V~a~dl~~----------~~~~v~~v~~~~~I~~L~~~~~l~~ 136 (263)
T PRK00783 84 GEGCPDCTVTLSLEVEGP-----------------KTVYSGDLKS----------SDPDVKPVDPNIPIVKLKEGQKLVL 136 (263)
T ss_pred CCCCCCcEEEEEEEecCC-----------------CcEEcccccc----------CCCCceecCCCcEEEEeCCCCEEEE
Confidence 468999999999999832 4699999985 2456789999999999999999999
Q ss_pred EEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEeccC
Q psy1865 89 TMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKK 145 (152)
Q Consensus 89 ~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~ 145 (152)
+|+|+||+|++||||||+++++||+.|.|.+.+.+.+ +..+++.||.++|.++++
T Consensus 137 e~~~~~G~G~~HAKw~p~~~~~yr~~p~I~i~~~C~~--C~~C~~~CP~~vi~~~~~ 191 (263)
T PRK00783 137 EAYARLGRGKEHAKWQPGSACGYKYYPRIEVSEDCDE--CEKCVEACPRGVLELKEG 191 (263)
T ss_pred EEEEEcCcccccCccCcceEeeecccccccccccCCc--hHHHHHhCCccccEecCC
Confidence 9999999999999999999999999999999555543 778999999999999764
No 6
>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=99.95 E-value=2.8e-27 Score=195.26 Aligned_cols=108 Identities=25% Similarity=0.480 Sum_probs=97.4
Q ss_pred CCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEE
Q psy1865 9 YEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDV 88 (152)
Q Consensus 9 ~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l 88 (152)
...|+.|++.|+|+++++ ..|||+||+| .+..+.|++++|+|+||++||+|+|
T Consensus 84 ~~~~~~~~~~~~l~~~~~-----------------~~v~s~dl~~----------~~~~v~~~~~~~~I~~l~~~~~l~~ 136 (259)
T cd07030 84 GAGCPLCTVTLTLSVEGP-----------------GTVYSGDLKS----------SDPDVKPVYDNIPIVKLGKGQKLVL 136 (259)
T ss_pred CCCCCCcEEEEEEEccCC-----------------ceEEcccccc----------CCCCccccCCCcEEEEeCCCCEEEE
Confidence 467889999999999854 4699999987 3456789999999999999999999
Q ss_pred EEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEeccC
Q psy1865 89 TMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIEKK 145 (152)
Q Consensus 89 ~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~ 145 (152)
+++|+||+||+||||+|+++++||++|.|.+++.+.+ +..+++.||.++|.++++
T Consensus 137 ~~~~~kg~g~~hakw~p~~~~~yr~~P~i~i~~~C~~--C~~C~~~CP~~vi~~d~~ 191 (259)
T cd07030 137 EAYARLGRGKEHAKWQPTTACGYKYYPVIEIDEDCDG--CGKCVEECPRGVLELEEG 191 (259)
T ss_pred EEEEecCccCCCCCCCCccEEEEEeecceechhhCCC--hHHHHHhCCccceEccCC
Confidence 9999999999999999999999999999999987765 778999999999998764
No 7
>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=99.92 E-value=8.6e-26 Score=183.79 Aligned_cols=111 Identities=31% Similarity=0.384 Sum_probs=100.3
Q ss_pred cCCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEE
Q psy1865 7 LKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEI 86 (152)
Q Consensus 7 ~~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I 86 (152)
+|+.+|+.|++.|+|+++|+ ..|||+||+|. .|+.+.|++++|+|++|++||+|
T Consensus 70 ~~~~~~~~~~~~~~L~~~gp-----------------~~V~a~Dl~~~---------~~~~v~~vnp~~~I~~L~~gq~l 123 (224)
T smart00662 70 ECEEGCEKCSVTLTLDVKGP-----------------GEVTAGDLKSD---------SDPDVEIVNPDIPIAKLREGQEL 123 (224)
T ss_pred cccccCCCceEEEEEEEEcC-----------------CcEEHHHcccC---------CCCCcEEeCCCcEEEEECCCCEE
Confidence 46789999999999999965 35999999972 15578899999999999999999
Q ss_pred EEEEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCccEEec
Q psy1865 87 DVTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPGVISIE 143 (152)
Q Consensus 87 ~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~ 143 (152)
+++++|+||+|++||||+|+++++|++.|.|.++..+++.++..+...||++++..+
T Consensus 124 ~~e~~~~~G~G~~hak~~p~~~~~~~~~~~i~id~~~~pv~~v~~~~~~~~~~~~~~ 180 (224)
T smart00662 124 ELEARAEKGRGYVHAKWSPVSTVEYRYIPRIPVDASFSPVDRVAYQVECPRVVQRTD 180 (224)
T ss_pred EEEEEEECCcccccCccccccCCCcCcCCEEEECCCCChhhheeeeccCCccceecc
Confidence 999999999999999999999999999999999998888888889999999888765
No 8
>cd07028 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and
Probab=99.92 E-value=2.3e-25 Score=180.64 Aligned_cols=91 Identities=35% Similarity=0.500 Sum_probs=79.5
Q ss_pred cCCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEE
Q psy1865 7 LKYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEI 86 (152)
Q Consensus 7 ~~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I 86 (152)
++...|+.|++.|+|+++++.+ .+..|||+||+|.+.+. +++.+.|++++|+|+||++||+|
T Consensus 84 ~~~~~~~~~~v~~~l~~~g~~~-------------~~~~V~s~DL~~~~~~~-----~~~~v~pv~~di~I~kL~~gq~i 145 (212)
T cd07028 84 ECEDHCDKCSVVLTLQAFAESE-------------STTNVYSKDLVIVSNLM-----GRNIGHPIIQDILICKLRKGQEI 145 (212)
T ss_pred cccccccceeEEEEEEccCCCC-------------CcceEEHHHcccCCccc-----cCCCeEEeCCCcEEEEECCCCEE
Confidence 3567788899999999997653 12579999999965443 34678899999999999999999
Q ss_pred EEEEEEeecCCcceeeeccceeEEeEeee
Q psy1865 87 DVTMFAVKSIGRDHAKFSPVATAFYRLLP 115 (152)
Q Consensus 87 ~l~~~A~kGiGk~HAKwsPv~~~~yr~~P 115 (152)
+|+|+|+||+|++|||||||++++|+++|
T Consensus 146 ~le~~~~~G~G~~hAk~sPV~~v~y~~~~ 174 (212)
T cd07028 146 KLTCVAKKGIGKEHAKFGPVAAIEFRYDP 174 (212)
T ss_pred EEEEEEECCCcCCCCEeCCceEEEEEEEc
Confidence 99999999999999999999999999999
No 9
>PF01000 RNA_pol_A_bac: RNA polymerase Rpb3/RpoA insert domain; InterPro: IPR011262 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha (RpoA) subunit homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. The dimerisation domains differ between the different subunit families. In eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain is comprised of a central insert domain, which interrupts an Rpb11-like domain (IPR009025 from INTERPRO), dividing it into two halves []. In eukaryotic Rpb11 and archaeal L subunits, the insert domain is lacking, leaving the Rpb11-like domain intact and contiguous.; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_O 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3GTK_C 1TWH_C 3HOV_C 3S17_C ....
Probab=99.75 E-value=3.2e-18 Score=125.21 Aligned_cols=70 Identities=31% Similarity=0.516 Sum_probs=63.4
Q ss_pred CCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEE
Q psy1865 8 KYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEID 87 (152)
Q Consensus 8 ~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~ 87 (152)
++.+|+.|++.|.|+++|+. .|||+||++ .+..+++++++++|++|++||+|+
T Consensus 43 ~~~~~~~~~~~~~L~~~g~~-----------------~V~a~di~~----------~~~~i~ivn~d~~I~tl~~~~~l~ 95 (112)
T PF01000_consen 43 CEEGCDDCSVTFSLKVKGPG-----------------EVTAGDIKL----------EPSGIEIVNPDIYIATLSEGQKLE 95 (112)
T ss_dssp SSSSTTTSEEEEEEEEESSS-----------------CEEGGGSEE----------SBTTEEESSTTSEEEEEESSTEEE
T ss_pred cccCCCCceEEEEEEecCCC-----------------ccccceeEe----------cCCceEEecCCeEEEEECCCCEEE
Confidence 56899999999999999763 499999998 356678999999999999999999
Q ss_pred EEEEEeecCCcceeeec
Q psy1865 88 VTMFAVKSIGRDHAKFS 104 (152)
Q Consensus 88 l~~~A~kGiGk~HAKws 104 (152)
|+|+|++|+|+.|||||
T Consensus 96 ~e~~i~~G~Gy~~ak~~ 112 (112)
T PF01000_consen 96 MELYIEKGRGYVHAKWS 112 (112)
T ss_dssp EEEEEEEEESEECCTS-
T ss_pred EEEEEECCCcccccccC
Confidence 99999999999999997
No 10
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=99.67 E-value=5.5e-17 Score=138.57 Aligned_cols=127 Identities=15% Similarity=0.140 Sum_probs=110.5
Q ss_pred CCCCCCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEE
Q psy1865 8 KYEPCEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEID 87 (152)
Q Consensus 8 ~~~~c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~ 87 (152)
|+.+|..|++.++|+|.|+...-+ +-+++.+++....||++++.|-+.+.+ ..++++.|+..|+++++|+++|.+.
T Consensus 101 g~v~a~d~~~~~~lEv~np~~~ia-~~~~~~~l~~~~~V~~G~gyv~~~~~~---~~~~~v~~i~~D~~~spv~kvqy~v 176 (317)
T COG0202 101 GEVTASDITVPLDLEVVNPDHVIA-TLTEDAKLEMELRVYSGDGYVPAEGNR---EDDPPVGPIAVDAPFSPVRKVQYIV 176 (317)
T ss_pred ccccHhhcccceeEEEECCCceee-eccCCcceEEEEEEEcCccEecccccc---ccCCCceeeeCCCceeeeeeceEEE
Confidence 566899999999999999866443 223367778889999999999665555 3667889999999999999999999
Q ss_pred EEEEEeecCCcceeeeccceeEEeEeeeeeEEccccChHHHHHHHhhCCCc
Q psy1865 88 VTMFAVKSIGRDHAKFSPVATAFYRLLPKITLTQEIEGEMAQRLQTMFSPG 138 (152)
Q Consensus 88 l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i~~~~~~~~~~~~~~~cp~~ 138 (152)
++|+|.+|+|++||||+|++..+|+++|.+.+-..+..++...++++||..
T Consensus 177 e~~r~~~~~~~Dhl~~~~~T~gsi~~~~a~~~aa~il~e~~~~~~~~~~~~ 227 (317)
T COG0202 177 EEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKA 227 (317)
T ss_pred EeEEEeccCCceeEEEEEeeccEeehHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 999999999999999999999999999988887778788999999999976
No 11
>PRK14979 DNA-directed RNA polymerase subunit D; Provisional
Probab=99.64 E-value=5e-16 Score=124.86 Aligned_cols=76 Identities=22% Similarity=0.440 Sum_probs=62.6
Q ss_pred CCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEe
Q psy1865 14 QDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAV 93 (152)
Q Consensus 14 ~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~ 93 (152)
.+++.|+|+++.+ ..|||+||++ .+. .|++++++|++|++||+|+|+|+|+
T Consensus 77 ~~~~~l~L~~~gp-----------------~~Vta~Di~~----------~~~--~ivnpdi~I~tL~~g~~l~~e~~~~ 127 (195)
T PRK14979 77 DEVITFTLSKEGP-----------------CTVYSSDLKS----------ENG--EVAFKNIPIVKLAEGQKLEIECEAL 127 (195)
T ss_pred CCcEEEEEEEeCC-----------------ceEEHHHcCC----------CCC--cccCCCcEEEEECCCCEEEEEEEEE
Confidence 4688999988621 4699999986 222 4789999999999999999999999
Q ss_pred ecCCcceeeeccceeEEeEeeeeeEE
Q psy1865 94 KSIGRDHAKFSPVATAFYRLLPKITL 119 (152)
Q Consensus 94 kGiGk~HAKwsPv~~~~yr~~P~i~i 119 (152)
+|+|++||||+|+ .+.|++.+.=++
T Consensus 128 ~G~Gy~hAk~~pv-da~y~~~~~dkl 152 (195)
T PRK14979 128 VGTGKIHAKWQPC-NAVYKQISNDEV 152 (195)
T ss_pred CCCccccccccce-eeEEecCCCcEE
Confidence 9999999999995 567877765444
No 12
>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=99.09 E-value=4.5e-10 Score=91.27 Aligned_cols=76 Identities=26% Similarity=0.300 Sum_probs=65.7
Q ss_pred CCCCeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEE
Q psy1865 12 CEQDTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMF 91 (152)
Q Consensus 12 c~~csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~ 91 (152)
|.+|++.++|+++++ ..|||+||.+ +..+.+++++++|++|.+||+|+++|+
T Consensus 81 ~~~~~~~~~l~~~gp-----------------~~V~a~Di~~-----------~~~i~ivnp~~~IatL~~~~~l~ie~~ 132 (215)
T cd06928 81 SEDEPQVLRLKVKGP-----------------GVVTAADIEL-----------PSGVEIVNPDQYIATLTEDASLEMELR 132 (215)
T ss_pred CCCceEEEEEEEecC-----------------eEEEhHhcCc-----------CCCcEEeCCCcEEEEECCCCEEEEEEE
Confidence 447899999999843 4699999986 224789999999999999999999999
Q ss_pred EeecCCcceeee-----------------ccceeEEeEeee
Q psy1865 92 AVKSIGRDHAKF-----------------SPVATAFYRLLP 115 (152)
Q Consensus 92 A~kGiGk~HAKw-----------------sPv~~~~yr~~P 115 (152)
|++|+|+.+|+| |||--+.|....
T Consensus 133 i~~G~Gy~~~~~~~~~~~~~~~~~iDa~f~PV~~vny~v~~ 173 (215)
T cd06928 133 IEKGRGYVPAEENKSEEKPIGFIPIDAIFSPVRKVNYSVES 173 (215)
T ss_pred EECcCcceeccccccccCCCceEEeCCCcCCeEEEEEEEEE
Confidence 999999999988 899989897554
No 13
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=99.01 E-value=8.1e-10 Score=94.30 Aligned_cols=73 Identities=26% Similarity=0.397 Sum_probs=62.5
Q ss_pred CeEEEEEEEEecCCCCCccCCCcccccccceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEee
Q psy1865 15 DTLQFQLKIKCTKSASFSHSSHADDMYEKHKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVK 94 (152)
Q Consensus 15 csV~f~L~V~c~~~~~~~~~~~~~~~~~~~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~k 94 (152)
|++.++|+++++ ..|||+||.+ ++.+.|++++++|++|++||+|+++++|++
T Consensus 93 ~~~~~~l~~~gp-----------------~~VtA~Di~~-----------~~~v~ivn~d~~IatL~~~~~l~ie~~~~k 144 (310)
T PRK05182 93 EPVTLTLSKKGP-----------------GEVTAGDIET-----------DGDVEIVNPDLVIATLNEGAKLEMELTVER 144 (310)
T ss_pred ceEEEEEEecCC-----------------eEEEHHHcCC-----------CCCcEEeCCCeEEEEECCCCEEEEEEEEEC
Confidence 899999999732 4799999985 234789999999999999999999999999
Q ss_pred cCCcceee----------------eccceeEEeEeee
Q psy1865 95 SIGRDHAK----------------FSPVATAFYRLLP 115 (152)
Q Consensus 95 GiGk~HAK----------------wsPv~~~~yr~~P 115 (152)
|+|..+|+ |+||.-+.|...+
T Consensus 145 G~Gy~~~~~~~~~~~~g~i~iDa~f~PV~~vny~ve~ 181 (310)
T PRK05182 145 GRGYVPAEENKEDAPIGRIPVDAIFSPVKKVNYTVEN 181 (310)
T ss_pred cCCCcccccccccCCcccEEecCCcCCccceEEEecc
Confidence 99987665 9999989996444
No 14
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=98.66 E-value=9.8e-08 Score=81.10 Aligned_cols=62 Identities=26% Similarity=0.332 Sum_probs=53.1
Q ss_pred ceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEeecCCccee-----------------eeccc
Q psy1865 44 HKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDHA-----------------KFSPV 106 (152)
Q Consensus 44 ~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~kGiGk~HA-----------------KwsPv 106 (152)
..|+++||+|. ++.+.++.++++|++|.+||+|++++++.+|+|..+| -||||
T Consensus 86 ~~VtA~Di~~~----------p~~ieivnpd~~IatL~~~~~L~iel~i~~G~Gy~~~~~~~~~~~~~~~i~iDa~FsPV 155 (297)
T TIGR02027 86 GVVTAGDIKAP----------PGDVEIVNPDLVIATLTEPADLEIELRVERGRGYVPAEENREEDRPVGVIAVDAIFSPV 155 (297)
T ss_pred EEEEhhhcccC----------CCCcEEeCCCeEEEEECCCCEEEEEEEEEcccccCcccccccccCccccccccccccCe
Confidence 57999999973 3457889999999999999999999999999997544 49999
Q ss_pred eeEEeEeee
Q psy1865 107 ATAFYRLLP 115 (152)
Q Consensus 107 ~~~~yr~~P 115 (152)
--+.|....
T Consensus 156 ~~Vny~ve~ 164 (297)
T TIGR02027 156 LKVNYEVEN 164 (297)
T ss_pred EEEEEEEee
Confidence 989997654
No 15
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=96.48 E-value=0.016 Score=50.20 Aligned_cols=61 Identities=21% Similarity=0.276 Sum_probs=53.2
Q ss_pred ceeeecCeEEeecCCCCCCCCCCCCcccCCCceEEEcCCCCEEEEEEEEeecCCcc--------------eeeeccceeE
Q psy1865 44 HKVFTKDIQWVPIGSQGDMYKSSDVGPIHDDILIAKLRPGHEIDVTMFAVKSIGRD--------------HAKFSPVATA 109 (152)
Q Consensus 44 ~~V~S~dL~~~p~~~q~~~~~~~~~~p~~~~I~I~KL~~GQ~I~l~~~A~kGiGk~--------------HAKwsPv~~~ 109 (152)
..|+++|+.+ ++.+..+.++..|+.|..|+.|++++...+|.|-. -|-||||--+
T Consensus 106 ~~vtA~Di~~-----------p~~ieivnpd~~Iatl~~~~~l~~el~ie~G~GY~~~~~~~~~~g~i~iDa~FsPV~kV 174 (327)
T CHL00013 106 KYVTAQDIIL-----------PPSVEIVDPTQHIATITEPIDLEIELKIEKGRGYRLKTPKNFQDGSFPIDAVFMPVRNV 174 (327)
T ss_pred eEEEeeeecc-----------CCCeEEeCCCeEEEEeCCCCEEEEEEEEECccCceeccccccCCCcEEeCCCCCCeeEE
Confidence 5799999975 34578899999999999999999999999999984 3479999999
Q ss_pred EeEeee
Q psy1865 110 FYRLLP 115 (152)
Q Consensus 110 ~yr~~P 115 (152)
.|...+
T Consensus 175 ny~Ve~ 180 (327)
T CHL00013 175 NYSIHS 180 (327)
T ss_pred EEEEEE
Confidence 997776
No 16
>PRK15449 ferredoxin-like protein FixX; Provisional
Probab=81.32 E-value=1.7 Score=31.41 Aligned_cols=39 Identities=10% Similarity=0.240 Sum_probs=27.9
Q ss_pred EEeEe---eeeeEEccccChHHHHHHHhhCCCccEEeccCCC
Q psy1865 109 AFYRL---LPKITLTQEIEGEMAQRLQTMFSPGVISIEKKPN 147 (152)
Q Consensus 109 ~~yr~---~P~i~i~~~~~~~~~~~~~~~cp~~Vf~i~~~~~ 147 (152)
..|.. .|+|.++.+......+.+++.||.|+|..++.+.
T Consensus 14 ~~y~vd~~~~HI~i~~~~~~~~~k~C~~aCPagA~~~~e~G~ 55 (95)
T PRK15449 14 NKFNVDEEHPHIVVKADADKQALELLVKACPAGLYKKQDDGS 55 (95)
T ss_pred ceeECCCCCCcEEEcCCCCchhhhHHHHHCCHhhcEeCCCCC
Confidence 45653 4899998665445566789999999998765443
No 17
>COG2440 FixX Ferredoxin-like protein [Energy production and conversion]
Probab=79.23 E-value=1.3 Score=32.34 Aligned_cols=37 Identities=11% Similarity=0.140 Sum_probs=25.6
Q ss_pred eeeeEEccccChHHH--HHHHhhCCCccEEeccCCCcee
Q psy1865 114 LPKITLTQEIEGEMA--QRLQTMFSPGVISIEKKPNAGV 150 (152)
Q Consensus 114 ~P~i~i~~~~~~~~~--~~~~~~cp~~Vf~i~~~~~a~v 150 (152)
.|+|.++++-.-... +.+.+.||.|+|...+.++..+
T Consensus 24 ~pHI~v~~~~~~~~~~~~~l~~aCPA~~Y~~~~~g~l~~ 62 (99)
T COG2440 24 HPHIIVKDPDDCQECEDKPLIKACPAGCYKLIDDGKLRF 62 (99)
T ss_pred CCcEecCCchhhhhccchhhhhcCCHHHeeECCCCcEEE
Confidence 488998853222222 3688999999999988665443
No 18
>COG0202 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]
Probab=57.41 E-value=25 Score=30.44 Aligned_cols=48 Identities=23% Similarity=0.303 Sum_probs=37.9
Q ss_pred CcccCCCceEEEcCCCCEEEEEEEEeecCCcce-----------------eeeccceeEEeEeee
Q psy1865 68 VGPIHDDILIAKLRPGHEIDVTMFAVKSIGRDH-----------------AKFSPVATAFYRLLP 115 (152)
Q Consensus 68 ~~p~~~~I~I~KL~~GQ~I~l~~~A~kGiGk~H-----------------AKwsPv~~~~yr~~P 115 (152)
+.-+.++..|+.|..|-+|.++.+...|.|... |=|+||.-+.|.-..
T Consensus 114 lEv~np~~~ia~~~~~~~l~~~~~V~~G~gyv~~~~~~~~~~~v~~i~~D~~~spv~kvqy~ve~ 178 (317)
T COG0202 114 LEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNREDDPPVGPIAVDAPFSPVRKVQYIVEE 178 (317)
T ss_pred EEEECCCceeeeccCCcceEEEEEEEcCccEeccccccccCCCceeeeCCCceeeeeeceEEEEe
Confidence 344688999999999999999999999999874 236677766665443
No 19
>PF04775 Bile_Hydr_Trans: Acyl-CoA thioester hydrolase/BAAT N-terminal region; InterPro: IPR006862 This entry presents the N-termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) []. This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism []. For example, in peroxisomes, the hydrolase acts on bile-CoA esters [].; GO: 0016290 palmitoyl-CoA hydrolase activity, 0006629 lipid metabolic process; PDB: 3HLK_B 3K2I_B.
Probab=45.67 E-value=41 Score=24.89 Aligned_cols=41 Identities=22% Similarity=0.347 Sum_probs=25.3
Q ss_pred CceEEEcCCCCEEEEEEEEeecCCcceeeeccceeEEeEeeeeeEE
Q psy1865 74 DILIAKLRPGHEIDVTMFAVKSIGRDHAKFSPVATAFYRLLPKITL 119 (152)
Q Consensus 74 ~I~I~KL~~GQ~I~l~~~A~kGiGk~HAKwsPv~~~~yr~~P~i~i 119 (152)
.|-|.=|.|||++.|++...-.-| ..|+ |-|.|+-.+.=.+
T Consensus 6 ~I~v~GL~p~~~vtl~a~~~~~~g---~~w~--S~A~f~Ad~~G~V 46 (126)
T PF04775_consen 6 DIRVSGLPPGQEVTLRARLTDDNG---VQWQ--SYATFRADENGIV 46 (126)
T ss_dssp EEEEES--TT-EEEEEEEEE-TTS----EEE--EEEEEE--TTS-E
T ss_pred EEEEeCCCCCCEEEEEEEEEeCCC---CEEE--EEEEEEcCCCCeE
Confidence 588889999999999999986433 5787 4567877665444
No 20
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=41.99 E-value=7.9 Score=26.99 Aligned_cols=19 Identities=16% Similarity=0.480 Sum_probs=10.7
Q ss_pred CceEEEcCCCCEEEEEEEE
Q psy1865 74 DILIAKLRPGHEIDVTMFA 92 (152)
Q Consensus 74 ~I~I~KL~~GQ~I~l~~~A 92 (152)
.=.+.+|+|||+|.+..-.
T Consensus 37 ~k~L~~L~pGq~l~f~~d~ 55 (85)
T PF04225_consen 37 AKPLTRLKPGQTLEFQLDE 55 (85)
T ss_dssp T--GGG--TT-EEEEEE-T
T ss_pred cchHhhCCCCCEEEEEECC
Confidence 3467899999999998754
No 21
>KOG1101|consensus
Probab=36.01 E-value=9.8 Score=29.46 Aligned_cols=11 Identities=45% Similarity=0.806 Sum_probs=9.8
Q ss_pred cceeeecccee
Q psy1865 98 RDHAKFSPVAT 108 (152)
Q Consensus 98 k~HAKwsPv~~ 108 (152)
.|||||+|-|.
T Consensus 72 ~EH~k~~p~C~ 82 (147)
T KOG1101|consen 72 EEHAKWSPECE 82 (147)
T ss_pred HHHHhhCCCCc
Confidence 68999999985
No 22
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=35.62 E-value=34 Score=22.83 Aligned_cols=26 Identities=27% Similarity=0.553 Sum_probs=18.3
Q ss_pred ccCCCceEEEcCCCCEEEEEEEEeec
Q psy1865 70 PIHDDILIAKLRPGHEIDVTMFAVKS 95 (152)
Q Consensus 70 p~~~~I~I~KL~~GQ~I~l~~~A~kG 95 (152)
++.++..+..|++||+|++...-..+
T Consensus 33 ~v~~~~~l~~l~~Gd~V~F~~~~~~~ 58 (70)
T PF11604_consen 33 PVADPVDLAGLKPGDKVRFTFERTDD 58 (70)
T ss_dssp E--TTSEESS-STT-EEEEEEEEETT
T ss_pred EcCChhhhhcCCCCCEEEEEEEECCC
Confidence 45678899999999999999876544
No 23
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=35.41 E-value=38 Score=23.14 Aligned_cols=18 Identities=17% Similarity=0.298 Sum_probs=14.8
Q ss_pred cCCCCEEEEEEEEeecCC
Q psy1865 80 LRPGHEIDVTMFAVKSIG 97 (152)
Q Consensus 80 L~~GQ~I~l~~~A~kGiG 97 (152)
-||||.|+++++++.--+
T Consensus 11 YrPGetV~~~~~~~~~~~ 28 (99)
T PF01835_consen 11 YRPGETVHFRAIVRDLDN 28 (99)
T ss_dssp E-TTSEEEEEEEEEEECT
T ss_pred cCCCCEEEEEEEEecccc
Confidence 489999999999988764
No 24
>smart00110 C1Q Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor.
Probab=30.60 E-value=1.1e+02 Score=22.80 Aligned_cols=20 Identities=15% Similarity=0.227 Sum_probs=17.5
Q ss_pred CCceEEEcCCCCEEEEEEEE
Q psy1865 73 DDILIAKLRPGHEIDVTMFA 92 (152)
Q Consensus 73 ~~I~I~KL~~GQ~I~l~~~A 92 (152)
.+=.|.+|.+|+++-|++..
T Consensus 93 S~s~vL~L~~GD~Vwl~l~~ 112 (135)
T smart00110 93 SGGALLQLRQGDQVWLELPD 112 (135)
T ss_pred cCcEEEEECCCCEEEEEEeC
Confidence 46689999999999999964
No 25
>PF07679 I-set: Immunoglobulin I-set domain; InterPro: IPR013098 The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulphide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains: alpha, delta, epsilon, gamma and mu, all consisting of a variable domain (VH) and three (in alpha, delta and gamma) or four (in epsilon and mu) constant domains (CH1 to CH4). Ig molecules are highly modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. The domains in Ig and Ig-like molecules are grouped into four types: V-set (variable; IPR013106 from INTERPRO), C1-set (constant-1; IPR003597 from INTERPRO), C2-set (constant-2; IPR008424 from INTERPRO) and I-set (intermediate; IPR013098 from INTERPRO) []. Structural studies have shown that these domains share a common core Greek-key beta-sandwich structure, with the types differing in the number of strands in the beta-sheets as well as in their sequence patterns [, ]. Immunoglobulin-like domains that are related in both sequence and structure can be found in several diverse protein families. Ig-like domains are involved in a variety of functions, including cell-cell recognition, cell-surface receptors, muscle structure and the immune system []. This entry represents I-set domains, which are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM). I-set domains are also present in several other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1 [], and the signalling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis [].; PDB: 3MTR_A 2EDK_A 3DMK_B 1KOA_A 3NCM_A 2NCM_A 2V9Q_A 2CR3_A 3QQN_A 3QR2_A ....
Probab=28.59 E-value=97 Score=19.93 Aligned_cols=26 Identities=4% Similarity=0.086 Sum_probs=19.4
Q ss_pred EEcCCCCEEEEEEEEeecCCcceeeec
Q psy1865 78 AKLRPGHEIDVTMFAVKSIGRDHAKFS 104 (152)
Q Consensus 78 ~KL~~GQ~I~l~~~A~kGiGk~HAKws 104 (152)
+....|+.+.|.|.+. |...-+.+|.
T Consensus 10 ~~v~~G~~~~l~c~~~-~~p~~~v~W~ 35 (90)
T PF07679_consen 10 VTVKEGESVTLECEVS-GNPPPTVTWY 35 (90)
T ss_dssp EEEETTSEEEEEEEEE-ESSSSEEEEE
T ss_pred EEEeCCCEEEEEEEEE-eCCCCccccc
Confidence 3567799999999996 6555566664
No 26
>COG3592 Uncharacterized conserved protein [Function unknown]
Probab=28.52 E-value=45 Score=23.06 Aligned_cols=22 Identities=9% Similarity=0.200 Sum_probs=18.1
Q ss_pred ccChHHHHHHHhhCCCccEEec
Q psy1865 122 EIEGEMAQRLQTMFSPGVISIE 143 (152)
Q Consensus 122 ~~~~~~~~~~~~~cp~~Vf~i~ 143 (152)
....++.+++...||.|++.+.
T Consensus 51 ~~~ve~i~~vi~sCPSGAl~Y~ 72 (74)
T COG3592 51 AVDVEEIVKVIDTCPSGALKYR 72 (74)
T ss_pred CCCHHHHHHHHHhCCchhhhee
Confidence 4666788899999999998764
No 27
>cd02198 YjgH_like YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=27.37 E-value=57 Score=23.09 Aligned_cols=26 Identities=27% Similarity=0.443 Sum_probs=21.1
Q ss_pred cccCCCceEEEcC-CCCEEEEEEEEee
Q psy1865 69 GPIHDDILIAKLR-PGHEIDVTMFAVK 94 (152)
Q Consensus 69 ~p~~~~I~I~KL~-~GQ~I~l~~~A~k 94 (152)
.|..--+.+..|. ||..|+++|+|.+
T Consensus 85 ~Pa~t~v~V~~L~~~~~~vEIe~~A~~ 111 (111)
T cd02198 85 YPAWTAVGVAWLARPGLLVEIKVVAVR 111 (111)
T ss_pred CCceehhhhhhcCCCCcEEEEEEEEEC
Confidence 5666667778996 7999999999974
No 28
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=27.24 E-value=97 Score=20.44 Aligned_cols=27 Identities=19% Similarity=0.287 Sum_probs=20.1
Q ss_pred EEcCCCCEEEEEEEEeecCCcceeeeccc
Q psy1865 78 AKLRPGHEIDVTMFAVKSIGRDHAKFSPV 106 (152)
Q Consensus 78 ~KL~~GQ~I~l~~~A~kGiGk~HAKwsPv 106 (152)
-.++.||+++++.... .-+.+..++||
T Consensus 51 ~~~~iGd~v~v~I~~i--~e~~~i~l~~~ 77 (77)
T cd04473 51 RDYEVGDEVIVQVTDI--PENGNIDLIPV 77 (77)
T ss_pred CcCCCCCEEEEEEEEE--CCCCcEEEEEC
Confidence 3489999999998776 34556677775
No 29
>cd05735 Ig8_DSCAM Eight immunoglobulin (Ig) domain of Down Syndrome Cell Adhesion molecule (DSCAM). Ig8_DSCAM: the eight immunoglobulin (Ig) domain of Down Syndrome Cell Adhesion molecule (DSCAM). DSCAM is a cell adhesion molecule expressed largely in the developing nervous system. The gene encoding DSCAM is located at human chromosome 21q22, the locus associated with the mental retardation phenotype of Down Syndrome. DSCAM is predicted to be the largest member of the IG superfamily. It has been demonstrated that DSCAM can mediate cation-independent homophilic intercellular adhesion.
Probab=26.41 E-value=92 Score=20.86 Aligned_cols=20 Identities=10% Similarity=0.104 Sum_probs=15.9
Q ss_pred CCEEEEEEEEeecCCcceeee
Q psy1865 83 GHEIDVTMFAVKSIGRDHAKF 103 (152)
Q Consensus 83 GQ~I~l~~~A~kGiGk~HAKw 103 (152)
||++.|+|.|. |.-.-+-.|
T Consensus 1 g~~~~l~C~~~-g~p~~~i~W 20 (88)
T cd05735 1 GQKKEMSCTAH-GEKPIIVRW 20 (88)
T ss_pred CCeEEEEEEEE-CCCCCEEEE
Confidence 89999999987 665566666
No 30
>TIGR03610 RutC pyrimidine utilization protein C. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the endoribonuclease L-PSP family defined by pfam01042.
Probab=26.20 E-value=79 Score=23.21 Aligned_cols=27 Identities=15% Similarity=0.193 Sum_probs=20.5
Q ss_pred cccCCCceEEEcCCCCEEEEEEEEeec
Q psy1865 69 GPIHDDILIAKLRPGHEIDVTMFAVKS 95 (152)
Q Consensus 69 ~p~~~~I~I~KL~~GQ~I~l~~~A~kG 95 (152)
.|..--|...-|+||..|+++|+|.+|
T Consensus 101 ~Pa~t~v~v~l~~p~~lVEIe~vA~~~ 127 (127)
T TIGR03610 101 KPARYCIQCGLVKPDALVEIASVAHIG 127 (127)
T ss_pred CCcEEEEEeccCCCCCEEEEEEEEEeC
Confidence 455554544567899999999999876
No 31
>PRK10665 nitrogen regulatory protein P-II 2; Provisional
Probab=25.79 E-value=1.3e+02 Score=21.99 Aligned_cols=45 Identities=20% Similarity=0.303 Sum_probs=26.9
Q ss_pred EEEEEeecCCcceeeeccce--eEEeEeeeeeEEccccChHHHHHHH
Q psy1865 88 VTMFAVKSIGRDHAKFSPVA--TAFYRLLPKITLTQEIEGEMAQRLQ 132 (152)
Q Consensus 88 l~~~A~kGiGk~HAKwsPv~--~~~yr~~P~i~i~~~~~~~~~~~~~ 132 (152)
|...=++|.|+++..-.-.. ...+.+.|++.|.--+.+++.++++
T Consensus 28 ~Tv~~V~G~G~q~g~~~~~rg~~~~~~~~~k~~ieivv~de~ve~vv 74 (112)
T PRK10665 28 LTVTEVKGFGRQKGHAELYRGAEYSVNFLPKVKIDVAIADDQLDEVI 74 (112)
T ss_pred EEEEeeEecCCCCCCcceeccceeeecccceEEEEEEEChHhHHHHH
Confidence 55666789999765432221 2234578888886545555555543
No 32
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=25.14 E-value=20 Score=21.48 Aligned_cols=24 Identities=21% Similarity=0.297 Sum_probs=21.1
Q ss_pred eEeeeeeEEccccChHHHHHHHhh
Q psy1865 111 YRLLPKITLTQEIEGEMAQRLQTM 134 (152)
Q Consensus 111 yr~~P~i~i~~~~~~~~~~~~~~~ 134 (152)
||++|..+|...++.++-+.++.+
T Consensus 1 Yr~D~DLeFL~~cs~edL~~L~~~ 24 (35)
T PF13099_consen 1 YRYDSDLEFLAECSNEDLKDLVDI 24 (35)
T ss_pred CCcCcchHHHHHCCHHHHHHHHHH
Confidence 789999999988998888888877
No 33
>cd05724 Ig2_Robo Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Ig2_Robo: domain similar to the second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit responsiveness, antago
Probab=24.80 E-value=87 Score=20.11 Aligned_cols=25 Identities=4% Similarity=0.018 Sum_probs=17.3
Q ss_pred EcCCCCEEEEEEEEeecCCcceeee
Q psy1865 79 KLRPGHEIDVTMFAVKSIGRDHAKF 103 (152)
Q Consensus 79 KL~~GQ~I~l~~~A~kGiGk~HAKw 103 (152)
.+..|+.+.|.|.+..|...-.-.|
T Consensus 7 ~~~~G~~v~l~C~~~~g~p~p~i~W 31 (86)
T cd05724 7 QVAVGEMAVLECSPPRGHPEPTVSW 31 (86)
T ss_pred EEeCCCCEEEEEECCCCCCCCEEEE
Confidence 4468999999999877754333333
No 34
>TIGR00004 endoribonuclease L-PSP, putative. This protein was described initially as an inhibitor of protein synthesis intiation but is now viewed as an endoribonuclease active on single-stranded mRNA. The cleavage of mRNA is responsible for the inhibition of protein synthesis. A role in purine regulation has also been suggested.
Probab=24.63 E-value=63 Score=23.19 Aligned_cols=26 Identities=27% Similarity=0.419 Sum_probs=20.4
Q ss_pred cccCCCceEEEcCCCCEEEEEEEEee
Q psy1865 69 GPIHDDILIAKLRPGHEIDVTMFAVK 94 (152)
Q Consensus 69 ~p~~~~I~I~KL~~GQ~I~l~~~A~k 94 (152)
.|..--|....|.+|..|+++++|.|
T Consensus 99 ~Pa~t~v~v~~L~~~~~vEIe~vA~~ 124 (124)
T TIGR00004 99 YPARSAVQVAALPKGVLVEIEAIAVK 124 (124)
T ss_pred CCceEEEECccCCCCCEEEEEEEEEC
Confidence 45554555678999999999999986
No 35
>PF00386 C1q: C1q domain; InterPro: IPR001073 This entry represents the C-terminal domain of C1q. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. C1q comprises 6 A, 6 B and 6 C chains. These share the same topology, each possessing a small, globular N-terminal domain, a collagen-like Gly/Pro-rich central region, and a conserved C-terminal region, the C1q domain []. The C1q protein is produced in collagen-producing cells and shows sequence and structural similarity to collagens VIII and X [, ]. This domain is also found in multimerin and EMILIN proteins.; PDB: 1O91_C 2JG8_D 2JG9_A 2WNV_A 2WNU_A 1PK6_A 4DOU_A 1C3H_C 1C28_C 2OII_A ....
Probab=22.88 E-value=97 Score=22.12 Aligned_cols=25 Identities=16% Similarity=0.206 Sum_probs=18.5
Q ss_pred CCCceEEEcCCCCEEEEEEEEeecC
Q psy1865 72 HDDILIAKLRPGHEIDVTMFAVKSI 96 (152)
Q Consensus 72 ~~~I~I~KL~~GQ~I~l~~~A~kGi 96 (152)
...-.|+.|.+|+++.|++..-.|+
T Consensus 87 ~s~s~vl~L~~GD~V~v~~~~~~~~ 111 (127)
T PF00386_consen 87 ASNSAVLQLNKGDTVWVRLDSGNGI 111 (127)
T ss_dssp EEEEEEEEE-TT-EEEEEEEEEEEE
T ss_pred EEEEEEEEeCCCCEEEEEEecCceE
Confidence 3456788999999999999987554
No 36
>PRK11401 putative endoribonuclease L-PSP; Provisional
Probab=22.66 E-value=88 Score=22.85 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=21.4
Q ss_pred cccCCCceEEEcCCCCEEEEEEEEeec
Q psy1865 69 GPIHDDILIAKLRPGHEIDVTMFAVKS 95 (152)
Q Consensus 69 ~p~~~~I~I~KL~~GQ~I~l~~~A~kG 95 (152)
.|..--|-...|.+|-.|+++|+|.++
T Consensus 102 ~Part~v~v~~L~~~~~VEIe~~A~~~ 128 (129)
T PRK11401 102 YPTRSCVQVARLPKDVKLEIEAIAVRS 128 (129)
T ss_pred CCceEEEEcccCCCCCeEEEEEEEEec
Confidence 455445556789999999999999876
No 37
>PF05187 ETF_QO: Electron transfer flavoprotein-ubiquinone oxidoreductase; InterPro: IPR007859 Electron-transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) in the inner mitochondrial membrane accepts electrons from electron-transfer flavoprotein which is located in the mitochondrial matrix and reduces ubiquinone in the mitochondrial membrane. The two redox centres in the protein, FAD and a [4Fe4S] cluster, are present in a 64 kDa monomer [].; GO: 0004174 electron-transferring-flavoprotein dehydrogenase activity, 0055114 oxidation-reduction process; PDB: 2GMJ_B 2GMH_B.
Probab=21.85 E-value=52 Score=24.33 Aligned_cols=15 Identities=27% Similarity=0.284 Sum_probs=8.9
Q ss_pred HHhhCCCccEEeccC
Q psy1865 131 LQTMFSPGVISIEKK 145 (152)
Q Consensus 131 ~~~~cp~~Vf~i~~~ 145 (152)
.+.-||.||+++.++
T Consensus 95 ~qryCPAgVYE~v~~ 109 (110)
T PF05187_consen 95 EQRYCPAGVYEIVED 109 (110)
T ss_dssp HHHH-TTS-EEEE--
T ss_pred hhhcCcceeEEEecc
Confidence 456799999998753
No 38
>CHL00030 rpl23 ribosomal protein L23
Probab=20.32 E-value=70 Score=22.85 Aligned_cols=16 Identities=31% Similarity=0.505 Sum_probs=13.6
Q ss_pred CCceEEEcCCCCEEEE
Q psy1865 73 DDILIAKLRPGHEIDV 88 (152)
Q Consensus 73 ~~I~I~KL~~GQ~I~l 88 (152)
--=.|++|.+||.|.+
T Consensus 72 ~KKAiVtL~~g~~I~~ 87 (93)
T CHL00030 72 YKRMIITLQPGYSIPL 87 (93)
T ss_pred cEEEEEEcCCcCEecc
Confidence 3578999999999976
Done!