Query 022690
Match_columns 293
No_of_seqs 194 out of 443
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:25:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022690.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022690hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1588 RNA-binding protein Sa 100.0 2.9E-64 6.3E-69 463.9 21.3 209 31-292 29-241 (259)
2 cd02395 SF1_like-KH Splicing f 100.0 9.6E-42 2.1E-46 284.3 13.0 119 142-264 1-120 (120)
3 KOG0119 Splicing factor 1/bran 100.0 2.6E-38 5.7E-43 310.9 11.5 197 56-268 56-261 (554)
4 COG5176 MSL5 Splicing factor ( 100.0 1.2E-30 2.6E-35 235.5 6.2 124 139-266 146-269 (269)
5 KOG1960 Predicted RNA-binding 98.5 5.4E-08 1.2E-12 95.9 2.5 97 139-249 208-304 (531)
6 cd02393 PNPase_KH Polynucleoti 98.4 1.1E-06 2.3E-11 65.1 7.4 58 143-235 4-61 (61)
7 cd00105 KH-I K homology RNA-bi 98.4 1.3E-06 2.9E-11 62.9 7.1 62 143-234 2-63 (64)
8 smart00322 KH K homology RNA-b 98.3 4.9E-06 1.1E-10 58.9 7.5 65 142-238 4-68 (69)
9 PF00013 KH_1: KH domain syndr 98.2 1E-06 2.3E-11 63.7 2.6 60 142-234 1-60 (60)
10 PF13014 KH_3: KH domain 98.1 2.2E-06 4.8E-11 58.8 3.0 28 157-184 1-28 (43)
11 cd02394 vigilin_like_KH K homo 98.0 1.1E-05 2.3E-10 58.7 5.0 60 143-234 2-61 (62)
12 cd02396 PCBP_like_KH K homolog 97.8 6.6E-05 1.4E-09 55.6 6.2 35 143-183 2-36 (65)
13 TIGR03665 arCOG04150 arCOG0415 97.6 8.6E-05 1.9E-09 65.4 4.7 53 157-240 99-151 (172)
14 PRK13763 putative RNA-processi 97.5 0.00018 3.9E-09 63.9 5.4 53 157-240 105-157 (180)
15 COG1094 Predicted RNA-binding 97.1 0.00097 2.1E-08 60.6 5.8 55 157-242 112-166 (194)
16 PRK13763 putative RNA-processi 97.1 0.00089 1.9E-08 59.5 5.5 64 143-240 5-71 (180)
17 TIGR02696 pppGpp_PNP guanosine 97.0 0.0021 4.5E-08 68.1 7.6 65 141-240 578-642 (719)
18 TIGR03665 arCOG04150 arCOG0415 96.7 0.0016 3.4E-08 57.5 3.9 57 156-240 7-65 (172)
19 TIGR03591 polynuc_phos polyrib 96.4 0.0055 1.2E-07 64.6 5.8 64 141-239 551-614 (684)
20 KOG2874 rRNA processing protei 96.2 0.0095 2.1E-07 57.3 6.1 77 159-268 161-238 (356)
21 KOG2193 IGF-II mRNA-binding pr 96.2 0.0016 3.4E-08 65.4 0.7 38 146-183 279-316 (584)
22 KOG1676 K-homology type RNA bi 95.8 0.015 3.2E-07 60.3 5.6 61 156-240 239-300 (600)
23 KOG1960 Predicted RNA-binding 95.6 0.0031 6.8E-08 62.9 -0.0 78 159-249 307-384 (531)
24 KOG1676 K-homology type RNA bi 95.5 0.03 6.6E-07 58.1 6.7 74 138-239 136-209 (600)
25 PLN00207 polyribonucleotide nu 95.4 0.013 2.7E-07 63.7 3.8 65 141-240 685-750 (891)
26 PRK04163 exosome complex RNA-b 95.3 0.02 4.4E-07 52.8 4.3 57 155-240 153-209 (235)
27 PRK11824 polynucleotide phosph 93.6 0.06 1.3E-06 57.0 3.5 56 156-240 563-618 (693)
28 KOG2191 RNA-binding protein NO 93.4 0.19 4.1E-06 49.6 6.3 37 141-183 39-75 (402)
29 KOG2814 Transcription coactiva 93.2 0.11 2.5E-06 50.8 4.5 61 155-235 65-127 (345)
30 KOG2190 PolyC-binding proteins 93.1 0.23 5E-06 50.8 6.8 40 140-185 137-176 (485)
31 KOG2193 IGF-II mRNA-binding pr 92.2 0.16 3.5E-06 51.5 4.2 31 155-185 207-237 (584)
32 PRK00106 hypothetical protein; 91.2 0.35 7.7E-06 50.1 5.5 62 145-239 229-290 (535)
33 TIGR03319 YmdA_YtgF conserved 90.4 0.4 8.7E-06 49.3 5.1 62 145-239 208-269 (514)
34 PRK12704 phosphodiesterase; Pr 90.0 0.6 1.3E-05 48.1 5.9 49 145-221 214-262 (520)
35 KOG2191 RNA-binding protein NO 89.6 2.1 4.6E-05 42.4 9.0 38 141-184 132-169 (402)
36 COG1185 Pnp Polyribonucleotide 88.1 0.65 1.4E-05 49.4 4.6 60 145-239 556-615 (692)
37 cd02134 NusA_KH NusA_K homolog 88.1 0.93 2E-05 33.4 4.2 36 141-182 25-60 (61)
38 KOG2190 PolyC-binding proteins 82.1 1.4 3E-05 45.3 3.7 42 138-185 335-376 (485)
39 KOG0336 ATP-dependent RNA heli 81.9 0.75 1.6E-05 47.0 1.6 29 154-182 54-82 (629)
40 PF13184 KH_5: NusA-like KH do 80.4 0.77 1.7E-05 35.1 0.9 31 152-182 13-44 (69)
41 KOG1067 Predicted RNA-binding 74.7 2.6 5.6E-05 44.5 3.0 53 158-240 608-660 (760)
42 cd02409 KH-II KH-II (K homolo 72.5 3.4 7.4E-05 29.2 2.4 23 158-180 36-58 (68)
43 KOG2113 Predicted RNA binding 68.4 4 8.6E-05 40.3 2.6 44 139-188 24-69 (394)
44 PRK12705 hypothetical protein; 64.5 5.5 0.00012 41.3 2.9 30 153-182 205-234 (508)
45 COG1094 Predicted RNA-binding 63.0 21 0.00046 32.8 6.1 40 143-188 10-50 (194)
46 PRK08406 transcription elongat 62.8 5.7 0.00012 34.2 2.3 28 157-184 42-69 (140)
47 cd02414 jag_KH jag_K homology 57.6 7 0.00015 29.8 1.7 21 158-178 35-55 (77)
48 COG1097 RRP4 RNA-binding prote 57.3 8.9 0.00019 36.3 2.7 29 155-183 154-182 (239)
49 KOG4797 Transcriptional regula 56.6 3.2 6.9E-05 35.1 -0.3 45 223-268 46-91 (123)
50 PRK12327 nusA transcription el 49.4 23 0.0005 35.2 4.3 40 144-184 234-274 (362)
51 PRK12329 nusA transcription el 49.1 21 0.00046 36.6 4.1 42 142-184 264-306 (449)
52 TIGR01953 NusA transcription t 48.1 28 0.00062 34.2 4.7 40 144-184 232-272 (341)
53 COG1702 PhoH Phosphate starvat 43.2 44 0.00096 33.3 5.1 31 155-185 23-53 (348)
54 KOG2208 Vigilin [Lipid transpo 40.8 19 0.0004 39.1 2.3 39 139-183 707-745 (753)
55 TIGR00436 era GTP-binding prot 39.9 29 0.00062 32.0 3.1 40 139-183 219-266 (270)
56 TIGR01952 nusA_arch NusA famil 39.2 23 0.0005 30.8 2.2 29 156-184 42-70 (141)
57 KOG2192 PolyC-binding hnRNP-K 37.8 59 0.0013 31.8 4.9 39 140-184 47-85 (390)
58 PF00126 HTH_1: Bacterial regu 37.4 26 0.00055 25.2 1.9 20 168-187 33-52 (60)
59 PRK00089 era GTPase Era; Revie 37.3 71 0.0015 29.4 5.3 41 138-183 223-271 (292)
60 PRK02821 hypothetical protein; 36.5 21 0.00045 28.1 1.4 21 157-177 41-61 (77)
61 COG0195 NusA Transcription elo 36.4 27 0.00059 31.8 2.3 34 152-185 81-114 (190)
62 PRK12328 nusA transcription el 35.4 35 0.00076 34.3 3.1 39 144-183 240-279 (374)
63 KOG0334 RNA helicase [RNA proc 34.7 27 0.00059 39.1 2.4 76 146-239 901-976 (997)
64 PRK00468 hypothetical protein; 34.6 23 0.0005 27.6 1.4 18 158-175 41-58 (75)
65 PF13083 KH_4: KH domain; PDB: 34.0 7.8 0.00017 29.0 -1.3 20 158-177 40-59 (73)
66 PRK15494 era GTPase Era; Provi 33.3 83 0.0018 30.4 5.2 41 138-183 270-318 (339)
67 PRK13348 chromosome replicatio 31.9 32 0.00069 31.2 2.1 21 168-188 36-56 (294)
68 PRK06418 transcription elongat 31.4 36 0.00078 30.4 2.2 27 159-185 72-98 (166)
69 KOG2113 Predicted RNA binding 31.3 26 0.00056 34.8 1.4 31 155-185 123-153 (394)
70 PRK09202 nusA transcription el 30.9 51 0.0011 33.9 3.5 40 144-184 234-274 (470)
71 PRK01064 hypothetical protein; 30.1 34 0.00073 26.9 1.6 20 158-177 41-60 (78)
72 PRK05424 rplA 50S ribosomal pr 29.7 1.4E+02 0.003 27.7 5.9 31 208-238 168-199 (230)
73 TIGR01169 rplA_bact ribosomal 29.1 1.9E+02 0.004 26.9 6.6 10 157-166 124-133 (227)
74 KOG2192 PolyC-binding hnRNP-K 29.0 1.7E+02 0.0038 28.7 6.5 42 134-183 310-351 (390)
75 COG0080 RplK Ribosomal protein 28.5 1.6E+02 0.0034 26.0 5.6 99 139-259 4-110 (141)
76 COG1837 Predicted RNA-binding 27.9 35 0.00076 26.9 1.4 18 158-175 41-58 (76)
77 PTZ00225 60S ribosomal protein 27.4 1.5E+02 0.0032 27.3 5.6 61 158-238 117-191 (214)
78 TIGR03298 argP transcriptional 26.0 39 0.00084 30.6 1.5 21 168-188 35-55 (292)
79 PRK03635 chromosome replicatio 24.0 55 0.0012 29.8 2.2 22 168-189 36-57 (294)
80 PRK08406 transcription elongat 24.0 35 0.00077 29.3 0.8 25 158-182 110-134 (140)
81 PF07582 AP_endonuc_2_N: AP en 24.0 94 0.002 23.0 3.0 31 212-242 18-48 (55)
82 PRK03601 transcriptional regul 23.5 60 0.0013 29.4 2.3 18 168-185 35-52 (275)
83 PRK11074 putative DNA-binding 22.8 66 0.0014 29.4 2.4 22 168-189 36-57 (300)
84 PRK12684 transcriptional regul 21.9 70 0.0015 29.6 2.4 20 168-187 36-56 (313)
85 COG0484 DnaJ DnaJ-class molecu 21.7 97 0.0021 31.2 3.5 36 174-221 300-335 (371)
86 PRK15421 DNA-binding transcrip 21.6 72 0.0016 29.8 2.5 18 168-185 36-53 (317)
87 TIGR01170 rplA_mito ribosomal 21.0 33 0.00072 29.7 0.1 18 150-167 101-118 (141)
88 PRK12683 transcriptional regul 20.7 76 0.0016 29.4 2.4 20 168-187 36-56 (309)
89 PRK12682 transcriptional regul 20.6 78 0.0017 29.1 2.4 20 168-187 36-56 (309)
No 1
>KOG1588 consensus RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification]
Probab=100.00 E-value=2.9e-64 Score=463.86 Aligned_cols=209 Identities=50% Similarity=0.758 Sum_probs=182.8
Q ss_pred hHHHHHHHHHHHHhhcCCcccchhHHHHHHHHHHHHHHhcCCCCCCCCcccCCCCCCCCCCCCCCCCCccccccchhhhh
Q 022690 31 DRERYLAELLAERQKLGPFVQVLPLCSRLLSQEIRRITGYNPSFVDHERFEHDSPFRSLGQPNGRPMDLEGLSAMQTEEN 110 (293)
Q Consensus 31 ~~~~YL~eLl~Ek~~L~~~~~vf~h~~rLL~~EI~RV~~~~~~~~~~~~~~~~Sp~~s~~~~n~~~~~~~~~~~~~~E~~ 110 (293)
...+||.+|++|+++|++|+. |+||.|||++||.||+....-.. ...+++.
T Consensus 29 ~~~~yl~el~~e~~~l~~~~~-~~~~~rLL~~Ei~rv~~~~~~~~----------------------------~~~~~~~ 79 (259)
T KOG1588|consen 29 KASKYLSELLAERKSLSPFFP-FPHAERLLDEEIERVQTSGRQHG----------------------------SKEPEEL 79 (259)
T ss_pred HHHHHHHHHHhhHHhcCcccc-hHHHHHHHHHHHHHHHhhhhhcc----------------------------CCCchhc
Confidence 357999999999999999987 99999999999999998621000 0001111
Q ss_pred cccccCCCCCCCCCCCCCCCCCCCCCCceEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCC
Q 022690 111 GHLQRMAPFQTPPSMGWQGIPGIPTTPVVKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKD 190 (293)
Q Consensus 111 ~~p~~~~~~~~~~~~~~~~~p~~~~~~~vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd 190 (293)
. ....++++.+|+++||+|||++||+||||||||||||||+||||++|||||+||||||+||
T Consensus 80 ~------------------~~~~~~~~~vk~~~Kv~vPv~~yP~fNFVGRILGPrGnSlkrLe~eTgCki~IrGrgSmrD 141 (259)
T KOG1588|consen 80 P------------------YADVYSGKPVKLTEKVLVPVKEYPKFNFVGRILGPRGNSLKRLEEETGCKIMIRGRGSMRD 141 (259)
T ss_pred c------------------cccCccCCceeEEEEEEeccCCCCCCccccccccCCcchHHHHHHHHCCeEEEecCCcccc
Confidence 0 0023577789999999999999999999999999999999999999999999999999999
Q ss_pred chhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHHHcCccCCC-CCC
Q 022690 191 SIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILENLLKPVDESLDHYKKQQLRELAMLNGTLREE-SPS 269 (293)
Q Consensus 191 ~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~~rl~~A~e~Ie~LL~pv~e~~D~lKr~QL~ELA~lNGt~r~~-~~~ 269 (293)
..||+++|++|+||||++||||+|++++|+++|++||++|+++|++||+|.+|+.| |++||+|||++||||..+ +.+
T Consensus 142 ~~KEE~lR~~p~yeHL~epLHVlIe~~~p~~ea~~rl~~AleeI~klL~P~~e~~d--k~~QL~ELa~lngt~~~~~~~~ 219 (259)
T KOG1588|consen 142 KAKEEELRGDPGYEHLNEPLHVLIETEAPPAEAYARLAYALEEIKKLLVPDHEDED--KREQLRELAILNGTYLRSESRK 219 (259)
T ss_pred hHHHHHhhcCcchHHhCCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhcCCCCCCch--HHHHHHHHhhcCCccccccccc
Confidence 99999999999999999999999999999999999999999999999999998887 999999999999995544 434
Q ss_pred CCCCCC---CCCCCCCcccccccccC
Q 022690 270 MSPSMS---PSMSPFNNAGMKRAKTG 292 (293)
Q Consensus 270 ~~~~~~---~~~s~~~~~~~~~~~~~ 292 (293)
++ |+++||++.|+||+|++
T Consensus 220 ----~~g~~~~~~~~~~~~~~r~~~~ 241 (259)
T KOG1588|consen 220 ----PSGGNGRGVPGNSAGGKRGKTG 241 (259)
T ss_pred ----cCCCCCcCCCCCCCCcccccCC
Confidence 44 48999999999999985
No 2
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=100.00 E-value=9.6e-42 Score=284.32 Aligned_cols=119 Identities=55% Similarity=0.907 Sum_probs=112.8
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchh
Q 022690 142 VIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPED 221 (293)
Q Consensus 142 ~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~ 221 (293)
++|||||+++||+|||||+||||+|+|+|+||++|||+|.|||+||+++.++++++++ +.|+|++|||||+|+|.++
T Consensus 1 ~~ki~iP~~~~P~~N~IG~IIGPgG~tiK~i~~eTg~kI~Irg~gs~~~~~~~~~~~~-~~~~~~~eplhV~I~a~~~-- 77 (120)
T cd02395 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRG-PKYAHLNEPLHVLITAETP-- 77 (120)
T ss_pred CCEEEcCcccCCCCCeeEEEECCCChHHHHHHHHHCCEEEEecCcccccccccccccC-cccccCCCCcEEEEEeCCc--
Confidence 3799999999999999999999999999999999999999999999999999998887 8999999999999999996
Q ss_pred HHHHHHHHHHHHHHhccCCCccc-hHHHHHHHHHHHHHHcCccC
Q 022690 222 IINSRLDHAVAILENLLKPVDES-LDHYKKQQLRELAMLNGTLR 264 (293)
Q Consensus 222 ~~~~rl~~A~e~Ie~LL~pv~e~-~D~lKr~QL~ELA~lNGt~r 264 (293)
+.+++++|+++|+.||.++.++ .|++|++||+|||++|||||
T Consensus 78 -~~e~~~~A~~~I~~ll~~~~~~~~~~~k~~ql~~la~~nGt~~ 120 (120)
T cd02395 78 -PEEALAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120 (120)
T ss_pred -HHHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHhcccCC
Confidence 3458999999999999998887 99999999999999999997
No 3
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=100.00 E-value=2.6e-38 Score=310.87 Aligned_cols=197 Identities=34% Similarity=0.511 Sum_probs=147.4
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCCcccCCCCCCCCCC-CCCCCC---CccccccchhhhhcccccC-CCCCCCCCCCCCCC
Q 022690 56 CSRLLSQEIRRITGYNPSFVDHERFEHDSPFRSLGQ-PNGRPM---DLEGLSAMQTEENGHLQRM-APFQTPPSMGWQGI 130 (293)
Q Consensus 56 ~~rLL~~EI~RV~~~~~~~~~~~~~~~~Sp~~s~~~-~n~~~~---~~~~~~~~~~E~~~~p~~~-~~~~~~~~~~~~~~ 130 (293)
+..|..|||.|.+..++ |......+.+||.++..+ .+++.. .......+.+|+......+ +-. ..| .+
T Consensus 56 ~l~~~iee~t~kLrt~d-~~~p~~~e~rSPsp~p~yda~g~R~ntRe~R~r~~Le~er~e~I~~~lk~n-----P~f-kp 128 (554)
T KOG0119|consen 56 SLNLRIEEITRKLRTGD-VGVPPPRELRSPSPEPVYDAKGKRLNTREQRARKKLEDERHEIIEEILKLN-----PGF-KP 128 (554)
T ss_pred hHHHHHHHhhhhhcccc-CCCCCCccccCCCcchhhhhhccchhhHHHHHHHHHHHHHHHHHHHHHHhC-----cCC-CC
Confidence 44566678888877755 322233445677666544 444431 1222345666665433221 111 112 55
Q ss_pred CCCCCCCceEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCC-CCCCC
Q 022690 131 PGIPTTPVVKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYE-HLNEP 209 (293)
Q Consensus 131 p~~~~~~~vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~e-hl~ep 209 (293)
|++..-+. ++++||||||++||+|||||+||||||+|+|+||+||||||+||||||+|+++ ...++.+|. ..+||
T Consensus 129 P~DYk~p~-~~~~Kv~IPvke~Pd~NFvGLiiGPRG~TqK~lE~etgAKI~IRGkgSvkEgk---~~~~d~~~~~~~~ep 204 (554)
T KOG0119|consen 129 PADYKPPA-KLHDKVYIPVKEFPDINFVGLIIGPRGNTQKRLERETGAKIAIRGKGSVKEGK---GRSDDLSYIPKENEP 204 (554)
T ss_pred CcccCccc-ccccceecchhhcCCcceeEEEecCCccHHHHHHHHhCCeEEEeccccccccc---cCCcccccccccccc
Confidence 66666666 89999999999999999999999999999999999999999999999999875 122445553 46899
Q ss_pred cEEEEEecCchhHHHHHHHHHHHHHHhccC---CCccchHHHHHHHHHHHHHHcCccCCCCC
Q 022690 210 LHVLVEAEFPEDIINSRLDHAVAILENLLK---PVDESLDHYKKQQLRELAMLNGTLREESP 268 (293)
Q Consensus 210 LHVlIsa~~p~~~~~~rl~~A~e~Ie~LL~---pv~e~~D~lKr~QL~ELA~lNGt~r~~~~ 268 (293)
|||+|++++.+ +|++|+++|++||. .++|+++++|+.||+|||-+|||+|+++.
T Consensus 205 LH~~Isadt~e-----ki~~Ai~vienli~~av~~~e~~n~l~~~Qlrela~lNgt~r~~d~ 261 (554)
T KOG0119|consen 205 LHCLISADTQE-----KIKKAIAVIENLIQSAVSVPEGQNDLKRLQLRELARLNGTLRDDDN 261 (554)
T ss_pred eeEEEecchHH-----HHHHHHHHHHHHHHhhccCccccccccHHHHHHHHHhCCCCCcccc
Confidence 99999999854 89999999999998 68999999999999999999999999984
No 4
>COG5176 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]
Probab=99.96 E-value=1.2e-30 Score=235.53 Aligned_cols=124 Identities=34% Similarity=0.566 Sum_probs=98.0
Q ss_pred eEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecC
Q 022690 139 VKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEF 218 (293)
Q Consensus 139 vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~ 218 (293)
.|.+.||||||++||+.||||+||||||.|+|+||+.|+|||.|||+||.|+++-...+ -++...+.++||+||+++.
T Consensus 146 sk~q~KiYIPV~eyPe~NFVGLliGPRG~Tlk~le~~s~akIaIRG~gsvKegk~ssd~--p~~~~N~e~~lhcLI~ads 223 (269)
T COG5176 146 SKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSVKEGKISSDT--PESLKNAEAVLHCLIEADS 223 (269)
T ss_pred ccccceEEeehhhCcccceeEEEecCCcchHHHHHHHhCCeEEEecccccccCcccccC--chhhhhhHHhHHHHhhcch
Confidence 57899999999999999999999999999999999999999999999999976433221 1222346799999999976
Q ss_pred chhHHHHHHHHHHHHHHhccCCCccchHHHHHHHHHHHHHHcCccCCC
Q 022690 219 PEDIINSRLDHAVAILENLLKPVDESLDHYKKQQLRELAMLNGTLREE 266 (293)
Q Consensus 219 p~~~~~~rl~~A~e~Ie~LL~pv~e~~D~lKr~QL~ELA~lNGt~r~~ 266 (293)
.-..+ ..+......|.+.-. ++++++++||-||++||-+|||+|++
T Consensus 224 edki~-~~ik~~~n~I~~a~~-~PeGqnDlkR~qlr~la~lngtlr~d 269 (269)
T COG5176 224 EDKIC-RLIKSQLNAIREARR-NPEGQNDLKRFQLRWLAHLNGTLRAD 269 (269)
T ss_pred hhhHH-HHHHHHHHHHHHHhc-CCcccchHHHHHHHHHHHhcceecCC
Confidence 43222 223333444444444 57899999999999999999999975
No 5
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=98.49 E-value=5.4e-08 Score=95.87 Aligned_cols=97 Identities=16% Similarity=-0.005 Sum_probs=82.7
Q ss_pred eEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecC
Q 022690 139 VKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEF 218 (293)
Q Consensus 139 vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~ 218 (293)
+++..|++|++| .|.||.-+..=|++..||..+|.+|+.++.||||||++.+.-+. ++.+||++++|+...
T Consensus 208 ~~Y~~k~~v~~~-~P~~~~K~~~~~r~d~~La~~~ie~~i~~l~~Gr~SG~iEP~~G--------~EsnEPMYI~i~h~~ 278 (531)
T KOG1960|consen 208 RYYPNKALATDK-DPPLYLKIVSHNRKDLTLALQEIESWINPLIDGRRSGRREPNEG--------NESNEPMYIFSTHGN 278 (531)
T ss_pred ccchhheecccC-CcchhhhhhccCccchhhhhhhhhhhhhhhhccccccccCcccc--------cccCCceeEEeecCC
Confidence 455669999999 79999999999999999999999999999999999998765432 247999999999998
Q ss_pred chhHHHHHHHHHHHHHHhccCCCccchHHHH
Q 022690 219 PEDIINSRLDHAVAILENLLKPVDESLDHYK 249 (293)
Q Consensus 219 p~~~~~~rl~~A~e~Ie~LL~pv~e~~D~lK 249 (293)
++ .+..|+.+|.+|+.-++-.+..+-
T Consensus 279 ~~-----g~~~A~r~~~nl~~~v~~~~sr~~ 304 (531)
T KOG1960|consen 279 GN-----GENGAPRRKWNLEEKVYINLSRGF 304 (531)
T ss_pred ch-----hhccchhHHHhHHHHHHHHhhhhh
Confidence 76 578999999999998775554443
No 6
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.42 E-value=1.1e-06 Score=65.13 Aligned_cols=58 Identities=21% Similarity=0.378 Sum_probs=45.2
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhH
Q 022690 143 IRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDI 222 (293)
Q Consensus 143 ~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~ 222 (293)
+.+.||. +++|+|||++|.|+|+||++|||+|.|-- .-.|.|++.+++
T Consensus 4 ~~i~Ip~------~~ig~iIGkgG~~ik~I~~~tg~~I~i~~------------------------~g~v~I~G~~~~-- 51 (61)
T cd02393 4 ETMKIPP------DKIRDVIGPGGKTIKKIIEETGVKIDIED------------------------DGTVYIAASDKE-- 51 (61)
T ss_pred EEEEeCh------hheeeeECCCchHHHHHHHHHCCEEEeCC------------------------CCEEEEEeCCHH--
Confidence 4566764 47899999999999999999999998742 014899997654
Q ss_pred HHHHHHHHHHHHH
Q 022690 223 INSRLDHAVAILE 235 (293)
Q Consensus 223 ~~~rl~~A~e~Ie 235 (293)
.++.|+++|+
T Consensus 52 ---~v~~A~~~I~ 61 (61)
T cd02393 52 ---AAEKAKKMIE 61 (61)
T ss_pred ---HHHHHHHHhC
Confidence 5778888764
No 7
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=98.39 E-value=1.3e-06 Score=62.92 Aligned_cols=62 Identities=27% Similarity=0.434 Sum_probs=47.0
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhH
Q 022690 143 IRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDI 222 (293)
Q Consensus 143 ~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~ 222 (293)
.+|.||. +++|+|+||+|.++++|+++|||+|.|...++ ...+-.|.|.+..
T Consensus 2 ~~i~ip~------~~~~~vIG~~G~~i~~I~~~s~~~I~i~~~~~------------------~~~~~~v~i~G~~---- 53 (64)
T cd00105 2 ERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSGS------------------GSEERIVTITGTP---- 53 (64)
T ss_pred EEEEEch------hhcceeECCCCHHHHHHHHHHCCEEEEcCCCC------------------CCCceEEEEEcCH----
Confidence 4677875 78999999999999999999999999987543 1244467777752
Q ss_pred HHHHHHHHHHHH
Q 022690 223 INSRLDHAVAIL 234 (293)
Q Consensus 223 ~~~rl~~A~e~I 234 (293)
..+..|..+|
T Consensus 54 --~~v~~a~~~i 63 (64)
T cd00105 54 --EAVEKAKELI 63 (64)
T ss_pred --HHHHHHHHHh
Confidence 2566676665
No 8
>smart00322 KH K homology RNA-binding domain.
Probab=98.26 E-value=4.9e-06 Score=58.89 Aligned_cols=65 Identities=28% Similarity=0.495 Sum_probs=49.1
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchh
Q 022690 142 VIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPED 221 (293)
Q Consensus 142 ~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~ 221 (293)
+.+|.||. +++|+|||++|.++++|++.|||+|.+.+.++ ..-.|.|.+. +
T Consensus 4 ~~~i~i~~------~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~--------------------~~~~v~i~g~-~-- 54 (69)
T smart00322 4 TIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPEDGS--------------------EERVVEITGP-P-- 54 (69)
T ss_pred EEEEEEcc------hhcceeECCCchHHHHHHHHHCCEEEECCCCC--------------------CccEEEEEcC-H--
Confidence 46677765 68899999999999999999999999976433 2335777765 2
Q ss_pred HHHHHHHHHHHHHHhcc
Q 022690 222 IINSRLDHAVAILENLL 238 (293)
Q Consensus 222 ~~~~rl~~A~e~Ie~LL 238 (293)
..+..|.+.|.+.+
T Consensus 55 ---~~v~~a~~~i~~~~ 68 (69)
T smart00322 55 ---ENVEKAAELILEIL 68 (69)
T ss_pred ---HHHHHHHHHHHHHh
Confidence 24667777777654
No 9
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=98.18 E-value=1e-06 Score=63.71 Aligned_cols=60 Identities=30% Similarity=0.563 Sum_probs=45.5
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchh
Q 022690 142 VIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPED 221 (293)
Q Consensus 142 ~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~ 221 (293)
+.+|.|| .+++|+|||++|.++|+|+++|||+|.|... ++.-.|.|++ +++
T Consensus 1 T~~i~vp------~~~~~~iIG~~G~~i~~I~~~t~~~I~i~~~---------------------~~~~~v~I~G-~~~- 51 (60)
T PF00013_consen 1 TERIEVP------SSLVGRIIGKKGSNIKEIEEETGVKIQIPDD---------------------DERDIVTISG-SPE- 51 (60)
T ss_dssp EEEEEEE------HHHHHHHHTGGGHHHHHHHHHHTSEEEEEST---------------------TEEEEEEEEE-SHH-
T ss_pred CEEEEEC------HHHcCEEECCCCCcHHHhhhhcCeEEEEcCC---------------------CCcEEEEEEe-CHH-
Confidence 3566776 4589999999999999999999999999553 1223688888 543
Q ss_pred HHHHHHHHHHHHH
Q 022690 222 IINSRLDHAVAIL 234 (293)
Q Consensus 222 ~~~~rl~~A~e~I 234 (293)
.+++|+++|
T Consensus 52 ----~v~~A~~~I 60 (60)
T PF00013_consen 52 ----QVEKAKKMI 60 (60)
T ss_dssp ----HHHHHHHHH
T ss_pred ----HHHHHHhhC
Confidence 567777765
No 10
>PF13014 KH_3: KH domain
Probab=98.11 E-value=2.2e-06 Score=58.82 Aligned_cols=28 Identities=36% Similarity=0.682 Sum_probs=26.8
Q ss_pred eeeeEeCCCCchHHHHHHhhCCeEEEec
Q 022690 157 FVGRILGPRGNSLKRVEAMTECRVFIRG 184 (293)
Q Consensus 157 fvGrILGPrG~TlKrle~eTgcKI~IRG 184 (293)
|+|+|||++|.|+|+|+++|||+|.|--
T Consensus 1 ~vg~iIG~~G~~I~~I~~~tg~~I~i~~ 28 (43)
T PF13014_consen 1 FVGRIIGKGGSTIKEIREETGAKIQIPP 28 (43)
T ss_pred CcCeEECCCChHHHHHHHHhCcEEEECC
Confidence 6899999999999999999999999977
No 11
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=98.00 E-value=1.1e-05 Score=58.72 Aligned_cols=60 Identities=12% Similarity=0.324 Sum_probs=44.7
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhH
Q 022690 143 IRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDI 222 (293)
Q Consensus 143 ~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~ 222 (293)
++|.||. .++|+|||++|.++++|+++|||+|.|-..+ +..=.|.|++. +
T Consensus 2 ~~i~Vp~------~~~~~iIG~~G~~i~~i~~~~g~~I~i~~~~--------------------~~~~~v~I~G~-~--- 51 (62)
T cd02394 2 EEVEIPK------KLHRFIIGKKGSNIRKIMEETGVKIRFPDPG--------------------SKSDTITITGP-K--- 51 (62)
T ss_pred eEEEeCH------HHhhhccCCCCCcHHHHHHHhCCEEEcCCCC--------------------CCCCEEEEEcC-H---
Confidence 3466654 4789999999999999999999999997643 12236888886 2
Q ss_pred HHHHHHHHHHHH
Q 022690 223 INSRLDHAVAIL 234 (293)
Q Consensus 223 ~~~rl~~A~e~I 234 (293)
..+..|+++|
T Consensus 52 --~~v~~A~~~i 61 (62)
T cd02394 52 --ENVEKAKEEI 61 (62)
T ss_pred --HHHHHHHHHh
Confidence 2566777765
No 12
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=97.80 E-value=6.6e-05 Score=55.64 Aligned_cols=35 Identities=29% Similarity=0.560 Sum_probs=30.9
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEe
Q 022690 143 IRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIR 183 (293)
Q Consensus 143 ~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IR 183 (293)
.|++||. +.+|+|||.+|.++|+|+++|||+|.|-
T Consensus 2 ~r~~ip~------~~vg~iIG~~G~~i~~i~~~tga~I~i~ 36 (65)
T cd02396 2 LRLLVPS------SQAGSIIGKGGSTIKEIREETGAKIRVS 36 (65)
T ss_pred EEEEECH------HHcCeeECCCcHHHHHHHHHHCCEEEEc
Confidence 4677774 4789999999999999999999999994
No 13
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=97.58 E-value=8.6e-05 Score=65.42 Aligned_cols=53 Identities=26% Similarity=0.441 Sum_probs=44.6
Q ss_pred eeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHh
Q 022690 157 FVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILEN 236 (293)
Q Consensus 157 fvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~~rl~~A~e~Ie~ 236 (293)
.+|||||+.|.|++.||..|||+|.|-|+ .|.|.+ +++ .++.|.+.|++
T Consensus 99 ~~griIG~~G~t~~~ie~~t~~~i~i~~~-------------------------~v~i~G-~~~-----~~~~A~~~i~~ 147 (172)
T TIGR03665 99 IKGRIIGEGGKTRRIIEELTGVSISVYGK-------------------------TVGIIG-DPE-----QVQIAREAIEM 147 (172)
T ss_pred HHhhhcCCCcHHHHHHHHHHCCeEEEcCC-------------------------EEEEEC-CHH-----HHHHHHHHHHH
Confidence 69999999999999999999999998541 477877 443 68889999999
Q ss_pred ccCC
Q 022690 237 LLKP 240 (293)
Q Consensus 237 LL~p 240 (293)
|+.-
T Consensus 148 li~~ 151 (172)
T TIGR03665 148 LIEG 151 (172)
T ss_pred HHcC
Confidence 9863
No 14
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.48 E-value=0.00018 Score=63.91 Aligned_cols=53 Identities=26% Similarity=0.471 Sum_probs=43.3
Q ss_pred eeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHh
Q 022690 157 FVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILEN 236 (293)
Q Consensus 157 fvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~~rl~~A~e~Ie~ 236 (293)
.+|||||+.|.|.|.||..|||+|.|-++ .|.|.+ ++. .++.|.+.|+.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~-------------------------~v~i~G-~~~-----~~~~A~~~I~~ 153 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGK-------------------------TVAIIG-DPE-----QVEIAREAIEM 153 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCC-------------------------EEEEEe-CHH-----HHHHHHHHHHH
Confidence 69999999999999999999999998541 166666 433 67889999999
Q ss_pred ccCC
Q 022690 237 LLKP 240 (293)
Q Consensus 237 LL~p 240 (293)
|+.-
T Consensus 154 li~g 157 (180)
T PRK13763 154 LIEG 157 (180)
T ss_pred HHcC
Confidence 8863
No 15
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=97.10 E-value=0.00097 Score=60.57 Aligned_cols=55 Identities=22% Similarity=0.383 Sum_probs=46.0
Q ss_pred eeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHh
Q 022690 157 FVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILEN 236 (293)
Q Consensus 157 fvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~~rl~~A~e~Ie~ 236 (293)
..|||||+.|.|.+.||.-|||.|.|.|+ +|.|-+. + ..++.|.+.|+.
T Consensus 112 ~kgRIIG~~GkTr~~IE~lt~~~I~V~g~-------------------------tVaiiG~-~-----~~v~iAr~AVem 160 (194)
T COG1094 112 IKGRIIGREGKTRRAIEELTGVYISVYGK-------------------------TVAIIGG-F-----EQVEIAREAVEM 160 (194)
T ss_pred hhceeeCCCchHHHHHHHHhCCeEEEeCc-------------------------EEEEecC-h-----hhhHHHHHHHHH
Confidence 57999999999999999999999999994 5666663 2 367889999999
Q ss_pred ccCCCc
Q 022690 237 LLKPVD 242 (293)
Q Consensus 237 LL~pv~ 242 (293)
|+.-.+
T Consensus 161 li~G~~ 166 (194)
T COG1094 161 LINGAP 166 (194)
T ss_pred HHcCCC
Confidence 997543
No 16
>PRK13763 putative RNA-processing protein; Provisional
Probab=97.09 E-value=0.00089 Score=59.50 Aligned_cols=64 Identities=23% Similarity=0.366 Sum_probs=50.5
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEE---ecCc
Q 022690 143 IRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVE---AEFP 219 (293)
Q Consensus 143 ~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIs---a~~p 219 (293)
..+.||.+ -+|.|+||.|.|+|.|+++|||+|.|--. .=.|.|. +.++
T Consensus 5 ~~i~IP~~------kig~iIG~gGk~Ik~I~e~tg~~I~i~~~-----------------------~g~V~I~~~~~~d~ 55 (180)
T PRK13763 5 EYVKIPKD------RIGVLIGKKGETKKEIEERTGVKLEIDSE-----------------------TGEVIIEPTDGEDP 55 (180)
T ss_pred EEEEcCHH------HhhhHhccchhHHHHHHHHHCcEEEEECC-----------------------CCeEEEEeCCCCCH
Confidence 45667644 58999999999999999999999999753 0156666 4554
Q ss_pred hhHHHHHHHHHHHHHHhccCC
Q 022690 220 EDIINSRLDHAVAILENLLKP 240 (293)
Q Consensus 220 ~~~~~~rl~~A~e~Ie~LL~p 240 (293)
. .+.+|+++|+.++..
T Consensus 56 ~-----~i~kA~~~I~ai~~g 71 (180)
T PRK13763 56 L-----AVLKARDIVKAIGRG 71 (180)
T ss_pred H-----HHHHHHHHHHHHhcC
Confidence 3 689999999999884
No 17
>TIGR02696 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase.
Probab=96.95 E-value=0.0021 Score=68.13 Aligned_cols=65 Identities=25% Similarity=0.506 Sum_probs=53.9
Q ss_pred EEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCch
Q 022690 141 RVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPE 220 (293)
Q Consensus 141 ~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~ 220 (293)
+...+.||.+ -+|.||||+|.|+|.|+++|||+|.|-- +=+|.|.+.+.+
T Consensus 578 ~~~~~~I~~~------ki~~vIG~gGk~I~~i~~~tg~~Idi~d------------------------~G~V~I~a~d~~ 627 (719)
T TIGR02696 578 RIITVKIPVD------KIGEVIGPKGKMINQIQDETGAEISIED------------------------DGTVYIGAADGP 627 (719)
T ss_pred eeEEEEeChH------HhhheeCCCcHhHHHHHHHHCCEEEEec------------------------CcEEEEEeCCHH
Confidence 4466778755 5899999999999999999999998743 337888887753
Q ss_pred hHHHHHHHHHHHHHHhccCC
Q 022690 221 DIINSRLDHAVAILENLLKP 240 (293)
Q Consensus 221 ~~~~~rl~~A~e~Ie~LL~p 240 (293)
++++|++.|+.+..+
T Consensus 628 -----~~~~A~~~I~~i~~~ 642 (719)
T TIGR02696 628 -----SAEAARAMINAIANP 642 (719)
T ss_pred -----HHHHHHHHHHHhhCc
Confidence 789999999999984
No 18
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=96.73 E-value=0.0016 Score=57.50 Aligned_cols=57 Identities=21% Similarity=0.301 Sum_probs=45.2
Q ss_pred CeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEE--EecCchhHHHHHHHHHHHH
Q 022690 156 NFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLV--EAEFPEDIINSRLDHAVAI 233 (293)
Q Consensus 156 NfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlI--sa~~p~~~~~~rl~~A~e~ 233 (293)
+.+|.||||+|.|+|.||++|||+|.|--. .=.|.| .+.++. .+.+|+++
T Consensus 7 ~kig~vIG~gG~~Ik~I~~~tgv~I~Id~~-----------------------~g~V~I~~~t~d~~-----~i~kA~~~ 58 (172)
T TIGR03665 7 DRIGVLIGKGGETKKEIEERTGVKLDIDSE-----------------------TGEVKIEEEDEDPL-----AVMKAREV 58 (172)
T ss_pred HHhhhHhCCchhHHHHHHHHhCcEEEEEcC-----------------------CceEEEecCCCCHH-----HHHHHHHH
Confidence 578999999999999999999999999742 014666 344443 68899999
Q ss_pred HHhccCC
Q 022690 234 LENLLKP 240 (293)
Q Consensus 234 Ie~LL~p 240 (293)
|+.+...
T Consensus 59 I~~i~~g 65 (172)
T TIGR03665 59 VKAIGRG 65 (172)
T ss_pred HHHHHcC
Confidence 9998874
No 19
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=96.36 E-value=0.0055 Score=64.61 Aligned_cols=64 Identities=19% Similarity=0.350 Sum_probs=50.4
Q ss_pred EEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCch
Q 022690 141 RVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPE 220 (293)
Q Consensus 141 ~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~ 220 (293)
+...+.||.+ .+|.||||+|.|+|.|+++|||+|.|-- +=+|.|.+.+.+
T Consensus 551 ~~~~~~I~~~------kI~~vIG~gGk~Ik~I~~~tg~~I~i~d------------------------dG~V~i~~~~~~ 600 (684)
T TIGR03591 551 RIETIKINPD------KIRDVIGPGGKVIREITEETGAKIDIED------------------------DGTVKIAASDGE 600 (684)
T ss_pred eEEEEecCHH------HHHhhcCCCcHHHHHHHHHHCCEEEEec------------------------CeEEEEEECcHH
Confidence 3455677644 6899999999999999999999999832 226778777743
Q ss_pred hHHHHHHHHHHHHHHhccC
Q 022690 221 DIINSRLDHAVAILENLLK 239 (293)
Q Consensus 221 ~~~~~rl~~A~e~Ie~LL~ 239 (293)
.+++|.+.|+.+..
T Consensus 601 -----~~~~a~~~I~~~~~ 614 (684)
T TIGR03591 601 -----AAEAAIKMIEGITA 614 (684)
T ss_pred -----HHHHHHHHHHhhhc
Confidence 68899999988865
No 20
>KOG2874 consensus rRNA processing protein [Translation, ribosomal structure and biogenesis; Cell cycle control, cell division, chromosome partitioning]
Probab=96.23 E-value=0.0095 Score=57.25 Aligned_cols=77 Identities=31% Similarity=0.492 Sum_probs=56.1
Q ss_pred eeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHhcc
Q 022690 159 GRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILENLL 238 (293)
Q Consensus 159 GrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~~rl~~A~e~Ie~LL 238 (293)
.|||||.|+|||.||--|.|-|.|.|. -| ++-+| +..|..+..+|++.+
T Consensus 161 qRLiGpng~TLKAlelLT~CYilVqG~-------------------------TV--saiGp----fkGlkevr~IV~DcM 209 (356)
T KOG2874|consen 161 QRLIGPNGSTLKALELLTNCYILVQGN-------------------------TV--SAIGP----FKGLKEVRKIVEDCM 209 (356)
T ss_pred HHhcCCCchhHHHHHHHhhcEEEeeCc-------------------------EE--EeecC----cchHHHHHHHHHHHH
Confidence 589999999999999999999999994 12 22232 246888899999998
Q ss_pred CCCccchHHHHH-HHHHHHHHHcCccCCCCC
Q 022690 239 KPVDESLDHYKK-QQLRELAMLNGTLREESP 268 (293)
Q Consensus 239 ~pv~e~~D~lKr-~QL~ELA~lNGt~r~~~~ 268 (293)
..+|.-++ +|. +--||||- +-++.+++|
T Consensus 210 ~NiHPiY~-IK~LmiKRel~k-d~~l~ne~W 238 (356)
T KOG2874|consen 210 KNIHPIYN-IKTLMIKRELAK-DPELANEDW 238 (356)
T ss_pred hccchHHH-HHHHHHHHHhhc-ChhhccccH
Confidence 88887775 443 22356653 456666666
No 21
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=96.19 E-value=0.0016 Score=65.40 Aligned_cols=38 Identities=32% Similarity=0.652 Sum_probs=34.9
Q ss_pred ecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEe
Q 022690 146 DVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIR 183 (293)
Q Consensus 146 ~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IR 183 (293)
.||++-.-.-||+|||||--|.++|.||++||+||.|-
T Consensus 279 e~pLk~lAHN~lvGRLIGKeGrnlKkIeq~TgTkITis 316 (584)
T KOG2193|consen 279 EIPLKILAHNNLVGRLIGKEGRNLKKIEQDTGTKITIS 316 (584)
T ss_pred hcchhhhhhcchhhhhhhhccccHHHHHhhcCCceeee
Confidence 57777777889999999999999999999999999994
No 22
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=95.79 E-value=0.015 Score=60.34 Aligned_cols=61 Identities=20% Similarity=0.462 Sum_probs=44.1
Q ss_pred CeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCc-EEEEEecCchhHHHHHHHHHHHHH
Q 022690 156 NFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPL-HVLVEAEFPEDIINSRLDHAVAIL 234 (293)
Q Consensus 156 NfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epL-HVlIsa~~p~~~~~~rl~~A~e~I 234 (293)
+=||.|||=.|.|+|+|+.+||+||.++= |. +| .-++ -+.|.+ .. +++.+|.++|
T Consensus 239 ~~VG~IIGkgGE~IKklq~etG~KIQfkp-----Dd--------~p-----~speR~~~IiG--~~----d~ie~Aa~lI 294 (600)
T KOG1676|consen 239 SKVGIIIGKGGEMIKKLQNETGAKIQFKP-----DD--------DP-----SSPERPAQIIG--TV----DQIEHAAELI 294 (600)
T ss_pred cceeeEEecCchHHHHHhhccCceeEeec-----CC--------CC-----CCccceeeeec--CH----HHHHHHHHHH
Confidence 36999999999999999999999999974 11 11 1122 223333 22 3788999999
Q ss_pred HhccCC
Q 022690 235 ENLLKP 240 (293)
Q Consensus 235 e~LL~p 240 (293)
.+||.-
T Consensus 295 ~eii~~ 300 (600)
T KOG1676|consen 295 NEIIAE 300 (600)
T ss_pred HHHHHH
Confidence 999874
No 23
>KOG1960 consensus Predicted RNA-binding protein, contains KH domains [RNA processing and modification]
Probab=95.61 E-value=0.0031 Score=62.94 Aligned_cols=78 Identities=27% Similarity=0.480 Sum_probs=65.5
Q ss_pred eeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHhcc
Q 022690 159 GRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILENLL 238 (293)
Q Consensus 159 GrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~~rl~~A~e~Ie~LL 238 (293)
--|.||.|.+.|.++.+|-+++.|.|-||.+..... ....++|.||+|.+.++. .|+.|+-++++++
T Consensus 307 ~~~~~p~~~y~~~~~~~~~~~~~~~g~~s~~i~p~~--------~~~~~~p~~~~~~~~~~~-----~~~~~~~~~~~~i 373 (531)
T KOG1960|consen 307 QAIVGPQGAYVKHIQQETRTRVQIKGQGSAFIEPST--------NRESDEPIHLCIMSHDPN-----AIQRAKVLCEDLI 373 (531)
T ss_pred cccccCCcccccccCCCCCcceeccCccceeecCCC--------CCCCCCCcccccccCChh-----hhhhhhhcccccC
Confidence 357899999999999999999999999999865422 224789999999998865 5777999999999
Q ss_pred CCCccchHHHH
Q 022690 239 KPVDESLDHYK 249 (293)
Q Consensus 239 ~pv~e~~D~lK 249 (293)
-+|+..+...|
T Consensus 374 ~~v~~qy~~~~ 384 (531)
T KOG1960|consen 374 ASVHQQYKAWK 384 (531)
T ss_pred CcccccCcccc
Confidence 99997776655
No 24
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=95.54 E-value=0.03 Score=58.12 Aligned_cols=74 Identities=19% Similarity=0.527 Sum_probs=57.0
Q ss_pred ceEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEec
Q 022690 138 VVKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAE 217 (293)
Q Consensus 138 ~vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~ 217 (293)
.++.+.+|.||-. =+|+|||=.|-|+|+|++.||||+.+-=-|+.-+. .+-||. |+++
T Consensus 136 ~~~ttqeI~IPa~------k~GlIIGKgGETikqlqe~sg~k~i~iqd~~~~~~--------------~~Kplr--itGd 193 (600)
T KOG1676|consen 136 SVETTQEILIPAN------KCGLIIGKGGETIKQLQEQSGVKMILVQDGSIATG--------------ADKPLR--ITGD 193 (600)
T ss_pred ccceeeeeccCcc------ceeeEeccCccHHHHHHhhcCCceEEEecCCcCCC--------------CCCcee--ecCC
Confidence 3566778889854 58999999999999999999999988776665432 234444 4443
Q ss_pred CchhHHHHHHHHHHHHHHhccC
Q 022690 218 FPEDIINSRLDHAVAILENLLK 239 (293)
Q Consensus 218 ~p~~~~~~rl~~A~e~Ie~LL~ 239 (293)
+ .++.+|+++|.++|.
T Consensus 194 -p-----~~ve~a~~lV~dil~ 209 (600)
T KOG1676|consen 194 -P-----DKVEQAKQLVADILR 209 (600)
T ss_pred -H-----HHHHHHHHHHHHHHH
Confidence 3 378999999999998
No 25
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=95.45 E-value=0.013 Score=63.69 Aligned_cols=65 Identities=20% Similarity=0.209 Sum_probs=52.5
Q ss_pred EEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCe-EEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCc
Q 022690 141 RVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECR-VFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFP 219 (293)
Q Consensus 141 ~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcK-I~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p 219 (293)
+...+.||. +-||.||||+|.|+|.|+++||++ |-|+ |+-+|.|.+.+.
T Consensus 685 ~i~~~~i~~------~ki~~vIG~GGktIk~I~eetg~~~Idi~------------------------ddg~V~I~a~d~ 734 (891)
T PLN00207 685 LIHIMKVKP------EKVNMIIGSGGKKVKSIIEETGVEAIDTQ------------------------DDGTVKITAKDL 734 (891)
T ss_pred eeEEEEcCH------HHHHHHhcCCchhHHHHHHHHCCCccCcC------------------------CCeeEEEEeCCH
Confidence 345677764 468999999999999999999998 6553 456888888875
Q ss_pred hhHHHHHHHHHHHHHHhccCC
Q 022690 220 EDIINSRLDHAVAILENLLKP 240 (293)
Q Consensus 220 ~~~~~~rl~~A~e~Ie~LL~p 240 (293)
+ +++.|++.|+.+..-
T Consensus 735 ~-----~i~~A~~~I~~l~~~ 750 (891)
T PLN00207 735 S-----SLEKSKAIISSLTMV 750 (891)
T ss_pred H-----HHHHHHHHHHHHhcC
Confidence 4 789999999998764
No 26
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=95.31 E-value=0.02 Score=52.81 Aligned_cols=57 Identities=16% Similarity=0.345 Sum_probs=46.2
Q ss_pred CCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHH
Q 022690 155 FNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAIL 234 (293)
Q Consensus 155 fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~~rl~~A~e~I 234 (293)
-+.+++||||+|.+++.|.++|+|+|.| |. .=.|+|.+.+.+ .+..|++.|
T Consensus 153 ~~~i~~lig~~g~~i~~l~~~~~~~I~i-g~-----------------------NG~VwI~~~~~~-----~~~~a~~~I 203 (235)
T PRK04163 153 PVKVPRVIGKKGSMINMLKEETGCDIIV-GQ-----------------------NGRIWIKGPDEE-----DEEIAIEAI 203 (235)
T ss_pred HHHHHhhcCCCChhHhhhhhhhCcEEEE-cC-----------------------CcEEEEeeCCHH-----HHHHHHHHH
Confidence 3579999999999999999999999988 31 127999998864 567788888
Q ss_pred HhccCC
Q 022690 235 ENLLKP 240 (293)
Q Consensus 235 e~LL~p 240 (293)
+.+-.-
T Consensus 204 ~~~e~~ 209 (235)
T PRK04163 204 KKIERE 209 (235)
T ss_pred HHHHhh
Confidence 877664
No 27
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=93.59 E-value=0.06 Score=57.03 Aligned_cols=56 Identities=18% Similarity=0.304 Sum_probs=45.5
Q ss_pred CeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHH
Q 022690 156 NFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILE 235 (293)
Q Consensus 156 NfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~~rl~~A~e~Ie 235 (293)
+-++.+|||+|.|+|.|+++||++|-|+ |+-+|.|.+.+.+ .+++|.+.|+
T Consensus 563 ~kI~~vIG~gg~~ik~I~~~~~~~idi~------------------------d~G~v~i~~~~~~-----~~~~a~~~I~ 613 (693)
T PRK11824 563 DKIRDVIGPGGKTIREITEETGAKIDIE------------------------DDGTVKIAATDGE-----AAEAAKERIE 613 (693)
T ss_pred HHHHHHhcCCchhHHHHHHHHCCccccC------------------------CCceEEEEcccHH-----HHHHHHHHHH
Confidence 4589999999999999999999988773 2346777777643 7889999999
Q ss_pred hccCC
Q 022690 236 NLLKP 240 (293)
Q Consensus 236 ~LL~p 240 (293)
.+...
T Consensus 614 ~~~~~ 618 (693)
T PRK11824 614 GITAE 618 (693)
T ss_pred Hhccc
Confidence 88863
No 28
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=93.44 E-value=0.19 Score=49.56 Aligned_cols=37 Identities=19% Similarity=0.415 Sum_probs=33.3
Q ss_pred EEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEe
Q 022690 141 RVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIR 183 (293)
Q Consensus 141 ~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IR 183 (293)
+..||+|| -+-+|-|||-.|.|+.+||++|||+|.+-
T Consensus 39 y~ikvLip------s~AaGsIIGKGG~ti~~lqk~tgariklS 75 (402)
T KOG2191|consen 39 YFLKVLIP------SYAAGSIIGKGGQTIVQLQKETGARIKLS 75 (402)
T ss_pred eEEEEEee------cccccceeccchHHHHHHHhccCcEEEec
Confidence 67899997 34789999999999999999999999885
No 29
>KOG2814 consensus Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription]
Probab=93.23 E-value=0.11 Score=50.77 Aligned_cols=61 Identities=16% Similarity=0.324 Sum_probs=44.9
Q ss_pred CCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhH--HHHHHHHHHH
Q 022690 155 FNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDI--INSRLDHAVA 232 (293)
Q Consensus 155 fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~--~~~rl~~A~e 232 (293)
--|+|.|+|=+|.|.|+||+||+|+|.+=-.+..++ |+-|++-.-.++ |..||+.++.
T Consensus 65 s~~~~~lig~~g~trkkle~Etq~~i~lp~p~~n~~--------------------~i~i~~~~~~~V~~a~~Ri~~~id 124 (345)
T KOG2814|consen 65 SSFIGWLIGKQGKTRKKLEEETQTNIFLPRPNTNKE--------------------EIKIIGISRNCVIQALERIAKLID 124 (345)
T ss_pred HHHhhhhhcccchHHHHHHHhhccceEccCCCCCcc--------------------eEEEeehhHHHHHHHHHHHHHHHH
Confidence 358999999999999999999999999865443322 677777554333 4557777766
Q ss_pred HHH
Q 022690 233 ILE 235 (293)
Q Consensus 233 ~Ie 235 (293)
-..
T Consensus 125 s~r 127 (345)
T KOG2814|consen 125 SDR 127 (345)
T ss_pred hhh
Confidence 665
No 30
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=93.14 E-value=0.23 Score=50.82 Aligned_cols=40 Identities=25% Similarity=0.439 Sum_probs=36.1
Q ss_pred EEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEecc
Q 022690 140 KRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGR 185 (293)
Q Consensus 140 k~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGr 185 (293)
..++|+.||- +-+|-|||=+|..+|.|.++|||+|.|.+.
T Consensus 137 ~v~~RLlVp~------sq~GslIGK~G~~Ik~Ire~TgA~I~v~~~ 176 (485)
T KOG2190|consen 137 EVTCRLLVPS------SQVGSLIGKGGSLIKEIREETGAKIRVSSD 176 (485)
T ss_pred ceEEEEEech------hheeeeeccCcHHHHHHHHhcCceEEecCC
Confidence 4578999984 569999999999999999999999999985
No 31
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=92.25 E-value=0.16 Score=51.48 Aligned_cols=31 Identities=26% Similarity=0.591 Sum_probs=28.5
Q ss_pred CCeeeeEeCCCCchHHHHHHhhCCeEEEecc
Q 022690 155 FNFVGRILGPRGNSLKRVEAMTECRVFIRGR 185 (293)
Q Consensus 155 fNfvGrILGPrG~TlKrle~eTgcKI~IRGr 185 (293)
--|+|-||||.|.|+|-|-+.|.|||-+--+
T Consensus 207 tqyvgaIIGkeG~TIknItkqTqsriD~hrk 237 (584)
T KOG2193|consen 207 TQYVGAIIGKEGATIKNITKQTQSRIDVHRK 237 (584)
T ss_pred cceeEEEecCCCccccCcchhhhheeeeeec
Confidence 5699999999999999999999999998753
No 32
>PRK00106 hypothetical protein; Provisional
Probab=91.21 E-value=0.35 Score=50.10 Aligned_cols=62 Identities=34% Similarity=0.528 Sum_probs=50.1
Q ss_pred EecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHH
Q 022690 145 LDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIIN 224 (293)
Q Consensus 145 v~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~ 224 (293)
|.+|-+ .+-|||||--|-+++.+|..||+-|.| .+.|=-|.||+.||.
T Consensus 229 v~lp~d-----emkGriIGreGrNir~~E~~tGvdlii-----------------------ddtp~~v~lS~fdpv---- 276 (535)
T PRK00106 229 VHLPDD-----NMKGRIIGREGRNIRTLESLTGIDVII-----------------------DDTPEVVVLSGFDPI---- 276 (535)
T ss_pred EEcCCh-----HhhcceeCCCcchHHHHHHHhCceEEE-----------------------cCCCCeEEEeCCChH----
Confidence 556544 478999999999999999999999988 245667999999986
Q ss_pred HHHHHHHHHHHhccC
Q 022690 225 SRLDHAVAILENLLK 239 (293)
Q Consensus 225 ~rl~~A~e~Ie~LL~ 239 (293)
|-.-|..-+++|+.
T Consensus 277 -RReiAr~~le~Li~ 290 (535)
T PRK00106 277 -RREIARMTLESLIK 290 (535)
T ss_pred -HHHHHHHHHHHHHH
Confidence 55667777777776
No 33
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=90.44 E-value=0.4 Score=49.27 Aligned_cols=62 Identities=29% Similarity=0.544 Sum_probs=48.1
Q ss_pred EecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHH
Q 022690 145 LDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIIN 224 (293)
Q Consensus 145 v~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~ 224 (293)
|.+|-+ .+-|||||--|-++|.+|..||+-|.|= +.|=-|.||+.||.
T Consensus 208 v~lp~d-----~~kgriigreGrnir~~e~~tgvd~iid-----------------------dtp~~v~ls~fdp~---- 255 (514)
T TIGR03319 208 VNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID-----------------------DTPEAVILSGFDPV---- 255 (514)
T ss_pred EEcCCh-----hhhccccCCCcchHHHHHHHhCceEEEc-----------------------CCCCeEEecCCchH----
Confidence 455544 4789999999999999999999999882 34557889999986
Q ss_pred HHHHHHHHHHHhccC
Q 022690 225 SRLDHAVAILENLLK 239 (293)
Q Consensus 225 ~rl~~A~e~Ie~LL~ 239 (293)
|=.-|..-+++|+.
T Consensus 256 -rreia~~~l~~li~ 269 (514)
T TIGR03319 256 -RREIARMALEKLIQ 269 (514)
T ss_pred -HHHHHHHHHHHHHH
Confidence 44556666666665
No 34
>PRK12704 phosphodiesterase; Provisional
Probab=90.03 E-value=0.6 Score=48.10 Aligned_cols=49 Identities=27% Similarity=0.554 Sum_probs=40.4
Q ss_pred EecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchh
Q 022690 145 LDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPED 221 (293)
Q Consensus 145 v~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~ 221 (293)
|.+|-+ .+-|||||--|-++|.+|..||+-|.|= +.|=-|+||+.+|..
T Consensus 214 v~lp~d-----~mkgriigreGrnir~~e~~tgvd~iid-----------------------dtp~~v~ls~~~~~r 262 (520)
T PRK12704 214 VNLPND-----EMKGRIIGREGRNIRALETLTGVDLIID-----------------------DTPEAVILSGFDPIR 262 (520)
T ss_pred eecCCc-----hhhcceeCCCcchHHHHHHHhCCeEEEc-----------------------CCCCeEEEecCChhh
Confidence 455544 4789999999999999999999999882 356679999999864
No 35
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=89.64 E-value=2.1 Score=42.40 Aligned_cols=38 Identities=24% Similarity=0.448 Sum_probs=32.9
Q ss_pred EEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEec
Q 022690 141 RVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRG 184 (293)
Q Consensus 141 ~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRG 184 (293)
++.||.+|-. -.|.|||+.|.|+|.+.+++||-|.|--
T Consensus 132 kqikivvPNs------tag~iigkggAtiK~~~Eqsga~iqisP 169 (402)
T KOG2191|consen 132 KQIKIVVPNS------TAGMIIGKGGATIKAIQEQSGAWIQISP 169 (402)
T ss_pred ceeEEeccCC------cccceecCCcchHHHHHHhhCcceEecc
Confidence 4578888854 4689999999999999999999999964
No 36
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=88.10 E-value=0.65 Score=49.41 Aligned_cols=60 Identities=22% Similarity=0.405 Sum_probs=45.4
Q ss_pred EecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHH
Q 022690 145 LDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIIN 224 (293)
Q Consensus 145 v~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~ 224 (293)
+-|+.+. ++-+|||.|.|+|.|.++|||+|.|--.|++ .|.+.+.
T Consensus 556 ~~i~~dK------I~dvIG~gGk~I~~I~eetg~~IdieddGtv------------------------~i~~s~~----- 600 (692)
T COG1185 556 IKIDPDK------IRDVIGPGGKTIKAITEETGVKIDIEDDGTV------------------------KIAASDG----- 600 (692)
T ss_pred EccCHHH------HhhccCCcccchhhhhhhhCcEEEecCCCcE------------------------EEEecch-----
Confidence 4455554 5678999999999999999999999766664 4455442
Q ss_pred HHHHHHHHHHHhccC
Q 022690 225 SRLDHAVAILENLLK 239 (293)
Q Consensus 225 ~rl~~A~e~Ie~LL~ 239 (293)
.+..+|++.|+.+..
T Consensus 601 ~~~~~ak~~I~~i~~ 615 (692)
T COG1185 601 ESAKKAKERIEAITR 615 (692)
T ss_pred HHHHHHHHHHHHHHh
Confidence 267788888888874
No 37
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=88.07 E-value=0.93 Score=33.41 Aligned_cols=36 Identities=19% Similarity=0.351 Sum_probs=30.1
Q ss_pred EEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEE
Q 022690 141 RVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFI 182 (293)
Q Consensus 141 ~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~I 182 (293)
...+|+|+. .-+|+.||.+|.+++.++..+|.+|-|
T Consensus 25 ~~~~v~V~~------~~~~~aIGk~G~nI~~~~~l~~~~I~v 60 (61)
T cd02134 25 KRARVVVPD------DQLGLAIGKGGQNVRLASKLLGEKIDI 60 (61)
T ss_pred cEEEEEECc------ccceeeECCCCHHHHHHHHHHCCCeEE
Confidence 345677765 458999999999999999999998876
No 38
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=82.12 E-value=1.4 Score=45.29 Aligned_cols=42 Identities=24% Similarity=0.395 Sum_probs=36.5
Q ss_pred ceEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEecc
Q 022690 138 VVKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGR 185 (293)
Q Consensus 138 ~vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGr 185 (293)
....+.++.|| .+++|.|||..|+.+-.|++.|||.|.|-++
T Consensus 335 ~~~v~~~l~vp------s~~igciiGk~G~~iseir~~tgA~I~I~~~ 376 (485)
T KOG2190|consen 335 TQTVTQRLLVP------SDLIGCIIGKGGAKISEIRQRTGASISILNK 376 (485)
T ss_pred cceeeeeeccC------ccccceeecccccchHHHHHhcCCceEEccc
Confidence 44456778886 5699999999999999999999999999884
No 39
>KOG0336 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=81.89 E-value=0.75 Score=47.05 Aligned_cols=29 Identities=31% Similarity=0.641 Sum_probs=26.3
Q ss_pred CCCeeeeEeCCCCchHHHHHHhhCCeEEE
Q 022690 154 NFNFVGRILGPRGNSLKRVEAMTECRVFI 182 (293)
Q Consensus 154 ~fNfvGrILGPrG~TlKrle~eTgcKI~I 182 (293)
.-||||.+||=.|+.+|+||..|+++|.|
T Consensus 54 ks~mvg~vigrggskik~iq~~tnt~iqi 82 (629)
T KOG0336|consen 54 KSEMVGKVIGRGGSKIKRIQNDTNTRIQI 82 (629)
T ss_pred hhhhhheeeccCcchhhhhhcccceeEEE
Confidence 35899999999999999999999988765
No 40
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=80.39 E-value=0.77 Score=35.11 Aligned_cols=31 Identities=23% Similarity=0.443 Sum_probs=24.0
Q ss_pred CCCCCeeeeEeCCCCchHHHHHHhh-CCeEEE
Q 022690 152 YPNFNFVGRILGPRGNSLKRVEAMT-ECRVFI 182 (293)
Q Consensus 152 ~P~fNfvGrILGPrG~TlKrle~eT-gcKI~I 182 (293)
.++++-+|..+|.+|..+|.|+++. |-||.|
T Consensus 13 ~~~~d~vG~~iG~~G~rik~i~~~L~gekIdv 44 (69)
T PF13184_consen 13 DPNIDPVGACIGKKGSRIKAISEELNGEKIDV 44 (69)
T ss_dssp STTS-HHHHHH-CCCCCHHHHHHHTTT-EEEE
T ss_pred CCCcCcceecCccccHHHHHHHHHhCCCeEEE
Confidence 4889999999999999999999998 544443
No 41
>KOG1067 consensus Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only]
Probab=74.69 E-value=2.6 Score=44.50 Aligned_cols=53 Identities=17% Similarity=0.269 Sum_probs=41.9
Q ss_pred eeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHHHHHHHHHHHHhc
Q 022690 158 VGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINSRLDHAVAILENL 237 (293)
Q Consensus 158 vGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~~rl~~A~e~Ie~L 237 (293)
+..+|||.|..+|+|+.|||+.-+| ++=|+-|-|.++. .|..|.+.|..+
T Consensus 608 ~~~lIGp~G~~~kki~~EtGai~~v-------------------------De~t~~i~A~~~~-----am~~Ak~~I~~i 657 (760)
T KOG1067|consen 608 RATLIGPGGVLKKKIEVETGAISQV-------------------------DEGTFSIFAPTQA-----AMEEAKEFIDGI 657 (760)
T ss_pred hheeecCccceeeeEeeeccceeee-------------------------cCceEEEEecCHH-----HHHHHHHHHHHH
Confidence 5678999999999999999943322 3347888888864 689999999988
Q ss_pred cCC
Q 022690 238 LKP 240 (293)
Q Consensus 238 L~p 240 (293)
..-
T Consensus 658 ~~~ 660 (760)
T KOG1067|consen 658 IKD 660 (760)
T ss_pred hcC
Confidence 874
No 42
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=72.53 E-value=3.4 Score=29.15 Aligned_cols=23 Identities=13% Similarity=0.485 Sum_probs=20.5
Q ss_pred eeeEeCCCCchHHHHHHhhCCeE
Q 022690 158 VGRILGPRGNSLKRVEAMTECRV 180 (293)
Q Consensus 158 vGrILGPrG~TlKrle~eTgcKI 180 (293)
.|++||.+|.+++.|+..++-.+
T Consensus 36 ~g~lIGk~G~~l~~l~~l~~~~~ 58 (68)
T cd02409 36 PGLVIGKKGQNIRALQKLLQKLL 58 (68)
T ss_pred CceEECCCCccHHHHHHHHHHHc
Confidence 58999999999999999998554
No 43
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=68.44 E-value=4 Score=40.31 Aligned_cols=44 Identities=25% Similarity=0.399 Sum_probs=33.9
Q ss_pred eEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEE--EeccCCc
Q 022690 139 VKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVF--IRGRGSV 188 (293)
Q Consensus 139 vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~--IRGrGS~ 188 (293)
..+++.|-+| ++ ||+.|.|++|.++|.|+++|.+.|. .||+--+
T Consensus 24 ~nvt~sv~vp---s~---~v~~ivg~qg~kikalr~KTqtyi~tPsr~eePi 69 (394)
T KOG2113|consen 24 QNVTESVEVP---SE---HVAEIVGRQGCKIKALRAKTQTYIKTPSRGEEPI 69 (394)
T ss_pred CccceeeecC---cc---cceeecccCccccchhhhhhcceeccCCCCCCCc
Confidence 4455666666 44 9999999999999999999999875 4554433
No 44
>PRK12705 hypothetical protein; Provisional
Probab=64.47 E-value=5.5 Score=41.28 Aligned_cols=30 Identities=30% Similarity=0.619 Sum_probs=26.7
Q ss_pred CCCCeeeeEeCCCCchHHHHHHhhCCeEEE
Q 022690 153 PNFNFVGRILGPRGNSLKRVEAMTECRVFI 182 (293)
Q Consensus 153 P~fNfvGrILGPrG~TlKrle~eTgcKI~I 182 (293)
|+=.+-|||||--|.+++.+|..||+-|.|
T Consensus 205 p~demkGriIGreGrNir~~E~~tGvdlii 234 (508)
T PRK12705 205 PSDAMKGRIIGREGRNIRAFEGLTGVDLII 234 (508)
T ss_pred CChHhhccccCccchhHHHHHHhhCCceEe
Confidence 344588999999999999999999998887
No 45
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=63.02 E-value=21 Score=32.76 Aligned_cols=40 Identities=30% Similarity=0.513 Sum_probs=32.5
Q ss_pred EEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEecc-CCc
Q 022690 143 IRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGR-GSV 188 (293)
Q Consensus 143 ~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGr-GS~ 188 (293)
+.|.||-+ =+|-|+|+.|.+.|.||+.++|+|.|=.+ ||+
T Consensus 10 ~~v~iPk~------R~~~lig~~g~v~k~ie~~~~~~~~iD~~~~~V 50 (194)
T COG1094 10 EAVKIPKD------RIGVLIGKWGEVKKAIEEKTGVKLRIDSKTGSV 50 (194)
T ss_pred eeeecCch------hheeeecccccchHHHHhhcCeEEEEECCCCeE
Confidence 44566644 37899999999999999999999999876 444
No 46
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=62.81 E-value=5.7 Score=34.21 Aligned_cols=28 Identities=21% Similarity=0.294 Sum_probs=26.3
Q ss_pred eeeeEeCCCCchHHHHHHhhCCeEEEec
Q 022690 157 FVGRILGPRGNSLKRVEAMTECRVFIRG 184 (293)
Q Consensus 157 fvGrILGPrG~TlKrle~eTgcKI~IRG 184 (293)
.+|..+|.+|..+|.|++..|-||-|=.
T Consensus 42 ~vG~~IG~~G~rI~~i~e~lgekIdVve 69 (140)
T PRK08406 42 DMGLAIGKGGENVKRLEEKLGKDIELVE 69 (140)
T ss_pred CccccCCcCchHHHHHHHHhCCceEEEE
Confidence 6899999999999999999999998877
No 47
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=57.56 E-value=7 Score=29.83 Aligned_cols=21 Identities=24% Similarity=0.646 Sum_probs=18.9
Q ss_pred eeeEeCCCCchHHHHHHhhCC
Q 022690 158 VGRILGPRGNSLKRVEAMTEC 178 (293)
Q Consensus 158 vGrILGPrG~TlKrle~eTgc 178 (293)
.|+|||-+|.|++.||--+..
T Consensus 35 ~g~LIGk~G~tL~AlQ~L~~~ 55 (77)
T cd02414 35 IGLLIGKRGKTLDALQYLANL 55 (77)
T ss_pred CCeEECCCCccHHHHHHHHHH
Confidence 599999999999999998763
No 48
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=57.31 E-value=8.9 Score=36.26 Aligned_cols=29 Identities=24% Similarity=0.524 Sum_probs=26.4
Q ss_pred CCeeeeEeCCCCchHHHHHHhhCCeEEEe
Q 022690 155 FNFVGRILGPRGNSLKRVEAMTECRVFIR 183 (293)
Q Consensus 155 fNfvGrILGPrG~TlKrle~eTgcKI~IR 183 (293)
.++|-|+||.+|+-++-|.+.|+|+|.|=
T Consensus 154 p~kVpRvig~~~sm~~~l~~~~~~~I~VG 182 (239)
T COG1097 154 PSKVPRVIGKKGSMLNMLKEKTGCEIIVG 182 (239)
T ss_pred hhhcceEecCCCcHHHHhhhhcCeEEEEe
Confidence 46788999999999999999999999983
No 49
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=56.61 E-value=3.2 Score=35.09 Aligned_cols=45 Identities=29% Similarity=0.505 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHhcc-CCCccchHHHHHHHHHHHHHHcCccCCCCC
Q 022690 223 INSRLDHAVAILENLL-KPVDESLDHYKKQQLRELAMLNGTLREESP 268 (293)
Q Consensus 223 ~~~rl~~A~e~Ie~LL-~pv~e~~D~lKr~QL~ELA~lNGt~r~~~~ 268 (293)
+|.||.+|+.+|+.-| --|.|+.+-+| .|.+||..-|..++.++.
T Consensus 46 IDNKIeQAMDLVKtHLmfAVREEVe~Lk-~qI~eL~er~~~Le~EN~ 91 (123)
T KOG4797|consen 46 IDNKIEQAMDLVKTHLMFAVREEVEVLK-EQIRELEERNSALERENS 91 (123)
T ss_pred echHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 3569999999999854 45667776666 999999998888876654
No 50
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=49.41 E-value=23 Score=35.19 Aligned_cols=40 Identities=20% Similarity=0.407 Sum_probs=32.5
Q ss_pred EEecCCCCCCCCCeeeeEeCCCCchHHHHHHhh-CCeEEEec
Q 022690 144 RLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMT-ECRVFIRG 184 (293)
Q Consensus 144 Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eT-gcKI~IRG 184 (293)
||-| ....|+++-+|..+|++|..++.|.++. |=||-|=-
T Consensus 234 KVAV-~s~~~~iDpvGa~iG~~G~rI~~i~~el~gekIdiv~ 274 (362)
T PRK12327 234 KIAV-RSNNPNVDAKGACVGPKGQRVQNIVSELKGEKIDIID 274 (362)
T ss_pred EEEE-EcCCCCCCchheeECCCChhHHHHHHHhCCCeEEEEE
Confidence 4444 2356899999999999999999999998 77777654
No 51
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=49.12 E-value=21 Score=36.60 Aligned_cols=42 Identities=17% Similarity=0.215 Sum_probs=33.5
Q ss_pred EEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhh-CCeEEEec
Q 022690 142 VIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMT-ECRVFIRG 184 (293)
Q Consensus 142 ~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eT-gcKI~IRG 184 (293)
..||-| ....|+++-||..+|++|+.++.|.++. |=||-|=-
T Consensus 264 RtKVAV-~S~d~~VDPvGacVG~kG~RI~~I~~eL~gEkIDVI~ 306 (449)
T PRK12329 264 RTKIAV-DTLERDVDPVGACIGARGSRIQAVVNELRGEKIDVIR 306 (449)
T ss_pred eeEEEE-EcCCCCCChhhccCCCCcchHHHHHHHhCCCeEEEEE
Confidence 345554 2356899999999999999999999998 77887654
No 52
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=48.10 E-value=28 Score=34.24 Aligned_cols=40 Identities=20% Similarity=0.366 Sum_probs=31.9
Q ss_pred EEecCCCCCCCCCeeeeEeCCCCchHHHHHHhh-CCeEEEec
Q 022690 144 RLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMT-ECRVFIRG 184 (293)
Q Consensus 144 Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eT-gcKI~IRG 184 (293)
||-| ....|+++-+|..+|++|..++.|.++. |=||-|=-
T Consensus 232 KvAV-~s~~~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 272 (341)
T TIGR01953 232 KIAV-ESNDENIDPVGACVGPKGSRIQAISKELNGEKIDIIE 272 (341)
T ss_pred EEEE-EcCCCCCCcceeeECCCCchHHHHHHHhCCCeEEEEE
Confidence 4544 2346899999999999999999999998 66666544
No 53
>COG1702 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]
Probab=43.20 E-value=44 Score=33.29 Aligned_cols=31 Identities=23% Similarity=0.337 Sum_probs=27.6
Q ss_pred CCeeeeEeCCCCchHHHHHHhhCCeEEEecc
Q 022690 155 FNFVGRILGPRGNSLKRVEAMTECRVFIRGR 185 (293)
Q Consensus 155 fNfvGrILGPrG~TlKrle~eTgcKI~IRGr 185 (293)
=|-+--|+||.|..++.||+.+|+.|.-||.
T Consensus 23 ~~~~~~l~G~~~~~l~l~e~~~gv~i~~rG~ 53 (348)
T COG1702 23 DNELVALFGPTDTNLSLLEIALGVSIVARGE 53 (348)
T ss_pred chhhhhhcCCCCccHHHHHHHhCcEEEeCCc
Confidence 3566779999999999999999999999994
No 54
>KOG2208 consensus Vigilin [Lipid transport and metabolism]
Probab=40.78 E-value=19 Score=39.13 Aligned_cols=39 Identities=15% Similarity=0.432 Sum_probs=30.7
Q ss_pred eEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEe
Q 022690 139 VKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIR 183 (293)
Q Consensus 139 vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IR 183 (293)
...+..++||.+ |-+-|+||+|.++++++.+++|-+.+-
T Consensus 707 ~~~~~~~~~p~~------~~~~~ig~~g~~~r~~~~~~~~~~~~~ 745 (753)
T KOG2208|consen 707 NLVTKEIEIPRS------LHRYLIGPKGSNLRQLEKEFNVNIVVP 745 (753)
T ss_pred cceeeEEeccHH------HhhhccCCCCccHHHHHHHhccceecC
Confidence 344556777765 456789999999999999999988764
No 55
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=39.92 E-value=29 Score=32.00 Aligned_cols=40 Identities=23% Similarity=0.416 Sum_probs=29.0
Q ss_pred eEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHH--------HHhhCCeEEEe
Q 022690 139 VKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRV--------EAMTECRVFIR 183 (293)
Q Consensus 139 vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrl--------e~eTgcKI~IR 183 (293)
+.....|+|.-+. --|-|||-+|.++|+| |+-.||||.+.
T Consensus 219 ~~i~~~i~v~~~s-----~k~iiig~~g~~ik~i~~~ar~~l~~~~~~~v~l~ 266 (270)
T TIGR00436 219 LKIHALISVERES-----QKKIIIGKNGSMIKAIGIAARKDILELFDCDVFLE 266 (270)
T ss_pred EEEEEEEEECcCC-----ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 4455666665554 3478999999999986 66678888764
No 56
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=39.19 E-value=23 Score=30.75 Aligned_cols=29 Identities=21% Similarity=0.367 Sum_probs=26.5
Q ss_pred CeeeeEeCCCCchHHHHHHhhCCeEEEec
Q 022690 156 NFVGRILGPRGNSLKRVEAMTECRVFIRG 184 (293)
Q Consensus 156 NfvGrILGPrG~TlKrle~eTgcKI~IRG 184 (293)
+-+|..+|++|..+|.|++..|=||-|=.
T Consensus 42 g~vG~~IG~~G~rIk~i~el~gekIdVVe 70 (141)
T TIGR01952 42 GEMGAAIGKGGENVKRLEELIGKSIELIE 70 (141)
T ss_pred CCccccCCCCchHHHHHHHhcCCeeEEEE
Confidence 36999999999999999999999998877
No 57
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=37.84 E-value=59 Score=31.84 Aligned_cols=39 Identities=15% Similarity=0.341 Sum_probs=31.1
Q ss_pred EEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEec
Q 022690 140 KRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRG 184 (293)
Q Consensus 140 k~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRG 184 (293)
++..+|++--+. .|.|+|-.|.++|+|..+.++.|.|--
T Consensus 47 r~e~ril~~sk~------agavigkgg~nik~lr~d~na~v~vpd 85 (390)
T KOG2192|consen 47 RVELRILLQSKN------AGAVIGKGGKNIKALRTDYNASVSVPD 85 (390)
T ss_pred ceeEEEEEeccc------ccceeccccccHHHHhhhccceeeccC
Confidence 345667775443 689999999999999999999998743
No 58
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=37.44 E-value=26 Score=25.18 Aligned_cols=20 Identities=20% Similarity=0.297 Sum_probs=16.1
Q ss_pred hHHHHHHhhCCeEEEeccCC
Q 022690 168 SLKRVEAMTECRVFIRGRGS 187 (293)
Q Consensus 168 TlKrle~eTgcKI~IRGrGS 187 (293)
.+++||++.|+++.+|..+.
T Consensus 33 ~i~~LE~~lg~~Lf~r~~~~ 52 (60)
T PF00126_consen 33 QIKQLEEELGVPLFERSGRG 52 (60)
T ss_dssp HHHHHHHHHTS-SEEECSSS
T ss_pred HHHHHHHHhCCeEEEECCCC
Confidence 57999999999999996543
No 59
>PRK00089 era GTPase Era; Reviewed
Probab=37.26 E-value=71 Score=29.45 Aligned_cols=41 Identities=29% Similarity=0.458 Sum_probs=29.6
Q ss_pred ceEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHH--------HHhhCCeEEEe
Q 022690 138 VVKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRV--------EAMTECRVFIR 183 (293)
Q Consensus 138 ~vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrl--------e~eTgcKI~IR 183 (293)
.++....|+|.-+.+ .+-|||-+|.++|+| |+-.||||.+.
T Consensus 223 ~~~i~~~i~v~~~~~-----k~i~ig~~g~~i~~i~~~ar~~l~~~~~~~v~l~ 271 (292)
T PRK00089 223 LVRIEATIYVERDSQ-----KGIIIGKGGAMLKKIGTEARKDIEKLLGKKVFLE 271 (292)
T ss_pred eEEEEEEEEEccCCc-----eeEEEeCCcHHHHHHHHHHHHHHHHHhCCCEEEE
Confidence 345566677755543 688999999999987 56677877764
No 60
>PRK02821 hypothetical protein; Provisional
Probab=36.53 E-value=21 Score=28.08 Aligned_cols=21 Identities=14% Similarity=0.450 Sum_probs=17.7
Q ss_pred eeeeEeCCCCchHHHHHHhhC
Q 022690 157 FVGRILGPRGNSLKRVEAMTE 177 (293)
Q Consensus 157 fvGrILGPrG~TlKrle~eTg 177 (293)
=+|||||=+|.|++.|-.--.
T Consensus 41 D~GrVIGk~Gr~i~AIRtlv~ 61 (77)
T PRK02821 41 DLGKVIGRGGRTATALRTVVA 61 (77)
T ss_pred hCcceeCCCCchHHHHHHHHH
Confidence 489999999999999876543
No 61
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=36.41 E-value=27 Score=31.78 Aligned_cols=34 Identities=21% Similarity=0.269 Sum_probs=29.7
Q ss_pred CCCCCeeeeEeCCCCchHHHHHHhhCCeEEEecc
Q 022690 152 YPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGR 185 (293)
Q Consensus 152 ~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGr 185 (293)
.++.+-+|..+|++|..+|.|.++.|=||-|=--
T Consensus 81 ~~~~d~vG~~iG~~G~rvk~i~~eLgekIdVVe~ 114 (190)
T COG0195 81 VVKIDPVGACIGKRGSRVKAVSEELGEKIDVVEW 114 (190)
T ss_pred ecCcCchhhhccCCChHHHHHHHHhCCceEEEEe
Confidence 3567889999999999999999999988887664
No 62
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=35.41 E-value=35 Score=34.25 Aligned_cols=39 Identities=15% Similarity=0.286 Sum_probs=31.2
Q ss_pred EEecCCCCCCCCCeeeeEeCCCCchHHHHHHhh-CCeEEEe
Q 022690 144 RLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMT-ECRVFIR 183 (293)
Q Consensus 144 Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eT-gcKI~IR 183 (293)
||-| ....|+++-+|..+|++|..++.|.++. |=||-|=
T Consensus 240 KVAV-~S~d~~iDPvGacIG~~G~rI~~I~~eL~gEkIDvI 279 (374)
T PRK12328 240 KVAL-FSNNPNIDPIGATVGVKGVRINAVSKELNGENIDCI 279 (374)
T ss_pred EEEE-EcCCCCCChHHhhcCCCcchHHHHHHHhCCCeEEEE
Confidence 4444 2366899999999999999999999998 6666554
No 63
>KOG0334 consensus RNA helicase [RNA processing and modification]
Probab=34.68 E-value=27 Score=39.06 Aligned_cols=76 Identities=24% Similarity=0.314 Sum_probs=55.1
Q ss_pred ecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchhHHHH
Q 022690 146 DVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPEDIINS 225 (293)
Q Consensus 146 ~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~~~~~ 225 (293)
-.+++.+| =|..+++.+=-- |.+|...|+|.|++||+=--... .| ....+-||.+|++.+. .
T Consensus 901 ~~~inD~P-q~~r~~vt~~~~--L~~i~e~~~~~it~rg~f~~~gk--------~p--~~gErklyl~ve~~~e-----~ 962 (997)
T KOG0334|consen 901 ELEINDFP-QNARWRVTYKEA--LLRISEPTAAGITTRGKFNPPGK--------EP--KPGERKLYLLVEGPDE-----L 962 (997)
T ss_pred eccccccc-hhcceeeechhh--hhhccCccccceeeccccCCCCC--------CC--CCcchhhhhhhhcchh-----H
Confidence 34567888 457888877554 99999999999999996322111 11 2357889999997663 3
Q ss_pred HHHHHHHHHHhccC
Q 022690 226 RLDHAVAILENLLK 239 (293)
Q Consensus 226 rl~~A~e~Ie~LL~ 239 (293)
-+++|++.++.+|.
T Consensus 963 ~vqra~~e~~r~l~ 976 (997)
T KOG0334|consen 963 SVQRAIEELERLLE 976 (997)
T ss_pred HHHHHHHHHHHHHH
Confidence 57889999988665
No 64
>PRK00468 hypothetical protein; Provisional
Probab=34.56 E-value=23 Score=27.59 Aligned_cols=18 Identities=22% Similarity=0.676 Sum_probs=16.0
Q ss_pred eeeEeCCCCchHHHHHHh
Q 022690 158 VGRILGPRGNSLKRVEAM 175 (293)
Q Consensus 158 vGrILGPrG~TlKrle~e 175 (293)
+|||||=+|.|++.|-.-
T Consensus 41 ~GrVIGk~Gr~i~AIRtv 58 (75)
T PRK00468 41 MGKVIGKQGRIAKAIRTV 58 (75)
T ss_pred CcceecCCChhHHHHHHH
Confidence 699999999999988664
No 65
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=34.02 E-value=7.8 Score=29.04 Aligned_cols=20 Identities=25% Similarity=0.695 Sum_probs=18.1
Q ss_pred eeeEeCCCCchHHHHHHhhC
Q 022690 158 VGRILGPRGNSLKRVEAMTE 177 (293)
Q Consensus 158 vGrILGPrG~TlKrle~eTg 177 (293)
.|+|||-+|.|++.||--++
T Consensus 40 ~g~lIGk~G~tl~ALq~l~~ 59 (73)
T PF13083_consen 40 AGRLIGKHGKTLNALQYLVN 59 (73)
T ss_dssp CHHHCTTHHHHHHHHHHHHH
T ss_pred cceEECCCCeeHHHHHHHHH
Confidence 79999999999999998665
No 66
>PRK15494 era GTPase Era; Provisional
Probab=33.25 E-value=83 Score=30.40 Aligned_cols=41 Identities=24% Similarity=0.292 Sum_probs=30.2
Q ss_pred ceEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHH--------HHhhCCeEEEe
Q 022690 138 VVKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRV--------EAMTECRVFIR 183 (293)
Q Consensus 138 ~vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrl--------e~eTgcKI~IR 183 (293)
.++....|||.-+. --|-|||-+|..+|+| |+-.||||.+.
T Consensus 270 ~~~i~~~i~v~~~s-----qk~iiiG~~g~~ik~i~~~ar~~le~~~~~~v~l~ 318 (339)
T PRK15494 270 SVKINQVIVVSRES-----YKTIILGKNGSKIKEIGAKSRMQMERFFGFPVHLF 318 (339)
T ss_pred eEEEEEEEEECCCC-----ceeEEEcCCcHHHHHHHHHHHHHHHHHhCCCeEEE
Confidence 34566677776554 4578999999999986 66678887764
No 67
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=31.88 E-value=32 Score=31.17 Aligned_cols=21 Identities=24% Similarity=0.370 Sum_probs=18.5
Q ss_pred hHHHHHHhhCCeEEEeccCCc
Q 022690 168 SLKRVEAMTECRVFIRGRGSV 188 (293)
Q Consensus 168 TlKrle~eTgcKI~IRGrGS~ 188 (293)
.+|+||++.|+++++|++|..
T Consensus 36 ~i~~LE~~lg~~Lf~R~r~i~ 56 (294)
T PRK13348 36 RIKALEESLGQPLLVRGRPCR 56 (294)
T ss_pred HHHHHHHHhCceeeecCCCCc
Confidence 689999999999999997643
No 68
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=31.36 E-value=36 Score=30.45 Aligned_cols=27 Identities=15% Similarity=0.123 Sum_probs=25.4
Q ss_pred eeEeCCCCchHHHHHHhhCCeEEEecc
Q 022690 159 GRILGPRGNSLKRVEAMTECRVFIRGR 185 (293)
Q Consensus 159 GrILGPrG~TlKrle~eTgcKI~IRGr 185 (293)
|.-||++|.++|+|++..|=+|.|=.-
T Consensus 72 g~aIGk~G~~ik~l~~~lgk~VevVE~ 98 (166)
T PRK06418 72 RIPIGKGGKIAKALSRKLGKKVRVVEK 98 (166)
T ss_pred cccccccchHHHHHHHHhCCcEEEEEc
Confidence 999999999999999999999998873
No 69
>KOG2113 consensus Predicted RNA binding protein, contains KH domain [General function prediction only]
Probab=31.26 E-value=26 Score=34.85 Aligned_cols=31 Identities=29% Similarity=0.629 Sum_probs=27.6
Q ss_pred CCeeeeEeCCCCchHHHHHHhhCCeEEEecc
Q 022690 155 FNFVGRILGPRGNSLKRVEAMTECRVFIRGR 185 (293)
Q Consensus 155 fNfvGrILGPrG~TlKrle~eTgcKI~IRGr 185 (293)
+-+||.+.||.|+|+|++|+.|..-|.--++
T Consensus 123 ~rvvglvv~~~~~ti~~iqq~tnt~I~T~v~ 153 (394)
T KOG2113|consen 123 LRVVGLVVGPKGATIKRIQQFTNTYIATPVR 153 (394)
T ss_pred ceeeeeccccccCccchheecccceEeeecc
Confidence 6799999999999999999999998876554
No 70
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=30.91 E-value=51 Score=33.93 Aligned_cols=40 Identities=20% Similarity=0.320 Sum_probs=32.5
Q ss_pred EEecCCCCCCCCCeeeeEeCCCCchHHHHHHhh-CCeEEEec
Q 022690 144 RLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMT-ECRVFIRG 184 (293)
Q Consensus 144 Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eT-gcKI~IRG 184 (293)
||-|= ...|+++-||..+|++|+.++.|.++. |=||-|=-
T Consensus 234 KvAV~-s~d~~iDpvga~vG~~G~ri~~i~~el~ge~Idiv~ 274 (470)
T PRK09202 234 KIAVK-SNDPRIDPVGACVGMRGSRIQAISNELGGEKIDIIL 274 (470)
T ss_pred EEEEE-cCCCCCChhHccCCCCCchHHHHHHHhCCCeEEEEE
Confidence 45442 567899999999999999999999998 77776643
No 71
>PRK01064 hypothetical protein; Provisional
Probab=30.12 E-value=34 Score=26.93 Aligned_cols=20 Identities=25% Similarity=0.718 Sum_probs=17.6
Q ss_pred eeeEeCCCCchHHHHHHhhC
Q 022690 158 VGRILGPRGNSLKRVEAMTE 177 (293)
Q Consensus 158 vGrILGPrG~TlKrle~eTg 177 (293)
+|++||=+|.|++.|..-..
T Consensus 41 ~g~vIGk~G~~i~air~l~~ 60 (78)
T PRK01064 41 IGKIIGKEGRTIKAIRTLLV 60 (78)
T ss_pred ceEEECCCCccHHHHHHHHH
Confidence 69999999999999988544
No 72
>PRK05424 rplA 50S ribosomal protein L1; Validated
Probab=29.69 E-value=1.4e+02 Score=27.73 Aligned_cols=31 Identities=6% Similarity=0.114 Sum_probs=17.5
Q ss_pred CCcEEEEEecC-chhHHHHHHHHHHHHHHhcc
Q 022690 208 EPLHVLVEAEF-PEDIINSRLDHAVAILENLL 238 (293)
Q Consensus 208 epLHVlIsa~~-p~~~~~~rl~~A~e~Ie~LL 238 (293)
.-+|+-|=..+ +.+.+.+-+...++.|.+.+
T Consensus 168 g~i~~~IG~~~m~~e~i~eNi~a~l~~i~~~~ 199 (230)
T PRK05424 168 GIIHAPIGKVSFDAEKLKENLKALIDAIKKAK 199 (230)
T ss_pred CEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhC
Confidence 45677775544 33344455666666666554
No 73
>TIGR01169 rplA_bact ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model.
Probab=29.11 E-value=1.9e+02 Score=26.88 Aligned_cols=10 Identities=80% Similarity=1.441 Sum_probs=8.6
Q ss_pred eeeeEeCCCC
Q 022690 157 FVGRILGPRG 166 (293)
Q Consensus 157 fvGrILGPrG 166 (293)
.+|+||||||
T Consensus 124 ~Lg~iLGPrG 133 (227)
T TIGR01169 124 KLGRILGPRG 133 (227)
T ss_pred Hhcccccccc
Confidence 3599999997
No 74
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=29.04 E-value=1.7e+02 Score=28.72 Aligned_cols=42 Identities=21% Similarity=0.470 Sum_probs=33.8
Q ss_pred CCCCceEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEe
Q 022690 134 PTTPVVKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIR 183 (293)
Q Consensus 134 ~~~~~vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IR 183 (293)
-.+|+. +..|-||-| +-|-|||-.|.-+|+|-.|+|+-|.|-
T Consensus 310 lGGPit--TaQvtip~d------lggsiigkggqri~~ir~esGA~Ikid 351 (390)
T KOG2192|consen 310 LGGPIT--TAQVTIPKD------LGGSIIGKGGQRIKQIRHESGASIKID 351 (390)
T ss_pred CCCcee--eeeEecccc------cCcceecccchhhhhhhhccCceEEec
Confidence 345655 355777754 679999999999999999999999874
No 75
>COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]
Probab=28.54 E-value=1.6e+02 Score=25.99 Aligned_cols=99 Identities=22% Similarity=0.224 Sum_probs=58.5
Q ss_pred eEEEEEEecCCCCCCCCCeeeeEeCCCCchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecC
Q 022690 139 VKRVIRLDVPVDKYPNFNFVGRILGPRGNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEF 218 (293)
Q Consensus 139 vk~~~Kv~IPv~~~P~fNfvGrILGPrG~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~ 218 (293)
+....|+-||--+-.----+|-=|||+|.++...-++.+.+- +| | -..+++|.|++..
T Consensus 4 ~~~~ikl~v~aGkA~p~PpvGPALG~~Gvni~~f~k~fN~~T--------~~------------~--~G~~vPV~Itv~~ 61 (141)
T COG0080 4 VVKIIKLQVPAGKANPSPPVGPALGQLGVNIMEFCKEFNAAT--------KD------------E--KGLPVPVVITVYE 61 (141)
T ss_pred cceEEEEEecccccCCCCCCCccccccCCCHHHHHHHHHHHh--------hc------------c--CCCeeeEEEEEEc
Confidence 345566777755433334689999999999999988876331 11 1 3578889888872
Q ss_pred chh-HHHHHHHHHHHHHHhccCCCcc-------chHHHHHHHHHHHHHH
Q 022690 219 PED-IINSRLDHAVAILENLLKPVDE-------SLDHYKKQQLRELAML 259 (293)
Q Consensus 219 p~~-~~~~rl~~A~e~Ie~LL~pv~e-------~~D~lKr~QL~ELA~l 259 (293)
... ....+.==|-.+|.+.+.-... -.-.+-+.|++|.|.+
T Consensus 62 drsftf~~ktPPas~LlkKa~g~~~Gs~~p~k~~vG~lt~~qv~eIA~~ 110 (141)
T COG0080 62 DRSFTFIVKTPPASALLKKAAGIEKGSGKPNKNKVGKLTLAQVREIAKT 110 (141)
T ss_pred CCcEEEEECCCCHHHHHHHHhCCCCCCCCCCcceeeeeeHHHHHHHHHH
Confidence 111 0000112255666666643211 1123558899998875
No 76
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=27.88 E-value=35 Score=26.90 Aligned_cols=18 Identities=17% Similarity=0.802 Sum_probs=15.9
Q ss_pred eeeEeCCCCchHHHHHHh
Q 022690 158 VGRILGPRGNSLKRVEAM 175 (293)
Q Consensus 158 vGrILGPrG~TlKrle~e 175 (293)
+|++||=+|.|++.|-.-
T Consensus 41 ~GkvIGk~GRti~AIRTl 58 (76)
T COG1837 41 MGKVIGKQGRTIQAIRTL 58 (76)
T ss_pred ccceecCCChhHHHHHHH
Confidence 799999999999998653
No 77
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=27.36 E-value=1.5e+02 Score=27.32 Aligned_cols=61 Identities=23% Similarity=0.202 Sum_probs=35.1
Q ss_pred eeeEeCCC-------------CchHHHHHHhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecC-chhHH
Q 022690 158 VGRILGPR-------------GNSLKRVEAMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEF-PEDII 223 (293)
Q Consensus 158 vGrILGPr-------------G~TlKrle~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~-p~~~~ 223 (293)
+||+|||+ +..+...-+++.++|.+|=+ -..-+|+.|=..+ ..+.+
T Consensus 117 lgk~LGp~~~p~gK~P~~~~~~~dl~~~i~~~k~~v~~r~~--------------------k~~~~~~~VGk~~m~~e~i 176 (214)
T PTZ00225 117 VPRLVGPHMHRMGKFPTVCSPSESLPDKVVELRSTVKFQLK--------------------KVLCLGTCVGHVEMTEEQL 176 (214)
T ss_pred hhhhcCCCCCcCCCCCcccCCccCHHHHHHHHhheeEEEec--------------------CccEEEeEEccCCCCHHHH
Confidence 59999999 33355555566655555532 1234677775544 23334
Q ss_pred HHHHHHHHHHHHhcc
Q 022690 224 NSRLDHAVAILENLL 238 (293)
Q Consensus 224 ~~rl~~A~e~Ie~LL 238 (293)
.+-+..+++.|...|
T Consensus 177 ~eNi~a~l~~l~~~~ 191 (214)
T PTZ00225 177 RQNVVMAINFLVSLL 191 (214)
T ss_pred HHHHHHHHHHHHHhC
Confidence 445666666666665
No 78
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=25.98 E-value=39 Score=30.59 Aligned_cols=21 Identities=14% Similarity=0.192 Sum_probs=18.1
Q ss_pred hHHHHHHhhCCeEEEeccCCc
Q 022690 168 SLKRVEAMTECRVFIRGRGSV 188 (293)
Q Consensus 168 TlKrle~eTgcKI~IRGrGS~ 188 (293)
.+|+||++.|++++.|+||-.
T Consensus 35 ~I~~LE~~lg~~Lf~R~r~~~ 55 (292)
T TIGR03298 35 RIKALEERLGQPLLVRTQPCR 55 (292)
T ss_pred HHHHHHHHhCchheecCCCCc
Confidence 479999999999999997543
No 79
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=24.02 E-value=55 Score=29.80 Aligned_cols=22 Identities=14% Similarity=0.178 Sum_probs=18.9
Q ss_pred hHHHHHHhhCCeEEEeccCCcC
Q 022690 168 SLKRVEAMTECRVFIRGRGSVK 189 (293)
Q Consensus 168 TlKrle~eTgcKI~IRGrGS~k 189 (293)
.+|+||++.||+++.|++|-.-
T Consensus 36 ~I~~LE~~lg~~LF~R~~~~~l 57 (294)
T PRK03635 36 RIKALEERVGQVLLVRTQPCRP 57 (294)
T ss_pred HHHHHHHHhCceeeecCCCCcc
Confidence 6899999999999999976443
No 80
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=23.98 E-value=35 Score=29.33 Aligned_cols=25 Identities=20% Similarity=0.420 Sum_probs=21.8
Q ss_pred eeeEeCCCCchHHHHHHhhCCeEEE
Q 022690 158 VGRILGPRGNSLKRVEAMTECRVFI 182 (293)
Q Consensus 158 vGrILGPrG~TlKrle~eTgcKI~I 182 (293)
.|+.||.+|.|++.++.-+|-++-|
T Consensus 110 ~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 110 KGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cchhhCCCCHHHHHHHHHhCCccCC
Confidence 6899999999999999999866543
No 81
>PF07582 AP_endonuc_2_N: AP endonuclease family 2 C terminus; InterPro: IPR011418 DNA damaging agents such as the anti-tumour drugs bleomycin and neocarzinostatin or those that generate oxygen radicals produce a variety of lesions in DNA. Amongst these is base-loss which forms apurinic/apyrimidinic (AP) sites or strand breaks with atypical 3' termini. DNA repair at the AP sites is initiated by specific endonuclease cleavage of the phosphodiester backbone. Such endonucleases are also generally capable of removing blocking groups from the 3' terminus of DNA strand breaks. AP endonucleases can be classified into two families based on sequence similarity []. This entry represents a highly-conserved sequence found at the C terminus of several apurinic/apyrimidinic (AP) endonucleases in a range of Gram-positive and Gram-negative bacteria. ; PDB: 3LMZ_A 2ZDS_D.
Probab=23.98 E-value=94 Score=22.95 Aligned_cols=31 Identities=23% Similarity=0.059 Sum_probs=17.4
Q ss_pred EEEEecCchhHHHHHHHHHHHHHHhccCCCc
Q 022690 212 VLVEAEFPEDIINSRLDHAVAILENLLKPVD 242 (293)
Q Consensus 212 VlIsa~~p~~~~~~rl~~A~e~Ie~LL~pv~ 242 (293)
|-|+.++..-.....+++|++.++++|..++
T Consensus 18 ~siE~ED~~~~~~~G~~~a~~~lr~~l~~~~ 48 (55)
T PF07582_consen 18 LSIEHEDALMDPEEGAREAAAFLRKLLIREP 48 (55)
T ss_dssp EEE---STTTSHHHHHHHHHHHHHTT-----
T ss_pred EEEEeecCCCCHHHHHHHHHHHHHHhcCCCC
Confidence 4566665444445689999999999998654
No 82
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=23.49 E-value=60 Score=29.39 Aligned_cols=18 Identities=22% Similarity=0.469 Sum_probs=16.1
Q ss_pred hHHHHHHhhCCeEEEecc
Q 022690 168 SLKRVEAMTECRVFIRGR 185 (293)
Q Consensus 168 TlKrle~eTgcKI~IRGr 185 (293)
.+|+||++.|++++.|..
T Consensus 35 ~I~~LE~~lG~~LF~R~~ 52 (275)
T PRK03601 35 RIRQLENQLGVNLFTRHR 52 (275)
T ss_pred HHHHHHHHhCCceEEECC
Confidence 589999999999999953
No 83
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=22.78 E-value=66 Score=29.41 Aligned_cols=22 Identities=18% Similarity=0.368 Sum_probs=17.7
Q ss_pred hHHHHHHhhCCeEEEeccCCcC
Q 022690 168 SLKRVEAMTECRVFIRGRGSVK 189 (293)
Q Consensus 168 TlKrle~eTgcKI~IRGrGS~k 189 (293)
.+|+||++.|+++++|...-+.
T Consensus 36 ~I~~LE~~lg~~LF~R~~r~~~ 57 (300)
T PRK11074 36 TVRQLEEWLAVPLFERRHRDVE 57 (300)
T ss_pred HHHHHHHHhCCeeEEeCCCCce
Confidence 6899999999999999543333
No 84
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=21.87 E-value=70 Score=29.61 Aligned_cols=20 Identities=20% Similarity=0.401 Sum_probs=17.3
Q ss_pred hHHHHHHhhCCeEEEe-ccCC
Q 022690 168 SLKRVEAMTECRVFIR-GRGS 187 (293)
Q Consensus 168 TlKrle~eTgcKI~IR-GrGS 187 (293)
.+|+||++.||++.+| |||-
T Consensus 36 ~ik~LE~~lg~~Lf~R~~r~~ 56 (313)
T PRK12684 36 AIIELEDELGVEIFTRHGKRL 56 (313)
T ss_pred HHHHHHHHhCCeeEEEcCCcc
Confidence 5899999999999999 4553
No 85
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=21.66 E-value=97 Score=31.17 Aligned_cols=36 Identities=28% Similarity=0.221 Sum_probs=26.5
Q ss_pred HhhCCeEEEeccCCcCCchhhhhccCCCCCCCCCCCcEEEEEecCchh
Q 022690 174 AMTECRVFIRGRGSVKDSIKEEKLKDKPGYEHLNEPLHVLVEAEFPED 221 (293)
Q Consensus 174 ~eTgcKI~IRGrGS~kd~~ke~~lrg~p~~ehl~epLHVlIsa~~p~~ 221 (293)
..+|+.+.|||+|--+... +-..+|+|.|.++.|.+
T Consensus 300 tq~G~~~rl~gkG~p~~~~------------~~~GDl~v~v~v~~P~~ 335 (371)
T COG0484 300 TQTGEVFRLRGKGMPKLRS------------GGRGDLYVRVKVETPKN 335 (371)
T ss_pred CccCcEEEEcCCCccccCC------------CCcCCEEEEEEEEcCCC
Confidence 3568899999998754221 22489999999999875
No 86
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=21.60 E-value=72 Score=29.78 Aligned_cols=18 Identities=22% Similarity=0.420 Sum_probs=16.2
Q ss_pred hHHHHHHhhCCeEEEecc
Q 022690 168 SLKRVEAMTECRVFIRGR 185 (293)
Q Consensus 168 TlKrle~eTgcKI~IRGr 185 (293)
.+|+||++.|+++++|..
T Consensus 36 ~Ik~LE~~lg~~LF~R~~ 53 (317)
T PRK15421 36 QFSDLEQRLGFRLFVRKS 53 (317)
T ss_pred HHHHHHHHhCCEEEEecC
Confidence 589999999999999953
No 87
>TIGR01170 rplA_mito ribosomal protein L1, mitochondrial. This model represents the mitochondrial homolog of bacterial ribosomal protein L1. Unlike chloroplast L1, this form was not sufficiently similar to bacterial forms to include in a single bacterial/organellar L1.
Probab=21.01 E-value=33 Score=29.67 Aligned_cols=18 Identities=39% Similarity=0.776 Sum_probs=14.5
Q ss_pred CCCCCCCeeeeEeCCCCc
Q 022690 150 DKYPNFNFVGRILGPRGN 167 (293)
Q Consensus 150 ~~~P~fNfvGrILGPrG~ 167 (293)
+-.|....+|+||||||.
T Consensus 101 ~~m~~l~~Lg~iLGprGl 118 (141)
T TIGR01170 101 DIVPELAQLRRLLGPKGL 118 (141)
T ss_pred HHHHHHHHhhcccccCcC
Confidence 345667789999999986
No 88
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=20.66 E-value=76 Score=29.41 Aligned_cols=20 Identities=30% Similarity=0.539 Sum_probs=17.5
Q ss_pred hHHHHHHhhCCeEEEe-ccCC
Q 022690 168 SLKRVEAMTECRVFIR-GRGS 187 (293)
Q Consensus 168 TlKrle~eTgcKI~IR-GrGS 187 (293)
.+|+||++.|+++++| |||-
T Consensus 36 ~I~~LE~~lg~~Lf~R~~r~~ 56 (309)
T PRK12683 36 QIKDLEDELGVEIFIRRGKRL 56 (309)
T ss_pred HHHHHHHHhCCeeEeeCCCCc
Confidence 6899999999999999 5664
No 89
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=20.63 E-value=78 Score=29.06 Aligned_cols=20 Identities=20% Similarity=0.331 Sum_probs=17.2
Q ss_pred hHHHHHHhhCCeEEEec-cCC
Q 022690 168 SLKRVEAMTECRVFIRG-RGS 187 (293)
Q Consensus 168 TlKrle~eTgcKI~IRG-rGS 187 (293)
.+|+||++.||++++|. +|-
T Consensus 36 ~I~~LE~~lg~~LF~R~~~~~ 56 (309)
T PRK12682 36 AIIELEEELGIEIFIRHGKRL 56 (309)
T ss_pred HHHHHHHHhCCeeEEECCCCc
Confidence 58999999999999995 554
Done!