Query 032941
Match_columns 130
No_of_seqs 102 out of 197
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 07:51:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032941.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032941hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00658 RPOL8c RNA polymera 100.0 4.5E-53 9.7E-58 321.4 13.8 117 4-120 2-120 (143)
2 KOG3400 RNA polymerase subunit 100.0 8.2E-53 1.8E-57 317.1 11.6 118 1-119 1-119 (143)
3 PF03870 RNA_pol_Rpb8: RNA pol 100.0 3.7E-52 7.9E-57 314.8 14.3 112 8-119 1-114 (138)
4 PTZ00167 RNA polymerase subuni 100.0 2.2E-50 4.7E-55 307.0 13.6 114 1-120 2-116 (144)
5 PRK14980 DNA-directed RNA poly 97.5 0.0019 4.1E-08 48.9 10.1 94 4-119 6-99 (127)
6 PF08530 PepX_C: X-Pro dipepti 82.4 4.7 0.0001 31.1 5.9 54 11-65 115-181 (218)
7 TIGR00976 /NonD putative hydro 59.4 20 0.00044 31.7 5.1 55 12-66 446-506 (550)
8 PF13745 HxxPF_rpt: HxxPF-repe 56.8 23 0.00049 22.9 3.9 31 18-50 54-84 (91)
9 PF11183 PmrD: Polymyxin resis 46.6 45 0.00097 23.6 4.2 30 28-58 17-47 (82)
10 PF08292 RNA_pol_Rbc25: RNA po 44.5 24 0.00052 26.1 2.7 50 6-64 25-74 (122)
11 COG3717 KduI 5-keto 4-deoxyuro 35.5 53 0.0012 27.9 3.7 56 71-127 186-260 (278)
12 PRK05659 sulfur carrier protei 32.3 67 0.0015 20.2 3.1 23 39-61 31-61 (66)
13 PRK06763 F0F1 ATP synthase sub 30.6 2.9E+02 0.0064 22.8 7.1 29 29-60 56-84 (213)
14 PRK00924 5-keto-4-deoxyuronate 30.0 47 0.001 28.1 2.6 33 94-127 212-258 (276)
15 PF13670 PepSY_2: Peptidase pr 29.2 40 0.00086 22.5 1.7 11 36-46 66-76 (83)
16 cd02847 Chitobiase_C_term Chit 28.6 49 0.0011 22.7 2.1 21 8-28 57-77 (78)
17 TIGR02722 lp_ uncharacterized 28.6 67 0.0014 25.0 3.1 28 86-114 140-167 (189)
18 PF11604 CusF_Ec: Copper bindi 27.2 88 0.0019 20.6 3.1 49 12-64 2-56 (70)
19 PRK13444 atpC F0F1 ATP synthas 26.2 1.4E+02 0.0031 21.8 4.3 32 10-41 5-37 (127)
20 PF02823 ATP-synt_DE_N: ATP sy 25.9 1.1E+02 0.0024 20.2 3.4 30 11-40 1-31 (80)
21 PF01834 XRCC1_N: XRCC1 N term 23.7 40 0.00087 26.3 1.0 14 20-34 124-137 (153)
22 PHA02146 hypothetical protein 23.2 50 0.0011 23.3 1.3 16 10-25 28-43 (86)
23 PF06257 DUF1021: Protein of u 23.1 71 0.0015 22.1 2.0 20 7-27 42-61 (76)
24 COG4263 NosZ Nitrous oxide red 22.5 1.2E+02 0.0026 28.3 3.9 39 86-128 576-614 (637)
25 PRK05371 x-prolyl-dipeptidyl a 22.2 1E+02 0.0022 29.3 3.5 29 37-65 711-739 (767)
26 PF00900 Ribosomal_S4e: Riboso 22.0 1.5E+02 0.0032 20.3 3.4 52 10-62 15-72 (77)
27 PF11485 DUF3211: Protein of u 21.9 67 0.0015 24.6 1.9 13 87-99 52-64 (136)
28 PF02760 HIN: HIN-200/IF120x d 20.7 2.8E+02 0.006 22.2 5.2 52 4-61 113-166 (170)
No 1
>smart00658 RPOL8c RNA polymerase subunit 8. subunit of RNA polymerase I, II and III
Probab=100.00 E-value=4.5e-53 Score=321.42 Aligned_cols=117 Identities=52% Similarity=0.847 Sum_probs=107.0
Q ss_pred ccceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCCccCCC-CCC
Q 032941 4 IVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPG-ARK 82 (130)
Q Consensus 4 ~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~~~~~~-~~~ 82 (130)
.+||||+|+|++|||+||||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++||+++++.+++. +.+
T Consensus 2 ~~lfeD~F~V~~iDp~gKkfdrVSRi~~~S~~~~~~l~LDiNtelyPv~~gd~~~l~La~tL~~dg~~d~~~~~~~~~~~ 81 (143)
T smart00658 2 IILFDDIFKVKSVDPDGKKFDKVSRIFAESEYLQMELTLDINSEIYPLAVGDKFTLVIASTLNEDGTPDSGENNPIALIK 81 (143)
T ss_pred ceeeeeEEEEEEECCCCCeEccEEEEEEEcCCCceEEEEEecceEEeccCCCEEEEEEecccccCCCCcccccccccccc
Confidence 5799999999999999999999999999999999999999999999999999999999999999999997766554 346
Q ss_pred CcccccceEEeeeEEEeeecCCC-CeEEEEEecCcceee
Q 032941 83 TLADKYEYIMHGKLFKIGDEGSG-KSLKAYETTTQSIHY 120 (130)
Q Consensus 83 sLaD~ydYVMyGKVYk~e~e~~~-~~~~vYiS~~~~~~~ 120 (130)
+|||+|||||||||||+|+++++ ++++|||||||+++.
T Consensus 82 ~Lad~ydYVM~GkvYk~e~~~~~~~~~~vy~SFGGLLm~ 120 (143)
T smart00658 82 SLADKYEYVMYGKVYRIEEDKTETEKLSVYVSFGGLLMR 120 (143)
T ss_pred chhhcCCEEeeeEEEEEEecCCCceEEEEEEEeccEeEE
Confidence 79999999999999999975543 499999999999873
No 2
>KOG3400 consensus RNA polymerase subunit 8 [Transcription]
Probab=100.00 E-value=8.2e-53 Score=317.15 Aligned_cols=118 Identities=52% Similarity=0.902 Sum_probs=111.2
Q ss_pred CCcccceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCCccCCCC
Q 032941 1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGA 80 (130)
Q Consensus 1 ms~~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~~~~~~~ 80 (130)
|+ ++||||||+|++|||||||||||||+.|.|++++|+|+||||++|||++.||+|+|+||+||++||+|++|||+|.+
T Consensus 1 Ma-~ilfdDiF~V~~vDpeGkkydrVsR~~~~S~~~~m~l~LDiNt~lyPl~~gdkf~l~iastL~eDgtpd~g~~~p~a 79 (143)
T KOG3400|consen 1 MA-GILFDDIFKVSDVDPEGKKYDRVSRIEAKSESFKMDLILDINTQLYPLATGDKFTLVIASTLNEDGTPDTGEYTPGA 79 (143)
T ss_pred Cc-chhhhhceeeeecCcccchhhheEeEEeeCCCceEEEEEecccEEEeeccCCEEEEEEecccccCCCccccccCccc
Confidence 55 69999999999999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CCCcccccceEEeeeEEEeeecC-CCCeEEEEEecCccee
Q 032941 81 RKTLADKYEYIMHGKLFKIGDEG-SGKSLKAYETTTQSIH 119 (130)
Q Consensus 81 ~~sLaD~ydYVMyGKVYk~e~e~-~~~~~~vYiS~~~~~~ 119 (130)
..+|||+|||||||||||+|.++ ..+..++|+||+++..
T Consensus 80 ~~~~ad~~eYvMyGkvYriE~~e~~~~~~~~YvSFGGLLM 119 (143)
T KOG3400|consen 80 KKPLADEYEYVMYGKVYRIEYDEGKTEKASAYVSFGGLLM 119 (143)
T ss_pred cccccceeeEEEeeEEEEEeccCCccceeeEEEeeceEEE
Confidence 77799999999999999999543 5788899999999864
No 3
>PF03870 RNA_pol_Rpb8: RNA polymerase Rpb8; InterPro: IPR005570 Rpb8 is a subunit common to the three yeast RNA polymerases, pol I, II and III. Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits.; GO: 0006351 transcription, DNA-dependent; PDB: 1TWH_H 1R9T_H 1I3Q_H 2B8K_H 1TWA_H 2NVY_H 4A3E_H 1Y77_H 3GTK_H 2E2J_H ....
Probab=100.00 E-value=3.7e-52 Score=314.81 Aligned_cols=112 Identities=53% Similarity=0.910 Sum_probs=99.6
Q ss_pred eeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCC-ccCCCCCCCccc
Q 032941 8 EDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTG-YYTPGARKTLAD 86 (130)
Q Consensus 8 eD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~-~~~~~~~~sLaD 86 (130)
||+|+|+++|||||||||||||.|+|++++|+|+|||||||||+++||+|+|+||+||++||+++++ |++..+++||||
T Consensus 1 eD~F~V~~vD~dGkkfdrVSRi~~~S~~~~m~l~LDiNtelyPl~~~d~~~l~La~tL~~dg~~d~~~~~~~~~~~slad 80 (138)
T PF03870_consen 1 EDIFTVTDVDPDGKKFDRVSRIFAKSESFDMELTLDINTELYPLKVGDKFTLALASTLNLDGTPDDGSWRPKGGEPSLAD 80 (138)
T ss_dssp EEEEEEEEEE---SSSSSEEEEEEEESSSS-EEEEEEETTTSSSTSSEEEEEEECSSS-SSSSSTTTSSSSTTCTTCCCT
T ss_pred CCeEEEEEECCCCCeeccEEEEEEEeCCCceEEEEEccccEEccCCCCEEEEEEecccccCCCCCccccccCCCCcchhh
Confidence 7999999999999999999999999999999999999999999999999999999999999999876 666557789999
Q ss_pred ccceEEeeeEEEeeecC-CCCeEEEEEecCccee
Q 032941 87 KYEYIMHGKLFKIGDEG-SGKSLKAYETTTQSIH 119 (130)
Q Consensus 87 ~ydYVMyGKVYk~e~e~-~~~~~~vYiS~~~~~~ 119 (130)
+|||||||||||+|+.+ .+++++|||||||+++
T Consensus 81 ~ydYVMyGkvYk~ee~~~~~~~~~vY~SFGGLLM 114 (138)
T PF03870_consen 81 DYDYVMYGKVYKFEEGSGGSDKVKVYASFGGLLM 114 (138)
T ss_dssp SSSEEEEEEEEEEEESSS-TSCEEEEEEETTEEE
T ss_pred heeeEeeeEEEeeeccCCCCceEEEEEEecceeE
Confidence 99999999999999643 4799999999999986
No 4
>PTZ00167 RNA polymerase subunit 8c; Provisional
Probab=100.00 E-value=2.2e-50 Score=307.00 Aligned_cols=114 Identities=34% Similarity=0.614 Sum_probs=103.7
Q ss_pred CCcccceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCC-ccCCC
Q 032941 1 MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTG-YYTPG 79 (130)
Q Consensus 1 ms~~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~-~~~~~ 79 (130)
|++++||||+|+|+++||+| |||||||.|+|++++|+|+|||||||||+++||+|+|+||+|| +|| ++++ |++.
T Consensus 2 ~~~~~LfeD~F~V~~iD~~g--fdrVSRI~a~S~~~~~~l~LDiNtelyPv~~gd~~~l~LastL-~dg-~d~~~~~~~- 76 (144)
T PTZ00167 2 SLPSCLFEDRFVVRSVDNSK--FERVSRIKAKSTGFDAELILDINSDLFPVREKQSLYIGLTNQL-SSG-PDDNVWESS- 76 (144)
T ss_pred CCCceEEEeeEEEEecCCCC--CceEEEEEEEeCCCceEEEEEecccEEeccCCCEEEEEEeccc-cCC-CCccccccc-
Confidence 45588999999999999976 9999999999999999999999999999999999999999999 999 5554 7665
Q ss_pred CCCCcccccceEEeeeEEEeeecCCCCeEEEEEecCcceee
Q 032941 80 ARKTLADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHY 120 (130)
Q Consensus 80 ~~~sLaD~ydYVMyGKVYk~e~e~~~~~~~vYiS~~~~~~~ 120 (130)
+++||||+|||||||||||||+++ +++++|||||||++..
T Consensus 77 ~~~tLad~ydYVM~GkvYk~ee~~-s~~~~vy~SFGGLLM~ 116 (144)
T PTZ00167 77 EPQSLMDQYEYVMYGKIFKFEEKS-SERRTLYASFGGLLMA 116 (144)
T ss_pred ccccccccCCEEcceEEEEeeecC-CCcEEEEEEcccEeEE
Confidence 588899999999999999999644 5799999999999873
No 5
>PRK14980 DNA-directed RNA polymerase subunit G; Provisional
Probab=97.48 E-value=0.0019 Score=48.86 Aligned_cols=94 Identities=10% Similarity=0.131 Sum_probs=74.6
Q ss_pred ccceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeeecCCCCCCCCCccCCCCCCC
Q 032941 4 IVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPDTGYYTPGARKT 83 (130)
Q Consensus 4 ~~LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~LastL~~dg~~~~~~~~~~~~~s 83 (130)
+.-+.-.=+|++|.| .+.-.-.|+.+.+ .+.++++|+|.+|=+.++||++.+.+.+.- +.
T Consensus 6 ~~~~~~~cKI~SIEk--g~l~~l~i~~~~C--~~~~v~fDi~~~L~~fsege~v~iiIS~ek----------------P~ 65 (127)
T PRK14980 6 AQEIILSCKINSIEK--GSLKNLSIIHMSC--NDFNISFDIIDSINIFSQKEKVKAIISKER----------------PS 65 (127)
T ss_pred hhheeeEEeeeeecc--cccCCcEEEEEec--CCeEEEEEehhhhheecCCCcEEEEEeccC----------------cc
Confidence 445667789999999 7788888888777 469999999999999999999999997742 22
Q ss_pred cccccceEEeeeEEEeeecCCCCeEEEEEecCccee
Q 032941 84 LADKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIH 119 (130)
Q Consensus 84 LaD~ydYVMyGKVYk~e~e~~~~~~~vYiS~~~~~~ 119 (130)
. .+.|+.=||-|...+. ..+++-.+=+|..|.+.
T Consensus 66 ~-~~~dFCghGyvV~~~k-~~~~~y~~iISl~GlLv 99 (127)
T PRK14980 66 Y-TNDDFCAHGYIVTESS-NNGNRYTTIISLFGLLV 99 (127)
T ss_pred c-ccceeecCcEEEEEEe-cCCCeEEEEEEeeeEEE
Confidence 3 3378888999988853 45788888888887654
No 6
>PF08530 PepX_C: X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain; InterPro: IPR013736 This domain is found at the C terminus of cocaine esterase CocE, several glutaryl-7-ACA acylases, and the putative diester hydrolase NonD of Streptomyces griseus (all hydrolases). The domain, which is a beta sandwich, is also found in serine peptidases belonging to MEROPS peptidase family S15: Xaa-Pro dipeptidyl-peptidases. Members of this entry, that are not characterised as peptidases, show extensive low-level similarity to the Xaa-Pro dipeptidyl-peptidases. ; GO: 0008239 dipeptidyl-peptidase activity; PDB: 2B4K_D 1RYY_F 2B9V_O 1NX9_B 3PUH_B 3I2I_A 3I2G_A 1JU4_A 3I2K_A 1L7R_A ....
Probab=82.43 E-value=4.7 Score=31.10 Aligned_cols=54 Identities=13% Similarity=0.315 Sum_probs=38.8
Q ss_pred EEeeeECCCCCccceEeeEEEEe-------------cCCceEEEEEecccccccccCCEEEEEEeeec
Q 032941 11 FVVEKIDPDGKKFDKVSRIEAHS-------------QNCDMYMLLDVNSELYPMRVGDKFTMALAHTL 65 (130)
Q Consensus 11 F~V~~iD~dGKkFDrVSRI~a~S-------------~~~~m~l~LDINteLyPl~~gdk~~l~LastL 65 (130)
-.+.+++|||+. ..|++-.++- .+--.++.+.++---|-+++|.+++|.|+++=
T Consensus 115 v~L~dv~pdG~~-~~it~G~l~~s~r~~~~~~~~~~pg~~~~~~i~L~p~~~~~~~GhrLrl~I~~~d 181 (218)
T PF08530_consen 115 VRLSDVDPDGTS-TLITRGWLRASHRESDEKPEPLEPGEPYDVTIELQPTAYVFPAGHRLRLSISSSD 181 (218)
T ss_dssp EEEEEEETTSSE-EEEEEEEEEGGGSSCSSST----TT-EEEEEEEEEEEEEEE-TT-EEEEEEESSB
T ss_pred EEEEEeCCCCCE-EEccceEEEcccccCccccccCCCCcEEEEEEEEchhccEECCCCEEEEEEEecC
Confidence 356799999875 4566655553 13235889999999999999999999999873
No 7
>TIGR00976 /NonD putative hydrolase, CocE/NonD family. This model represents a protein subfamily that includes the cocaine esterase CocE, several glutaryl-7-ACA acylases, and the putative diester hydrolase NonD of Streptomyces griseus (all hydrolases). This family shows extensive, low-level similarity to a family of xaa-pro dipeptidyl-peptidases, and local similarity by PSI-BLAST to many other hydrolases.
Probab=59.37 E-value=20 Score=31.74 Aligned_cols=55 Identities=13% Similarity=0.293 Sum_probs=37.9
Q ss_pred EeeeECCCCCcc---ceEeeEEEE-e--cCCceEEEEEecccccccccCCEEEEEEeeecC
Q 032941 12 VVEKIDPDGKKF---DKVSRIEAH-S--QNCDMYMLLDVNSELYPMRVGDKFTMALAHTLN 66 (130)
Q Consensus 12 ~V~~iD~dGKkF---DrVSRI~a~-S--~~~~m~l~LDINteLyPl~~gdk~~l~LastL~ 66 (130)
++.+++|||+.. +-+-|+.-. + .+.-.++++++..--|-+++|.+++|.|+++=.
T Consensus 446 ~L~dV~pdG~~~~i~~g~lr~~~r~~~~~G~~~~v~i~l~~~~~~f~~Ghrlrl~I~ssd~ 506 (550)
T TIGR00976 446 KLTDVDPDGRAIALDEGICRVRYRRTSVNGEIYEVDIDLGATANLFAPGHRLRVEVGSSNF 506 (550)
T ss_pred EEEEECCCCeEEecccceeeeecccccCCCceEEEEEeccccceEECCCCEEEEEEEccCC
Confidence 456899999752 112222211 1 133467888989999999999999999998754
No 8
>PF13745 HxxPF_rpt: HxxPF-repeated domain; PDB: 2JGP_A.
Probab=56.82 E-value=23 Score=22.91 Aligned_cols=31 Identities=26% Similarity=0.528 Sum_probs=17.1
Q ss_pred CCCCccceEeeEEEEecCCceEEEEEecccccc
Q 032941 18 PDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYP 50 (130)
Q Consensus 18 ~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyP 50 (130)
+.+.|||=. +.+......+.+.+++|++||-
T Consensus 54 ~~~~~~DL~--l~~~~~~~~l~~~~~Y~~~lf~ 84 (91)
T PF13745_consen 54 NGGAKFDLT--LEVREDGDGLRLQLEYNTDLFS 84 (91)
T ss_dssp -SB-SSSEE--EEEEE-SS-EEEEEEEETTT--
T ss_pred ccceeeeEE--EEEEecCCeEEEEEEEEhHhCC
Confidence 445567765 3344444578889999998884
No 9
>PF11183 PmrD: Polymyxin resistance protein PmrD; InterPro: IPR020146 The Salmonella PmrA/PmrB two-component system is required for resistance to the cationic peptide antibiotic olymyxin B, resistance to Fe(3+)-mediated killing, growth in soil, virulence in mice, and infection of chicken macrophages. PmrA-activated genes encode periplasmic and integral membrane proteins as well as cytoplasmic products mediating the modification of the lipopolysaccharide, suggesting a role for the PmrA/PmrB system in remodeling of the Gram-negative envelope. The PmrA/PmrB two-component system of Salmonella enterica is activated by Fe(3+), which is sensed by the PmrB protein, and by low Mg(2+), which is sensed by the PhoQ protein. The low Mg(2+) activation requires pmrD, a PhoPPhoQ-activated gene that activates the response regulator PmrA at a posttranscriptional level. However, under conditions that activate the PmrA protein independently of pmrD, such as exposure to Fe3, lower levels of pmrD transcription occur. It has been demonstrated that PmrA binds to the pmrD promoter, suppressing transcription. Negative regulation of the PhoP/PhoQ-activated pmrD gene by the PmrA/ PmrB system closes a regulatory circuit designed to maintain proper cellular levels of activated PmrA protein, and constitutes a singular example of a multicomponent feedback loop []. ; PDB: 2RQX_A 2JSO_A.
Probab=46.60 E-value=45 Score=23.64 Aligned_cols=30 Identities=23% Similarity=0.366 Sum_probs=20.7
Q ss_pred eEEEEe-cCCceEEEEEecccccccccCCEEE
Q 032941 28 RIEAHS-QNCDMYMLLDVNSELYPMRVGDKFT 58 (130)
Q Consensus 28 RI~a~S-~~~~m~l~LDINteLyPl~~gdk~~ 58 (130)
.+.+.+ .+..+.|+.-|++ -+++++||+|+
T Consensus 17 ~~l~l~~a~g~LkmIAEv~s-~~~l~~GD~Lt 47 (82)
T PF11183_consen 17 HVLLLCDAGGALKMIAEVTS-DFRLQEGDKLT 47 (82)
T ss_dssp EEEEEEETTTTCEEEEEEEE-SS---TT-EEE
T ss_pred EEEEEecCCCCeEEEEEeec-CcccCCCCCcc
Confidence 455555 4567999999999 89999999996
No 10
>PF08292 RNA_pol_Rbc25: RNA polymerase III subunit Rpc25; InterPro: IPR013238 Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [].; PDB: 2CKZ_D 3AYH_B.
Probab=44.53 E-value=24 Score=26.13 Aligned_cols=50 Identities=16% Similarity=0.405 Sum_probs=32.5
Q ss_pred ceeeeEEeeeECCCCCccceEeeEEEEecCCceEEEEEecccccccccCCEEEEEEeee
Q 032941 6 LFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64 (130)
Q Consensus 6 LFeD~F~V~~iD~dGKkFDrVSRI~a~S~~~~m~l~LDINteLyPl~~gdk~~l~Last 64 (130)
.|+|||.-.+.=|++..||.-.++-.-.-. ..+-+.+..|+.+++...+-
T Consensus 25 FFddI~IP~~~L~~ps~fd~~~~~W~W~~~---------~~~~l~~d~ge~IRFRV~~~ 74 (122)
T PF08292_consen 25 FFDDIFIPPSLLPEPSRFDEEEQAWVWEYD---------EEQELFFDIGEEIRFRVESE 74 (122)
T ss_dssp CEEEEEEECCCC-TTEEEECCCTEEEEEES---------SSEEEEE-TT-EEEEEEEEE
T ss_pred ccccEEECHHHCCCCCccCccCCEEEEECC---------CCceeEccCCCEEEEEEeEE
Confidence 689999999999999999877666554332 44455555666666665443
No 11
>COG3717 KduI 5-keto 4-deoxyuronate isomerase [Carbohydrate transport and metabolism]
Probab=35.48 E-value=53 Score=27.87 Aligned_cols=56 Identities=25% Similarity=0.430 Sum_probs=33.3
Q ss_pred CCCCccCCC--CCCCcccccceEEe---eeEEEeeecCCCCeE-------EEEEecCccee-------eeeeeeee
Q 032941 71 PDTGYYTPG--ARKTLADKYEYIMH---GKLFKIGDEGSGKSL-------KAYETTTQSIH-------YYFIWACV 127 (130)
Q Consensus 71 ~~~~~~~~~--~~~sLaD~ydYVMy---GKVYk~e~e~~~~~~-------~vYiS~~~~~~-------~~~~~~~~ 127 (130)
|..-|..-. -..-+++-|=|.=- -+||++..+.. +.. .+=+|-+-||| |=||||.+
T Consensus 186 pgsvWNTMP~H~HdRRmE~YlYF~m~e~srVfH~MGqP~-ETRHiv~~NEqAViSP~WSIHSG~GT~~YtFIWaMa 260 (278)
T COG3717 186 PGSVWNTMPCHVHDRRMEVYLYFDMDEDSRVFHMMGQPQ-ETRHIVMHNEQAVISPPWSIHSGVGTANYTFIWAMA 260 (278)
T ss_pred CCCccccCCccccccceeEEEEecCCCcceEEEecCCCC-ceeEEEEeccceeeCCCceeecCccccceEEEEEec
Confidence 445566432 11124455555422 47899975542 222 24578888999 99999975
No 12
>PRK05659 sulfur carrier protein ThiS; Validated
Probab=32.35 E-value=67 Score=20.21 Aligned_cols=23 Identities=30% Similarity=0.573 Sum_probs=17.4
Q ss_pred EEEEEecccccc--------cccCCEEEEEE
Q 032941 39 YMLLDVNSELYP--------MRVGDKFTMAL 61 (130)
Q Consensus 39 ~l~LDINteLyP--------l~~gdk~~l~L 61 (130)
.+.+.+|-++.| |+.||++.+.=
T Consensus 31 ~vav~vNg~iv~r~~~~~~~l~~gD~vei~~ 61 (66)
T PRK05659 31 RVAVEVNGEIVPRSQHASTALREGDVVEIVH 61 (66)
T ss_pred eEEEEECCeEeCHHHcCcccCCCCCEEEEEE
Confidence 445668887777 89999998863
No 13
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=30.56 E-value=2.9e+02 Score=22.76 Aligned_cols=29 Identities=21% Similarity=0.358 Sum_probs=22.0
Q ss_pred EEEEecCCceEEEEEecccccccccCCEEEEE
Q 032941 29 IEAHSQNCDMYMLLDVNSELYPMRVGDKFTMA 60 (130)
Q Consensus 29 I~a~S~~~~m~l~LDINteLyPl~~gdk~~l~ 60 (130)
|+++.-+..+.+.+|-++.. +.||.+...
T Consensus 56 iesk~yn~~v~i~~d~~~nv---KVGD~VKaT 84 (213)
T PRK06763 56 IKSKQYEEPVSVYIDSLSNV---KVGDEVKAT 84 (213)
T ss_pred EEeccCCCceEEEecCCCCc---ccCcEEEEc
Confidence 44444455699999999887 999998875
No 14
>PRK00924 5-keto-4-deoxyuronate isomerase; Provisional
Probab=29.96 E-value=47 Score=28.14 Aligned_cols=33 Identities=30% Similarity=0.608 Sum_probs=24.0
Q ss_pred eeEEEeeecCCCCe--E-----EEEEecCccee-------eeeeeeee
Q 032941 94 GKLFKIGDEGSGKS--L-----KAYETTTQSIH-------YYFIWACV 127 (130)
Q Consensus 94 GKVYk~e~e~~~~~--~-----~vYiS~~~~~~-------~~~~~~~~ 127 (130)
++||.+..+. .+. + .+=+|-+-||| |=||||..
T Consensus 212 qrV~h~mG~p-dETrh~~v~n~~aVisP~wsih~g~gt~~y~fiw~m~ 258 (276)
T PRK00924 212 ARVFHFMGEP-QETRHIVVHNEQAVISPSWSIHSGVGTSNYTFIWGMA 258 (276)
T ss_pred ceEEecCCCc-cceeeEEEECCCEEECCCcceecCcCccccEEEEEec
Confidence 8999987533 222 2 35688888999 99999964
No 15
>PF13670 PepSY_2: Peptidase propeptide and YPEB domain This Prosite motif covers only the active site. This is family M4 in the peptidase classification.
Probab=29.22 E-value=40 Score=22.45 Aligned_cols=11 Identities=9% Similarity=0.126 Sum_probs=5.6
Q ss_pred CceEEEEEecc
Q 032941 36 CDMYMLLDVNS 46 (130)
Q Consensus 36 ~~m~l~LDINt 46 (130)
..+++.+|-+|
T Consensus 66 ~~~ev~vD~~t 76 (83)
T PF13670_consen 66 KKVEVYVDPAT 76 (83)
T ss_pred CEEEEEEcCCC
Confidence 34555555443
No 16
>cd02847 Chitobiase_C_term Chitobiase C-terminus domain. Chitobiase (AKA N-acetylglucosaminidase) digests the beta, 1-4 glycosidic bonds of the N-acetylglucosamine (NAG) oligomers found in chitin, an important structural element of fungal cell wall and arthropod exoskeletons. It is thought to proceed through an acid-base reaction mechanism, in which one protein carboxylate acts as catalytic acid, while the nucleophile is the polar acetamido group of the sugar in a substrate-assisted reaction with retention of the anomeric configuration. The C-terminus of chitobiase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chit
Probab=28.65 E-value=49 Score=22.70 Aligned_cols=21 Identities=19% Similarity=0.378 Sum_probs=17.3
Q ss_pred eeeEEeeeECCCCCccceEee
Q 032941 8 EDIFVVEKIDPDGKKFDKVSR 28 (130)
Q Consensus 8 eD~F~V~~iD~dGKkFDrVSR 28 (130)
.+.++|..+.++|+++.|+..
T Consensus 57 ~~~v~vr~~s~~G~r~sR~~~ 77 (78)
T cd02847 57 SGDVQIRSVSFDGKRVSRVTS 77 (78)
T ss_pred cccEEEEEEcCCCCeecceee
Confidence 467889999999999888754
No 17
>TIGR02722 lp_ uncharacterized proteobacterial lipoprotein. Members of this protein family are restricted to the Proteobacteria, and all are predicted lipoproteins. In genomes that contain the thiK gene for the salvage enzyme thiamin kinase, the member of this family is encoded nearby.
Probab=28.56 E-value=67 Score=24.99 Aligned_cols=28 Identities=21% Similarity=0.243 Sum_probs=18.6
Q ss_pred cccceEEeeeEEEeeecCCCCeEEEEEec
Q 032941 86 DKYEYIMHGKLFKIGDEGSGKSLKAYETT 114 (130)
Q Consensus 86 D~ydYVMyGKVYk~e~e~~~~~~~vYiS~ 114 (130)
-.-||+++|+|-.+... .+....+|+.+
T Consensus 140 ~gADy~L~G~I~~~~~~-~~~~~~~~~~~ 167 (189)
T TIGR02722 140 VGADYSLYGKISSIVKS-DGSRKLVYYKF 167 (189)
T ss_pred hCCCEEEEEEEEEEEee-cCCCceEEEEE
Confidence 35799999999988743 23334555543
No 18
>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=27.15 E-value=88 Score=20.60 Aligned_cols=49 Identities=27% Similarity=0.399 Sum_probs=29.4
Q ss_pred EeeeECCCCCccceEeeEEEE---e-cCCceEEEEEe--cccccccccCCEEEEEEeee
Q 032941 12 VVEKIDPDGKKFDKVSRIEAH---S-QNCDMYMLLDV--NSELYPMRVGDKFTMALAHT 64 (130)
Q Consensus 12 ~V~~iD~dGKkFDrVSRI~a~---S-~~~~m~l~LDI--NteLyPl~~gdk~~l~Last 64 (130)
+|++||+++++ | .|.-. + .=..|+|.+.+ +.++=.+++||++++.+..+
T Consensus 2 ~V~~vd~~~~~---i-ti~H~pIp~l~wpaMTM~F~v~~~~~l~~l~~Gd~V~F~~~~~ 56 (70)
T PF11604_consen 2 VVKSVDPEAGT---I-TISHEPIPELGWPAMTMDFPVADPVDLAGLKPGDKVRFTFERT 56 (70)
T ss_dssp EEEEEETTTTE---E-EEEE--BCCCTB-SEEEEEE--TTSEESS-STT-EEEEEEEEE
T ss_pred EEEEEecCCCE---E-EEecCccccCCCCCeEEEEEcCChhhhhcCCCCCEEEEEEEEC
Confidence 57888886652 2 12111 1 12346666665 68889999999999999874
No 19
>PRK13444 atpC F0F1 ATP synthase subunit epsilon; Provisional
Probab=26.20 E-value=1.4e+02 Score=21.80 Aligned_cols=32 Identities=16% Similarity=0.210 Sum_probs=27.0
Q ss_pred eEEeeeECCCCCccc-eEeeEEEEecCCceEEE
Q 032941 10 IFVVEKIDPDGKKFD-KVSRIEAHSQNCDMYML 41 (130)
Q Consensus 10 ~F~V~~iD~dGKkFD-rVSRI~a~S~~~~m~l~ 41 (130)
.|.++=+-|+|..|+ +|.++.+.+..+++.+.
T Consensus 5 ~~~l~IvtP~~~~~~~~v~~V~~p~~~G~~gIL 37 (127)
T PRK13444 5 KLTVSVISPEKILYKGEVDSLIVPGSEGFFGIL 37 (127)
T ss_pred ceEEEEEcCCceEEeceEEEEEEECCccCeEec
Confidence 588999999998888 79999999888777653
No 20
>PF02823 ATP-synt_DE_N: ATP synthase, Delta/Epsilon chain, beta-sandwich domain; InterPro: IPR020546 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This family represents subunits called delta (in mitochondrial ATPase) or epsilon (in bacteria or chloroplast ATPase). The interaction site of subunit C of the F0 complex with the delta or epsilon subunit of the F1 complex may be important for connecting the rotor of F1 (gamma subunit) to the rotor of F0 (C subunit) []. In bacterial species, the delta subunit is the equivalent of the Oligomycin sensitive subunit (OSCP, IPR000711 from INTERPRO) in metazoans. The C-terminal domain of the epsilon subunit appears to act as an inhibitor of ATPase activity []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046933 hydrogen ion transporting ATP synthase activity, rotational mechanism, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015986 ATP synthesis coupled proton transport, 0045261 proton-transporting ATP synthase complex, catalytic core F(1); PDB: 2WSS_H 1E79_H 2JDI_H 2W6I_H 2W6H_H 2W6J_H 2CK3_H 2V7Q_H 1H8E_H 2XND_H ....
Probab=25.93 E-value=1.1e+02 Score=20.17 Aligned_cols=30 Identities=17% Similarity=0.396 Sum_probs=24.0
Q ss_pred EEeeeECCCCCccc-eEeeEEEEecCCceEE
Q 032941 11 FVVEKIDPDGKKFD-KVSRIEAHSQNCDMYM 40 (130)
Q Consensus 11 F~V~~iD~dGKkFD-rVSRI~a~S~~~~m~l 40 (130)
|+++=+-|+|..|+ .|.++.+.+.++++.+
T Consensus 1 l~l~IvtP~~~~~~~~v~~v~~~t~~G~~gI 31 (80)
T PF02823_consen 1 LKLKIVTPDGIFFEGEVESVVLPTTDGEFGI 31 (80)
T ss_dssp EEEEEEESSSEEEEEEESEEEEEBSSSEEEE
T ss_pred CEEEEEcCCceEEeeEEEEEEEECCCcChhh
Confidence 56677789888887 7999999988777664
No 21
>PF01834 XRCC1_N: XRCC1 N terminal domain; InterPro: IPR002706 DNA-repair protein Xrcc1 functions in the repair of single-strand DNA breaks in mammalian cells and forms a repair complex with beta-Pol, ligase III and PARP []. The NMR solution structure of the Xrcc1 N-terminal domain (Xrcc1 NTD) shows that the structural core is a beta-sandwich with beta-strands connected by loops, three helices and two short two-stranded beta-sheets at each connection side. The Xrcc1 NTD specifically binds single-strand break DNA (gapped and nicked) and a gapped DNA-beta-Pol complex [].; GO: 0003684 damaged DNA binding, 0000012 single strand break repair, 0005634 nucleus; PDB: 3K77_E 3K75_C 3LQC_A 1XNA_A 1XNT_A.
Probab=23.67 E-value=40 Score=26.32 Aligned_cols=14 Identities=29% Similarity=0.551 Sum_probs=10.2
Q ss_pred CCccceEeeEEEEec
Q 032941 20 GKKFDKVSRIEAHSQ 34 (130)
Q Consensus 20 GKkFDrVSRI~a~S~ 34 (130)
++|+||| ||.|+-.
T Consensus 124 ~~kWDrv-kivC~QP 137 (153)
T PF01834_consen 124 EEKWDRV-KIVCSQP 137 (153)
T ss_dssp HS-EEEE-EEEEE-T
T ss_pred hcCccEE-EEEEeCC
Confidence 4789999 9999843
No 22
>PHA02146 hypothetical protein
Probab=23.18 E-value=50 Score=23.25 Aligned_cols=16 Identities=38% Similarity=0.607 Sum_probs=13.2
Q ss_pred eEEeeeECCCCCccce
Q 032941 10 IFVVEKIDPDGKKFDK 25 (130)
Q Consensus 10 ~F~V~~iD~dGKkFDr 25 (130)
-|+|+++|.||..|.|
T Consensus 28 ef~v~~~d~dgd~~s~ 43 (86)
T PHA02146 28 EFTVTNIDDDGDLYTY 43 (86)
T ss_pred EEEeeccccCCCeEee
Confidence 4899999999977654
No 23
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=23.05 E-value=71 Score=22.12 Aligned_cols=20 Identities=40% Similarity=0.918 Sum_probs=12.3
Q ss_pred eeeeEEeeeECCCCCccceEe
Q 032941 7 FEDIFVVEKIDPDGKKFDKVS 27 (130)
Q Consensus 7 FeD~F~V~~iD~dGKkFDrVS 27 (130)
|-.+|.|. +|.+...|+|||
T Consensus 42 YPsvFvV~-l~~~~~~~~rvS 61 (76)
T PF06257_consen 42 YPSVFVVE-LDQEENQFERVS 61 (76)
T ss_dssp -SSEEEEE-ES-S-SS-EEEE
T ss_pred cCcEEEEE-EccCCCceEEEE
Confidence 44578875 888877888887
No 24
>COG4263 NosZ Nitrous oxide reductase [Energy production and conversion]
Probab=22.48 E-value=1.2e+02 Score=28.32 Aligned_cols=39 Identities=23% Similarity=0.313 Sum_probs=25.0
Q ss_pred cccceEEeeeEEEeeecCCCCeEEEEEecCcceeeeeeeeeee
Q 032941 86 DKYEYIMHGKLFKIGDEGSGKSLKAYETTTQSIHYYFIWACVI 128 (130)
Q Consensus 86 D~ydYVMyGKVYk~e~e~~~~~~~vYiS~~~~~~~~~~~~~~~ 128 (130)
|.-+|+.||-|- -+-+-.+++-.|-++|+.||--|-||.
T Consensus 576 d~Ved~thgfv~----p~~~v~~~v~pq~tasvtf~a~kpgv~ 614 (637)
T COG4263 576 DEVEDLTHGFVI----PNYGVNMEVKPQRTASVTFYADKPGVA 614 (637)
T ss_pred ceeccccceeee----ccCceEEEEccCCceEEEEEccCCeee
Confidence 556777777653 123556666677777777777777663
No 25
>PRK05371 x-prolyl-dipeptidyl aminopeptidase; Provisional
Probab=22.20 E-value=1e+02 Score=29.28 Aligned_cols=29 Identities=17% Similarity=0.209 Sum_probs=26.6
Q ss_pred ceEEEEEecccccccccCCEEEEEEeeec
Q 032941 37 DMYMLLDVNSELYPMRVGDKFTMALAHTL 65 (130)
Q Consensus 37 ~m~l~LDINteLyPl~~gdk~~l~LastL 65 (130)
-++++++.+.-.|-+++|.+++|.|++|=
T Consensus 711 ~~~v~i~L~pt~~~~~~GHRLrL~I~ssd 739 (767)
T PRK05371 711 WYDVTFDLQPTDYVLPAGHQLGLVLYSTD 739 (767)
T ss_pred EEEEEEecccceeeeCCCCEEEEEEEecC
Confidence 37899999999999999999999999874
No 26
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.
Probab=21.99 E-value=1.5e+02 Score=20.26 Aligned_cols=52 Identities=19% Similarity=0.395 Sum_probs=32.5
Q ss_pred eEEeeeECCCCCccceEeeEEEEe--cCCceEEEE-Eecccccc---cccCCEEEEEEe
Q 032941 10 IFVVEKIDPDGKKFDKVSRIEAHS--QNCDMYMLL-DVNSELYP---MRVGDKFTMALA 62 (130)
Q Consensus 10 ~F~V~~iD~dGKkFDrVSRI~a~S--~~~~m~l~L-DINteLyP---l~~gdk~~l~La 62 (130)
.|.+..|+++-.+| |..||..+. .+....|.+ |=.+=+|| ++.+|++-+-|.
T Consensus 15 r~~l~~I~~eea~~-KLckV~~k~~~~gG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~ 72 (77)
T PF00900_consen 15 RFVLHPISEEEAKY-KLCKVRNKTTGKGGKPQLNTHDGRNIRYPDPDIKTNDTVVIDLP 72 (77)
T ss_dssp -EEEEEE-TTGGGE-EEEEEEEEEEEGGGEEEEEETTTEEEES-SST--TTEEEEEETT
T ss_pred cEEEEECCHHHccC-eEEEEeEEEEecCCcEEEEecCceEEEcCcCCccCCCEEEEECC
Confidence 58899999976643 344555543 355677777 77888888 677888877664
No 27
>PF11485 DUF3211: Protein of unknown function (DUF3211); InterPro: IPR021578 This archaeal family of proteins has no known function. ; PDB: 2EJX_A.
Probab=21.89 E-value=67 Score=24.56 Aligned_cols=13 Identities=15% Similarity=0.554 Sum_probs=11.0
Q ss_pred ccceEEeeeEEEe
Q 032941 87 KYEYIMHGKLFKI 99 (130)
Q Consensus 87 ~ydYVMyGKVYk~ 99 (130)
.+++.|||+||+=
T Consensus 52 ~~~~~~~G~vy~s 64 (136)
T PF11485_consen 52 GFPFEMKGNVYVS 64 (136)
T ss_dssp TEEEEEEEEEEEE
T ss_pred eEEEEEEEEEEEc
Confidence 4889999999965
No 28
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.
Probab=20.68 E-value=2.8e+02 Score=22.15 Aligned_cols=52 Identities=13% Similarity=0.110 Sum_probs=33.7
Q ss_pred ccceeeeEEeeeECCCCCccceEeeEE--EEecCCceEEEEEecccccccccCCEEEEEE
Q 032941 4 IVLFEDIFVVEKIDPDGKKFDKVSRIE--AHSQNCDMYMLLDVNSELYPMRVGDKFTMAL 61 (130)
Q Consensus 4 ~~LFeD~F~V~~iD~dGKkFDrVSRI~--a~S~~~~m~l~LDINteLyPl~~gdk~~l~L 61 (130)
+.+..-.|.|....-. =.++. -+-.++.|++...=+-.--++++||||+|.-
T Consensus 113 Gt~V~G~F~v~KK~v~------~~~~~YeI~DnTG~MeVvv~G~~~ni~CEeGDKLrL~c 166 (170)
T PF02760_consen 113 GTFVNGLFTVHKKTVN------KKNTIYEIQDNTGKMEVVVYGKWHNIKCEEGDKLRLFC 166 (170)
T ss_dssp TEEEEEEEEEEEEEEE------SSEEEEEEEETTEEEEEEEEGGGCGCC--TT-EEEEEE
T ss_pred CcEEeEEEEEEEEEEc------CCeEEEEEecCCCcEEEEEeccCcccccCCCCeEEEEE
Confidence 5677888988755431 11222 2245668999998888888999999999874
Done!