Query 022312
Match_columns 299
No_of_seqs 178 out of 1253
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 02:35:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022312.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022312hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00147 rpl4 ribosomal protei 100.0 2.8E-68 6.1E-73 483.3 17.8 197 98-298 6-207 (215)
2 PRK05319 rplD 50S ribosomal pr 100.0 5.7E-68 1.2E-72 478.0 18.4 198 99-298 1-198 (205)
3 PRK14547 rplD 50S ribosomal pr 100.0 8.2E-67 1.8E-71 492.5 18.4 200 98-298 1-201 (298)
4 PF00573 Ribosomal_L4: Ribosom 100.0 2.9E-65 6.4E-70 456.1 13.8 184 114-298 1-187 (192)
5 PRK14907 rplD 50S ribosomal pr 100.0 5.2E-64 1.1E-68 471.4 15.5 183 112-298 102-288 (295)
6 COG0088 RplD Ribosomal protein 100.0 3.9E-60 8.5E-65 429.7 14.8 199 98-297 1-203 (214)
7 PRK04042 rpl4lp 50S ribosomal 100.0 3.4E-59 7.4E-64 432.3 15.9 192 99-298 1-247 (254)
8 KOG1624 Mitochondrial/chloropl 100.0 8.9E-59 1.9E-63 430.0 16.9 238 56-297 13-255 (290)
9 TIGR03672 rpl4p_arch 50S ribos 100.0 2.5E-58 5.5E-63 425.7 16.4 192 99-298 1-246 (251)
10 PLN00185 60S ribosomal protein 100.0 7.7E-51 1.7E-55 394.7 17.3 195 99-297 7-262 (405)
11 PTZ00428 60S ribosomal protein 100.0 9E-47 2E-51 364.7 16.2 195 98-297 4-256 (381)
12 KOG1475 Ribosomal protein RPL1 100.0 1.1E-29 2.3E-34 238.4 10.6 195 98-295 4-252 (363)
13 PTZ00428 60S ribosomal protein 95.5 0.0085 1.8E-07 59.5 2.5 55 156-218 60-130 (381)
14 COG1618 Predicted nucleotide k 74.2 20 0.00044 32.5 8.2 85 196-280 79-165 (179)
15 KOG0333 U5 snRNP-like RNA heli 50.7 42 0.00092 35.6 6.5 88 173-267 472-565 (673)
16 PF03266 NTPase_1: NTPase; In 48.5 30 0.00065 30.3 4.5 69 216-284 94-163 (168)
17 COG1136 SalX ABC-type antimicr 41.3 78 0.0017 29.6 6.2 56 202-263 148-207 (226)
18 PRK10681 DNA-binding transcrip 38.2 2.2E+02 0.0047 26.4 8.7 59 206-274 77-139 (252)
19 PF07015 VirC1: VirC1 protein; 36.6 1.4E+02 0.003 28.2 7.1 75 220-295 3-92 (231)
20 PHA02324 hypothetical protein 35.2 29 0.00064 24.7 1.8 27 140-166 19-46 (47)
21 PF13514 AAA_27: AAA domain 34.8 89 0.0019 35.2 6.5 65 201-268 1032-1101(1111)
22 PF02463 SMC_N: RecF/RecN/SMC 33.5 49 0.0011 29.1 3.5 64 201-268 143-208 (220)
23 TIGR00201 comF comF family pro 24.8 60 0.0013 28.6 2.5 50 196-245 128-180 (190)
24 PRK13695 putative NTPase; Prov 23.9 3.8E+02 0.0083 22.7 7.3 66 217-282 96-162 (174)
25 cd03273 ABC_SMC2_euk Eukaryoti 22.7 2.2E+02 0.0047 25.9 5.8 65 203-270 173-240 (251)
26 PF07693 KAP_NTPase: KAP famil 21.9 1.1E+02 0.0024 28.4 3.7 50 220-270 175-225 (325)
27 cd03228 ABCC_MRP_Like The MRP 21.8 2.4E+02 0.0052 23.9 5.6 48 203-253 103-152 (171)
28 cd03251 ABCC_MsbA MsbA is an e 21.4 2.1E+02 0.0047 25.3 5.4 49 202-253 144-194 (234)
29 cd03369 ABCC_NFT1 Domain 2 of 20.7 2.6E+02 0.0057 24.3 5.7 50 201-253 130-181 (207)
30 cd03247 ABCC_cytochrome_bd The 20.1 2.6E+02 0.0057 23.8 5.5 49 202-253 104-154 (178)
No 1
>CHL00147 rpl4 ribosomal protein L4; Validated
Probab=100.00 E-value=2.8e-68 Score=483.31 Aligned_cols=197 Identities=34% Similarity=0.505 Sum_probs=187.0
Q ss_pred ceeeEEEccCCCe-eeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeeeecCCCCCccccCCCCccCCCCCC
Q 022312 98 DLVIPVTNFFNED-KGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176 (299)
Q Consensus 98 ~~~v~V~n~~ge~-~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~TKtRaEVsGsGrKp~rQKGTGrAR~Gs~r 176 (299)
.++++|+|++|+. +|+++|+++|| .+++.|+||++|+||++++|||||+||||+||+|||||||||||||||||||+|
T Consensus 6 ~~~~~v~~~~g~~~~~~~~l~~~vf-~~~~~~ll~~~v~~~~a~~R~gt~~tKtR~eV~G~grKp~~QKGTGrAR~Gs~r 84 (215)
T CHL00147 6 FLNYPVIDLTGKEKSETIKLKLNVL-EKSGNYLLHRALVRQNNNQRQGTASTKTRSEVRGGGRKPWKQKGTGRARAGSNR 84 (215)
T ss_pred eeeEEEEccCCCeecceEEeCHHHh-CCchHhHHHHHHHHHHHHHhhcccccCccccccCCCCCCcccCCCCccCCCCCc
Confidence 4689999999999 89999999999 557799999999999999999999999999999999999999999999999999
Q ss_pred CCcccCcccccCCCCccccccccHHHHHHHHHHHHHHHHHcCCeEEEecCC--CCCCCHHHHHHHHHhccCC--CcEEEE
Q 022312 177 GPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLE--VPSHKTKFIVNYYNQMENT--KKVLLC 252 (299)
Q Consensus 177 sP~~rGGG~afGPkPR~y~~klNKK~rrlAlksALSak~~~g~LiVVD~l~--~~~~KTK~~~~~Lk~l~~~--k~~LiV 252 (299)
||+|||||++|||+||+|+++||||+|++|+++|||+| +++|+|||+++ ++.+|||+++++|++++.. +++|||
T Consensus 85 sP~~rgGG~afgP~pR~y~~klnKKvrrlAl~sALS~k--~~~l~VVd~~~~~~~~~KTK~~~~~L~~l~~~~~~~~L~V 162 (215)
T CHL00147 85 SPLWKGGGVIFGPKPKTYSNKLNKKERRLALRTLLYNK--SNNITVVENFESSITNPKTKAFINLLKKLNINLDQKILII 162 (215)
T ss_pred CCcccCCEeecCCCCcchhhhcCHHHHHHHHHHHHHHh--hCCeEEEcccccccCCCCHHHHHHHHHHcCCCcCCceEEE
Confidence 99999999999999999999999999999999999998 45899999999 9999999999999999863 579999
Q ss_pred ecCCcchhHHHHhhCCCCceEEecCCCccccccccceEEEeeeccC
Q 022312 253 DGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKK 298 (299)
Q Consensus 253 ~~~~~~enl~~A~RNIp~V~v~~~~~LNv~dLl~~~~ifI~~~a~~ 298 (299)
+ ++.|+|+.+|+||||+|+++++++|||||||.+++++|+++|.+
T Consensus 163 ~-~~~~~nl~~S~rNlp~V~v~~~~~lNv~dLL~~~~vvit~~Al~ 207 (215)
T CHL00147 163 V-PEKTENLYLSTRNLKNVELISADTLNIKSLLKAKQIIITKEALK 207 (215)
T ss_pred E-CCCchHHHHHHhCCCCcEEEecCCccHHHHhcCCcEEEEHHHHH
Confidence 8 46789999999999999999999999999999999999999863
No 2
>PRK05319 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=5.7e-68 Score=478.03 Aligned_cols=198 Identities=45% Similarity=0.642 Sum_probs=192.7
Q ss_pred eeeEEEccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeeeecCCCCCccccCCCCccCCCCCCCC
Q 022312 99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGP 178 (299)
Q Consensus 99 ~~v~V~n~~ge~~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~TKtRaEVsGsGrKp~rQKGTGrAR~Gs~rsP 178 (299)
|+++|||++|+..|+++||++||+.|+|.||||++|+||++++|||||+||+|+||+|+|||||+||||||||+|++++|
T Consensus 1 ~~~~v~~~~g~~~~~i~l~~~vF~~~~r~dll~~~v~~~~~~~Rqgta~tk~r~ev~GsgrK~~~QKGTGrAR~Gs~rsP 80 (205)
T PRK05319 1 MELKVLNLDGKEAGEVELSDAVFGVEPNEALLHQVVVAQLANARQGTHATKTRSEVSGGGKKPWRQKGTGRARQGSIRSP 80 (205)
T ss_pred CeeEEEcCCCCCcceEEcCHHHhCCCccHHHHHHHHHHHHHhcccCcccCCcccccCCCCCCCCCCCCCCccCcCcccCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCcccccCCCCccccccccHHHHHHHHHHHHHHHHHcCCeEEEecCCCCCCCHHHHHHHHHhccCCCcEEEEecCCcc
Q 022312 179 QFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIH 258 (299)
Q Consensus 179 ~~rGGG~afGPkPR~y~~klNKK~rrlAlksALSak~~~g~LiVVD~l~~~~~KTK~~~~~Lk~l~~~k~~LiV~~~~~~ 258 (299)
+|||||+||||+||+|+++||||+|++|+++|||+++.+++|+|||+++++.+|||+++++|+++++ +++|||+ ++.+
T Consensus 81 ~~rGGg~afgpkpr~~~~klnkK~~~lAl~~aLs~k~~~~~l~Vvd~~~~~~~KTk~~~~~l~~lg~-~~~Lii~-~~~~ 158 (205)
T PRK05319 81 QWRGGGVVFGPKPRDYSQKLNKKVRRLALRSALSEKAREGRLVVVDDLSLEAPKTKELAAKLKNLGL-KKVLIVT-DEVD 158 (205)
T ss_pred cccCCeeeCCCCccchhhhcCHHHHHHHHHHHHHHHHhcCCeEEEeccccCCCCHHHHHHHHHHcCC-CceEEEE-CCCc
Confidence 9999999999999999999999999999999999999999999999999999999999999999997 7799998 4678
Q ss_pred hhHHHHhhCCCCceEEecCCCccccccccceEEEeeeccC
Q 022312 259 EKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKK 298 (299)
Q Consensus 259 enl~~A~RNIp~V~v~~~~~LNv~dLl~~~~ifI~~~a~~ 298 (299)
+|+.+|+||||+|+++++++||+||||+++.++|+++|.+
T Consensus 159 ~n~~~a~rNi~~v~v~~~~~ln~~dll~~~~vv~t~~Al~ 198 (205)
T PRK05319 159 ENLYLSARNLPNVDVLPAQGLNVYDLLRADKVVLTKAAVK 198 (205)
T ss_pred hHHHHHHhCCCCcEEEecCCccHHHhcCCCcEEEEHHHHH
Confidence 9999999999999999999999999999999999998864
No 3
>PRK14547 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=8.2e-67 Score=492.52 Aligned_cols=200 Identities=38% Similarity=0.535 Sum_probs=190.9
Q ss_pred ceeeEEEccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeeeecCCCCCccccCCCCccCCCCCCC
Q 022312 98 DLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRG 177 (299)
Q Consensus 98 ~~~v~V~n~~ge~~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~TKtRaEVsGsGrKp~rQKGTGrAR~Gs~rs 177 (299)
||+++|||++|+.+|+|+||++||+.++|.||||++|+||++++|||||+||||+||+|||||||+||||||||+||+||
T Consensus 1 M~~~~v~~~~g~~~g~ieL~~~vF~~~~r~dllh~vv~~q~a~~Rqgt~~tKtRaEV~G~GkKP~rQKGTGrAR~Gs~rs 80 (298)
T PRK14547 1 MATCDVLDWQGKKVGSAELPLKVFDVETNIPLIHQVVVAQMAAARQGTHHTKTRAEVRGGGKKPWRQKGTGRARQGSIRA 80 (298)
T ss_pred CceeEEeccCCCCcceEECCHHHhCCCccHHHHHHHHHHHHHhhhcCCCCCCceeeccCCCCCccCCCCCcccCcCCccC
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccCcccccCCCCccccccccHHHHHHHHHHHHHHHHHcCCeEEEecCC-CCCCCHHHHHHHHHhccCCCcEEEEecCC
Q 022312 178 PQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLE-VPSHKTKFIVNYYNQMENTKKVLLCDGGC 256 (299)
Q Consensus 178 P~~rGGG~afGPkPR~y~~klNKK~rrlAlksALSak~~~g~LiVVD~l~-~~~~KTK~~~~~Lk~l~~~k~~LiV~~~~ 256 (299)
|+|||||++|||+||+|+++||||+|++||++|||+++++++|+|||++. ++.+|||+++++|++++..+++|||+ ++
T Consensus 81 P~wrGGGvafGPkpR~y~~klNKK~rrlAlrsALS~k~~~~~liVVd~~~~~~~~KTK~~~~~L~~l~~~~~lLiv~-~~ 159 (298)
T PRK14547 81 PQWRGGGTVHGPRPREYNQRTPKKMRQAALRGALSDRARDNRLIVVESLQDGDPPSTKAVAQALSVMEDQRALLVVA-ER 159 (298)
T ss_pred CceeCCeeecCCCCchhhhhcCHHHHHHHHHHHHHHHHhcCCEEEEeCccccCCcCHHHHHHHHHhcccCceEEEEe-cC
Confidence 99999999999999999999999999999999999999999999999996 89999999999999998546677776 45
Q ss_pred cchhHHHHhhCCCCceEEecCCCccccccccceEEEeeeccC
Q 022312 257 IHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYYFLDFDFKK 298 (299)
Q Consensus 257 ~~enl~~A~RNIp~V~v~~~~~LNv~dLl~~~~ifI~~~a~~ 298 (299)
.++++.+|+||||+|+++++++|||||||.++.|+|+++|.+
T Consensus 160 ~~~~~~ls~RNL~~V~v~~~~~lNv~dLl~~~~vViT~~Al~ 201 (298)
T PRK14547 160 SDAVERLSVRNLARVHVLGADQLNTYDVLNVDWVVFTQSALE 201 (298)
T ss_pred ccHHHHHHHhCCCCcEEEecCCccHHHHhCCCCEEEEHHHHH
Confidence 677888999999999999999999999999999999998864
No 4
>PF00573 Ribosomal_L4: Ribosomal protein L4/L1 family; InterPro: IPR002136 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 ribosomal L4/L1 from eukaryotes and plants and L4 from bacteria. L4 from yeast has been shown to bind rRNA []. These proteins have 246 (plant) to 427 (human) amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZR_D 1VSA_D 3D5D_F 3MS1_E 3F1F_F 3PYO_E 3MRZ_E 3F1H_F 3PYR_E 1VSP_D ....
Probab=100.00 E-value=2.9e-65 Score=456.09 Aligned_cols=184 Identities=48% Similarity=0.717 Sum_probs=174.4
Q ss_pred EEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeeeecCCCCCccccCCCCccCCCCCCCCcccCcccccCCCC-c
Q 022312 114 MVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKP-R 192 (299)
Q Consensus 114 ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~TKtRaEVsGsGrKp~rQKGTGrAR~Gs~rsP~~rGGG~afGPkP-R 192 (299)
|+|||+||+.|+|.||||+||+||++++||||++||+|+||+|+|||||+||||||||+|+++||+|||||++|||+| |
T Consensus 1 i~L~~~vF~~~~r~~llh~~v~~~~~~~Rqgt~~tktr~ev~g~grKp~~QKGTGrAR~Gs~rsP~~rgGg~afgPkp~r 80 (192)
T PF00573_consen 1 IELSPDVFNVPVRPDLLHRAVVWQLANRRQGTASTKTRSEVSGSGRKPWPQKGTGRARQGSIRSPQWRGGGVAFGPKPPR 80 (192)
T ss_dssp -ES-CGGGGSSTSHHHHHHHHHHHHHHTSSBT-SSSTSTTSSSSSSSSSSSSSSSSSSSSSCTSTTSTTSSBSSSSSSTS
T ss_pred CCCCHHHhCCCCcHHHHHHHHHHHHHhccCCccCCccceEEecccCcccCCCCCcccccCccccceeeccEEecCCcccc
Confidence 689999999999999999999999999999999999999999999999999999999999999999999999999998 9
Q ss_pred cccccccHHHHHHHHHHHHHHHHHcCCeEEEecCC-CCCCCHHHHHHHHHhccC-CCcEEEEecCCcchhHHHHhhCCCC
Q 022312 193 SHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLE-VPSHKTKFIVNYYNQMEN-TKKVLLCDGGCIHEKLKLATQNLHY 270 (299)
Q Consensus 193 ~y~~klNKK~rrlAlksALSak~~~g~LiVVD~l~-~~~~KTK~~~~~Lk~l~~-~k~~LiV~~~~~~enl~~A~RNIp~ 270 (299)
+|+++||||+|++|+++|||+|+.+++|+|||+++ ++.+|||+++++|+++++ ++++|||++ +.|+++.+|+||||+
T Consensus 81 ~~~~klnkK~r~lAl~~aLs~k~~~~~l~vvd~~~~~~~~kTk~~~~~L~~~~~~~~~~L~V~~-~~~~~~~~a~rNl~~ 159 (192)
T PF00573_consen 81 DYSYKLNKKVRRLALRSALSAKAAEGNLIVVDNFSPLEEPKTKDLVKLLKKLGLKGKSVLFVVG-EENENLFRASRNLPG 159 (192)
T ss_dssp BCSHHHHHHHHHHHHHHHHHHHHHTTHHHHCTSCSSSSSSSHHHHHHHHHHTTTSSSSEEEEES-STSHCHHHHHCTSTT
T ss_pred cceecCChHHHHHHHHHHHHHhhcccceEEeeccccccccCHHHHHHHHHHhhhcccceEEEec-CCchHHHHHHHccCC
Confidence 99999999999999999999999999999999998 999999999999999998 678999994 679999999999999
Q ss_pred ceEEecCCCccccccccceEEEeeeccC
Q 022312 271 VNVLPSVVRSTTQSFLIYYYFLDFDFKK 298 (299)
Q Consensus 271 V~v~~~~~LNv~dLl~~~~ifI~~~a~~ 298 (299)
|+++++++|||||||++++++|+++|.+
T Consensus 160 v~~~~~~~lnv~dll~~~~lv~t~~Al~ 187 (192)
T PF00573_consen 160 VDVLPVEGLNVYDLLKADKLVITKSALE 187 (192)
T ss_dssp EEEEESTG--HHHHCHSSEEEEEHHHHH
T ss_pred eEEEecCcEeHHHHhCCCcEEEEHHHHH
Confidence 9999999999999999999999999864
No 5
>PRK14907 rplD 50S ribosomal protein L4; Provisional
Probab=100.00 E-value=5.2e-64 Score=471.36 Aligned_cols=183 Identities=34% Similarity=0.475 Sum_probs=174.7
Q ss_pred eeEEcCccccCCC-CchhHHHHHHHHHHHHcccCCCCCceeeeecCCCCCccccCCCCccCCCCCCCCcccCcccccCCC
Q 022312 112 GFMVLAGDVFDVP-IRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPK 190 (299)
Q Consensus 112 g~ieLp~~VF~~p-ir~dilh~vv~~q~anrRqGta~TKtRaEVsGsGrKp~rQKGTGrAR~Gs~rsP~~rGGG~afGPk 190 (299)
..++|+++||+.+ ++.++||++|+||++++|||||+||+|+||+|||||||||||||||||||+|||+|||||++|||+
T Consensus 102 ~~ieL~~~vF~~e~~~~~llh~~V~~q~A~~RqGT~~TKtRsEVsGggkKPwrQKGTGRAR~GS~RSP~wrGGGvaFGPk 181 (295)
T PRK14907 102 NTSKLPKKLFASEKIYSQAIFDTILSERASRRQGTHKVKTRAEVSGTGKKPWRQKGTGRARAGSTRSPIFVGGGRAFGPT 181 (295)
T ss_pred ceEEeCHHHhCCCccchhHHHHHHHHHHHHhccccccccchhhccCCCCCCcccCCCCccCCCCCcCCcccCCeeecCCC
Confidence 3599999999999 899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred C-ccccccccHHHHHHHHHHHHHHHHHcCCeEEEecCCCCCCCHHHHHHHHHhccCC--CcEEEEecCCcchhHHHHhhC
Q 022312 191 P-RSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENT--KKVLLCDGGCIHEKLKLATQN 267 (299)
Q Consensus 191 P-R~y~~klNKK~rrlAlksALSak~~~g~LiVVD~l~~~~~KTK~~~~~Lk~l~~~--k~~LiV~~~~~~enl~~A~RN 267 (299)
| |+|+++||||+|++||++|||+++++ +|+|||+|+++.+|||+++++|++++.+ +++|||+ .|+|+.+|+||
T Consensus 182 P~RdY~~KLNKKvRrLALrsALS~ka~~-~LvVVd~~~le~~KTK~l~~~L~~lgl~~~k~vLiV~---~denl~lSaRN 257 (295)
T PRK14907 182 PERNYKLKVNKKVRFNAFVSALTLLANS-KAVLVDDFKLEKISTKDLIKKLTKLKINNLKHILIVS---NDENIFKSARN 257 (295)
T ss_pred CccchhhhcCHHHHHHHHHHHHHHhccC-CEEEEecccCCCCCHHHHHHHHHHcCcccCCceEEEE---CCchHHHHHhC
Confidence 8 99999999999999999999999876 7999999999999999999999999863 4799998 26799999999
Q ss_pred CCCceEEecCCCccccccccceEEEeeeccC
Q 022312 268 LHYVNVLPSVVRSTTQSFLIYYYFLDFDFKK 298 (299)
Q Consensus 268 Ip~V~v~~~~~LNv~dLl~~~~ifI~~~a~~ 298 (299)
||+|+|+++++|||||||.+++|||+.+|.+
T Consensus 258 Lp~V~Vl~~~~LNVydLL~~~~vViT~~Al~ 288 (295)
T PRK14907 258 LQNVIVVKPTSLSVELLIAADVLVLSKESIE 288 (295)
T ss_pred CCCceEeecCCccHHHHhcCCcEEEeHHHHH
Confidence 9999999999999999999999999999864
No 6
>COG0088 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.9e-60 Score=429.72 Aligned_cols=199 Identities=42% Similarity=0.577 Sum_probs=189.7
Q ss_pred ceeeEEEccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCCceeeeecCCCCCccccCCCCccCCCCCCC
Q 022312 98 DLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRG 177 (299)
Q Consensus 98 ~~~v~V~n~~ge~~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~TKtRaEVsGsGrKp~rQKGTGrAR~Gs~rs 177 (299)
||+++|||++|+.+|++++++.||..+.+.||||+||+||++++|||||++|+|+||+|+|+|||+|||||+||+|++++
T Consensus 1 m~k~~v~~~~G~~~g~~~~~~~vf~~~~~~dli~~av~a~~a~~RQgt~~~k~rgevs~~g~Kp~~QkgtgraR~gs~rs 80 (214)
T COG0088 1 MMKLKVYDLDGEEVGEVELLPEVFGPERNEDLIHRAVLAQLANRRQGTHSTKTRGEVSGGGKKPWGQKGTGRARQGSIRS 80 (214)
T ss_pred CCcceEeCCCCCCccccccChhhccCCchHHHHHHHHHHHHHhhhccCCCCCCcccccccCcCCCCCCcCCcCCCCCCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccCcccccCCCC-ccccccccHHHHHHHHHHHHHHHHHcCCeEEEecCCCC-CCCHHHHHHHHHhccCCC-cEEEEec
Q 022312 178 PQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVP-SHKTKFIVNYYNQMENTK-KVLLCDG 254 (299)
Q Consensus 178 P~~rGGG~afGPkP-R~y~~klNKK~rrlAlksALSak~~~g~LiVVD~l~~~-~~KTK~~~~~Lk~l~~~k-~~LiV~~ 254 (299)
|+|||||++|||+| |+|+++||||||++||++|||+++++++|+++|++.++ .+|||+++++|++++.+. .+|++.
T Consensus 81 P~~rGGg~a~gPkp~r~~~~klnkK~rrlAl~sAls~ka~~~~lv~~~~~~~~~~~kTK~~~~~lk~l~~~~~~~l~~~- 159 (214)
T COG0088 81 PQWRGGGVAHGPKPERDYSQKLNKKERRLALRSALSAKARAGKLVVVRGHVFEDAPKTKELVEFLKKLGLDVKRLLIVK- 159 (214)
T ss_pred CeeecCccccCCCCccchhhhcCHHHHHHHHHHHHHHhccCCCEEEEecccccCCccHHHHHHHHHHhhhhhceeEEee-
Confidence 99999999999999 99999999999999999999999999999999999999 999999999999987654 466665
Q ss_pred CCcchhHHHHhhCCCCceEEecCC-CccccccccceEEEeeecc
Q 022312 255 GCIHEKLKLATQNLHYVNVLPSVV-RSTTQSFLIYYYFLDFDFK 297 (299)
Q Consensus 255 ~~~~enl~~A~RNIp~V~v~~~~~-LNv~dLl~~~~ifI~~~a~ 297 (299)
...++|+.++.|||+++.++.+.+ +|+||++.+++++|+++|.
T Consensus 160 ~~~~~n~~ls~Rnl~~~~~~~~~~~~~~~Dv~~~~~l~i~~~A~ 203 (214)
T COG0088 160 GERDGNGKLSARNLKNVKVVLVVGGLPVVDVLRADKLVITKLAP 203 (214)
T ss_pred cccccceeecccCCCCceeeeeeccccceEEEeecceeeeHhhh
Confidence 467889999999999999999998 9999999999999999885
No 7
>PRK04042 rpl4lp 50S ribosomal protein L4P; Provisional
Probab=100.00 E-value=3.4e-59 Score=432.27 Aligned_cols=192 Identities=29% Similarity=0.305 Sum_probs=181.8
Q ss_pred eeeEEEccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCC-----CCCceeeeecCCCC---CccccCCCCcc
Q 022312 99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGT-----HSTKTISEVSGTGK---KPWRQKGTGRA 170 (299)
Q Consensus 99 ~~v~V~n~~ge~~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGt-----a~TKtRaEVsGsGr---Kp~rQKGTGrA 170 (299)
|+++|||++|+.+|+++||+ ||+.++|.|+||+||+||++|+|||| |+||||+||||+|| |||||||||||
T Consensus 1 ~~v~v~~~~g~~~g~i~L~~-vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~ta~tKtraev~G~Gr~~~Kp~rQKGTGrA 79 (254)
T PRK04042 1 MKAKVYDLDGEVVGEIELPA-VFEEPVRPDLIRRAVLAAQTARLQPKGRDPLAGKRTSAESWGSGRGIARVPRLKGGSRA 79 (254)
T ss_pred CeeEEEcCCCCCcceEehhH-hhCCCCcHHHHHHHHHHHHHhccCCCCCCccccCccceeEcCCCCCcCcCCccCCCCCc
Confidence 68999999999999999995 99999999999999999999999994 88999999999999 99999999999
Q ss_pred CCCCCCCCcccCcccccCCCC-ccccccccHHHHHHHHHHHHHHHHHcC---------------CeEEEecCCCCCCCHH
Q 022312 171 RHGTLRGPQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKIALSARAAEG---------------KLLVFEDLEVPSHKTK 234 (299)
Q Consensus 171 R~Gs~rsP~~rGGG~afGPkP-R~y~~klNKK~rrlAlksALSak~~~g---------------~LiVVD~l~~~~~KTK 234 (299)
| |+|+|||||++|||+| |+|+++||||+|++|+++|||+++.++ +|+|||+++ +.+|||
T Consensus 80 r----rsP~~rGGgv~fgPkp~R~y~~klnkK~rrlAlrsALs~k~~~~lv~~~~~~~~~~~e~~lvvvd~~~-~~~KTK 154 (254)
T PRK04042 80 A----FVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATANPELVKARGHVFEGVPELPLVVVDDFE-SLKKTK 154 (254)
T ss_pred c----ccCccCcCCeeCCCCCCcccccccCHHHHHHHHHHHHHHhhhhhhhhhcCccccCCCccCEEEEcccc-cccCHH
Confidence 8 9999999999999999 999999999999999999999999984 899999999 999999
Q ss_pred HHHHHHHhccCC---------------------------CcEEEEecCCcchhHHHHhhCCCCceEEecCCCcccccccc
Q 022312 235 FIVNYYNQMENT---------------------------KKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLI 287 (299)
Q Consensus 235 ~~~~~Lk~l~~~---------------------------k~~LiV~~~~~~enl~~A~RNIp~V~v~~~~~LNv~dLl~~ 287 (299)
+++++|++++.+ +++|||++ + |+++.+|+||||+|+++++++||+|||+.+
T Consensus 155 ~~~~~Lk~lg~~~~~~~~~~~~~~~~~kgk~r~~~~~~~~~~LiV~~-~-d~~~~~s~RNi~~v~v~~~~~lnv~dLl~~ 232 (254)
T PRK04042 155 EVRELLEKLGLYDDVERAKEGKKIRAGKGKMRGRRYKKPKSVLIVVS-D-DSPIVKAARNLPGVDVVTVDNLNVEHLAPG 232 (254)
T ss_pred HHHHHHHHcCCcccchhhhccceecccccccccccccCCCccEEEEc-C-CcceeehhcCCCCCEEEecCCccHHHhhCc
Confidence 999999999863 36999994 5 889999999999999999999999999998
Q ss_pred ----ceEEEeeeccC
Q 022312 288 ----YYYFLDFDFKK 298 (299)
Q Consensus 288 ----~~ifI~~~a~~ 298 (299)
+.+|++.+|.+
T Consensus 233 ~~~~~~vv~t~~Al~ 247 (254)
T PRK04042 233 GHPGRLTVWTESAIE 247 (254)
T ss_pred CCCCCeEEEEHHHHH
Confidence 77999998854
No 8
>KOG1624 consensus Mitochondrial/chloroplast ribosomal protein L4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=8.9e-59 Score=430.04 Aligned_cols=238 Identities=41% Similarity=0.635 Sum_probs=218.5
Q ss_pred hhhcccccccccCCCCCCCCCCCcccccccccCcccccCCC--cceeeEEEccCCCeeeeEEcCccccCCCCchhHHHHH
Q 022312 56 FLASRKFSTTILTPDSSEGAFPSDLLLKKTVLTPDITIGLH--QDLVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRV 133 (299)
Q Consensus 56 ~~~~~~~~~~~~~~~~~~~~~p~~l~~~~~~~~~~~~~~~~--~~~~v~V~n~~ge~~g~ieLp~~VF~~pir~dilh~v 133 (299)
++..|.++++..++ ...+++. +-...+.+|+.....+ +...+++..+++|++|.++||+++|.+++|.||||++
T Consensus 13 ~ss~~~l~ss~~~~---~~~~~s~-l~~~~~~~p~~p~~~~p~qa~v~~~~~~e~E~~gl~~l~~dvf~~~~RrDIlhra 88 (290)
T KOG1624|consen 13 FSSKRNLVSSTQSP---PEQITSA-LHKESTLKPELPVSIPPKQAWVEPLDFFELEKVGLVDLHPDVFAEPPRRDILHRA 88 (290)
T ss_pred HHHHHHHHhhccCC---ccccccc-cccccccCcCCCCCcChhhheeeeccccccccceeeecChhhhccchHHHHHHHH
Confidence 44556777776553 2456666 6666777777766655 7788888899999999999999999999999999999
Q ss_pred HHHHHHHcccCCCCCceeeeecCCCCCccccCCCCccCCCCCCCCcccCcccccCCC-CccccccccHHHHHHHHHHHHH
Q 022312 134 VRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLRGPQFRGGTTMHGPK-PRSHAIKLNKKVRRLGLKIALS 212 (299)
Q Consensus 134 v~~q~anrRqGta~TKtRaEVsGsGrKp~rQKGTGrAR~Gs~rsP~~rGGG~afGPk-PR~y~~klNKK~rrlAlksALS 212 (299)
|+||.+|+|+|||+||||+||+|||||||+||||||||+|+.|||+++|||++|||+ ||+|++|||+|+|.+||++|||
T Consensus 89 v~wq~~nrrvgtastktRaEv~ggGrKp~~QKgtGrAr~Gs~rsP~r~gGg~~~gpr~P~d~~~~Lp~kvr~lgl~~ALS 168 (290)
T KOG1624|consen 89 VVWQLDNRRVGTASTKTRAEVRGGGRKPWPQKGTGRARVGSLRSPQRRGGGVAHGPRGPRDYSYKLPSKVRSLGLKIALS 168 (290)
T ss_pred HHHhhcccccccccCCccccccCCCCCcCcccCCCcccccCccCcccCCCccccCCCCCcchhhhccHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999 9999999999999999999999
Q ss_pred HHHHcCCeEEEecCCCCCCCHHHHHHHHHhccCCCcEEEEecC--CcchhHHHHhhCCCCceEEecCCCccccccccceE
Q 022312 213 ARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGG--CIHEKLKLATQNLHYVNVLPSVVRSTTQSFLIYYY 290 (299)
Q Consensus 213 ak~~~g~LiVVD~l~~~~~KTK~~~~~Lk~l~~~k~~LiV~~~--~~~enl~~A~RNIp~V~v~~~~~LNv~dLl~~~~i 290 (299)
++++|+.++|+|++.++++|||...+++...+++.++|+|+.. +.++|+.+|.+||++++++++.+|||||+|++|.+
T Consensus 169 ~~~a~~~l~I~d~~~L~t~~pk~~~~l~~~~~~g~~vl~v~~~~~~~~e~l~~as~~L~~~n~ip~~glnv~s~lk~dtl 248 (290)
T KOG1624|consen 169 AKLAQDDLHIVDELGLPTGKPKYLLNLLAQRNWGTSVLFVDEDHFEFDENLALASRRLGYLNLIPVGGLNVFSILKHDTL 248 (290)
T ss_pred HHHhCCceEEecccCCCCCCcHHHHHHHHHHhcCCeeEEeccchhhchHHHHHHhhccCeeEeecccccchhhhhhcCce
Confidence 9999999999999999999999999999999998889999853 47899999999999999999999999999999999
Q ss_pred EEeeecc
Q 022312 291 FLDFDFK 297 (299)
Q Consensus 291 fI~~~a~ 297 (299)
+|+.+|.
T Consensus 249 vlt~~aV 255 (290)
T KOG1624|consen 249 VLTREAV 255 (290)
T ss_pred EecHHHH
Confidence 9999874
No 9
>TIGR03672 rpl4p_arch 50S ribosomal protein L4P. One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome.
Probab=100.00 E-value=2.5e-58 Score=425.68 Aligned_cols=192 Identities=29% Similarity=0.325 Sum_probs=181.3
Q ss_pred eeeEEEccCCCeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCC-----CCCceeeeecCCCC---CccccCCCCcc
Q 022312 99 LVIPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGT-----HSTKTISEVSGTGK---KPWRQKGTGRA 170 (299)
Q Consensus 99 ~~v~V~n~~ge~~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGt-----a~TKtRaEVsGsGr---Kp~rQKGTGrA 170 (299)
|+++|||++|+..|+++|| +||+.|+|.|+||+||+||++|+|||| |+||||+||||+|| |||||||||||
T Consensus 1 m~~~v~~~~g~~~~~i~l~-~vF~~~~~~~lv~~vv~~~~an~Rqgt~~~~~a~tKtraev~G~Grg~aKp~rQKGTGrA 79 (251)
T TIGR03672 1 MKAKVYDLDGEVVGEIELP-AVFEEPVRPDLIKRAVLAAQTNRLQPYGADPYAGKRTSAESWGSGRGIARVPRIKGGSRA 79 (251)
T ss_pred CceEEEccCCCCcceEehH-HhhCCCccHHHHHHHHHHHHHhccCCCCCCcccCcccceeEccCCCCcCCCCccCCCCcc
Confidence 6899999999999999999 599999999999999999999999999 56999999999999 99999999999
Q ss_pred CCCCCCCCcccCcccccCCCC-ccccccccHHHHHHHHHHHHHHHHHcC--------------CeEEEecCCCCCCCHHH
Q 022312 171 RHGTLRGPQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKIALSARAAEG--------------KLLVFEDLEVPSHKTKF 235 (299)
Q Consensus 171 R~Gs~rsP~~rGGG~afGPkP-R~y~~klNKK~rrlAlksALSak~~~g--------------~LiVVD~l~~~~~KTK~ 235 (299)
+|+|+|||||++|||+| |+|+++||||+|++|+++|||+++.++ +|+|||+++ +.+|||+
T Consensus 80 ----~rsP~~rGGGv~fgPkp~R~y~~klNkK~rrlAl~sALs~k~~~~lv~~~~~~~~~~e~~lvVvd~~~-~~~KTK~ 154 (251)
T TIGR03672 80 ----ARVPQAVGGRRAHPPKVEKDLHEKINKKERRLAIRSAIAATADPELVKARGHVFEGDELPIVVVDDFE-SLKKTKE 154 (251)
T ss_pred ----eecCccCcCCeeCCCCCCcccceecCHHHHHHHHHHHHHHhcchhhhhhcccccccccccEEEEeCCC-CCCCHHH
Confidence 69999999999999999 999999999999999999999999988 899999999 9999999
Q ss_pred HHHHHHhccCC---------------------------CcEEEEecCCcchhHHHHhhCCCCceEEecCCCcccccccc-
Q 022312 236 IVNYYNQMENT---------------------------KKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSFLI- 287 (299)
Q Consensus 236 ~~~~Lk~l~~~---------------------------k~~LiV~~~~~~enl~~A~RNIp~V~v~~~~~LNv~dLl~~- 287 (299)
++++|++++.+ +++|||++ + ++++.+|+||||+|+++++++||+|||+.+
T Consensus 155 ~~~~Lk~l~~~~~~~~~~~~~~~~~~kgk~~~r~~~~~~~~LiV~~-~-~~~l~~s~RNi~~V~v~~~~~lNv~dLl~~~ 232 (251)
T TIGR03672 155 VRELLEALGVYDDIERAKEGKKIRAGKGKMRGRRYKEPKSVLIVVG-D-DSGISKAARNLPGVDVVTVNNLNVEHLAPGG 232 (251)
T ss_pred HHHHHHHcCCccccchhhccceeeccccccccccccCCCccEEEEc-C-CcchhhhhcCCCCCEEEecCCccHHHhhCcC
Confidence 99999999863 36999984 4 689999999999999999999999999999
Q ss_pred ---ceEEEeeeccC
Q 022312 288 ---YYYFLDFDFKK 298 (299)
Q Consensus 288 ---~~ifI~~~a~~ 298 (299)
+.++++.+|.+
T Consensus 233 ~~~~~vv~t~~Al~ 246 (251)
T TIGR03672 233 HPGRLTVWTESAIE 246 (251)
T ss_pred CCCCeEEEEHHHHH
Confidence 77999998853
No 10
>PLN00185 60S ribosomal protein L4-1; Provisional
Probab=100.00 E-value=7.7e-51 Score=394.71 Aligned_cols=195 Identities=25% Similarity=0.234 Sum_probs=177.8
Q ss_pred eeeEEEccCC----CeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCC-----ceeeeecCCCCCcc---ccC-
Q 022312 99 LVIPVTNFFN----EDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHST-----KTISEVSGTGKKPW---RQK- 165 (299)
Q Consensus 99 ~~v~V~n~~g----e~~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~T-----KtRaEVsGsGrKp~---rQK- 165 (299)
..|+|||++| +.+|+++|| +||+.|+|+||||+||+++++|+||||+.+ +|++||||+||||| |||
T Consensus 7 p~v~V~~~~g~~~~~~~~~v~Lp-~VF~~piR~dlv~~v~~~~~~n~RQp~~~~~~AG~qtsAeswGtGR~vaRiPR~kg 85 (405)
T PLN00185 7 PLVSVQSLDGDMATDKSATVALP-DVMTAPIRPDIVNFVHTNISKNSRQPYAVSKKAGHQTSAESWGTGRAVSRIPRVPG 85 (405)
T ss_pred CeeEEEcCCCCccccccceeehH-HHhCCCCCHHHHHHHHHHHHHhccCCCCCCcccCCcceeeecCCCCCceecccccC
Confidence 4689999999 678999999 999999999999999999999999999998 99999999999999 999
Q ss_pred -CCCccCCCCCCCCcccCcccccCCCC--ccccccccHHHHHHHHHHHHHHHHH------cC-Ce-------EEEecCCC
Q 022312 166 -GTGRARHGTLRGPQFRGGTTMHGPKP--RSHAIKLNKKVRRLGLKIALSARAA------EG-KL-------LVFEDLEV 228 (299)
Q Consensus 166 -GTGrAR~Gs~rsP~~rGGG~afGPkP--R~y~~klNKK~rrlAlksALSak~~------~g-~L-------iVVD~l~~ 228 (299)
||||||||++ |+|+|||++|||+| |+|+++||+|+|++|++||||+++. .| +| +||||+..
T Consensus 86 gGT~RAgqGa~--~~~~rGGr~FgP~p~~R~~~~KvNkK~rRlAl~SALAa~a~~~lV~arGH~i~~v~e~pLVV~d~~e 163 (405)
T PLN00185 86 GGTHRAGQGAF--GNMCRGGRMFAPTKTWRRWHRKVNVNQKRYAVVSALAASAVPSLVMARGHKIENVPEVPLVVSDSAE 163 (405)
T ss_pred CCCCcCCccCc--CCcCCCCeeCCCCCCccccccccCHHHHHHHHHHHHHhhccchhhhcccccccccccCCEEEEeCcc
Confidence 8999999998 99999999999999 9999999999999999999999993 33 22 57777767
Q ss_pred CCCCHHHHHHHHHhccCC---------------------------CcEEEEecCCcchhHHHHhhCCCCceEEecCCCcc
Q 022312 229 PSHKTKFIVNYYNQMENT---------------------------KKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRST 281 (299)
Q Consensus 229 ~~~KTK~~~~~Lk~l~~~---------------------------k~~LiV~~~~~~enl~~A~RNIp~V~v~~~~~LNv 281 (299)
+.+|||+++++|++++.+ +++|||++ +.++++.+|+||||+|+++++++||+
T Consensus 164 ~~~KTK~av~~Lk~lg~~~d~~k~~~s~~iRaGkGKmR~Rr~~~~kg~LIV~~-~~~~~l~kA~RNIPgV~v~~v~~LNv 242 (405)
T PLN00185 164 SIEKTSAAIKILKQIGAYADVEKAKDSKGIRAGKGKMRNRRYVSRKGPLVVYG-TEGAKIVKAFRNIPGVELCSVDRLNL 242 (405)
T ss_pred CCcCHHHHHHHHHHcCCcccchhhhcccccccccccccccccccCCceEEEEc-CCchhhhhhhcCCCCCeEEecCCccH
Confidence 789999999999999852 35999994 56778999999999999999999999
Q ss_pred ccccccce----EEEeeecc
Q 022312 282 TQSFLIYY----YFLDFDFK 297 (299)
Q Consensus 282 ~dLl~~~~----ifI~~~a~ 297 (299)
|||+++++ +|++++|.
T Consensus 243 ~dLapggh~gr~vI~TesA~ 262 (405)
T PLN00185 243 LQLAPGGHLGRFVIWTKSAF 262 (405)
T ss_pred HHHhccCCCCCEEEEEhHHH
Confidence 99999885 99998874
No 11
>PTZ00428 60S ribosomal protein L4; Provisional
Probab=100.00 E-value=9e-47 Score=364.68 Aligned_cols=195 Identities=23% Similarity=0.218 Sum_probs=162.7
Q ss_pred ceeeEEEccCC-CeeeeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCCC-----ceeeeecCCCCCcc---ccC--C
Q 022312 98 DLVIPVTNFFN-EDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHST-----KTISEVSGTGKKPW---RQK--G 166 (299)
Q Consensus 98 ~~~v~V~n~~g-e~~g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~T-----KtRaEVsGsGrKp~---rQK--G 166 (299)
-++++|||.+| +..|+++|| +||+.|+|+||||+||++|++|+||||+.+ ++++|+||+||+++ ||| |
T Consensus 4 r~~v~V~~~~g~~~~~~v~Lp-~VF~~pir~dlV~~vv~~~~aN~RQgta~s~~ag~~tsakswGTGRA~aripR~kg~G 82 (381)
T PTZ00428 4 RPVVSVYSASDKSVVGTVPLP-AVFTAPIRPDLVQFVHTNMAKNRRQAYAVKPLAGMQHSAESWGTGRAVARIPRVSGGG 82 (381)
T ss_pred CCeeEEEcCCCCcccceEehH-HhhCCCCcHHHHHHHHHHHHHhccCCCCcCCCCCCCCCceecCCCCCccccccccCCC
Confidence 47899999998 668999999 899999999999999999999999999998 55666666666666 666 5
Q ss_pred CCccCCCCCCCCcccCcccccCCCC--ccccccccHHHHHHHHHHHHHHHHH-------cCCe-------EEEecCCCCC
Q 022312 167 TGRARHGTLRGPQFRGGTTMHGPKP--RSHAIKLNKKVRRLGLKIALSARAA-------EGKL-------LVFEDLEVPS 230 (299)
Q Consensus 167 TGrAR~Gs~rsP~~rGGG~afGPkP--R~y~~klNKK~rrlAlksALSak~~-------~g~L-------iVVD~l~~~~ 230 (299)
|+||+||++ +| |++||++|||+| |+|+++||+|+|++|+++|||+++. .++| +||||+....
T Consensus 83 T~Rs~qGa~-~n-~~rGG~~FgP~~~~R~~~~KvNkK~rR~Al~SALaa~a~~~lv~argh~i~~v~e~plVV~d~~e~~ 160 (381)
T PTZ00428 83 THRSGQGAF-GN-MCRGGRMFAPTKTWRRWHRKVNLNQKRHAVASALAASGVPALVMARGHRISNVPEVPLVVSDSVESY 160 (381)
T ss_pred CCcCccccc-CC-cCCCceEcCCCCCccccccccCHHHHHHHHHHHHHhhccchhhhcccccccccccCCEEEEcCcCCC
Confidence 556666655 44 666666999999 9999999999999999999999974 2233 5566654455
Q ss_pred CCHHHHHHHHHhccCC---------------------------CcEEEEecCCcchhHHHHhhCCCCceEEecCCCcccc
Q 022312 231 HKTKFIVNYYNQMENT---------------------------KKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQ 283 (299)
Q Consensus 231 ~KTK~~~~~Lk~l~~~---------------------------k~~LiV~~~~~~enl~~A~RNIp~V~v~~~~~LNv~d 283 (299)
+|||+++++|++++.+ +++|||++ + |+++.+|+||||+|+++++++||+||
T Consensus 161 ~KTK~av~~Lk~lg~~~d~~k~~~s~~~R~gkGk~R~rr~~~~~g~LIV~~-~-d~~l~~A~RNIpgV~v~~v~~LNv~d 238 (381)
T PTZ00428 161 EKTKEAVAFLKALGAFDDVNRVNDSKKIRAGKGKMRNRRYVMRRGPLVVYA-N-DNGVTKAFRNIPGVDLCNVTRLNLLQ 238 (381)
T ss_pred CCHHHHHHHHHHcCCcccchhhhcccccccccccccccccccCCceEEEEc-C-CcchhhhhcCCCCcEEEecCCccHHH
Confidence 8999999999999853 23999993 3 78899999999999999999999999
Q ss_pred ccccce----EEEeeecc
Q 022312 284 SFLIYY----YFLDFDFK 297 (299)
Q Consensus 284 Ll~~~~----ifI~~~a~ 297 (299)
|+.+++ +|++.+|.
T Consensus 239 Lapggh~gr~vI~TesA~ 256 (381)
T PTZ00428 239 LAPGGHVGRFIIWTKSAF 256 (381)
T ss_pred HhccCCCCCEEEEEhHHH
Confidence 999764 88888764
No 12
>KOG1475 consensus Ribosomal protein RPL1/RPL2/RL4L4 [RNA processing and modification]
Probab=99.96 E-value=1.1e-29 Score=238.40 Aligned_cols=195 Identities=23% Similarity=0.214 Sum_probs=165.8
Q ss_pred ceeeEEEccCCCee-eeEEcCccccCCCCchhHHHHHHHHHHHHcccCCCC-----CceeeeecCCCCCcc---ccCCCC
Q 022312 98 DLVIPVTNFFNEDK-GFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHS-----TKTISEVSGTGKKPW---RQKGTG 168 (299)
Q Consensus 98 ~~~v~V~n~~ge~~-g~ieLp~~VF~~pir~dilh~vv~~q~anrRqGta~-----TKtRaEVsGsGrKp~---rQKGTG 168 (299)
...|.||+.+|+.+ +.+.|| +||..|+|+||++.++.....|+||.++. .+|.+|+||+||... |.+|.|
T Consensus 4 rp~vtvy~~~g~~s~~~l~lp-~vf~aPiRpdlv~~v~~~~~~n~rQpyAVs~kAG~QtSAESWGTGRAvaRiPRV~GGG 82 (363)
T KOG1475|consen 4 RPLVTVYSLDGEASKKTLTLP-AVFSAPIRPDLVNFVHTQVRKNRRQPYAVSEKAGHQTSAESWGTGRAVARIPRVGGGG 82 (363)
T ss_pred cceeeEEeccccccccccccc-ceeccCCcHHHHHHHHHHHhhccccchhhhhhhccccchhhcccccceecccccCCCC
Confidence 35789999999975 579999 99999999999999999999999998875 889999999999988 688888
Q ss_pred ccCCCCCCCCcccCcccccCCC--CccccccccHHHHHHHHHHHHHHHHHc------C-------C-eEEEecCCCCCCC
Q 022312 169 RARHGTLRGPQFRGGTTMHGPK--PRSHAIKLNKKVRRLGLKIALSARAAE------G-------K-LLVFEDLEVPSHK 232 (299)
Q Consensus 169 rAR~Gs~rsP~~rGGG~afGPk--PR~y~~klNKK~rrlAlksALSak~~~------g-------~-LiVVD~l~~~~~K 232 (299)
..|.|+.--..++.||.+|.|. .|.|+.++|..+++.|+.+|+++.+.. | + -+||+|-.....|
T Consensus 83 T~RsGQgAFgNmCR~GrMfaPtKt~RrW~rkVn~n~Kr~A~asaiaasavpaLv~arGHrIe~VpelPlVVsd~ve~~~K 162 (363)
T KOG1475|consen 83 THRSGQGAFGNMCRGGRMFAPTKTWRRWHRKVNENEKRYAIASAIAASAVPALVMARGHRIEEVPELPLVVSDKVESFRK 162 (363)
T ss_pred cccccchhhhhhcccccccCchhhHHHHhhhhhhhhhhhHHHhhhhhhhhhHHHHhcCccccccccCceEeehhhHHHHh
Confidence 8888887656666667777776 499999999999999999999998762 1 1 2566665557889
Q ss_pred HHHHHHHHHhccCC---------------------------CcEEEEecCCcchhHHHHhhCCCCceEEecCCCcccccc
Q 022312 233 TKFIVNYYNQMENT---------------------------KKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQSF 285 (299)
Q Consensus 233 TK~~~~~Lk~l~~~---------------------------k~~LiV~~~~~~enl~~A~RNIp~V~v~~~~~LNv~dLl 285 (299)
||+++.+|++++.+ +++|||++ +|..+.+||||||||++++++.||+++|.
T Consensus 163 TkeAV~~Lk~~~a~~di~kv~~S~~~RaGKGKmRNRr~~QrrGPlVVy~--Ed~~ivkAFRNIpGV~~~nV~~LnlLkLA 240 (363)
T KOG1475|consen 163 TKEAVALLKKLKAWNDIKKVYNSRRLRAGKGKMRNRRYIQRRGPLVVYN--EDNGIVKAFRNIPGVELMNVERLNLLKLA 240 (363)
T ss_pred HHHHHHHHHHhccHHHHHHHHhhcccccCccchhhhhhhhhcCCEEEEe--cCcchhhhhcCCCcceeechhhhhhhhcC
Confidence 99999999998642 57999993 57779999999999999999999999999
Q ss_pred ccce--EEEeee
Q 022312 286 LIYY--YFLDFD 295 (299)
Q Consensus 286 ~~~~--ifI~~~ 295 (299)
+..+ .||-|+
T Consensus 241 PGghlGRfvIWT 252 (363)
T KOG1475|consen 241 PGGHLGRFVIWT 252 (363)
T ss_pred CCcccceeEEee
Confidence 9998 455443
No 13
>PTZ00428 60S ribosomal protein L4; Provisional
Probab=95.49 E-value=0.0085 Score=59.48 Aligned_cols=55 Identities=31% Similarity=0.357 Sum_probs=38.7
Q ss_pred CCCCCccccCCCCccCC--------CCCCCCcccCcccccCCCC---cccc-----ccccHHHHHHHHHHHHHHHHHcC
Q 022312 156 GTGKKPWRQKGTGRARH--------GTLRGPQFRGGTTMHGPKP---RSHA-----IKLNKKVRRLGLKIALSARAAEG 218 (299)
Q Consensus 156 GsGrKp~rQKGTGrAR~--------Gs~rsP~~rGGG~afGPkP---R~y~-----~klNKK~rrlAlksALSak~~~g 218 (299)
++++||| ||||||+ |+.||||= +|||-- +-|. .+..+|+=+.--+.||..-++.-
T Consensus 60 ~tsaksw---GTGRA~aripR~kg~GT~Rs~qG-----a~~n~~rGG~~FgP~~~~R~~~~KvNkK~rR~Al~SALaa~ 130 (381)
T PTZ00428 60 QHSAESW---GTGRAVARIPRVSGGGTHRSGQG-----AFGNMCRGGRMFAPTKTWRRWHRKVNLNQKRHAVASALAAS 130 (381)
T ss_pred CCCceec---CCCCCccccccccCCCCCcCccc-----ccCCcCCCceEcCCCCCccccccccCHHHHHHHHHHHHHhh
Confidence 7899999 9999998 66666651 335543 4455 34567777777888888777653
No 14
>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=74.19 E-value=20 Score=32.49 Aligned_cols=85 Identities=16% Similarity=0.088 Sum_probs=53.4
Q ss_pred ccccHHHHHHHHHHHHHHHHHcCCeEEEecCCCCCCCHHHHHHHHHhccCCCcEEEEe-cCCcchhHHHHhhCCCCceE-
Q 022312 196 IKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCD-GGCIHEKLKLATQNLHYVNV- 273 (299)
Q Consensus 196 ~klNKK~rrlAlksALSak~~~g~LiVVD~l~~~~~KTK~~~~~Lk~l~~~k~~LiV~-~~~~~enl~~A~RNIp~V~v- 273 (299)
|-+|-+.-.--.--||.-.+.+-+++|||..---+-|++.+.+.+...-.+.++||.+ .-.....+..-.+++..+-+
T Consensus 79 Y~V~v~~le~i~~~al~rA~~~aDvIIIDEIGpMElks~~f~~~ve~vl~~~kpliatlHrrsr~P~v~~ik~~~~v~v~ 158 (179)
T COG1618 79 YGVNVEGLEEIAIPALRRALEEADVIIIDEIGPMELKSKKFREAVEEVLKSGKPLIATLHRRSRHPLVQRIKKLGGVYVF 158 (179)
T ss_pred EEeeHHHHHHHhHHHHHHHhhcCCEEEEecccchhhccHHHHHHHHHHhcCCCcEEEEEecccCChHHHHhhhcCCEEEE
Confidence 4455554432333455544455689999987545668888888888753344556544 11223458889999999888
Q ss_pred EecCCCc
Q 022312 274 LPSVVRS 280 (299)
Q Consensus 274 ~~~~~LN 280 (299)
+..++=|
T Consensus 159 lt~~NR~ 165 (179)
T COG1618 159 LTPENRN 165 (179)
T ss_pred Eccchhh
Confidence 6655544
No 15
>KOG0333 consensus U5 snRNP-like RNA helicase subunit [RNA processing and modification]
Probab=50.74 E-value=42 Score=35.62 Aligned_cols=88 Identities=18% Similarity=0.214 Sum_probs=57.2
Q ss_pred CCCCCCcccCcccccCCCCcc--ccccccHHHHHHHHHHHHHHHHHcCCeEEEecCCCCCCCHHH-HHHHHHhccCCCcE
Q 022312 173 GTLRGPQFRGGTTMHGPKPRS--HAIKLNKKVRRLGLKIALSARAAEGKLLVFEDLEVPSHKTKF-IVNYYNQMENTKKV 249 (299)
Q Consensus 173 Gs~rsP~~rGGG~afGPkPR~--y~~klNKK~rrlAlksALSak~~~g~LiVVD~l~~~~~KTK~-~~~~Lk~l~~~k~~ 249 (299)
+-.+-|.|+-+|.++.|.||- ..+.+.--.++.+|.-+|...+ +..++|+=+ ..|+-+ +.+.|.+++. .+
T Consensus 472 ~ylr~pv~vtig~~gk~~~rveQ~v~m~~ed~k~kkL~eil~~~~-~ppiIIFvN----~kk~~d~lAk~LeK~g~--~~ 544 (673)
T KOG0333|consen 472 SYLRRPVVVTIGSAGKPTPRVEQKVEMVSEDEKRKKLIEILESNF-DPPIIIFVN----TKKGADALAKILEKAGY--KV 544 (673)
T ss_pred HHhhCCeEEEeccCCCCccchheEEEEecchHHHHHHHHHHHhCC-CCCEEEEEe----chhhHHHHHHHHhhccc--eE
Confidence 346889999999999999974 4455555666888888888763 345555432 334433 4556666664 46
Q ss_pred EEEecC---CcchhHHHHhhC
Q 022312 250 LLCDGG---CIHEKLKLATQN 267 (299)
Q Consensus 250 LiV~~~---~~~enl~~A~RN 267 (299)
...+|+ +..++....+|+
T Consensus 545 ~tlHg~k~qeQRe~aL~~fr~ 565 (673)
T KOG0333|consen 545 TTLHGGKSQEQRENALADFRE 565 (673)
T ss_pred EEeeCCccHHHHHHHHHHHHh
Confidence 666753 334666667777
No 16
>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []. It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.
Probab=48.47 E-value=30 Score=30.27 Aligned_cols=69 Identities=9% Similarity=0.062 Sum_probs=38.9
Q ss_pred HcCCeEEEecCCCCCCCHHHHHHHHHh-ccCCCcEEEEecCCcchhHHHHhhCCCCceEEecCCCccccc
Q 022312 216 AEGKLLVFEDLEVPSHKTKFIVNYYNQ-MENTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTTQS 284 (299)
Q Consensus 216 ~~g~LiVVD~l~~~~~KTK~~~~~Lk~-l~~~k~~LiV~~~~~~enl~~A~RNIp~V~v~~~~~LNv~dL 284 (299)
.+.+++|+|.+=.-+-+.+.+.+.+.+ |...+.+|-+.....+..+....++.+++.++.+..-|--.|
T Consensus 94 ~~~~liviDEIG~mEl~~~~F~~~v~~~l~s~~~vi~vv~~~~~~~~l~~i~~~~~~~i~~vt~~NRd~l 163 (168)
T PF03266_consen 94 SSSDLIVIDEIGKMELKSPGFREAVEKLLDSNKPVIGVVHKRSDNPFLEEIKRRPDVKIFEVTEENRDAL 163 (168)
T ss_dssp HCCHEEEE---STTCCC-CHHHHHHHHHHCTTSEEEEE--SS--SCCHHHHHTTTTSEEEE--TTTCCCH
T ss_pred CCCCEEEEeccchhhhcCHHHHHHHHHHHcCCCcEEEEEecCCCcHHHHHHHhCCCcEEEEeChhHHhhH
Confidence 567899999864334455555555555 343334454542222666999999999999999988885443
No 17
>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=41.33 E-value=78 Score=29.61 Aligned_cols=56 Identities=14% Similarity=0.302 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHHHcCCeEEEecC--CCCCCCHHHHHHHHHhccC--CCcEEEEecCCcchhHHH
Q 022312 202 VRRLGLKIALSARAAEGKLLVFEDL--EVPSHKTKFIVNYYNQMEN--TKKVLLCDGGCIHEKLKL 263 (299)
Q Consensus 202 ~rrlAlksALSak~~~g~LiVVD~l--~~~~~KTK~~~~~Lk~l~~--~k~~LiV~~~~~~enl~~ 263 (299)
..|.|+.-||.. +-+|++.|.- +++....+.+.++|+++.. +..+++|+ +|..+..
T Consensus 148 qQRVAIARAL~~---~P~iilADEPTgnLD~~t~~~V~~ll~~~~~~~g~tii~VT---Hd~~lA~ 207 (226)
T COG1136 148 QQRVAIARALIN---NPKIILADEPTGNLDSKTAKEVLELLRELNKERGKTIIMVT---HDPELAK 207 (226)
T ss_pred HHHHHHHHHHhc---CCCeEEeeCccccCChHHHHHHHHHHHHHHHhcCCEEEEEc---CCHHHHH
Confidence 455777777765 4678888874 5788889999999999853 33566665 4555544
No 18
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=38.19 E-value=2.2e+02 Score=26.37 Aligned_cols=59 Identities=15% Similarity=0.041 Sum_probs=31.1
Q ss_pred HHHHHHHHHH----HcCCeEEEecCCCCCCCHHHHHHHHHhccCCCcEEEEecCCcchhHHHHhhCCCCceEE
Q 022312 206 GLKIALSARA----AEGKLLVFEDLEVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHYVNVL 274 (299)
Q Consensus 206 AlksALSak~----~~g~LiVVD~l~~~~~KTK~~~~~Lk~l~~~k~~LiV~~~~~~enl~~A~RNIp~V~v~ 274 (299)
..|.+|+.++ .+|..+.+|+-. .+-.+.+.|.. .+.+-||+ ++-++...+.+-|+++++
T Consensus 77 ~~K~~IA~~Aa~lI~~g~tIflD~Gt----T~~~la~~L~~---~~~ltvvT---nsl~i~~~l~~~~~~~vi 139 (252)
T PRK10681 77 EEKRRAAQLAATLVEPNQTLFFDCGT----TTPWIIEAIDN---ELPFTAVC---YSLNTFLALQEKPHCRAI 139 (252)
T ss_pred HHHHHHHHHHHhhcCCCCEEEEECCc----cHHHHHHhcCC---CCCeEEEE---CCHHHHHHHhhCCCCEEE
Confidence 3344444444 478889999754 23344444432 12345555 244455555556666655
No 19
>PF07015 VirC1: VirC1 protein; InterPro: IPR009744 This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon, which enhances T-DNA processing probably, does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA [].
Probab=36.63 E-value=1.4e+02 Score=28.17 Aligned_cols=75 Identities=13% Similarity=0.185 Sum_probs=40.8
Q ss_pred eEEEecCCCCCCCHHHHHHHHHhcc-CCCcEEEEecCCcchhHHHHhhCC------C-CceEEecCCCcc-cccc-----
Q 022312 220 LLVFEDLEVPSHKTKFIVNYYNQME-NTKKVLLCDGGCIHEKLKLATQNL------H-YVNVLPSVVRST-TQSF----- 285 (299)
Q Consensus 220 LiVVD~l~~~~~KTK~~~~~Lk~l~-~~k~~LiV~~~~~~enl~~A~RNI------p-~V~v~~~~~LNv-~dLl----- 285 (299)
+|++=+..--..||-.+..+...+- .++++.+|+ .+.|.++....+|- + .+.|...+.+.. .+.+
T Consensus 3 vItf~s~KGGaGKTT~~~~LAs~la~~G~~V~lID-aDpn~pl~~W~~~a~~~~~~~~~~~V~~~~e~~~l~~~~e~a~~ 81 (231)
T PF07015_consen 3 VITFASSKGGAGKTTAAMALASELAARGARVALID-ADPNQPLAKWAENAQRPGAWPDRIEVYEADELTILEDAYEAAEA 81 (231)
T ss_pred eEEEecCCCCCcHHHHHHHHHHHHHHCCCeEEEEe-CCCCCcHHHHHHhccccCCCCCCeeEEeccchhhHHHHHHHHHh
Confidence 3444455556667777666666653 346777777 45666666664432 1 234554444432 2221
Q ss_pred -ccceEEEeee
Q 022312 286 -LIYYYFLDFD 295 (299)
Q Consensus 286 -~~~~ifI~~~ 295 (299)
-++++||+.+
T Consensus 82 ~~~d~VlvDle 92 (231)
T PF07015_consen 82 SGFDFVLVDLE 92 (231)
T ss_pred cCCCEEEEeCC
Confidence 2466777764
No 20
>PHA02324 hypothetical protein
Probab=35.17 E-value=29 Score=24.71 Aligned_cols=27 Identities=37% Similarity=0.573 Sum_probs=22.5
Q ss_pred HcccCCC-CCceeeeecCCCCCccccCC
Q 022312 140 KRQQGTH-STKTISEVSGTGKKPWRQKG 166 (299)
Q Consensus 140 nrRqGta-~TKtRaEVsGsGrKp~rQKG 166 (299)
+.|||.- +||-.+..+.+-|||||.-|
T Consensus 19 ~TRQG~G~~TKysATsRN~akK~YRGQG 46 (47)
T PHA02324 19 KTRQGQGKNTKYSATSRNNAKKPYRGQG 46 (47)
T ss_pred cccccCCccceeeeeccccccCcccCCC
Confidence 5788865 59999999999999998654
No 21
>PF13514 AAA_27: AAA domain
Probab=34.75 E-value=89 Score=35.18 Aligned_cols=65 Identities=18% Similarity=0.399 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHHHH-cC-Ce-EEEecC--CCCCCCHHHHHHHHHhccCCCcEEEEecCCcchhHHHHhhCC
Q 022312 201 KVRRLGLKIALSARAA-EG-KL-LVFEDL--EVPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNL 268 (299)
Q Consensus 201 K~rrlAlksALSak~~-~g-~L-iVVD~l--~~~~~KTK~~~~~Lk~l~~~k~~LiV~~~~~~enl~~A~RNI 268 (299)
-+--+||+.|+...+. ++ .+ +|+||. +++...++.++++|..+....=+|+.+ ..+.+...++.+
T Consensus 1032 dQLYLALRLA~~e~~~~~~~~lP~IlDD~fvnfDd~R~~~~l~~L~~ls~~~QVI~FT---ch~~l~~~a~~~ 1101 (1111)
T PF13514_consen 1032 DQLYLALRLALAELLAEQGEPLPFILDDIFVNFDDERARAALELLAELSRRRQVIYFT---CHEHLVELAREV 1101 (1111)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCcEEeeCCccccCHHHHHHHHHHHHHhccCCeEEEEe---ccHHHHHHHHHh
Confidence 4456999999999993 33 33 888984 578889999999999997644466665 345566656654
No 22
>PF02463 SMC_N: RecF/RecN/SMC N terminal domain; InterPro: IPR003395 This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression []. The domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.; PDB: 3HTK_A 1W1W_C 2WD5_A 3L51_A 1XEW_Y 3KTA_B 3NWC_B 1XEX_A 1GXL_C 1GXK_A ....
Probab=33.52 E-value=49 Score=29.13 Aligned_cols=64 Identities=11% Similarity=0.293 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHcCCeEEEecCC--CCCCCHHHHHHHHHhccCCCcEEEEecCCcchhHHHHhhCC
Q 022312 201 KVRRLGLKIALSARAAEGKLLVFEDLE--VPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNL 268 (299)
Q Consensus 201 K~rrlAlksALSak~~~g~LiVVD~l~--~~~~KTK~~~~~Lk~l~~~k~~LiV~~~~~~enl~~A~RNI 268 (299)
+.-.+|+..|+.. .....++++|+.+ ++....+.+.++|+.+....-++|++ .++.+...+.++
T Consensus 143 ~~~~Lal~lA~~~-~~~~p~~ilDEvd~~LD~~~~~~l~~~l~~~~~~~Q~ii~T---h~~~~~~~a~~~ 208 (220)
T PF02463_consen 143 SLVALALLLALQR-YKPSPFLILDEVDAALDEQNRKRLADLLKELSKQSQFIITT---HNPEMFEDADKL 208 (220)
T ss_dssp HHHHHHHHHHHHT-CS--SEEEEESTTTTS-HHHHHHHHHHHHHHTTTSEEEEE----S-HHHHTT-SEE
T ss_pred ccccccccccccc-ccccccccccccccccccccccccccccccccccccccccc---cccccccccccc
Confidence 4444555555333 2345789999875 66777888999999886433344444 455555544443
No 23
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=24.85 E-value=60 Score=28.62 Aligned_cols=50 Identities=16% Similarity=0.220 Sum_probs=33.6
Q ss_pred ccccHHHHHHHHHHHHHHH---HHcCCeEEEecCCCCCCCHHHHHHHHHhccC
Q 022312 196 IKLNKKVRRLGLKIALSAR---AAEGKLLVFEDLEVPSHKTKFIVNYYNQMEN 245 (299)
Q Consensus 196 ~klNKK~rrlAlksALSak---~~~g~LiVVD~l~~~~~KTK~~~~~Lk~l~~ 245 (299)
..+++++|+.-++.+++.+ ....++++|||.--.-....++.+.|++.|.
T Consensus 128 ~~l~~~~R~~n~~~~f~~~~~~~~~~~vllvDDV~TTGaTl~~~~~~L~~~Ga 180 (190)
T TIGR00201 128 SKLKATLRFLNLENAFDLKNNSFQGRNIVLVDDVVTTGATLHEIARLLLELGA 180 (190)
T ss_pred ccCCHHHHHHHHhCcEEccCCCCCCCEEEEEeeeeccHHHHHHHHHHHHHcCC
Confidence 4567788877777776543 2223689999975433344778888888776
No 24
>PRK13695 putative NTPase; Provisional
Probab=23.90 E-value=3.8e+02 Score=22.67 Aligned_cols=66 Identities=9% Similarity=0.026 Sum_probs=38.8
Q ss_pred cCCeEEEecCCCCCCCHHHHHHHHHhcc-CCCcEEEEecCCcchhHHHHhhCCCCceEEecCCCccc
Q 022312 217 EGKLLVFEDLEVPSHKTKFIVNYYNQME-NTKKVLLCDGGCIHEKLKLATQNLHYVNVLPSVVRSTT 282 (299)
Q Consensus 217 ~g~LiVVD~l~~~~~KTK~~~~~Lk~l~-~~k~~LiV~~~~~~enl~~A~RNIp~V~v~~~~~LNv~ 282 (299)
..+++++|.+-..+..+..+.+.+.++- ....++++........+..-...++.+.+..+..-|=-
T Consensus 96 ~~~~lllDE~~~~e~~~~~~~~~l~~~~~~~~~~i~v~h~~~~~~~~~~i~~~~~~~i~~~~~~~r~ 162 (174)
T PRK13695 96 EADVIIIDEIGKMELKSPKFVKAVEEVLDSEKPVIATLHRRSVHPFVQEIKSRPGGRVYELTPENRD 162 (174)
T ss_pred CCCEEEEECCCcchhhhHHHHHHHHHHHhCCCeEEEEECchhhHHHHHHHhccCCcEEEEEcchhhh
Confidence 5689999975333445555566666643 33445554422212235556778888888877666643
No 25
>cd03273 ABC_SMC2_euk Eukaryotic SMC2 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (fo
Probab=22.70 E-value=2.2e+02 Score=25.88 Aligned_cols=65 Identities=9% Similarity=0.139 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHHcC-CeEEEecCC--CCCCCHHHHHHHHHhccCCCcEEEEecCCcchhHHHHhhCCCC
Q 022312 203 RRLGLKIALSARAAEG-KLLVFEDLE--VPSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHY 270 (299)
Q Consensus 203 rrlAlksALSak~~~g-~LiVVD~l~--~~~~KTK~~~~~Lk~l~~~k~~LiV~~~~~~enl~~A~RNIp~ 270 (299)
++.++..||+.-+..+ +++++|.-. ++....+.+.++|+.+..+..+++|. ++..+...+..+=+
T Consensus 173 qr~~la~al~~~~~~~~~illlDEPt~~ld~~~~~~~~~~l~~~~~g~~ii~iS---H~~~~~~~~d~v~~ 240 (251)
T cd03273 173 SLVALSLILALLLFKPAPMYILDEVDAALDLSHTQNIGRMIKTHFKGSQFIVVS---LKEGMFNNANVLFR 240 (251)
T ss_pred HHHHHHHHHHHhhccCCCEEEEeCCCcCCCHHHHHHHHHHHHHHcCCCEEEEEE---CCHHHHHhCCEEEE
Confidence 4567777776433334 799999743 55555677788888774433466665 23334444554433
No 26
>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].
Probab=21.86 E-value=1.1e+02 Score=28.36 Aligned_cols=50 Identities=10% Similarity=0.111 Sum_probs=30.4
Q ss_pred eEEEecCCC-CCCCHHHHHHHHHhccCCCcEEEEecCCcchhHHHHhhCCCC
Q 022312 220 LLVFEDLEV-PSHKTKFIVNYYNQMENTKKVLLCDGGCIHEKLKLATQNLHY 270 (299)
Q Consensus 220 LiVVD~l~~-~~~KTK~~~~~Lk~l~~~k~~LiV~~~~~~enl~~A~RNIp~ 270 (299)
+++|||++- +..+-.++.+.++.+.....+.+|.. -..+.+..|..+.-+
T Consensus 175 ViiIDdLDR~~~~~i~~~l~~ik~~~~~~~i~~Il~-~D~~~l~~ai~~~~~ 225 (325)
T PF07693_consen 175 VIIIDDLDRCSPEEIVELLEAIKLLLDFPNIIFILA-FDPEILEKAIEKNYG 225 (325)
T ss_pred EEEEcchhcCCcHHHHHHHHHHHHhcCCCCeEEEEE-ecHHHHHHHHHhhcC
Confidence 578899873 44445666666666544355555552 235567777776554
No 27
>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=21.80 E-value=2.4e+02 Score=23.93 Aligned_cols=48 Identities=15% Similarity=0.350 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHcCCeEEEecCC--CCCCCHHHHHHHHHhccCCCcEEEEe
Q 022312 203 RRLGLKIALSARAAEGKLLVFEDLE--VPSHKTKFIVNYYNQMENTKKVLLCD 253 (299)
Q Consensus 203 rrlAlksALSak~~~g~LiVVD~l~--~~~~KTK~~~~~Lk~l~~~k~~LiV~ 253 (299)
+++++..||+. +-+++++|+-. ++......+.++|+.+..+..+|++.
T Consensus 103 ~rl~la~al~~---~p~llllDEP~~gLD~~~~~~l~~~l~~~~~~~tii~~s 152 (171)
T cd03228 103 QRIAIARALLR---DPPILILDEATSALDPETEALILEALRALAKGKTVIVIA 152 (171)
T ss_pred HHHHHHHHHhc---CCCEEEEECCCcCCCHHHHHHHHHHHHHhcCCCEEEEEe
Confidence 55677777764 56899999743 55555677888888875434455554
No 28
>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=21.42 E-value=2.1e+02 Score=25.26 Aligned_cols=49 Identities=8% Similarity=0.304 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHcCCeEEEecC--CCCCCCHHHHHHHHHhccCCCcEEEEe
Q 022312 202 VRRLGLKIALSARAAEGKLLVFEDL--EVPSHKTKFIVNYYNQMENTKKVLLCD 253 (299)
Q Consensus 202 ~rrlAlksALSak~~~g~LiVVD~l--~~~~~KTK~~~~~Lk~l~~~k~~LiV~ 253 (299)
.+++++..||+. +-+++++|+- .++...+..+.++|+++..+..++++.
T Consensus 144 ~qrv~la~al~~---~p~lllLDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~s 194 (234)
T cd03251 144 RQRIAIARALLK---DPPILILDEATSALDTESERLVQAALERLMKNRTTFVIA 194 (234)
T ss_pred HHHHHHHHHHhc---CCCEEEEeCccccCCHHHHHHHHHHHHHhcCCCEEEEEe
Confidence 356777777775 4579999974 366666788889998875434555555
No 29
>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1). NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.
Probab=20.74 E-value=2.6e+02 Score=24.31 Aligned_cols=50 Identities=16% Similarity=0.179 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHHcCCeEEEecCC--CCCCCHHHHHHHHHhccCCCcEEEEe
Q 022312 201 KVRRLGLKIALSARAAEGKLLVFEDLE--VPSHKTKFIVNYYNQMENTKKVLLCD 253 (299)
Q Consensus 201 K~rrlAlksALSak~~~g~LiVVD~l~--~~~~KTK~~~~~Lk~l~~~k~~LiV~ 253 (299)
..+|+++..||.. +-+++++|+-. ++....+.+.++|+++..+..++++.
T Consensus 130 ~~qrv~laral~~---~p~llllDEP~~~LD~~~~~~l~~~l~~~~~~~tiii~t 181 (207)
T cd03369 130 QRQLLCLARALLK---RPRVLVLDEATASIDYATDALIQKTIREEFTNSTILTIA 181 (207)
T ss_pred HHHHHHHHHHHhh---CCCEEEEeCCcccCCHHHHHHHHHHHHHhcCCCEEEEEe
Confidence 3567888888864 56899999743 44445567788888874334455555
No 30
>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.
Probab=20.05 E-value=2.6e+02 Score=23.79 Aligned_cols=49 Identities=10% Similarity=0.224 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHcCCeEEEecC--CCCCCCHHHHHHHHHhccCCCcEEEEe
Q 022312 202 VRRLGLKIALSARAAEGKLLVFEDL--EVPSHKTKFIVNYYNQMENTKKVLLCD 253 (299)
Q Consensus 202 ~rrlAlksALSak~~~g~LiVVD~l--~~~~~KTK~~~~~Lk~l~~~k~~LiV~ 253 (299)
.+++++..||+. +-+++++|+- .++....+.+.++|+++..+..++++.
T Consensus 104 ~qrv~laral~~---~p~~lllDEP~~~LD~~~~~~l~~~l~~~~~~~tii~~s 154 (178)
T cd03247 104 RQRLALARILLQ---DAPIVLLDEPTVGLDPITERQLLSLIFEVLKDKTLIWIT 154 (178)
T ss_pred HHHHHHHHHHhc---CCCEEEEECCcccCCHHHHHHHHHHHHHHcCCCEEEEEe
Confidence 356677777765 4589999974 355555677888888875433455555
Done!