Query 026466
Match_columns 238
No_of_seqs 52 out of 54
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 08:22:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026466.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026466hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10236 hypothetical protein; 100.0 7.3E-33 1.6E-37 245.4 9.1 110 59-179 7-126 (237)
2 COG4735 Uncharacterized protei 99.4 4.1E-14 8.9E-19 124.5 -0.8 71 98-178 14-86 (211)
3 COG4735 Uncharacterized protei 97.2 8.5E-05 1.9E-09 66.3 0.4 47 132-178 1-49 (211)
4 PF13099 DUF3944: Domain of un 95.3 0.015 3.2E-07 39.3 2.5 21 64-84 7-27 (35)
5 PF03250 Tropomodulin: Tropomo 84.9 1.3 2.9E-05 38.1 4.1 31 53-83 109-139 (147)
6 PF03981 Ubiq_cyt_C_chap: Ubiq 70.5 2.8 6E-05 33.2 1.7 46 115-179 4-50 (141)
7 PF02173 pKID: pKID domain; I 55.6 8.4 0.00018 27.1 1.7 13 138-150 18-30 (41)
8 PF15008 DUF4518: Domain of un 54.1 21 0.00046 33.2 4.5 92 60-181 6-97 (262)
9 PF06603 UpxZ: UpxZ family of 50.1 57 0.0012 27.1 5.9 96 117-238 5-105 (106)
10 PF11248 DUF3046: Protein of u 47.2 36 0.00077 25.7 4.0 44 115-158 5-62 (63)
11 PF04542 Sigma70_r2: Sigma-70 45.6 40 0.00086 22.5 3.8 35 142-179 5-39 (71)
12 PRK14082 hypothetical protein; 43.2 17 0.00037 27.8 1.8 30 162-191 33-62 (65)
13 TIGR02989 Sig-70_gvs1 RNA poly 42.0 34 0.00075 26.5 3.4 37 141-180 9-45 (159)
14 PRK09532 DNA polymerase III su 41.2 17 0.00037 38.4 2.0 50 106-158 410-460 (874)
15 cd06406 PB1_P67 A PB1 domain i 39.9 23 0.0005 27.7 2.1 39 137-189 18-56 (80)
16 PF01371 Trp_repressor: Trp re 38.9 47 0.001 26.0 3.7 23 64-86 8-30 (87)
17 PRK07279 dnaE DNA polymerase I 37.2 23 0.0005 38.4 2.3 51 106-159 343-394 (1034)
18 PLN02502 lysyl-tRNA synthetase 36.5 1.2E+02 0.0026 30.7 7.0 91 89-179 304-432 (553)
19 PRK05898 dnaE DNA polymerase I 36.0 30 0.00066 37.4 2.9 49 106-157 337-386 (971)
20 cd06134 RNaseT DEDDh 3'-5' exo 35.5 28 0.00061 29.2 2.1 34 145-178 151-189 (189)
21 PRK02983 lysS lysyl-tRNA synth 35.0 1E+02 0.0022 33.7 6.5 114 66-180 821-975 (1094)
22 PF04891 NifQ: NifQ; InterPro 33.4 56 0.0012 28.4 3.7 53 100-156 97-149 (167)
23 cd02642 R3H_encore_like R3H do 32.8 78 0.0017 22.7 3.8 43 115-157 3-48 (63)
24 PRK07374 dnaE DNA polymerase I 32.2 35 0.00075 37.5 2.7 50 106-158 412-462 (1170)
25 PRK07135 dnaE DNA polymerase I 30.2 36 0.00078 36.8 2.3 50 106-158 335-385 (973)
26 PF02836 Glyco_hydro_2_C: Glyc 30.1 38 0.00083 29.9 2.1 39 117-155 35-73 (298)
27 TIGR00594 polc DNA-directed DN 29.5 42 0.0009 36.2 2.7 49 106-157 405-454 (1022)
28 PF07176 DUF1400: Alpha/beta h 28.4 73 0.0016 26.0 3.4 36 55-90 26-61 (127)
29 PF14144 DOG1: Seed dormancy c 28.3 60 0.0013 24.8 2.7 24 60-83 3-28 (80)
30 PRK05673 dnaE DNA polymerase I 27.8 39 0.00084 36.9 2.1 51 106-159 401-452 (1135)
31 PRK06759 RNA polymerase factor 27.6 1.2E+02 0.0027 23.4 4.4 35 141-179 12-46 (154)
32 PF12616 DUF3775: Protein of u 25.9 2E+02 0.0043 22.1 5.1 27 60-86 3-29 (75)
33 PF09379 FERM_N: FERM N-termin 25.5 50 0.0011 23.4 1.7 18 140-157 17-34 (80)
34 cd00014 CH Calponin homology d 25.4 1.3E+02 0.0028 21.8 4.0 26 141-167 62-87 (107)
35 PF11470 TUG-UBL1: GLUT4 regul 25.1 47 0.001 24.7 1.5 20 139-158 16-35 (65)
36 PRK09643 RNA polymerase sigma 25.1 91 0.002 25.7 3.4 36 141-179 35-70 (192)
37 cd02646 R3H_G-patch R3H domain 24.9 97 0.0021 21.9 3.1 44 117-160 1-46 (58)
38 TIGR01298 RNaseT ribonuclease 24.5 65 0.0014 27.4 2.5 49 129-179 140-193 (200)
39 PRK06920 dnaE DNA polymerase I 24.5 59 0.0013 35.6 2.8 49 106-157 386-435 (1107)
40 PRK12513 RNA polymerase sigma 24.1 70 0.0015 26.0 2.5 37 141-180 34-70 (194)
41 PRK06826 dnaE DNA polymerase I 23.4 65 0.0014 35.4 2.8 50 106-158 401-451 (1151)
42 PF06757 Ins_allergen_rp: Inse 23.2 3.9E+02 0.0084 22.5 6.9 55 59-127 30-87 (179)
43 cd01817 RGS12_RBD Ubiquitin do 22.8 65 0.0014 24.9 2.0 29 130-158 8-38 (73)
44 KOG3354 Gluconate kinase [Carb 22.6 50 0.0011 29.7 1.5 40 109-148 62-104 (191)
45 PF00685 Sulfotransfer_1: Sulf 22.5 2.3E+02 0.005 23.0 5.3 15 144-158 185-199 (267)
46 KOG2805 tRNA (5-methylaminomet 22.2 88 0.0019 30.8 3.2 33 147-179 60-92 (377)
47 PF02196 RBD: Raf-like Ras-bin 21.6 75 0.0016 23.4 2.0 28 132-159 12-40 (71)
48 TIGR00462 genX lysyl-tRNA synt 21.6 4.3E+02 0.0093 24.2 7.3 84 89-176 80-185 (304)
49 PF13873 Myb_DNA-bind_5: Myb/S 21.6 2.2E+02 0.0048 20.2 4.5 44 109-153 33-76 (78)
50 PRK11924 RNA polymerase sigma 21.3 1.1E+02 0.0024 23.8 3.0 36 142-180 22-57 (179)
51 PF09177 Syntaxin-6_N: Syntaxi 21.3 2.3E+02 0.005 21.6 4.8 54 60-125 41-94 (97)
52 PRK07247 DNA polymerase III su 21.0 1.6E+02 0.0034 25.5 4.2 38 140-179 131-170 (195)
53 PRK05672 dnaE2 error-prone DNA 20.7 63 0.0014 35.1 2.0 50 106-158 394-444 (1046)
54 TIGR03640 cas1_DVULG CRISPR-as 20.6 1.5E+02 0.0033 27.5 4.2 42 109-153 283-324 (340)
55 PRK12528 RNA polymerase sigma 20.5 1.4E+02 0.0029 23.5 3.4 37 141-180 12-48 (161)
56 PRK09191 two-component respons 20.1 1.6E+02 0.0034 24.4 3.9 35 142-179 10-44 (261)
No 1
>PRK10236 hypothetical protein; Provisional
Probab=99.98 E-value=7.3e-33 Score=245.41 Aligned_cols=110 Identities=22% Similarity=0.326 Sum_probs=103.3
Q ss_pred CcHHHHHHHHhhChHHHHHHHHHhcc-----cCCCCccchhcc-cc---CCcchHHHHhhhHHHHHHHHHHHHHHhhhcc
Q 026466 59 FDPELRSVLELATDSELYELERILFG-----PSYFSPLLKSFT-KR---ADVDYVMIEQDLEEREDFIASLESRFLFLAA 129 (238)
Q Consensus 59 ~~~ELr~~LeLATdEEL~~Lt~ILf~-----~r~fsPLlkS~~-k~---~~~Dy~~i~~~~~~R~~~~~~IE~RFrfLAA 129 (238)
.|++| +||..|++|||.+|++||++ .|+++.|+++.. |+ |++||. +||+.||+|||||||
T Consensus 7 ~D~DL-~fL~~cs~edL~~Lv~~Lt~d~dG~~R~te~lt~~~~yk~~~~~~~~~~----------~yw~~Ia~elq~fGg 75 (237)
T PRK10236 7 NDSDL-DFLQHCSEEQLANFARLLTHNEKGKTRLSSVLMRNELFKSMEGHPEQHR----------RNWQLIAGELQHFGG 75 (237)
T ss_pred cCccH-HHHHhCCHHHHHHHHHHHhcCCCCCEeehhhhcccHHHHhhcccchhHH----------HHHHHHHHHHHHhcc
Confidence 47777 59999999999999999999 788999999965 66 999999 999999999999999
Q ss_pred cc-cchhcCCCchHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhc
Q 026466 130 DA-RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (238)
Q Consensus 130 D~-~TvLRG~~vsYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~s 179 (238)
|| +|+|||+||+|||||+|||+||||||++++||++||+|||+|+|++.-
T Consensus 76 nt~~n~lRG~Gv~YreIL~DVc~~LKV~y~~~~st~~iE~~il~kll~~a~ 126 (237)
T PRK10236 76 DSIANKLRGHGKLYRAILLDVSKRLKLKADKEMSTFEIEQQLLEQFLRNTW 126 (237)
T ss_pred hHHHHHHhcCCccHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 99 779999999999999999999999999999999999999999998764
No 2
>COG4735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.38 E-value=4.1e-14 Score=124.53 Aligned_cols=71 Identities=15% Similarity=0.351 Sum_probs=67.6
Q ss_pred cCCc-chHHHHhhhHHHHHHHHHHHHHHhhhcccc-cchhcCCCchHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHH
Q 026466 98 RADV-DYVMIEQDLEEREDFIASLESRFLFLAADA-RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLL 175 (238)
Q Consensus 98 ~~~~-Dy~~i~~~~~~R~~~~~~IE~RFrfLAAD~-~TvLRG~~vsYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL 175 (238)
|++. ||. +||+.|.+++|++++|+ ++.|||.|+.||+||+|+|||||++|+++++|.+||+.++++|+
T Consensus 14 r~g~~~~~----------ky~k~ia~elq~~gg~s~anflr~~G~lyk~il~d~~~~Lk~k~~k~~~tt~Iee~ll~~il 83 (211)
T COG4735 14 REGLIQVC----------KYLKRIAEELQTTGGLSAANFLRDLGQLYKKILCDEKDKLKVKVQKELGTTEIEEPLLLQIL 83 (211)
T ss_pred HhhHHHHH----------HHHHhhHHHHHHhccHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhccccccchhHHHHH
Confidence 6666 888 99999999999999999 99999999999999999999999999999999999999999999
Q ss_pred hhh
Q 026466 176 QEY 178 (238)
Q Consensus 176 ~~~ 178 (238)
.+-
T Consensus 84 ~~~ 86 (211)
T COG4735 84 RNP 86 (211)
T ss_pred HhH
Confidence 654
No 3
>COG4735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=97.23 E-value=8.5e-05 Score=66.27 Aligned_cols=47 Identities=30% Similarity=0.285 Sum_probs=43.7
Q ss_pred cchhcCC--CchHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhh
Q 026466 132 RSTLRGW--RPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEY 178 (238)
Q Consensus 132 ~TvLRG~--~vsYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~ 178 (238)
+|++||+ +++||+-++||||+++++|...+.|-++|.++|+|.+++-
T Consensus 1 lt~~l~~~~~~k~r~g~~~~~ky~k~ia~elq~~gg~s~anflr~~G~l 49 (211)
T COG4735 1 LTVLLGRSEQFKYREGLIQVCKYLKRIAEELQTTGGLSAANFLRDLGQL 49 (211)
T ss_pred CchhhccchhhHHHhhHHHHHHHHHhhHHHHHHhccHHHHHHHHHHHHH
Confidence 4788996 9999999999999999999999999999999999999653
No 4
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=95.34 E-value=0.015 Score=39.34 Aligned_cols=21 Identities=24% Similarity=0.275 Sum_probs=19.8
Q ss_pred HHHHHhhChHHHHHHHHHhcc
Q 026466 64 RSVLELATDSELYELERILFG 84 (238)
Q Consensus 64 r~~LeLATdEEL~~Lt~ILf~ 84 (238)
-+||..|++|+|++|++||++
T Consensus 7 LeFL~~cs~edL~~L~~~Lt~ 27 (35)
T PF13099_consen 7 LEFLAECSNEDLKDLVDILTH 27 (35)
T ss_pred hHHHHHCCHHHHHHHHHHHhc
Confidence 379999999999999999997
No 5
>PF03250 Tropomodulin: Tropomodulin; InterPro: IPR004934 Actin filaments have an intrinsic polarity, each with a fast-growing (barbed) end and a slow-growing (pointed) end. To regulate the dynamics at these ends, capping proteins have evolved that specifically bind to either the barbed or the pointed ends of the filament, where they block the association and dissociation of monomers. Pointed ends, for which actin monomers have significantly lower association and dissociation rate-constants than for barbed, are capped by either the Arp2/3 complex or tropomodulins []. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments []. Limited proteolysis shows this protein is composed of two domains. The unstructured tropomyosin-binding region at the N terminus has an actin pointed-end-capping activity that is dramatically up-regulated by tropomyosin coating of the actin filament[]. The second region is found near the C terminus. This tropomyosin-independent capping-domain caps pure actin. ; GO: 0005523 tropomyosin binding, 0005856 cytoskeleton
Probab=84.94 E-value=1.3 Score=38.07 Aligned_cols=31 Identities=45% Similarity=0.549 Sum_probs=27.0
Q ss_pred cCCCCCCcHHHHHHHHhhChHHHHHHHHHhc
Q 026466 53 SKGQGAFDPELRSVLELATDSELYELERILF 83 (238)
Q Consensus 53 ~~~~~~~~~ELr~~LeLATdEEL~~Lt~ILf 83 (238)
....-..++||.++|.-||++||.+|+.||-
T Consensus 109 ~ee~v~ldpeleeaL~~Atd~El~dlAaILG 139 (147)
T PF03250_consen 109 KEEQVTLDPELEEALSNATDAELCDLAAILG 139 (147)
T ss_pred cccccccCHHHHHHHhcCcHHHHHHHHHHHh
Confidence 3345577899999999999999999999995
No 6
>PF03981 Ubiq_cyt_C_chap: Ubiquinol-cytochrome C chaperone ; InterPro: IPR021150 Saccharomyces cerevisiae ubiquinol-cytochrome C chaperone is required for assembly of coenzyme QF-2-cytochrome C reductase. It appears to be found in a number of different organisms including Homo sapiens, Caenorhabditis elegans and Rhizobium meliloti. This entry also contains bacterial proteins belonging to the UPF0174 family.
Probab=70.46 E-value=2.8 Score=33.16 Aligned_cols=46 Identities=17% Similarity=0.283 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhhhcccc-cchhcCCCchHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhc
Q 026466 115 DFIASLESRFLFLAADA-RSTLRGWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (238)
Q Consensus 115 ~~~~~IE~RFrfLAAD~-~TvLRG~~vsYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~s 179 (238)
.+.+.+++||++++.+. +...| ||..+ .+..++|++||.++.++.-
T Consensus 4 ~~~dt~~~~f~~~~lh~~l~~~R----------------Lk~~~---~~~~~~~q~l~~~~~~d~~ 50 (141)
T PF03981_consen 4 GVPDTFAGRFQMLGLHVWLVLRR----------------LKAEG---KEGKELEQALFDKFFEDMD 50 (141)
T ss_pred CCccCHHHHHHHHHHHHHHHHHH----------------Hcccc---ccHHHHHHHHHHHHHHHHH
Confidence 35688999999999998 55555 77777 4569999999999997654
No 7
>PF02173 pKID: pKID domain; InterPro: IPR003102 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB [].; GO: 0005515 protein binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1KDX_B.
Probab=55.57 E-value=8.4 Score=27.11 Aligned_cols=13 Identities=46% Similarity=0.810 Sum_probs=11.2
Q ss_pred CCchHHHHHHHHH
Q 026466 138 WRPSYRNVLLAVR 150 (238)
Q Consensus 138 ~~vsYReVLl~VC 150 (238)
++||||.||-++-
T Consensus 18 RRPSYRKIlndLs 30 (41)
T PF02173_consen 18 RRPSYRKILNDLS 30 (41)
T ss_dssp TSTHHHHHHHHHH
T ss_pred hCchHHHHHHHhc
Confidence 6999999998873
No 8
>PF15008 DUF4518: Domain of unknown function (DUF4518)
Probab=54.08 E-value=21 Score=33.19 Aligned_cols=92 Identities=23% Similarity=0.336 Sum_probs=66.0
Q ss_pred cHHHHHHHHhhChHHHHHHHHHhcccCCCCccchhccccCCcchHHHHhhhHHHHHHHHHHHHHHhhhcccccchhcCCC
Q 026466 60 DPELRSVLELATDSELYELERILFGPSYFSPLLKSFTKRADVDYVMIEQDLEEREDFIASLESRFLFLAADARSTLRGWR 139 (238)
Q Consensus 60 ~~ELr~~LeLATdEEL~~Lt~ILf~~r~fsPLlkS~~k~~~~Dy~~i~~~~~~R~~~~~~IE~RFrfLAAD~~TvLRG~~ 139 (238)
+..+|++|.+.+++||..|++..+.+- ..| ++|+.=++.| .-+-.|+..+||.+.
T Consensus 6 r~G~rdlL~~l~~~~LlaL~~TVTn~~-i~~--------------------e~~~EAi~aI----L~~s~~a~~LL~rkk 60 (262)
T PF15008_consen 6 REGCRDLLGLLDNDDLLALADTVTNRL-IKP--------------------ESRQEAIDAI----LLYSQDAEELLRRKK 60 (262)
T ss_pred HHHHHHHHhcCChHHHHHHHHHHhcCc-eec--------------------CCHHHHHHHH----HHhCcCHHHHHhccc
Confidence 456899999999999999999999664 444 2333333332 334567788888766
Q ss_pred chHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhccc
Q 026466 140 PSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASE 181 (238)
Q Consensus 140 vsYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~ss~ 181 (238)
| +|+||..--..-+|..+...+-.+|=+ |.++-..+.
T Consensus 61 V-~RelLFkYLa~kgv~v~p~s~K~~LI~----~~l~~W~~~ 97 (262)
T PF15008_consen 61 V-KRELLFKYLASKGVIVPPDSEKADLIQ----RVLQYWSSQ 97 (262)
T ss_pred c-cHHHHHHHHHHcCCCCCCCccHHHHHH----HHHHHHhcc
Confidence 5 799999999999999998888666544 445444433
No 9
>PF06603 UpxZ: UpxZ family of transcription anti-terminator antagonists; InterPro: IPR010570 This family consists of several hypothetical proteins of unknown function and seems to be specific to Bacteroides species.
Probab=50.12 E-value=57 Score=27.07 Aligned_cols=96 Identities=29% Similarity=0.451 Sum_probs=62.2
Q ss_pred HHHHHHHHhhhcccccchhcCCCchHHHHH----HHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhcccccCCCCCcccc
Q 026466 117 IASLESRFLFLAADARSTLRGWRPSYRNVL----LAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGSWEN 192 (238)
Q Consensus 117 ~~~IE~RFrfLAAD~~TvLRG~~vsYReVL----l~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~ss~~~g~~~~~~~~ 192 (238)
++.++-++.|+|-||-- -|-+=+ -+|-++-+-=|+.+-+|.|-||++-|.||--|+ .++ .
T Consensus 5 L~~~ah~Ll~lG~dg~p-------iYsD~~~rLN~ev~~~~~~Ly~~~G~t~EeeA~lCLaLLmGYn----at~---y-- 68 (106)
T PF06603_consen 5 LQSLAHELLYLGMDGSP-------IYSDDFSRLNKEVYEQSNDLYSQHGSTPEEEANLCLALLMGYN----ATI---Y-- 68 (106)
T ss_pred HHHHHHHHHhcCCCCCe-------eehHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcc----chh---h--
Confidence 46678889999999832 232222 234444444588899999999999999999887 222 1
Q ss_pred cccccccchhhhhh-hhhHHHHHHHhhhchhhHHHHHHHHHHhhhcC
Q 026466 193 SEASDAQNSLELGL-SQWKVQALAAFNAGAVELKSMMLKVYLLHLCY 238 (238)
Q Consensus 193 ~~~~~~~~s~~~gl-~~w~~~~~aa~klG~~el~s~~lk~~~~~~~~ 238 (238)
...+.+.-.|.=| ..|.+. .-|.+-+||+=++-.||
T Consensus 69 -d~geke~~~Q~vL~Rs~~vL---------~~Lp~SlLK~~Llt~Cy 105 (106)
T PF06603_consen 69 -DNGEKEEKKQEVLDRSWEVL---------DKLPASLLKVQLLTYCY 105 (106)
T ss_pred -hCccHHHHHHHHHHHHHHHH---------HhCCcHHHHHHHHHHHc
Confidence 1223333333333 235443 35778899999999998
No 10
>PF11248 DUF3046: Protein of unknown function (DUF3046); InterPro: IPR021408 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=47.15 E-value=36 Score=25.66 Aligned_cols=44 Identities=30% Similarity=0.369 Sum_probs=34.8
Q ss_pred HHHHHHHHHH-----hhhcccc-cchhcCC--------CchHHHHHHHHHhhcCCCCC
Q 026466 115 DFIASLESRF-----LFLAADA-RSTLRGW--------RPSYRNVLLAVRKNLNIPCS 158 (238)
Q Consensus 115 ~~~~~IE~RF-----rfLAAD~-~TvLRG~--------~vsYReVLl~VC~kLKV~ys 158 (238)
.||+.++.+| +.++.|- .+-|-|+ |+.=|+|=..||+-++||-+
T Consensus 5 eFw~~~~~~FG~~~~~~la~dhvL~~LGgrT~~eAL~~G~dpr~VW~AlC~~~dVP~~ 62 (63)
T PF11248_consen 5 EFWQLMEEEFGPAYGRSLARDHVLSELGGRTAAEALEAGVDPRDVWRALCDAFDVPEE 62 (63)
T ss_pred HHHHHHHHHhCchhHHHHHHhcchhhcCCcCHHHHHHcCCCHHHHHHHHHHHcCCCCC
Confidence 6888888887 4556665 5666553 89999999999999999954
No 11
>PF04542 Sigma70_r2: Sigma-70 region 2 ; InterPro: IPR007627 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [, ]. The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation [, ].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1OR7_B 1H3L_B 2Z2S_C 2Q1Z_C 2O7G_B 1SMY_F 1IW7_P 2BE5_F 2A6E_F 2CW0_F ....
Probab=45.59 E-value=40 Score=22.53 Aligned_cols=35 Identities=23% Similarity=0.353 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhc
Q 026466 142 YRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (238)
Q Consensus 142 YReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~s 179 (238)
|...+..+|.+. ++.....+|+-+|.|+.+++.-.
T Consensus 5 ~~~~l~~~~~~~---~~~~~~~eD~~qe~~~~l~~~~~ 39 (71)
T PF04542_consen 5 YYPLLYRYARRY---TGDPEDAEDLVQEAFIKLWRAID 39 (71)
T ss_dssp THHHHHHHHHTC---TTCSSHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH---hCCHhhHHHHhhHHHHHHHhhhh
Confidence 667788888887 55557999999999999996554
No 12
>PRK14082 hypothetical protein; Provisional
Probab=43.24 E-value=17 Score=27.79 Aligned_cols=30 Identities=30% Similarity=0.531 Sum_probs=22.3
Q ss_pred ChHHHHHHHHHHHHhhhcccccCCCCCccc
Q 026466 162 STEDLEAEIFLHLLQEYASEESGVFPGSWE 191 (238)
Q Consensus 162 sT~dLEaEIFLhLL~~~ss~~~g~~~~~~~ 191 (238)
.-+|||+||=++++++--.-.--..||-|+
T Consensus 33 eREDLeQElk~Ki~eK~~~~~~~e~PGF~e 62 (65)
T PRK14082 33 EREDLEQELKIKIIEKADMLLCQEVPGFWE 62 (65)
T ss_pred hHHHHHHHHHHHHHHHHHHhhcccCCcHHH
Confidence 579999999999998754444455666665
No 13
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=41.96 E-value=34 Score=26.51 Aligned_cols=37 Identities=16% Similarity=0.248 Sum_probs=29.2
Q ss_pred hHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhcc
Q 026466 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYAS 180 (238)
Q Consensus 141 sYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~ss 180 (238)
.|+..|..+|.++.. .....+||.+|+|+++++....
T Consensus 9 ~~~~~l~~~~~~~~~---~~~~aEDivQe~~l~l~~~~~~ 45 (159)
T TIGR02989 9 RHQRSLRAFVRSLVP---DRDDADDVLQETFVTAWRKFDE 45 (159)
T ss_pred HhHHHHHHHHHHHcC---ChhhHHHHHHHHHHHHHHHHHh
Confidence 477888888888843 4457799999999999987653
No 14
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=41.19 E-value=17 Score=38.45 Aligned_cols=50 Identities=22% Similarity=0.357 Sum_probs=38.8
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhcccccc-hhcCCCchHHHHHHHHHhhcCCCCC
Q 026466 106 IEQDLEEREDFIASLESRFLFLAADARS-TLRGWRPSYRNVLLAVRKNLNIPCS 158 (238)
Q Consensus 106 i~~~~~~R~~~~~~IE~RFrfLAAD~~T-vLRG~~vsYReVLl~VC~kLKV~ys 158 (238)
++.+.+.|+..++-+.+++ |-|.+. +.-=....-|.++-|||+.|++|+.
T Consensus 410 iDf~~~rR~~Vi~Yv~ekY---G~~~Va~I~Tf~T~~ak~airdv~rvlg~~~~ 460 (874)
T PRK09532 410 TDFCIERRDEMIKYVTEKY---GEDRVAQIITFNRMTSKAVLKDVARVLDIPYG 460 (874)
T ss_pred eecccccHHHHHHHHHHHh---CcccEEEEeehhhhHHHHHHHHHHHHhCCCHH
Confidence 6667889999999999985 666633 2222467789999999999999874
No 15
>cd06406 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain
Probab=39.91 E-value=23 Score=27.72 Aligned_cols=39 Identities=28% Similarity=0.343 Sum_probs=29.9
Q ss_pred CCCchHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhcccccCCCCCc
Q 026466 137 GWRPSYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYASEESGVFPGS 189 (238)
Q Consensus 137 G~~vsYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~ss~~~g~~~~~ 189 (238)
..+++|.++.-.|++|||++ . .++.=.|.++.+|.+.-.
T Consensus 18 p~~~~y~~L~~ki~~kLkl~-~-------------e~i~LsYkde~s~~~v~l 56 (80)
T cd06406 18 ARGLSYATLLQKISSKLELP-A-------------EHITLSYKSEASGEDVIL 56 (80)
T ss_pred CCCCCHHHHHHHHHHHhCCC-c-------------hhcEEEeccCCCCCccCc
Confidence 47999999999999999998 2 123446888877776444
No 16
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=38.92 E-value=47 Score=26.04 Aligned_cols=23 Identities=26% Similarity=0.476 Sum_probs=13.2
Q ss_pred HHHHHhhChHHHHHHHHHhcccC
Q 026466 64 RSVLELATDSELYELERILFGPS 86 (238)
Q Consensus 64 r~~LeLATdEEL~~Lt~ILf~~r 86 (238)
..++.+-+.||.+++.+-|..+.
T Consensus 8 ~~i~~l~~~ee~~~f~~dL~T~~ 30 (87)
T PF01371_consen 8 EAILSLKDEEECYDFFEDLCTPD 30 (87)
T ss_dssp HHHHCHHCHHCHHHHHHHHSSHH
T ss_pred HHHHHcCCHHHHHHHHHHhCCHH
Confidence 34455556666666666665433
No 17
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=37.16 E-value=23 Score=38.39 Aligned_cols=51 Identities=16% Similarity=0.168 Sum_probs=40.6
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhcccc-cchhcCCCchHHHHHHHHHhhcCCCCCC
Q 026466 106 IEQDLEEREDFIASLESRFLFLAADA-RSTLRGWRPSYRNVLLAVRKNLNIPCSS 159 (238)
Q Consensus 106 i~~~~~~R~~~~~~IE~RFrfLAAD~-~TvLRG~~vsYReVLl~VC~kLKV~ys~ 159 (238)
|+.+.+.|+..++-+.++ +|.|. +.+.-=....-|.++-|||+-|++|+..
T Consensus 343 iDf~~~rR~eVi~Yv~~k---YG~~~VAqI~Tfgt~~aK~aiRDv~Rvlg~~~~~ 394 (1034)
T PRK07279 343 IDLPDIYRSEFLRYVRNR---YGSDHSAQIVTFSTFGAKQAIRDVFKRFGVPEYE 394 (1034)
T ss_pred eeCccccHHHHHHHHHHH---hCcccEEEEeehhhhHHHHHHHHHHHHhCCCHHH
Confidence 677788999999999888 57787 3333334778899999999999998753
No 18
>PLN02502 lysyl-tRNA synthetase
Probab=36.52 E-value=1.2e+02 Score=30.68 Aligned_cols=91 Identities=15% Similarity=0.235 Sum_probs=57.7
Q ss_pred Cccchhcc--ccCCcchHHHHh--hhHHHHHHHHHHHHHHhhhccc------------ccchhcCC-CchHHHHH-----
Q 026466 89 SPLLKSFT--KRADVDYVMIEQ--DLEEREDFIASLESRFLFLAAD------------ARSTLRGW-RPSYRNVL----- 146 (238)
Q Consensus 89 sPLlkS~~--k~~~~Dy~~i~~--~~~~R~~~~~~IE~RFrfLAAD------------~~TvLRG~-~vsYReVL----- 146 (238)
.|-+.++. .+|.+.+.|++. .-.+-+..++.+|+=++++... .....+-+ +++|.+.|
T Consensus 304 g~~FRnE~~~~rH~pEFtmlE~y~a~~d~~dlm~~~E~li~~i~~~v~~~~~~~~~~~~i~~~~p~~rit~~e~l~~~~g 383 (553)
T PLN02502 304 GRQFRNEGISTRHNPEFTTCEFYQAYADYNDMMELTEEMVSGMVKELTGSYKIKYHGIEIDFTPPFRRISMISLVEEATG 383 (553)
T ss_pred cCeeeCCCCCCccccceeehhhhhhcCCHHHHHHHHHHHHHHHHHHHhcccccccCCccccCCCCceeccHHHHHHHHhC
Confidence 45565554 688888887544 2236667788888777666521 11221222 55565543
Q ss_pred ----------------HHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhc
Q 026466 147 ----------------LAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (238)
Q Consensus 147 ----------------l~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~s 179 (238)
..+|++.++.+....+..++=.++|-++++.+-
T Consensus 384 ~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~l~~~~ve~~l 432 (553)
T PLN02502 384 IDFPADLKSDEANAYLIAACEKFDVKCPPPQTTGRLLNELFEEFLEETL 432 (553)
T ss_pred CCCCcCCCHHHHHHHHHHHHHHcCCCCCCCCCHhHHHHHHHHHHHHhhc
Confidence 446778888888777888888888888776544
No 19
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=36.01 E-value=30 Score=37.38 Aligned_cols=49 Identities=16% Similarity=0.129 Sum_probs=38.2
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhcccccchh-cCCCchHHHHHHHHHhhcCCCC
Q 026466 106 IEQDLEEREDFIASLESRFLFLAADARSTL-RGWRPSYRNVLLAVRKNLNIPC 157 (238)
Q Consensus 106 i~~~~~~R~~~~~~IE~RFrfLAAD~~TvL-RG~~vsYReVLl~VC~kLKV~y 157 (238)
++.+.+.|+..++-+.+| +|.|.+..+ -=....-|.++-|||+-|++|+
T Consensus 337 iDf~~~rR~eVi~Yv~~k---YG~~~VaqI~Tf~T~~aK~AiRDv~Rvlg~~~ 386 (971)
T PRK05898 337 TDIMDERRDEVVEYLFEK---YGNDHVAHIITFQRIKAKMAIRDVGRILGIDL 386 (971)
T ss_pred cccchhhHHHHHHHHHHH---hCcccEEEEeehhhhHHHHHHHHHHHHhCCCH
Confidence 566677799999999988 477773333 2247778999999999999986
No 20
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=35.48 E-value=28 Score=29.25 Aligned_cols=34 Identities=24% Similarity=0.340 Sum_probs=25.9
Q ss_pred HHHHHHhhcCCCCC-----CCCChHHHHHHHHHHHHhhh
Q 026466 145 VLLAVRKNLNIPCS-----SKLSTEDLEAEIFLHLLQEY 178 (238)
Q Consensus 145 VLl~VC~kLKV~ys-----~klsT~dLEaEIFLhLL~~~ 178 (238)
-|-.+|++++|+.. ..++....-+++|+++++++
T Consensus 151 ~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~~~ 189 (189)
T cd06134 151 VLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVNRW 189 (189)
T ss_pred cHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHHhC
Confidence 48999999999853 22355666789999999874
No 21
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=35.01 E-value=1e+02 Score=33.71 Aligned_cols=114 Identities=12% Similarity=0.132 Sum_probs=72.5
Q ss_pred HHHhhChHHHHHHHHHhcccCCC--Cccchhcc--ccCCcchHHHHhh--hHHHHHHHHHHHHHHhhhcccc-----c--
Q 026466 66 VLELATDSELYELERILFGPSYF--SPLLKSFT--KRADVDYVMIEQD--LEEREDFIASLESRFLFLAADA-----R-- 132 (238)
Q Consensus 66 ~LeLATdEEL~~Lt~ILf~~r~f--sPLlkS~~--k~~~~Dy~~i~~~--~~~R~~~~~~IE~RFrfLAAD~-----~-- 132 (238)
+|..+++=-|+.|.--=+ .|.| +|-+.++. .+|++.+.|+|.- -.|-+..++.+|+=+++++-.- .
T Consensus 821 yLriSPELylKrLivgG~-erVFEIg~~FRnE~~~~rHnpEFTmLE~y~a~~dy~d~m~l~E~li~~i~~~v~~~~~~~~ 899 (1094)
T PRK02983 821 YLRIAPELYLKRLCVGGV-ERVFELGRNFRNEGVDATHNPEFTLLEAYQAHADYDTMRDLTRELIQNAAQAAHGAPVVMR 899 (1094)
T ss_pred hhhcChHHHHHHHHhccc-CceEEEcceecCCCCCCCccccccchhhhhhcCCHHHHHHHHHHHHHHHHHHHhCCcEEee
Confidence 555555554554432112 3333 45555554 6788888875432 2356678888887777663211 0
Q ss_pred ---------chhcC--CCchHHHHHH-----------------HHHhhcCCCCCCCCChHHHHHHHHHHHHhhhcc
Q 026466 133 ---------STLRG--WRPSYRNVLL-----------------AVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYAS 180 (238)
Q Consensus 133 ---------TvLRG--~~vsYReVLl-----------------~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~ss 180 (238)
--+.+ ++++|.|.+. ++|++.+|++....+..+|-.++|.++++.+-.
T Consensus 900 ~~~~~~~~~i~~~~pf~rit~~eai~~~~g~~~~~~~~~~~l~~~~~~~~i~~~~~~~~~~l~~~l~~~~ve~~~~ 975 (1094)
T PRK02983 900 PDGDGVLEPVDISGPWPVVTVHDAVSEALGEEIDPDTPLAELRKLCDAAGIPYRTDWDAGAVVLELYEHLVEDRTT 975 (1094)
T ss_pred CCccccccccccCCCceEEEHHHHHHHHhCCCCCCCCCHHHHHHHHHHcCCCCCCCCCHhHHHHHHHHHHHHhhcC
Confidence 01223 3888988774 478899999988888889999999998886653
No 22
>PF04891 NifQ: NifQ; InterPro: IPR006975 NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co) [], which is an integral part of the active site of dinitrogenase []. The conserved C-terminal cysteine residues may be involved in metal binding [].; GO: 0030151 molybdenum ion binding, 0009399 nitrogen fixation
Probab=33.43 E-value=56 Score=28.42 Aligned_cols=53 Identities=21% Similarity=0.215 Sum_probs=44.9
Q ss_pred CcchHHHHhhhHHHHHHHHHHHHHHhhhcccccchhcCCCchHHHHHHHHHhhcCCC
Q 026466 100 DVDYVMIEQDLEEREDFIASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNLNIP 156 (238)
Q Consensus 100 ~~Dy~~i~~~~~~R~~~~~~IE~RFrfLAAD~~TvLRG~~vsYReVLl~VC~kLKV~ 156 (238)
++||.-.+-...+|+..=..+...|-=||+--..=+|=|+..||| +|+.-++.
T Consensus 97 ~~~HLWqDLGL~~R~eLs~Lm~r~Fp~Laa~N~~~MrWKKFfYrq----lCe~eG~~ 149 (167)
T PF04891_consen 97 GPDHLWQDLGLRSRAELSALMRRHFPPLAARNTRNMRWKKFFYRQ----LCEREGLY 149 (167)
T ss_pred CCCccHHhcCCCCHHHHHHHHHHHhHHHHHhccCCCcHHHHHHHH----HHHHcCCC
Confidence 568888888999999999999999999998777677778999997 47777665
No 23
>cd02642 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=32.79 E-value=78 Score=22.71 Aligned_cols=43 Identities=23% Similarity=0.322 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhhhcccc-cchhc--CCCchHHHHHHHHHhhcCCCC
Q 026466 115 DFIASLESRFLFLAADA-RSTLR--GWRPSYRNVLLAVRKNLNIPC 157 (238)
Q Consensus 115 ~~~~~IE~RFrfLAAD~-~TvLR--G~~vsYReVLl~VC~kLKV~y 157 (238)
.|+-.||+.|.=|..|+ ...++ .-..-+|-++-+||++.|..-
T Consensus 3 ~~~l~~E~~i~~Fi~~~~~~~~~f~pm~sy~RllvH~la~~~gL~s 48 (63)
T cd02642 3 LFVLKLEKDLLAFIKDSTRQSLELPPMNSYYRLLAHRVAQYYGLDH 48 (63)
T ss_pred hHHHHHHHHHHHHHhCCCCCeeEcCCCCcHHHHHHHHHHHHhCCee
Confidence 58888999999999988 55444 458899999999999988654
No 24
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=32.23 E-value=35 Score=37.49 Aligned_cols=50 Identities=24% Similarity=0.303 Sum_probs=39.1
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhcccccc-hhcCCCchHHHHHHHHHhhcCCCCC
Q 026466 106 IEQDLEEREDFIASLESRFLFLAADARS-TLRGWRPSYRNVLLAVRKNLNIPCS 158 (238)
Q Consensus 106 i~~~~~~R~~~~~~IE~RFrfLAAD~~T-vLRG~~vsYReVLl~VC~kLKV~ys 158 (238)
|+...+.|+..++-+.++ +|.|.+. +.-=....-|.++-|||+-|++|++
T Consensus 412 iDf~~~rR~eVi~Yv~~k---YG~~~VaqI~TfgT~~ak~aiRDv~Rvlg~~~~ 462 (1170)
T PRK07374 412 TDFCIERRGEVIDYVTRR---YGEDKVAQIITFNRMTSKAVLKDVARVLDIPYG 462 (1170)
T ss_pred cccccccHHHHHHHHHHH---hCcccEEEEEehhhhHHHHHHHHHHHHhCCCHH
Confidence 666778999999999888 4777733 3322467789999999999999875
No 25
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=30.21 E-value=36 Score=36.77 Aligned_cols=50 Identities=16% Similarity=0.201 Sum_probs=39.0
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhcccccc-hhcCCCchHHHHHHHHHhhcCCCCC
Q 026466 106 IEQDLEEREDFIASLESRFLFLAADARS-TLRGWRPSYRNVLLAVRKNLNIPCS 158 (238)
Q Consensus 106 i~~~~~~R~~~~~~IE~RFrfLAAD~~T-vLRG~~vsYReVLl~VC~kLKV~ys 158 (238)
|+.+.+.|+..++-+.+++ |.|.+. +.-=....-|.++-|||+-|++|+.
T Consensus 335 iDf~~~rR~eVi~Yv~~kY---G~~~VaqI~Tf~t~~ak~Airdv~Rvlg~~~~ 385 (973)
T PRK07135 335 IDIQDDRRDEVIDYIFEKY---GYEHCATISTFQTLGAKSAIRDVGRMLGIPES 385 (973)
T ss_pred eeCchhhHHHHHHHHHHHh---CcccEEEEeehhhhHHHHHHHHHHHHhCCCHH
Confidence 5566788999999999884 777733 3222477889999999999999874
No 26
>PF02836 Glyco_hydro_2_C: Glycosyl hydrolases family 2, TIM barrel domain; InterPro: IPR006103 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities; beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. Beta-galactosidase from E. coli has a TIM-barrel-like core surrounded by four other largely beta domains [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3CMG_A 3FN9_C 1YQ2_A 3K4D_B 3LPG_B 3LPF_A 3K4A_B 3K46_B 3GM8_A 3DEC_A ....
Probab=30.07 E-value=38 Score=29.89 Aligned_cols=39 Identities=10% Similarity=0.096 Sum_probs=27.4
Q ss_pred HHHHHHHHhhhcccccchhcCCCchHHHHHHHHHhhcCC
Q 026466 117 IASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNLNI 155 (238)
Q Consensus 117 ~~~IE~RFrfLAAD~~TvLRG~~vsYReVLl~VC~kLKV 155 (238)
-+.++..++.+-+=++|++|-..-.+.+-.++.||++||
T Consensus 35 ~~~~~~d~~l~k~~G~N~iR~~h~p~~~~~~~~cD~~Gi 73 (298)
T PF02836_consen 35 DEAMERDLELMKEMGFNAIRTHHYPPSPRFYDLCDELGI 73 (298)
T ss_dssp HHHHHHHHHHHHHTT-SEEEETTS--SHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHHhcCcceEEcccccCcHHHHHHHhhcCC
Confidence 345667777777666999997666677889999999998
No 27
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.47 E-value=42 Score=36.19 Aligned_cols=49 Identities=20% Similarity=0.234 Sum_probs=38.3
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhcccccc-hhcCCCchHHHHHHHHHhhcCCCC
Q 026466 106 IEQDLEEREDFIASLESRFLFLAADARS-TLRGWRPSYRNVLLAVRKNLNIPC 157 (238)
Q Consensus 106 i~~~~~~R~~~~~~IE~RFrfLAAD~~T-vLRG~~vsYReVLl~VC~kLKV~y 157 (238)
|+...+.|+..++-+.++ +|.|.+. +.-=....-|.++-|||+-|++|+
T Consensus 405 iDf~~~rR~eVi~Yv~~k---YG~~~VaqI~Tf~t~~ak~Airdv~rvlg~~~ 454 (1022)
T TIGR00594 405 IDFCDERRDEVIEYVADK---YGHDNVAQIITFGTMKAKAALRDVARVLDIPY 454 (1022)
T ss_pred cccccccHHHHHHHHHHH---hCccCEEEEeehhhhHHHHHHHHHHHHhCCCH
Confidence 666778999999999988 5777633 222246778999999999999985
No 28
>PF07176 DUF1400: Alpha/beta hydrolase of unknown function (DUF1400); InterPro: IPR010802 This domain is specific to cyanobacterial proteins, its function and the function of the proteins it is associated with, are uncharacterised.
Probab=28.37 E-value=73 Score=25.97 Aligned_cols=36 Identities=28% Similarity=0.421 Sum_probs=32.0
Q ss_pred CCCCCcHHHHHHHHhhChHHHHHHHHHhcccCCCCc
Q 026466 55 GQGAFDPELRSVLELATDSELYELERILFGPSYFSP 90 (238)
Q Consensus 55 ~~~~~~~ELr~~LeLATdEEL~~Lt~ILf~~r~fsP 90 (238)
..|...+||+..+.+.+.++.++|-++|..+=-++|
T Consensus 26 ~tG~~~~~L~~~~~ll~~~~~~~lr~~L~~~~~~~~ 61 (127)
T PF07176_consen 26 ETGEISPELAFYLNLLSPQQRQQLRELLNTPIPIDP 61 (127)
T ss_pred HcCCCCHHHHHHHHhcCHhhHHHHHHHHcCCCCCCH
Confidence 367889999999999999999999999998766666
No 29
>PF14144 DOG1: Seed dormancy control
Probab=28.28 E-value=60 Score=24.84 Aligned_cols=24 Identities=33% Similarity=0.379 Sum_probs=19.3
Q ss_pred cHHHHHHHHhh--ChHHHHHHHHHhc
Q 026466 60 DPELRSVLELA--TDSELYELERILF 83 (238)
Q Consensus 60 ~~ELr~~LeLA--TdEEL~~Lt~ILf 83 (238)
++|||.+|... +|+||+.|++=..
T Consensus 3 l~eLr~al~~~~~~~~~L~~lV~~~~ 28 (80)
T PF14144_consen 3 LNELRAALQSHADSDDELRSLVDKVM 28 (80)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 67999999887 5999999887543
No 30
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=27.80 E-value=39 Score=36.91 Aligned_cols=51 Identities=18% Similarity=0.215 Sum_probs=39.7
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhccccc-chhcCCCchHHHHHHHHHhhcCCCCCC
Q 026466 106 IEQDLEEREDFIASLESRFLFLAADAR-STLRGWRPSYRNVLLAVRKNLNIPCSS 159 (238)
Q Consensus 106 i~~~~~~R~~~~~~IE~RFrfLAAD~~-TvLRG~~vsYReVLl~VC~kLKV~ys~ 159 (238)
|+...+.|+..++-+.++ +|.|.+ .+.-=....-|.++-|||+-|++|+..
T Consensus 401 iDf~~~rR~eVi~Yv~~k---YG~~~VaqI~Tfgt~~ak~aiRDv~Rvlg~~~~~ 452 (1135)
T PRK05673 401 IDFCQDRRDEVIRYVAEK---YGRDAVAQIITFGTMKAKAVIRDVGRVLGMPYGF 452 (1135)
T ss_pred CcCccccHHHHHHHHHHH---hCcccEEEEeehhhhHHHHHHHHHHHHhCCCHHH
Confidence 666788999999999887 477773 333324778899999999999999753
No 31
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=27.58 E-value=1.2e+02 Score=23.36 Aligned_cols=35 Identities=20% Similarity=0.264 Sum_probs=27.7
Q ss_pred hHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhc
Q 026466 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (238)
Q Consensus 141 sYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~s 179 (238)
.|...+..+|.+++. ....+|+=+|.|+.+.+...
T Consensus 12 ~y~~~l~~~~~~~~~----~~~aeDi~Qe~~l~l~~~~~ 46 (154)
T PRK06759 12 LYEGLIVNQIKKLGI----YQDYEEYYQCGLIGLWHAYE 46 (154)
T ss_pred HHHHHHHHHHHHhCC----cccHHHHHHHHHHHHHHHHH
Confidence 477888889988742 24779999999999997665
No 32
>PF12616 DUF3775: Protein of unknown function (DUF3775); InterPro: IPR022254 This domain family is found in bacteria, and is approximately 80 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=25.88 E-value=2e+02 Score=22.11 Aligned_cols=27 Identities=30% Similarity=0.366 Sum_probs=24.0
Q ss_pred cHHHHHHHHhhChHHHHHHHHHhcccC
Q 026466 60 DPELRSVLELATDSELYELERILFGPS 86 (238)
Q Consensus 60 ~~ELr~~LeLATdEEL~~Lt~ILf~~r 86 (238)
-+|||.+++-.+++|.-+|+.+..==|
T Consensus 3 ~~el~~~I~~l~~deqaeLvALmwiGR 29 (75)
T PF12616_consen 3 EEELRSFIEDLNEDEQAELVALMWIGR 29 (75)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHhcC
Confidence 479999999999999999999987544
No 33
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=25.45 E-value=50 Score=23.37 Aligned_cols=18 Identities=17% Similarity=0.191 Sum_probs=14.9
Q ss_pred chHHHHHHHHHhhcCCCC
Q 026466 140 PSYRNVLLAVRKNLNIPC 157 (238)
Q Consensus 140 vsYReVLl~VC~kLKV~y 157 (238)
-+=++++-+||++|+|.-
T Consensus 17 ~t~~~l~~~v~~~l~l~e 34 (80)
T PF09379_consen 17 TTGQDLLEQVCDKLGLKE 34 (80)
T ss_dssp SBHHHHHHHHHHHHTTSS
T ss_pred CcHHHHHHHHHHHcCCCC
Confidence 345899999999999973
No 34
>cd00014 CH Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).
Probab=25.42 E-value=1.3e+02 Score=21.79 Aligned_cols=26 Identities=27% Similarity=0.442 Sum_probs=21.1
Q ss_pred hHHHHHHHHHhhcCCCCCCCCChHHHH
Q 026466 141 SYRNVLLAVRKNLNIPCSSKLSTEDLE 167 (238)
Q Consensus 141 sYReVLl~VC~kLKV~ys~klsT~dLE 167 (238)
.--+..+++|+++|||.. ..+++||-
T Consensus 62 ~Ni~~~l~~~~~~gi~~~-~~~~~Dl~ 87 (107)
T cd00014 62 ENINLALNFAEKLGVPVV-NFDAEDLV 87 (107)
T ss_pred HHHHHHHHHHHHcCCcee-ccCHHHHh
Confidence 344677899999999987 78999986
No 35
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=25.14 E-value=47 Score=24.66 Aligned_cols=20 Identities=20% Similarity=0.218 Sum_probs=14.7
Q ss_pred CchHHHHHHHHHhhcCCCCC
Q 026466 139 RPSYRNVLLAVRKNLNIPCS 158 (238)
Q Consensus 139 ~vsYReVLl~VC~kLKV~ys 158 (238)
.-+-.|||.++|+|+|++-+
T Consensus 16 ~~~l~~VL~eac~k~~l~~~ 35 (65)
T PF11470_consen 16 NTTLNQVLEEACKKFGLDPS 35 (65)
T ss_dssp TSBHHHHHHHHHHHTT--GG
T ss_pred CCCHHHHHHHHHHHcCCCcc
Confidence 34567999999999998754
No 36
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=25.09 E-value=91 Score=25.72 Aligned_cols=36 Identities=14% Similarity=0.141 Sum_probs=26.0
Q ss_pred hHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhc
Q 026466 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (238)
Q Consensus 141 sYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~s 179 (238)
.|+..|..+|.++- ......+|+=+|+|+.+.....
T Consensus 35 ~y~~~l~~~~~~~~---~~~~~AeDlvQEvfl~l~~~~~ 70 (192)
T PRK09643 35 RHHRRLWAVARRTS---GTREDAADALQDAMLSAHRAAG 70 (192)
T ss_pred HHHHHHHHHHHHHc---CCHhhHHHHHHHHHHHHHHHHH
Confidence 46677777776653 3456779999999999986544
No 37
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=24.90 E-value=97 Score=21.86 Aligned_cols=44 Identities=16% Similarity=0.208 Sum_probs=34.0
Q ss_pred HHHHHHHHhhhcccccchhcC--CCchHHHHHHHHHhhcCCCCCCC
Q 026466 117 IASLESRFLFLAADARSTLRG--WRPSYRNVLLAVRKNLNIPCSSK 160 (238)
Q Consensus 117 ~~~IE~RFrfLAAD~~TvLRG--~~vsYReVLl~VC~kLKV~ys~k 160 (238)
++.|+.+|+-|-+|....+.= =...-|.++-++|+.+++...+.
T Consensus 1 ~~~i~~~i~~F~~~~~~~~~fppm~~~~R~~vH~lA~~~~L~S~S~ 46 (58)
T cd02646 1 IEDIKDEIEAFLLDSRDSLSFPPMDKHGRKTIHKLANCYNLKSKSR 46 (58)
T ss_pred ChHHHHHHHHHHhCCCceEecCCCCHHHHHHHHHHHHHcCCccccc
Confidence 467899999999888544442 27778999999999999876543
No 38
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=24.55 E-value=65 Score=27.45 Aligned_cols=49 Identities=16% Similarity=0.122 Sum_probs=33.4
Q ss_pred ccccchhcCCCchHHHHHHHHHhhcCCCCC-----CCCChHHHHHHHHHHHHhhhc
Q 026466 129 ADARSTLRGWRPSYRNVLLAVRKNLNIPCS-----SKLSTEDLEAEIFLHLLQEYA 179 (238)
Q Consensus 129 AD~~TvLRG~~vsYReVLl~VC~kLKV~ys-----~klsT~dLEaEIFLhLL~~~s 179 (238)
=|++.+-|..-+.| -|-.+|++++|+.. ..++-...=+++|+++++++.
T Consensus 140 lDTl~lar~~~~~~--~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~~~ 193 (200)
T TIGR01298 140 FDTATLAGLAYGQT--VLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNRWK 193 (200)
T ss_pred EEHHHHHHHHcCcc--cHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHHHH
Confidence 34544444322333 39999999999853 234556667899999999986
No 39
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=24.54 E-value=59 Score=35.61 Aligned_cols=49 Identities=8% Similarity=0.173 Sum_probs=38.6
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhcccccchh-cCCCchHHHHHHHHHhhcCCCC
Q 026466 106 IEQDLEEREDFIASLESRFLFLAADARSTL-RGWRPSYRNVLLAVRKNLNIPC 157 (238)
Q Consensus 106 i~~~~~~R~~~~~~IE~RFrfLAAD~~TvL-RG~~vsYReVLl~VC~kLKV~y 157 (238)
|+...+.|+..++-+.+++ |.|.+.-+ -=....-|.++-|||+-|++|+
T Consensus 386 iDF~~~rR~eVi~Yv~~kY---G~~~VaqI~TfgT~~ak~AiRDv~Rvlg~~~ 435 (1107)
T PRK06920 386 IDFPDTRRDEMIRYVKDKY---GQLRVAQIVTFGTLAAKAAIRDIARVMGLPP 435 (1107)
T ss_pred cccccccHHHHHHHHHHHh---CcccEEEEeeehhhHHHHHHHHHHHHhCCCH
Confidence 6666788999999998884 77774333 2247788999999999999987
No 40
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=24.12 E-value=70 Score=26.04 Aligned_cols=37 Identities=22% Similarity=0.255 Sum_probs=28.1
Q ss_pred hHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhcc
Q 026466 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYAS 180 (238)
Q Consensus 141 sYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~ss 180 (238)
.|+..|..+|.++- ......+|+=+|+|+.+++....
T Consensus 34 ~y~~~l~~~~~~~~---~~~~daeDlvQe~fi~l~~~~~~ 70 (194)
T PRK12513 34 RHRTGLYRFLLRLA---RDRALAEDIFQETWLRVIRARAQ 70 (194)
T ss_pred HHHHHHHHHHHHHh---CCHHHHHHHHHHHHHHHHHHHHh
Confidence 57777777887763 34557899999999999976543
No 41
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=23.39 E-value=65 Score=35.39 Aligned_cols=50 Identities=20% Similarity=0.276 Sum_probs=39.5
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhcccccc-hhcCCCchHHHHHHHHHhhcCCCCC
Q 026466 106 IEQDLEEREDFIASLESRFLFLAADARS-TLRGWRPSYRNVLLAVRKNLNIPCS 158 (238)
Q Consensus 106 i~~~~~~R~~~~~~IE~RFrfLAAD~~T-vLRG~~vsYReVLl~VC~kLKV~ys 158 (238)
|+.+.+.|+..++-+.+++ |.|.+. +.-=.....|.++-|||+-|++|+.
T Consensus 401 iDf~~~rR~eVi~Yv~~kY---G~~~VaqI~TfgT~~ak~AirDv~Rvlg~~~~ 451 (1151)
T PRK06826 401 IDFCYERRQEVIDYVVEKY---GKDRVAQIITFGTMAARAAIRDVGRALNYPYA 451 (1151)
T ss_pred ccCccccHHHHHHHHHHHh---CccCEEEEEehhhhHHHHHHHHHHHHhCCCHH
Confidence 6677889999999999885 777633 3222477889999999999999875
No 42
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=23.17 E-value=3.9e+02 Score=22.47 Aligned_cols=55 Identities=20% Similarity=0.253 Sum_probs=32.4
Q ss_pred CcHHHHHHHHhhChHHHHHHHHHhcccCCCCccchhcc---ccCCcchHHHHhhhHHHHHHHHHHHHHHhhh
Q 026466 59 FDPELRSVLELATDSELYELERILFGPSYFSPLLKSFT---KRADVDYVMIEQDLEEREDFIASLESRFLFL 127 (238)
Q Consensus 59 ~~~ELr~~LeLATdEEL~~Lt~ILf~~r~fsPLlkS~~---k~~~~Dy~~i~~~~~~R~~~~~~IE~RFrfL 127 (238)
.|+|.|.+++....+|..++.+-+.. .|=.+... +.++.|-. .|++.|+..+..-
T Consensus 30 ~D~efq~~~~yl~s~~f~~l~~~l~~----~pE~~~l~~yL~~~gldv~----------~~i~~i~~~l~~~ 87 (179)
T PF06757_consen 30 EDAEFQAAVRYLNSSEFKQLWQQLEA----LPEVKALLDYLESAGLDVY----------YYINQINDLLGLP 87 (179)
T ss_pred cCHHHHHHHHHHcChHHHHHHHHHHc----CHHHHHHHHHHHHCCCCHH----------HHHHHHHHHHcCC
Confidence 35666666666666666666666653 33233332 55666666 6777777776443
No 43
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=22.83 E-value=65 Score=24.92 Aligned_cols=29 Identities=17% Similarity=0.224 Sum_probs=24.3
Q ss_pred cc-cchhcCC-CchHHHHHHHHHhhcCCCCC
Q 026466 130 DA-RSTLRGW-RPSYRNVLLAVRKNLNIPCS 158 (238)
Q Consensus 130 D~-~TvLRG~-~vsYReVLl~VC~kLKV~ys 158 (238)
|+ .|+..=+ |.+-|++|...|+|-++++.
T Consensus 8 dg~~T~V~vrpG~ti~d~L~kllekRgl~~~ 38 (73)
T cd01817 8 DGSTTVVPTRPGESIRDLLSGLCEKRGINYA 38 (73)
T ss_pred CCCeEEEEecCCCCHHHHHHHHHHHcCCChh
Confidence 65 6666654 99999999999999999965
No 44
>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]
Probab=22.57 E-value=50 Score=29.74 Aligned_cols=40 Identities=15% Similarity=0.220 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHHHHHHhhhcccc-cchhcCC--CchHHHHHHH
Q 026466 109 DLEEREDFIASLESRFLFLAADA-RSTLRGW--RPSYRNVLLA 148 (238)
Q Consensus 109 ~~~~R~~~~~~IE~RFrfLAAD~-~TvLRG~--~vsYReVLl~ 148 (238)
.-+||=-|++.|....+-=.|++ ..||--- +-.||+||..
T Consensus 62 nD~DR~pWL~~i~~~~~~~l~~~q~vVlACSaLKk~YRdILr~ 104 (191)
T KOG3354|consen 62 NDDDRWPWLKKIAVELRKALASGQGVVLACSALKKKYRDILRH 104 (191)
T ss_pred CcccccHHHHHHHHHHHHHhhcCCeEEEEhHHHHHHHHHHHHh
Confidence 44567799999999998887777 4454432 7799999988
No 45
>PF00685 Sulfotransfer_1: Sulfotransferase domain; InterPro: IPR000863 This family includes a range of sulphotransferase proteins including flavonyl 3-sulphotransferase, aryl sulphotransferase, alcohol sulphotransferase, oestrogen sulphotransferase and phenol-sulphating phenol sulphotransferase. These enzymes are responsible for the transfer of sulphate groups to specific compounds.; GO: 0008146 sulfotransferase activity; PDB: 3MGC_A 3MGB_A 3MG9_A 1G3M_B 1HY3_B 2QP4_A 3F3Y_C 1EFH_A 1OV4_A 1J99_A ....
Probab=22.51 E-value=2.3e+02 Score=23.03 Aligned_cols=15 Identities=27% Similarity=0.328 Sum_probs=11.4
Q ss_pred HHHHHHHhhcCCCCC
Q 026466 144 NVLLAVRKNLNIPCS 158 (238)
Q Consensus 144 eVLl~VC~kLKV~ys 158 (238)
+++-+||+.||++++
T Consensus 185 ~~l~~I~~FLgl~~~ 199 (267)
T PF00685_consen 185 KELKRICDFLGLPFS 199 (267)
T ss_dssp HHHHHHHHHTTSS--
T ss_pred HHHHHHHHHHhhccc
Confidence 567789999999987
No 46
>KOG2805 consensus tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=22.20 E-value=88 Score=30.75 Aligned_cols=33 Identities=30% Similarity=0.413 Sum_probs=29.6
Q ss_pred HHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhc
Q 026466 147 LAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (238)
Q Consensus 147 l~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~s 179 (238)
-.||++|+||+-+--=+.|-=..+|..+|+.|.
T Consensus 60 ~~Vc~~LnI~~~~Vnf~kEYW~~Vfs~~L~~Y~ 92 (377)
T KOG2805|consen 60 KRVCKQLNIPLHQVNFVKEYWNDVFSPFLEEYE 92 (377)
T ss_pred HHHHHHhCCeeEEEeeHHHHHHHHHHHHHHHHh
Confidence 469999999999887788888889999999998
No 47
>PF02196 RBD: Raf-like Ras-binding domain; InterPro: IPR003116 This is the Ras-binding domain found in proteins related to Ras. It is found in association with the PE-bind and pkinase domains.; GO: 0005057 receptor signaling protein activity, 0007165 signal transduction; PDB: 1RFA_A 1C1Y_B 3KUD_B 1GUA_B 3KUC_B 2L05_A 3NY5_D 1RRB_A 1WFY_A 1WXM_A.
Probab=21.58 E-value=75 Score=23.43 Aligned_cols=28 Identities=14% Similarity=0.077 Sum_probs=21.1
Q ss_pred cchhcC-CCchHHHHHHHHHhhcCCCCCC
Q 026466 132 RSTLRG-WRPSYRNVLLAVRKNLNIPCSS 159 (238)
Q Consensus 132 ~TvLRG-~~vsYReVLl~VC~kLKV~ys~ 159 (238)
.|+..= -|.+.|++|..+|+|-+++++.
T Consensus 12 ~t~V~vrpg~ti~d~L~~~~~kr~L~~~~ 40 (71)
T PF02196_consen 12 RTVVQVRPGMTIRDALSKACKKRGLNPEC 40 (71)
T ss_dssp EEEEEE-TTSBHHHHHHHHHHTTT--CCC
T ss_pred EEEEEEcCCCCHHHHHHHHHHHcCCCHHH
Confidence 555554 4899999999999999998864
No 48
>TIGR00462 genX lysyl-tRNA synthetase-like protein GenX. Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located near a homolog of lysine-2,3-aminomutase. Its function is unknown.
Probab=21.57 E-value=4.3e+02 Score=24.25 Aligned_cols=84 Identities=19% Similarity=0.298 Sum_probs=54.2
Q ss_pred Cccchhcc--ccCCcchHHHHhh--hHHHHHHHHHHHHHHhhhcccccchhcC-C-CchHHHHH----------------
Q 026466 89 SPLLKSFT--KRADVDYVMIEQD--LEEREDFIASLESRFLFLAADARSTLRG-W-RPSYRNVL---------------- 146 (238)
Q Consensus 89 sPLlkS~~--k~~~~Dy~~i~~~--~~~R~~~~~~IE~RFrfLAAD~~TvLRG-~-~vsYReVL---------------- 146 (238)
.|-..++. .+|.+.+.|++.- -.+-+..++.+|+=++++... +.. + +++|.+++
T Consensus 80 gp~FRaE~~~~rHl~EFtmLE~e~~~~d~~d~m~~~e~li~~i~~~----~~~~~~~it~~ea~~~~~~~~~~~~~~~~~ 155 (304)
T TIGR00462 80 CKVFRNGERGRRHNPEFTMLEWYRPGFDYHDLMDEVEALLQELLGD----PFAPWERLSYQEAFLRYAGIDPLTASLDEL 155 (304)
T ss_pred cCceeCCCCCCCcccHHHhHHHHHHcCCHHHHHHHHHHHHHHHHHh----cCCCcEEEEHHHHHHHHhCCCcccCCHHHH
Confidence 45554443 6888888886552 336778888888888877642 233 2 78898875
Q ss_pred HHHHhhcCCCCCCCCChHHHHHHHHHHHHh
Q 026466 147 LAVRKNLNIPCSSKLSTEDLEAEIFLHLLQ 176 (238)
Q Consensus 147 l~VC~kLKV~ys~klsT~dLEaEIFLhLL~ 176 (238)
.+..++.++......+-.++...+|-++++
T Consensus 156 ~~~~~~~g~~~~~~~d~~~~~e~~l~~~ie 185 (304)
T TIGR00462 156 AAAAAAHGVRASEEDDRDDLLDLLFSEKVE 185 (304)
T ss_pred HHHHHHcCCCCCCCCChhHHHHHHHHHHHH
Confidence 345667777666555555555566655553
No 49
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=21.56 E-value=2.2e+02 Score=20.25 Aligned_cols=44 Identities=11% Similarity=0.245 Sum_probs=30.1
Q ss_pred hhHHHHHHHHHHHHHHhhhcccccchhcCCCchHHHHHHHHHhhc
Q 026466 109 DLEEREDFIASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNL 153 (238)
Q Consensus 109 ~~~~R~~~~~~IE~RFrfLAAD~~TvLRG~~vsYReVLl~VC~kL 153 (238)
...+++..|+.|..+|-=++.- .-....++--|+++...+.+++
T Consensus 33 ~~~~k~~~W~~I~~~lN~~~~~-~Rs~~~lkkkW~nlk~~~Kk~~ 76 (78)
T PF13873_consen 33 SNKEKRKAWEEIAEELNALGPG-KRSWKQLKKKWKNLKSKAKKKL 76 (78)
T ss_pred HHHHHHHHHHHHHHHHHhcCCC-CCCHHHHHHHHHHHHHHHHHHh
Confidence 4677899999999999876663 2222334666777776666654
No 50
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=21.34 E-value=1.1e+02 Score=23.78 Aligned_cols=36 Identities=19% Similarity=0.132 Sum_probs=23.3
Q ss_pred HHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhcc
Q 026466 142 YRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYAS 180 (238)
Q Consensus 142 YReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~ss 180 (238)
|+.-|..++.++. ......+|+-+|+|+.++++..+
T Consensus 22 y~~~l~~~~~~~~---~~~~~aeDl~qe~~~~l~~~~~~ 57 (179)
T PRK11924 22 HAPDLLRYARRQL---GDRALAEDAVQEAFLRAWRKADL 57 (179)
T ss_pred HHHHHHHHHHHHh---CCHhhHHHHHHHHHHHHHHHHhh
Confidence 5555556665553 24446788888888888766543
No 51
>PF09177 Syntaxin-6_N: Syntaxin 6, N-terminal; InterPro: IPR015260 Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport []. ; GO: 0048193 Golgi vesicle transport, 0016020 membrane; PDB: 1LVF_B 2C5I_T 2C5J_A 2C5K_T 4DND_A.
Probab=21.32 E-value=2.3e+02 Score=21.59 Aligned_cols=54 Identities=20% Similarity=0.398 Sum_probs=34.0
Q ss_pred cHHHHHHHHhhChHHHHHHHHHhcccCCCCccchhccccCCcchHHHHhhhHHHHHHHHHHHHHHh
Q 026466 60 DPELRSVLELATDSELYELERILFGPSYFSPLLKSFTKRADVDYVMIEQDLEEREDFIASLESRFL 125 (238)
Q Consensus 60 ~~ELr~~LeLATdEEL~~Lt~ILf~~r~fsPLlkS~~k~~~~Dy~~i~~~~~~R~~~~~~IE~RFr 125 (238)
-.||+..|+-+ +++|.||.+-.---. -|| ..|.--......|.+|+..++.++.
T Consensus 41 ~~eL~~~l~~i-e~~L~DL~~aV~ive-~np----------~kF~l~~~Ei~~Rr~fv~~~~~~i~ 94 (97)
T PF09177_consen 41 KRELRNALQSI-EWDLEDLEEAVRIVE-KNP----------SKFNLSEEEISRRRQFVSAIRNQIK 94 (97)
T ss_dssp HHHHHHHHHHH-HHHHHHHHHHHHHHH-CCH----------HHHT-HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHHHHH-hCc----------cccCCCHHHHHHHHHHHHHHHHHHH
Confidence 35777777765 456777666544311 234 3332245578899999999998875
No 52
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=21.01 E-value=1.6e+02 Score=25.48 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=29.2
Q ss_pred chHHHHHHHHHhhcCCCCCCCCChHHHH--HHHHHHHHhhhc
Q 026466 140 PSYRNVLLAVRKNLNIPCSSKLSTEDLE--AEIFLHLLQEYA 179 (238)
Q Consensus 140 vsYReVLl~VC~kLKV~ys~klsT~dLE--aEIFLhLL~~~s 179 (238)
.+|| |-.+|++++|+....-.-.|-+ ++||++++.+-.
T Consensus 131 ~~~~--L~~La~~~gi~~~~HrAl~DA~~ta~v~~~ll~~~~ 170 (195)
T PRK07247 131 ANLK--LQTVADFLGIKGRGHNSLEDARMTARVYESFLESDQ 170 (195)
T ss_pred CCCC--HHHHHHhcCCCCCCcCCHHHHHHHHHHHHHHHhhcc
Confidence 3566 9999999999987766655555 899999986543
No 53
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=20.75 E-value=63 Score=35.07 Aligned_cols=50 Identities=18% Similarity=0.210 Sum_probs=37.1
Q ss_pred HHhhhHHHHHHHHHHHHHHhhhcccccc-hhcCCCchHHHHHHHHHhhcCCCCC
Q 026466 106 IEQDLEEREDFIASLESRFLFLAADARS-TLRGWRPSYRNVLLAVRKNLNIPCS 158 (238)
Q Consensus 106 i~~~~~~R~~~~~~IE~RFrfLAAD~~T-vLRG~~vsYReVLl~VC~kLKV~ys 158 (238)
|+...+.|+..++-+.++ +|.|.+. +.-=....-|.++-|||+-|++++.
T Consensus 394 iDf~~~rR~~Vi~Yv~~k---YG~~~VaqI~Tf~T~~ak~AirDv~Rvlg~~~~ 444 (1046)
T PRK05672 394 VDFEHDRREEVIQYVYRR---YGRDRAAQVANVITYRPRSAVRDVAKALGLSPG 444 (1046)
T ss_pred eecccccHHHHHHHHHHH---hCcccEEEEeehhhhHHHHHHHHHHHHhCCCHH
Confidence 556678899999999998 4777632 2221355669999999999999864
No 54
>TIGR03640 cas1_DVULG CRISPR-associated endonuclease Cas1, DVULG subtype. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the DVULG subtype of CRISPR/Cas system.
Probab=20.55 E-value=1.5e+02 Score=27.52 Aligned_cols=42 Identities=10% Similarity=0.013 Sum_probs=28.0
Q ss_pred hhHHHHHHHHHHHHHHhhhcccccchhcCCCchHHHHHHHHHhhc
Q 026466 109 DLEEREDFIASLESRFLFLAADARSTLRGWRPSYRNVLLAVRKNL 153 (238)
Q Consensus 109 ~~~~R~~~~~~IE~RFrfLAAD~~TvLRG~~vsYReVLl~VC~kL 153 (238)
..+.|..|++.+|.|++== -..--.|+++|||.++..=|.+|
T Consensus 283 ~~~grk~~i~~~e~~l~~~---~~~~~~~~~~s~~~~i~~qa~~l 324 (340)
T TIGR03640 283 TDDARKTVLVAYQERKQEE---ITHPFLGEKVPLGLLPHVQARLL 324 (340)
T ss_pred CHHHHHHHHHHHHHHHhhh---eeCccCCCcccHHHHHHHHHHHH
Confidence 5677888888888887511 11113367899998887666654
No 55
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=20.50 E-value=1.4e+02 Score=23.54 Aligned_cols=37 Identities=16% Similarity=0.177 Sum_probs=27.0
Q ss_pred hHHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhcc
Q 026466 141 SYRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYAS 180 (238)
Q Consensus 141 sYReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~ss 180 (238)
.|..-|..+|.++- ......+||=+|+|+++.++...
T Consensus 12 ~~~~~l~~~~~~~~---~~~~~AeDivQe~flk~~~~~~~ 48 (161)
T PRK12528 12 AHHHWLTGWLRRRL---GCPQSAADLAQDTFVKVLVARET 48 (161)
T ss_pred HHHHHHHHHHHHHc---CCcccHHHHHHHHHHHHHhcccc
Confidence 36677778887653 23347899999999999976543
No 56
>PRK09191 two-component response regulator; Provisional
Probab=20.09 E-value=1.6e+02 Score=24.39 Aligned_cols=35 Identities=20% Similarity=0.110 Sum_probs=24.4
Q ss_pred HHHHHHHHHhhcCCCCCCCCChHHHHHHHHHHHHhhhc
Q 026466 142 YRNVLLAVRKNLNIPCSSKLSTEDLEAEIFLHLLQEYA 179 (238)
Q Consensus 142 YReVLl~VC~kLKV~ys~klsT~dLEaEIFLhLL~~~s 179 (238)
|...|...|.++ .......+||-+++|+++..+..
T Consensus 10 ~~~~l~~~~~~~---~~~~~~aeDi~qd~~~~~~~~~~ 44 (261)
T PRK09191 10 HLPYLRRYARAL---TGSQSSGDAYVAATLEALLADPS 44 (261)
T ss_pred HhHHHHHHHHHh---cCChhhHHHHHHHHHHHHHHhHH
Confidence 455555555554 23446789999999999987654
Done!