Query 020955
Match_columns 319
No_of_seqs 258 out of 1407
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:28:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020955.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020955hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1544 Ribosome-associated pr 99.9 5.8E-27 1.2E-31 194.0 13.1 99 99-204 1-99 (110)
2 PRK10324 translation inhibitor 99.9 1.9E-26 4.1E-31 191.8 14.6 98 99-205 1-98 (113)
3 PRK10470 ribosome hibernation 99.9 2E-26 4.3E-31 185.1 14.0 95 99-202 1-95 (95)
4 TIGR00741 yfiA ribosomal subun 99.9 1.1E-24 2.4E-29 173.8 14.0 95 99-202 1-95 (95)
5 PF02482 Ribosomal_S30AE: Sigm 99.9 3.2E-23 6.9E-28 165.4 12.8 97 100-202 1-97 (97)
6 cd00552 RaiA RaiA ("ribosome-a 99.9 4.8E-22 1E-26 157.8 12.8 93 100-198 1-93 (93)
7 PHA03308 transcriptional regul 86.2 0.51 1.1E-05 50.7 2.6 9 109-117 1300-1308(1463)
8 PF10500 SR-25: Nuclear RNA-sp 81.3 0.97 2.1E-05 42.1 2.0 36 247-288 155-190 (225)
9 PHA03309 transcriptional regul 76.7 1.9 4.2E-05 47.3 2.8 8 87-94 1871-1878(2033)
10 KOG1420 Ca2+-activated K+ chan 72.1 2.8 6.1E-05 44.4 2.6 8 90-97 112-119 (1103)
11 PHA03308 transcriptional regul 71.4 3.6 7.9E-05 44.5 3.3 16 122-137 1361-1376(1463)
12 PF13031 DUF3892: Protein of u 68.2 26 0.00057 27.2 6.9 65 240-307 16-84 (85)
13 PF04370 DUF508: Domain of unk 64.1 5.6 0.00012 34.7 2.4 10 98-107 52-61 (156)
14 KOG1711 Mitochondrial/chloropl 59.4 4.8 0.0001 37.4 1.3 18 249-266 93-110 (218)
15 PHA03309 transcriptional regul 59.3 8.3 0.00018 42.7 3.2 7 42-48 1836-1842(2033)
16 PF05717 TnpB_IS66: IS66 Orf2 58.8 11 0.00024 31.2 3.2 37 259-296 28-64 (107)
17 PF03776 MinE: Septum formatio 54.8 65 0.0014 24.5 6.7 58 99-163 9-69 (70)
18 PF11419 DUF3194: Protein of u 53.2 35 0.00075 27.5 5.1 15 131-145 33-47 (87)
19 COG3111 Periplasmic protein wi 53.1 11 0.00023 32.4 2.2 46 264-310 70-120 (128)
20 PLN03014 carbonic anhydrase 46.5 16 0.00035 36.4 2.7 21 276-296 304-327 (347)
21 PF04965 GPW_gp25: Gene 25-lik 41.7 92 0.002 24.4 6.0 40 103-144 36-75 (99)
22 TIGR03357 VI_zyme type VI secr 41.5 1.1E+02 0.0024 25.5 6.8 50 112-163 64-113 (133)
23 KOG2130 Phosphatidylserine-spe 37.1 20 0.00042 35.6 1.6 7 15-21 342-348 (407)
24 PF14671 DSPn: Dual specificit 36.3 23 0.0005 30.8 1.8 30 249-278 95-124 (141)
25 KOG3915 Transcription regulato 34.7 41 0.00088 35.0 3.5 19 247-265 372-390 (641)
26 PF04415 DUF515: Protein of un 33.2 33 0.00071 35.1 2.5 11 38-48 298-308 (416)
27 PF06918 DUF1280: Protein of u 32.5 3E+02 0.0065 25.7 8.7 80 113-196 133-222 (224)
28 cd02418 Peptidase_C39B A sub-f 31.5 1.1E+02 0.0024 24.6 5.1 37 259-295 70-108 (136)
29 PRK14128 iraD DNA replication/ 31.5 2.3E+02 0.0051 21.5 7.5 47 113-163 7-53 (69)
30 PRK10053 hypothetical protein; 30.6 38 0.00082 29.2 2.2 31 264-296 74-105 (130)
31 cd04623 CBS_pair_10 The CBS do 29.2 90 0.002 23.5 4.0 34 251-284 9-42 (113)
32 cd04619 CBS_pair_6 The CBS dom 28.6 97 0.0021 24.0 4.1 35 250-284 8-42 (114)
33 KOG4368 Predicted RNA binding 28.0 55 0.0012 35.0 3.2 13 84-96 691-703 (757)
34 PF02120 Flg_hook: Flagellar h 28.0 1.4E+02 0.0031 22.4 4.9 55 133-194 12-66 (85)
35 TIGR01215 minE cell division t 26.6 2.5E+02 0.0054 22.0 6.0 49 108-163 31-80 (81)
36 PTZ00112 origin recognition co 26.6 33 0.00072 38.8 1.4 12 264-275 455-466 (1164)
37 PF04370 DUF508: Domain of unk 26.3 60 0.0013 28.5 2.6 12 42-53 29-40 (156)
38 cd02423 Peptidase_C39G A sub-f 25.9 1.7E+02 0.0037 23.2 5.2 39 259-297 69-108 (129)
39 PF14492 EFG_II: Elongation Fa 24.1 81 0.0018 23.9 2.8 28 254-281 21-48 (75)
40 smart00116 CBS Domain in cysta 23.7 1.1E+02 0.0024 18.7 3.0 26 250-275 7-32 (49)
41 PF02575 YbaB_DNA_bd: YbaB/Ebf 23.5 2.4E+02 0.0053 21.8 5.6 24 175-198 58-81 (93)
42 TIGR00156 conserved hypothetic 23.2 64 0.0014 27.6 2.3 45 264-310 70-120 (126)
43 TIGR00253 RNA_bind_YhbY putati 23.1 1.9E+02 0.0041 23.5 4.8 45 239-287 42-87 (95)
44 TIGR02889 spore_YpeB germinati 23.0 96 0.0021 31.9 3.9 17 245-261 366-382 (435)
45 cd02413 40S_S3_KH K homology R 22.2 3.8E+02 0.0083 20.8 6.8 42 113-171 6-47 (81)
46 PRK00296 minE cell division to 22.1 3.5E+02 0.0077 21.5 6.2 45 112-163 36-81 (86)
47 cd04593 CBS_pair_EriC_assoc_ba 22.0 1.6E+02 0.0036 22.4 4.3 34 250-283 8-41 (115)
48 PF09313 DUF1971: Domain of un 21.8 1.1E+02 0.0024 24.2 3.1 30 269-298 38-67 (82)
49 PF01514 YscJ_FliF: Secretory 21.7 1.9E+02 0.0041 26.4 5.2 53 114-167 112-165 (206)
50 PLN03014 carbonic anhydrase 21.4 75 0.0016 31.8 2.6 13 270-282 312-324 (347)
51 COG2098 Uncharacterized protei 21.2 4.9E+02 0.011 22.0 6.9 65 105-172 29-101 (116)
52 COG1724 Predicted RNA binding 20.9 2E+02 0.0043 22.1 4.2 40 249-293 4-43 (66)
53 PRK15463 cold shock-like prote 20.8 1.2E+02 0.0026 23.0 3.1 20 280-299 8-27 (70)
54 PF06933 SSP160: Special lobe- 20.4 91 0.002 32.1 3.0 12 95-106 222-233 (756)
55 COG1539 FolB Dihydroneopterin 20.4 2.2E+02 0.0049 23.9 5.0 40 103-146 65-104 (121)
56 PF03714 PUD: Bacterial pullan 20.2 57 0.0012 26.2 1.3 14 277-290 2-15 (103)
57 PF07118 DUF1374: Protein of u 20.1 1.6E+02 0.0035 23.9 3.8 30 265-294 55-86 (92)
58 PF07466 DUF1517: Protein of u 20.1 94 0.002 30.1 3.0 11 254-264 243-253 (289)
No 1
>COG1544 Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=5.8e-27 Score=194.03 Aligned_cols=99 Identities=40% Similarity=0.559 Sum_probs=92.4
Q ss_pred eEEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHH
Q 020955 99 VKLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVY 178 (319)
Q Consensus 99 MkI~ItgRnvelTdaLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~~g~~IrAee~a~D~Y 178 (319)
|+++|+|+|+++||+||+||++||+| |++||.+++.++|+|.++++ +..+.|||+|++++ ++|+|++.++|||
T Consensus 1 m~~~IsG~nieit~a~r~~Ve~Kl~k-l~r~~~~~~~~~v~l~~e~~-----~~~~~ve~ti~~~~-g~l~a~~~~~d~Y 73 (110)
T COG1544 1 MKLNISGKNVEITEAIREYVEEKLAK-LERYFDDIINVDVTLSKEKN-----RSRFKVEATIHLPG-GILRAEAEHEDMY 73 (110)
T ss_pred CeeEEeeeeeeeCHHHHHHHHHHHHH-HHhhhccCccEEEEEEeecc-----ccceEEEEEEEcCC-ceEEEeecCCCHH
Confidence 89999999999999999999999999 89999888899999999974 13489999999995 5999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhhccC
Q 020955 179 ASIDLVSSIIQRKLRKIKEKESDHGR 204 (319)
Q Consensus 179 aAID~A~dKLeRQLrK~KeKlkd~~r 204 (319)
+|||.|+|||||||||||+|+++|++
T Consensus 74 aAID~a~dKLerqlrK~K~K~~~~~~ 99 (110)
T COG1544 74 AAIDLAIDKLERQLRKHKEKLKDHRR 99 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhc
Confidence 99999999999999999999999974
No 2
>PRK10324 translation inhibitor protein RaiA; Provisional
Probab=99.94 E-value=1.9e-26 Score=191.78 Aligned_cols=98 Identities=22% Similarity=0.355 Sum_probs=92.4
Q ss_pred eEEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHH
Q 020955 99 VKLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVY 178 (319)
Q Consensus 99 MkI~ItgRnvelTdaLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~~g~~IrAee~a~D~Y 178 (319)
|+|+|+|||+++|++|++||++|++| |+||++++.+|+|+|+.+++. ++|||+|+++ |..|+|++.++|||
T Consensus 1 M~I~Itgr~v~~tdalr~~ie~Kl~k-L~k~~~~i~~~~V~l~~e~~~-------~~veitv~~~-g~~l~ae~~~~D~y 71 (113)
T PRK10324 1 MTMNITSKQMEITPAIRQHVADRLAK-LEKWQTHLINPHIILSKEPQG-------FVADATINTP-NGVLVASGKHEDMY 71 (113)
T ss_pred CEEEEEEEcCcCCHHHHHHHHHHHHH-HHHhcCCCceEEEEEEEcCCC-------eEEEEEEECC-CCeEEEEEecCCHH
Confidence 99999999999999999999999999 999999999999999998642 7899999998 67899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhhccCC
Q 020955 179 ASIDLVSSIIQRKLRKIKEKESDHGRH 205 (319)
Q Consensus 179 aAID~A~dKLeRQLrK~KeKlkd~~r~ 205 (319)
+|||.|+++|+|||+|+|+|+.+|+.+
T Consensus 72 ~AID~a~dklerQLrK~K~k~~~~~~~ 98 (113)
T PRK10324 72 TAINELINKLERQLNKLQHKGEARRAA 98 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 999999999999999999999988643
No 3
>PRK10470 ribosome hibernation promoting factor HPF; Provisional
Probab=99.94 E-value=2e-26 Score=185.07 Aligned_cols=95 Identities=28% Similarity=0.417 Sum_probs=89.9
Q ss_pred eEEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHH
Q 020955 99 VKLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVY 178 (319)
Q Consensus 99 MkI~ItgRnvelTdaLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~~g~~IrAee~a~D~Y 178 (319)
|+|+|+|||+++|++|++||++|+++ |+||+++|..++|+|+.+++. +.|||+++++ |..++|++.++|||
T Consensus 1 M~i~i~~r~i~~t~al~~~v~~kl~k-L~r~~~~i~~~~V~l~~~~~~-------~~~ei~~~~~-g~~l~a~~~~~d~y 71 (95)
T PRK10470 1 MQLNITGHNVEITEALREFVTAKFAK-LEQYFDRINQVYVVLKVEKVT-------HISDATLHVN-GGEIHASAEGQDMY 71 (95)
T ss_pred CEEEEEEEeeccCHHHHHHHHHHHHH-HHHhcCCCceEEEEEEEecCC-------eEEEEEEEeC-CCEEEEEEecCcHH
Confidence 89999999999999999999999998 999999999999999987642 7899999998 68999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhhc
Q 020955 179 ASIDLVSSIIQRKLRKIKEKESDH 202 (319)
Q Consensus 179 aAID~A~dKLeRQLrK~KeKlkd~ 202 (319)
+|||.|+++|+|||+|+|+|+++|
T Consensus 72 ~Aid~a~~klerqL~k~k~k~~~~ 95 (95)
T PRK10470 72 AAIDGLIDKLARQLTKHKDKLKQH 95 (95)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccC
Confidence 999999999999999999998764
No 4
>TIGR00741 yfiA ribosomal subunit interface protein. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes.
Probab=99.92 E-value=1.1e-24 Score=173.82 Aligned_cols=95 Identities=38% Similarity=0.608 Sum_probs=90.0
Q ss_pred eEEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHH
Q 020955 99 VKLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVY 178 (319)
Q Consensus 99 MkI~ItgRnvelTdaLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~~g~~IrAee~a~D~Y 178 (319)
|+|+|+|||+++|++|++||++|+++ |+||++.+..++|+|+.+++. ++|+|+|+++ |..|+|++.++|+|
T Consensus 1 M~i~i~~~~~~~t~~l~~~i~~k~~k-l~k~~~~i~~~~V~l~~e~~~-------~~~~i~v~~~-g~~l~a~~~~~d~~ 71 (95)
T TIGR00741 1 MNINITGKNVEITEALREYVEEKLAR-LERYFTHIINVDVVLSKERNR-------FKVEATIYTP-GGVIRASAEHEDMY 71 (95)
T ss_pred CEEEEEEeccccCHHHHHHHHHHHHH-HHHhcCCCceEEEEEEEecCc-------eEEEEEEEcC-CCEEEEEEecCcHH
Confidence 99999999999999999999999999 999999999999999988653 8999999999 56999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhhc
Q 020955 179 ASIDLVSSIIQRKLRKIKEKESDH 202 (319)
Q Consensus 179 aAID~A~dKLeRQLrK~KeKlkd~ 202 (319)
+|||.|+++|+|||+|+|+|+++|
T Consensus 72 ~Aid~a~~klerql~k~k~k~~~~ 95 (95)
T TIGR00741 72 AAIDLAIDKLERQLRKLKEKRKEH 95 (95)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhcC
Confidence 999999999999999999998765
No 5
>PF02482 Ribosomal_S30AE: Sigma 54 modulation protein / S30EA ribosomal protein; InterPro: IPR003489 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the sigma-54 modulation protein family and the S30Ae family of ribosomal proteins which includes the light-repressed protein (lrtA) [].; GO: 0005488 binding, 0044238 primary metabolic process; PDB: 1L4S_A 1VOX_a 1VOV_a 3V2E_Y 3V2C_Y 1N3G_A 1VOS_a 1VOZ_a 1VOQ_a 1IMU_A ....
Probab=99.90 E-value=3.2e-23 Score=165.38 Aligned_cols=97 Identities=38% Similarity=0.499 Sum_probs=85.0
Q ss_pred EEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHHH
Q 020955 100 KLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVYA 179 (319)
Q Consensus 100 kI~ItgRnvelTdaLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~~g~~IrAee~a~D~Ya 179 (319)
+|+|+|||+++|++|++||++||++ |++|++++..++|+|+.++ .++..++|+|+|.++ |..|+|++.++|+|+
T Consensus 1 ~i~i~~~~~~~t~~l~~~i~~kl~k-l~~~~~~i~~~~V~l~~~~----~~~~~~~v~i~i~~~-~~~l~a~~~~~d~~~ 74 (97)
T PF02482_consen 1 NIQITGRNFELTDALREYIEEKLEK-LERFFDDIIEAHVTLSKEK----SEGKGYRVEITIHVP-GHVLVAEESAEDLYA 74 (97)
T ss_dssp EEEEEECSS---HHHHHHHHHHHHH-HHTTSSC-SEEEEEEEEE------ETTEEEEEEEEEET-TEEEEEEEEESSHHH
T ss_pred CEEEEEEcccCCHHHHHHHHHHHHH-HHhhcCCCeeEEEEEEEee----ccCCCEEEEEEEEeC-CceEEEEEecCCHHH
Confidence 6899999999999999999999999 9999999999999999972 223569999999997 689999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhHhhhc
Q 020955 180 SIDLVSSIIQRKLRKIKEKESDH 202 (319)
Q Consensus 180 AID~A~dKLeRQLrK~KeKlkd~ 202 (319)
|||.|+++|+|||+|+|+|+++|
T Consensus 75 Aid~a~dkl~rql~k~k~k~~~h 97 (97)
T PF02482_consen 75 AIDEAFDKLERQLRKYKEKLRDH 97 (97)
T ss_dssp HHHHHHHHHHHHHHHHHHCCCT-
T ss_pred HHHHHHHHHHHHHHHHHHHhhcC
Confidence 99999999999999999999876
No 6
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=99.88 E-value=4.8e-22 Score=157.82 Aligned_cols=93 Identities=42% Similarity=0.580 Sum_probs=86.8
Q ss_pred EEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHHH
Q 020955 100 KLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVYA 179 (319)
Q Consensus 100 kI~ItgRnvelTdaLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~~g~~IrAee~a~D~Ya 179 (319)
+|+|+|||+++|++|++||++++++ |+||++++..++|+|+.++++ +..++|+|+|+++ |..|+|++.++|+|+
T Consensus 1 ~i~i~~r~~~~t~al~~~i~~k~~k-l~r~~~~i~~~~V~l~~~~~~----~~~~~v~i~v~~~-g~~~~a~~~~~d~~~ 74 (93)
T cd00552 1 NINITGRNIEVTDALREYVEEKLEK-LEKYFDRIISVDVVLSVEKNH----GKRFKVEITIHLP-GGVLRAEASAEDLYA 74 (93)
T ss_pred CEEEEEEcccCCHHHHHHHHHHHHH-HHHhcCCCceEEEEEEEecCC----CCceEEEEEEEeC-CCEEEEEEccCCHHH
Confidence 4899999999999999999999999 999999999999999998752 3358999999998 789999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhH
Q 020955 180 SIDLVSSIIQRKLRKIKEK 198 (319)
Q Consensus 180 AID~A~dKLeRQLrK~KeK 198 (319)
|||.|+++|+|||+|+|+|
T Consensus 75 Aid~a~~kl~rqL~k~k~k 93 (93)
T cd00552 75 AIDLAVDKLERQLRKYKEK 93 (93)
T ss_pred HHHHHHHHHHHHHHHhccC
Confidence 9999999999999999986
No 7
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=86.17 E-value=0.51 Score=50.71 Aligned_cols=9 Identities=11% Similarity=-0.149 Sum_probs=3.8
Q ss_pred ccCHHHHHH
Q 020955 109 ELTDTVKNH 117 (319)
Q Consensus 109 elTdaLrey 117 (319)
.|...+|.|
T Consensus 1300 ~LPpe~Ka~ 1308 (1463)
T PHA03308 1300 RLPIRDRVY 1308 (1463)
T ss_pred CCChHHhhh
Confidence 344444444
No 8
>PF10500 SR-25: Nuclear RNA-splicing-associated protein; InterPro: IPR019532 SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissue types. At the N terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localisation signals strongly implies that this is a nuclear protein that may contribute to RNA splicing []. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1; also see IPR019093 from INTERPRO) signalling pathway [].
Probab=81.33 E-value=0.97 Score=42.13 Aligned_cols=36 Identities=22% Similarity=0.341 Sum_probs=23.6
Q ss_pred ccCCCCCHHHHHHHHhcCCCcEEEEeeCCCCceeEEEEecCC
Q 020955 247 FEMPPLTVSEAIEQLENVDHDFYGFRNEETGEINIVYKRKAG 288 (319)
Q Consensus 247 f~lkPMSveEAV~QMEllghdF~vF~N~eTg~vnVVYRRkDG 288 (319)
-.|.|||-||=-.+=-.+ -=-+|+|||+..+| +.||
T Consensus 155 ~am~PmTkEEyearQSvI----RrVvDpETGRtRLI--kGdG 190 (225)
T PF10500_consen 155 QAMAPMTKEEYEARQSVI----RRVVDPETGRTRLI--KGDG 190 (225)
T ss_pred hhcCCCCHHHHHHHHhhh----eeeecCCCCceeee--cccc
Confidence 457899988755443332 33458888888877 5555
No 9
>PHA03309 transcriptional regulator ICP4; Provisional
Probab=76.73 E-value=1.9 Score=47.35 Aligned_cols=8 Identities=13% Similarity=0.455 Sum_probs=3.7
Q ss_pred ceeeecCC
Q 020955 87 PVRMSWDG 94 (319)
Q Consensus 87 ~~~~~~~~ 94 (319)
..-|-|.-
T Consensus 1871 anpfrwap 1878 (2033)
T PHA03309 1871 ANPFRWAP 1878 (2033)
T ss_pred CCccccCc
Confidence 44445543
No 10
>KOG1420 consensus Ca2+-activated K+ channel Slowpoke, alpha subunit [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=72.13 E-value=2.8 Score=44.38 Aligned_cols=8 Identities=38% Similarity=0.887 Sum_probs=4.8
Q ss_pred eecCCCCC
Q 020955 90 MSWDGPLS 97 (319)
Q Consensus 90 ~~~~~~~~ 97 (319)
-.|+|.+.
T Consensus 112 kdwageli 119 (1103)
T KOG1420|consen 112 KDWAGELI 119 (1103)
T ss_pred hhhhccee
Confidence 35777644
No 11
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=71.38 E-value=3.6 Score=44.52 Aligned_cols=16 Identities=6% Similarity=-0.176 Sum_probs=8.5
Q ss_pred HHHHHhhhCCCceEEE
Q 020955 122 VGKAVLKHSHLVREVD 137 (319)
Q Consensus 122 l~K~L~Ky~~~i~~a~ 137 (319)
+-+++..|+.+...++
T Consensus 1361 vlriisdyypdapgar 1376 (1463)
T PHA03308 1361 VLRIISDYYPDAPGAR 1376 (1463)
T ss_pred HHHHHhhhCCCCcchh
Confidence 3344666666554444
No 12
>PF13031 DUF3892: Protein of unknown function (DUF3892)
Probab=68.16 E-value=26 Score=27.24 Aligned_cols=65 Identities=25% Similarity=0.282 Sum_probs=44.5
Q ss_pred eEEEeeeccCCCC---CHHHHHHHHhcCCCcEEEEeeCCCCceeEEEEecCCcEEEEEeCCCC-cccccccc
Q 020955 240 EIVRMKFFEMPPL---TVSEAIEQLENVDHDFYGFRNEETGEINIVYKRKAGGYGVIIPKGNG-KAKKLEPL 307 (319)
Q Consensus 240 ~IVr~K~f~lkPM---SveEAV~QMEllghdF~vF~N~eTg~vnVVYRRkDG~YGLIeP~~~~-~~~~~~~~ 307 (319)
.|+..+.-.-... +.++||..+|.-.+.||+= +...-.+.|+ +..+| ---|....|| +..-|..|
T Consensus 16 ~I~~v~~~~g~~~~~~s~~~~i~~ie~g~~~~yv~-~~~~~~V~V~-~~~~G-~kYirT~~Dg~~~dNLl~L 84 (85)
T PF13031_consen 16 RITHVKLNNGGVPWKYSREEAIAWIENGKWSFYVE-GGWIAGVNVV-TSRNG-EKYIRTDADGTESDNLLSL 84 (85)
T ss_pred ceEEEECCCCCccccccHHHHHHHHHcCCceEEeC-CCCCccEEEE-ECCCC-CeeEeeCCCCCCCchhhcc
Confidence 4666664445666 9999999999987899988 7767777777 33455 4446776665 44444443
No 13
>PF04370 DUF508: Domain of unknown function (DUF508) ; InterPro: IPR007465 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=64.11 E-value=5.6 Score=34.72 Aligned_cols=10 Identities=10% Similarity=-0.127 Sum_probs=4.8
Q ss_pred ceEEEEEeee
Q 020955 98 SVKLIIQGKN 107 (319)
Q Consensus 98 ~MkI~ItgRn 107 (319)
|.++...--|
T Consensus 52 MVhVKFilLh 61 (156)
T PF04370_consen 52 MVHVKFILLH 61 (156)
T ss_pred EEEEEEEEEe
Confidence 3445555444
No 14
>KOG1711 consensus Mitochondrial/chloroplast ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=59.37 E-value=4.8 Score=37.41 Aligned_cols=18 Identities=39% Similarity=0.486 Sum_probs=15.4
Q ss_pred CCCCCHHHHHHHHhcCCC
Q 020955 249 MPPLTVSEAIEQLENVDH 266 (319)
Q Consensus 249 lkPMSveEAV~QMEllgh 266 (319)
+.-|++|||+|||++.+.
T Consensus 93 irgm~v~~AL~Ql~~s~k 110 (218)
T KOG1711|consen 93 IRGMSVEEALMQLEFSDK 110 (218)
T ss_pred HcCCCHHHHHHHhhcchH
Confidence 568999999999998753
No 15
>PHA03309 transcriptional regulator ICP4; Provisional
Probab=59.28 E-value=8.3 Score=42.70 Aligned_cols=7 Identities=43% Similarity=0.506 Sum_probs=2.7
Q ss_pred CCCCCCc
Q 020955 42 SSSVSPF 48 (319)
Q Consensus 42 ~~~~~~~ 48 (319)
|+|..|+
T Consensus 1836 srsatps 1842 (2033)
T PHA03309 1836 SRSATPS 1842 (2033)
T ss_pred cccCCCC
Confidence 3333333
No 16
>PF05717 TnpB_IS66: IS66 Orf2 like protein; InterPro: IPR008878 Thess proteins are found in insertion sequences related to IS66. The function of these proteins is uncertain, but they are probably essential for transposition []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=58.76 E-value=11 Score=31.18 Aligned_cols=37 Identities=22% Similarity=0.405 Sum_probs=27.9
Q ss_pred HHHhcCCCcEEEEeeCCCCceeEEEEecCCcEEEEEeC
Q 020955 259 EQLENVDHDFYGFRNEETGEINIVYKRKAGGYGVIIPK 296 (319)
Q Consensus 259 ~QMEllghdF~vF~N~eTg~vnVVYRRkDG~YGLIeP~ 296 (319)
+.++..+.+.|||.|..-.++.|+|.- +++|-|+.-.
T Consensus 28 ~~~dp~~g~~fvF~nr~r~riKiL~wd-~~G~~L~~KR 64 (107)
T PF05717_consen 28 LGLDPFSGDLFVFCNRRRDRIKILYWD-GDGFWLYYKR 64 (107)
T ss_pred hcCCCCcceEEEEEeccCCceEEEecc-CCceEEeeee
Confidence 456767788999999999999999984 4455555444
No 17
>PF03776 MinE: Septum formation topological specificity factor MinE; InterPro: IPR005527 Cytokinesis needs to be regulated spatially in order to ensure that it occurs between the daughter genomes. In prokaryotes such as Escherichia coli, cytokinesis is initiated by FtsZ, a tubulin-like protein that assembles into a ring structure at the cell centre called the Z ring. A fundamental problem in prokaryotic cell biology is to understand how the midcell division site is identified. Two major negative regulatory systems are known to be involved in preventing Z-ring assembly at all sites except the midcell. One of these systems, called nucleoid occlusion, blocks Z-ring assembly in the area occupied by an unsegregated nucleoid until a critical stage in chromosome replication or segregation is reached. The other system consists of three proteins, MinC, MinD and MinE, which prevent assembly of Z rings in regions of the cell not covered by the nucleoid, such as the cell poles. MinC is an inhibitor of FtsZ polymerisation, resulting in the inhibition of Z ring assembly in the cell; MinD greatly enhances the inhibitory effects of MinC in vivo; and MinE antagonizes the effects of MinC and MinD []. MinE is a small bifunctional protein. The amino terminus of MinE is required to interact with MinD, while the carboxyl terminus is required for `topological specificity' - that is, the ability of MinE to antagonise MinCD inhibition of Z rings at the midcell position but not at the poles.; GO: 0032955 regulation of barrier septum formation, 0051301 cell division; PDB: 2KXO_A 3MCD_B 3KU7_A 3R9J_C 3R9I_E 1EV0_B.
Probab=54.80 E-value=65 Score=24.50 Aligned_cols=58 Identities=16% Similarity=0.178 Sum_probs=37.4
Q ss_pred eEEEEEeeecccCH--HHHHHHHHHHHHHHhhhCC-CceEEEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020955 99 VKLIIQGKNLELTD--TVKNHVEEKVGKAVLKHSH-LVREVDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (319)
Q Consensus 99 MkI~ItgRnvelTd--aLreyIeeKl~K~L~Ky~~-~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~ 163 (319)
+++.+.......++ .+-+.+.+-|-.++.||.+ ....++|.++.+++ .-.-+++|.++
T Consensus 9 Lk~iL~~dR~~~~~~~~~l~~lk~eil~viskYv~i~~~~v~v~l~~~~~-------~~~L~~nIpl~ 69 (70)
T PF03776_consen 9 LKLILAHDRGGLSPQPDYLEQLKKEILEVISKYVEIDEEDVEVQLERDDD-------MSVLEANIPLP 69 (70)
T ss_dssp EEEEEEEECCSC-CTTSSHHHHHHHHHHHHHHHS---CCCEEEEEEECTT-------EEEEEEEEEE-
T ss_pred HHHHHHHHccCCCCcHHHHHHHHHHHHHHHHhheecCcccEEEEEEECCC-------ceEEEEEEEcC
Confidence 67777777777777 7777888888888999986 23567777774432 24555555543
No 18
>PF11419 DUF3194: Protein of unknown function (DUF3194); InterPro: IPR024502 This family of proteins has no known function however the structure has been determined. The protein consists of two alpha-helices packed on the same side of a central beta-hairpin [].; PDB: 1PU1_A.
Probab=53.23 E-value=35 Score=27.52 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=10.6
Q ss_pred CCceEEEEEEEeecC
Q 020955 131 HLVREVDVRLSVRGG 145 (319)
Q Consensus 131 ~~i~~a~V~Ls~e~~ 145 (319)
..+...+|++..+.+
T Consensus 33 sEV~DlDVtv~~~~~ 47 (87)
T PF11419_consen 33 SEVKDLDVTVRFEYG 47 (87)
T ss_dssp TTEEEEEEEEEEEES
T ss_pred hhcccceeEEEEecC
Confidence 357778888877754
No 19
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=53.09 E-value=11 Score=32.40 Aligned_cols=46 Identities=30% Similarity=0.543 Sum_probs=32.5
Q ss_pred CCCcEEEEeeCCCCceeEEEEecCCcEEEEEeCC----CCcccc-ccccccc
Q 020955 264 VDHDFYGFRNEETGEINIVYKRKAGGYGVIIPKG----NGKAKK-LEPLEVE 310 (319)
Q Consensus 264 lghdF~vF~N~eTg~vnVVYRRkDG~YGLIeP~~----~~~~~~-~~~~~~~ 310 (319)
+|+|-|+|+|. +|++||.--.+.++=-=|.|.. .||.+| |...+++
T Consensus 70 i~~D~y~FrD~-sGeI~VeIdd~~w~g~tv~P~dkV~I~GevDk~~~~~eId 120 (128)
T COG3111 70 IGDDRYVFRDA-SGEINVDIDDKVWNGQTVTPKDKVRIQGEVDKDWNSVEID 120 (128)
T ss_pred eCCceEEEEcC-CccEEEEecccccCCcccCcccEEEEEeEEcCCCccceeE
Confidence 59999999998 9999999887766655577752 355543 4544443
No 20
>PLN03014 carbonic anhydrase
Probab=46.54 E-value=16 Score=36.39 Aligned_cols=21 Identities=14% Similarity=0.313 Sum_probs=11.5
Q ss_pred CCceeE---EEEecCCcEEEEEeC
Q 020955 276 TGEINI---VYKRKAGGYGVIIPK 296 (319)
Q Consensus 276 Tg~vnV---VYRRkDG~YGLIeP~ 296 (319)
.|++.| +|--.+|.+-++++.
T Consensus 304 ~G~L~I~G~~YDi~TG~V~~l~~~ 327 (347)
T PLN03014 304 KGTLALKGGYYDFVKGAFELWGLE 327 (347)
T ss_pred cCCcEEEEEEEECCCceEEEeccc
Confidence 444443 455566666666654
No 21
>PF04965 GPW_gp25: Gene 25-like lysozyme; InterPro: IPR007048 The family of sequences represented by this entry include proteins from Bacteriophage T4 and related phage, which may be structural components of the outer wedge of the baseplate that has acidic lysozyme activity [, ]. They also include anti-adapter protein IraD, from bacteria, that inhibit RpoS proteolysis by regulating RssB activity [].; PDB: 2IA7_A.
Probab=41.67 E-value=92 Score=24.36 Aligned_cols=40 Identities=8% Similarity=0.204 Sum_probs=28.6
Q ss_pred EEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeec
Q 020955 103 IQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRG 144 (319)
Q Consensus 103 ItgRnvelTdaLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~ 144 (319)
+.+.++ ++.....+...|..+|.+|-+++...+|.+....
T Consensus 36 ~~~~~~--~~~~~~~i~~~I~~aI~~~EPRl~~~~V~~~~~~ 75 (99)
T PF04965_consen 36 LIFEPI--SPDTRQAIRREIREAIQRFEPRLKVVSVEVEEDD 75 (99)
T ss_dssp ---S-----HHHHHHHHHHHHHHHHHH-TTEEEEEEEEE-TT
T ss_pred HcCCCC--CHHHHHHHHHHHHHHHHHhCCcEEEEEEEEEecC
Confidence 445555 8899999999999999999999999999998744
No 22
>TIGR03357 VI_zyme type VI secretion system lysozyme-related protein. The description for PFAM family pfam04965 cites acidic lysozyme activity for some phage-encoded members. This family represents a different subgroup of the proteins from pfam04965, where all members are associated with bacterial type VI secretion system genomic contexts.
Probab=41.47 E-value=1.1e+02 Score=25.54 Aligned_cols=50 Identities=12% Similarity=0.044 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020955 112 DTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (319)
Q Consensus 112 daLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~ 163 (319)
...+..|...|.+++.+|-+++..++|.+..+... .+.-.+.++.++...
T Consensus 64 ~~~~~~i~~~I~~aI~r~EPRl~~~~V~~~~~~~~--~~~l~f~I~~~l~~~ 113 (133)
T TIGR03357 64 ADDRRRIRRAIEQAIERYEPRLSSVRVTALEDEED--PLALRFRIEAELDVD 113 (133)
T ss_pred HHHHHHHHHHHHHHHHhcCCCcCceEEEEecCCCC--ccEEEEEEEEEEEeC
Confidence 66777888888888999999999988888743321 222235666666655
No 23
>KOG2130 consensus Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics; Signal transduction mechanisms]
Probab=37.07 E-value=20 Score=35.63 Aligned_cols=7 Identities=0% Similarity=-0.211 Sum_probs=2.6
Q ss_pred CCCCccc
Q 020955 15 PVPSSCY 21 (319)
Q Consensus 15 ~~~~~~~ 21 (319)
++.-..|
T Consensus 342 e~~~~~~ 348 (407)
T KOG2130|consen 342 ESTGLAS 348 (407)
T ss_pred cccCccc
Confidence 3333333
No 24
>PF14671 DSPn: Dual specificity protein phosphatase, N-terminal half; PDB: 1OHD_A 1OHE_A 1OHC_A.
Probab=36.27 E-value=23 Score=30.84 Aligned_cols=30 Identities=23% Similarity=0.396 Sum_probs=16.9
Q ss_pred CCCCCHHHHHHHHhcCCCcEEEEeeCCCCc
Q 020955 249 MPPLTVSEAIEQLENVDHDFYGFRNEETGE 278 (319)
Q Consensus 249 lkPMSveEAV~QMEllghdF~vF~N~eTg~ 278 (319)
..-||++||...+...+-+|.-|||+-.|.
T Consensus 95 ~l~~spe~A~~~l~~~~p~~~pFRDAs~g~ 124 (141)
T PF14671_consen 95 YLGMSPEEAYKPLASIQPPFMPFRDASYGP 124 (141)
T ss_dssp TS---HHHHHHHHTTTT-----B--SSSSS
T ss_pred hcCCCHHHHHHHHHhcCCCCCCCCCCCCCC
Confidence 357999999999999999999999997664
No 25
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=34.70 E-value=41 Score=35.00 Aligned_cols=19 Identities=26% Similarity=0.637 Sum_probs=14.2
Q ss_pred ccCCCCCHHHHHHHHhcCC
Q 020955 247 FEMPPLTVSEAIEQLENVD 265 (319)
Q Consensus 247 f~lkPMSveEAV~QMEllg 265 (319)
+.+.|-++++|..||+-+.
T Consensus 372 vslppasv~mamnqmnhl~ 390 (641)
T KOG3915|consen 372 VSLPPASVEMAMNQMNHLQ 390 (641)
T ss_pred ccCCchhhHHHhhhhhhhh
Confidence 4567888888888887543
No 26
>PF04415 DUF515: Protein of unknown function (DUF515) ; InterPro: IPR007509 This is a family of hypothetical archaeal proteins.
Probab=33.16 E-value=33 Score=35.05 Aligned_cols=11 Identities=82% Similarity=0.573 Sum_probs=4.2
Q ss_pred CCCCCCCCCCc
Q 020955 38 SSSSSSSVSPF 48 (319)
Q Consensus 38 ~~~~~~~~~~~ 48 (319)
+++++++-+|.
T Consensus 298 s~s~ss~~s~~ 308 (416)
T PF04415_consen 298 SSSSSSSYSPG 308 (416)
T ss_pred eeecccccCCC
Confidence 33333333443
No 27
>PF06918 DUF1280: Protein of unknown function (DUF1280); InterPro: IPR009689 This family represents a conserved region approximately 200 residues long within a number of proteins of unknown function that seem to be specific to Caenorhabditis elegans.
Probab=32.53 E-value=3e+02 Score=25.69 Aligned_cols=80 Identities=11% Similarity=0.160 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHHHhhh----CCCceEEEEEEEeecCcCCCCCceeE-EEEEEEc-----CCCceEEEEeeccCHHHHHH
Q 020955 113 TVKNHVEEKVGKAVLKH----SHLVREVDVRLSVRGGEFGKGPRIRR-CEVTLFT-----KKHGVVRAEEDAETVYASID 182 (319)
Q Consensus 113 aLreyIeeKl~K~L~Ky----~~~i~~a~V~Ls~e~~~~~kg~~~~~-vEItV~~-----~~g~~IrAee~a~D~YaAID 182 (319)
.+++.+..||+. |.+. ++..+.-+|.|..-+. +|+..++ |-+..++ +.+..+.+=-.++|-|.++.
T Consensus 133 dv~~~l~~rle~-l~~~~~L~~~~~t~d~I~l~igGD---kGg~~tKl~~~i~Nv~~PNs~~~~~~~~~~~g~D~~~~l~ 208 (224)
T PF06918_consen 133 DVEKLLSRRLEQ-LSKSGKLIFDDGTGDEIWLGIGGD---KGGDETKLCLQIENVDKPNSPHNLLLLGLYEGDDNYENLK 208 (224)
T ss_pred CHHHHHHHHHHH-HHHcCCceeCCCCCCCEEEEEccc---CCCCceEEEEEEeccCCCCCcCcEEEEEEEcCCCCHHHHH
Confidence 578899999988 6643 3333445677776554 4444444 3333332 23456788889999999999
Q ss_pred HHHHHHHHHHHHHH
Q 020955 183 LVSSIIQRKLRKIK 196 (319)
Q Consensus 183 ~A~dKLeRQLrK~K 196 (319)
..+..+-.||..++
T Consensus 209 ~~~~~v~~qln~L~ 222 (224)
T PF06918_consen 209 KYLGPVFEQLNNLT 222 (224)
T ss_pred HHHHHHHHHHhccc
Confidence 99999999987654
No 28
>cd02418 Peptidase_C39B A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=31.46 E-value=1.1e+02 Score=24.59 Aligned_cols=37 Identities=19% Similarity=0.156 Sum_probs=30.2
Q ss_pred HHHhcCCCcEEEEee--CCCCceeEEEEecCCcEEEEEe
Q 020955 259 EQLENVDHDFYGFRN--EETGEINIVYKRKAGGYGVIIP 295 (319)
Q Consensus 259 ~QMEllghdF~vF~N--~eTg~vnVVYRRkDG~YGLIeP 295 (319)
.++.-+..+++++.+ ...|..-||++.+++.+-+.+|
T Consensus 70 ~~l~~~~~P~I~~~~~~~~~~~~~Vl~~~~~~~~~i~dp 108 (136)
T cd02418 70 FELKDIPLPFIAHVIKEWKLNHYVVVYKIKKKKILIADP 108 (136)
T ss_pred hhHhcCCCCEEEEEccCCCCCeEEEEEEEcCCEEEEECC
Confidence 456667899999976 5668999999998888777788
No 29
>PRK14128 iraD DNA replication/recombination/repair protein; Provisional
Probab=31.46 E-value=2.3e+02 Score=21.50 Aligned_cols=47 Identities=15% Similarity=0.131 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020955 113 TVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (319)
Q Consensus 113 aLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~ 163 (319)
.-+..|+..|..++.+|-+++..++|.+....+ +.-.|.++..|...
T Consensus 7 ~~r~~i~~~I~~aI~~fEPRL~~v~V~~~~~~~----~~L~F~I~a~L~~~ 53 (69)
T PRK14128 7 RLQSWYCRQLRSALLFHEPRIAALQVNLKEAYC----HTLAISLEAMLYHD 53 (69)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCceEEEEecCCC----CEEEEEEEEEEEcC
Confidence 356788889999999999999998888874432 23346677777643
No 30
>PRK10053 hypothetical protein; Provisional
Probab=30.60 E-value=38 Score=29.16 Aligned_cols=31 Identities=32% Similarity=0.531 Sum_probs=23.4
Q ss_pred CCCcEEEEeeCCCCceeEEEEecCCcEEE-EEeC
Q 020955 264 VDHDFYGFRNEETGEINIVYKRKAGGYGV-IIPK 296 (319)
Q Consensus 264 lghdF~vF~N~eTg~vnVVYRRkDG~YGL-IeP~ 296 (319)
+|++-|+|+|. ||+|+|---.+.+ -|. |.|.
T Consensus 74 lg~d~Y~F~D~-tG~I~VeID~~~w-~G~~v~p~ 105 (130)
T PRK10053 74 KGDDRYVFRDK-SGEINVIIPAAVF-DGREVQPD 105 (130)
T ss_pred eCCceEEEECC-CCcEEEEeCHHHc-CCCcCCCC
Confidence 58999999997 9999998766655 343 4553
No 31
>cd04623 CBS_pair_10 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=29.21 E-value=90 Score=23.54 Aligned_cols=34 Identities=15% Similarity=0.095 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHhcCCCcEEEEeeCCCCceeEEEE
Q 020955 251 PLTVSEAIEQLENVDHDFYGFRNEETGEINIVYK 284 (319)
Q Consensus 251 PMSveEAV~QMEllghdF~vF~N~eTg~vnVVYR 284 (319)
-.+++||+.+|...++..++-.|.+..-+.+++.
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~V~~~~~~~~Giv~~ 42 (113)
T cd04623 9 DATVAEAAKLMAEKNIGAVVVVDDGGRLVGIFSE 42 (113)
T ss_pred CCcHHHHHHHHHHcCCCeEEEECCCCCEEEEEeh
Confidence 4789999999988888777777765445666765
No 32
>cd04619 CBS_pair_6 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=28.62 E-value=97 Score=23.95 Aligned_cols=35 Identities=14% Similarity=0.052 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHHhcCCCcEEEEeeCCCCceeEEEE
Q 020955 250 PPLTVSEAIEQLENVDHDFYGFRNEETGEINIVYK 284 (319)
Q Consensus 250 kPMSveEAV~QMEllghdF~vF~N~eTg~vnVVYR 284 (319)
.-+++.||+..|...++.+++..|.+..-+.+|.+
T Consensus 8 ~~~~l~~a~~~~~~~~~~~~~Vvd~~g~~~G~vt~ 42 (114)
T cd04619 8 VNATLQRAAKILGEPGIDLVVVCDPHGKLAGVLTK 42 (114)
T ss_pred CCCcHHHHHHHHHhcCCCEEEEECCCCCEEEEEeh
Confidence 46889999999988899999888876555666664
No 33
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=28.00 E-value=55 Score=34.97 Aligned_cols=13 Identities=31% Similarity=0.744 Sum_probs=10.1
Q ss_pred CCcceeeecCCCC
Q 020955 84 KPLPVRMSWDGPL 96 (319)
Q Consensus 84 ~~~~~~~~~~~~~ 96 (319)
+-.-++|.|+|..
T Consensus 691 hQml~KMGWsG~G 703 (757)
T KOG4368|consen 691 HQMLVKMGWSGSG 703 (757)
T ss_pred hhhHhhcCcccCC
Confidence 4457899999985
No 34
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=27.97 E-value=1.4e+02 Score=22.43 Aligned_cols=55 Identities=9% Similarity=0.025 Sum_probs=28.6
Q ss_pred ceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHHHHHHHHHHHHHHHHHH
Q 020955 133 VREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVYASIDLVSSIIQRKLRK 194 (319)
Q Consensus 133 i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~~g~~IrAee~a~D~YaAID~A~dKLeRQLrK 194 (319)
...+.+.|..+.-. ...+.|.+... +..++-....++.++.|....+.|...|..
T Consensus 12 ~~~~~l~L~p~~LG------~v~v~l~~~~~-~l~v~~~~~~~~~~~~L~~~~~~L~~~L~~ 66 (85)
T PF02120_consen 12 SWELSLQLDPPELG------SVEVKLRLQGG-NLSVQFTAENPETKELLRQNLPELKERLQA 66 (85)
T ss_dssp --EEEE--SSGGG--------EEEEEEEETT-EEEEEEE--SSHHHHHHHHTHHHHHHHHHT
T ss_pred ceEEEEEEcccccC------cEEEEEEEeCC-EEEEEEEECCHHHHHHHHHHHHHHHHHHHH
Confidence 44555666554421 13444444433 346777777788888777777777766653
No 35
>TIGR01215 minE cell division topological specificity factor MinE. This protein is involved in the process of cell division. This protein prevents the proteins MinC and MinD to inhibit cell division at internal sites, but allows inhibiton at polar sites. This allows for correct cell division at the proper sites.
Probab=26.61 E-value=2.5e+02 Score=22.03 Aligned_cols=49 Identities=14% Similarity=0.161 Sum_probs=30.9
Q ss_pred cccCHHHHHHHHHHHHHHHhhhCC-CceEEEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020955 108 LELTDTVKNHVEEKVGKAVLKHSH-LVREVDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (319)
Q Consensus 108 velTdaLreyIeeKl~K~L~Ky~~-~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~ 163 (319)
..+++.+-+.+.+-|-.++.||++ +...++|.++.+++ .-..+++|.++
T Consensus 31 ~~~~p~~l~~mk~dil~VIskY~~id~~~v~v~l~~~~~-------~~~L~~nI~l~ 80 (81)
T TIGR01215 31 AQLAPEYLEELRKEILEVISKYVEIDPEMVEVSLESQGD-------MSVLEANITLP 80 (81)
T ss_pred cCCCHHHHHHHHHHHHHHHHHheecchHhEEEEEEeCCC-------eeEEEEEeEcC
Confidence 347777778888888888999987 23445555554432 24555555543
No 36
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=26.57 E-value=33 Score=38.77 Aligned_cols=12 Identities=17% Similarity=0.260 Sum_probs=6.6
Q ss_pred CCCcEEEEeeCC
Q 020955 264 VDHDFYGFRNEE 275 (319)
Q Consensus 264 lghdF~vF~N~e 275 (319)
+|.|.++|....
T Consensus 455 ~g~dv~~~~~~~ 466 (1164)
T PTZ00112 455 IGDDVLIFCTGN 466 (1164)
T ss_pred cCCcEEEEEcCC
Confidence 455666665543
No 37
>PF04370 DUF508: Domain of unknown function (DUF508) ; InterPro: IPR007465 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=26.31 E-value=60 Score=28.49 Aligned_cols=12 Identities=25% Similarity=0.113 Sum_probs=5.7
Q ss_pred CCCCCCcccccc
Q 020955 42 SSSVSPFVTPRK 53 (319)
Q Consensus 42 ~~~~~~~~~~~~ 53 (319)
+..+-|..+|.+
T Consensus 29 ~~~Sip~~ty~s 40 (156)
T PF04370_consen 29 SKTSIPSYTYSS 40 (156)
T ss_pred cccccccccccC
Confidence 334445555553
No 38
>cd02423 Peptidase_C39G A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are
Probab=25.93 E-value=1.7e+02 Score=23.21 Aligned_cols=39 Identities=13% Similarity=0.050 Sum_probs=30.6
Q ss_pred HHHhcCCCcEEEEeeC-CCCceeEEEEecCCcEEEEEeCC
Q 020955 259 EQLENVDHDFYGFRNE-ETGEINIVYKRKAGGYGVIIPKG 297 (319)
Q Consensus 259 ~QMEllghdF~vF~N~-eTg~vnVVYRRkDG~YGLIeP~~ 297 (319)
.+|..+..+|+++.+. ..+...||++..++.+-+.+|..
T Consensus 69 ~~L~~~~lP~i~~~~~~~~~~~vvl~~~~~~~~~i~dp~~ 108 (129)
T cd02423 69 DKLNALQIPVIVLVNNGGYGHFVVIKGIDGDRVLVGDPAL 108 (129)
T ss_pred HHHhhCCCCEEEEEecCCCceEEEEEEEeCCEEEEECCCC
Confidence 3556667899999853 46799999998888888888854
No 39
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=24.07 E-value=81 Score=23.93 Aligned_cols=28 Identities=39% Similarity=0.547 Sum_probs=23.7
Q ss_pred HHHHHHHHhcCCCcEEEEeeCCCCceeE
Q 020955 254 VSEAIEQLENVDHDFYGFRNEETGEINI 281 (319)
Q Consensus 254 veEAV~QMEllghdF~vF~N~eTg~vnV 281 (319)
+.+|+.+|..-|-.|-+.+|.+||++-|
T Consensus 21 l~~aL~~l~~eDP~l~~~~d~et~e~~l 48 (75)
T PF14492_consen 21 LSEALQKLSEEDPSLRVERDEETGELIL 48 (75)
T ss_dssp HHHHHHHHHHH-TTSEEEEETTTSEEEE
T ss_pred HHHHHHHHHhcCCeEEEEEcchhceEEE
Confidence 4689999999999999999999998654
No 40
>smart00116 CBS Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease.
Probab=23.73 E-value=1.1e+02 Score=18.65 Aligned_cols=26 Identities=31% Similarity=0.316 Sum_probs=20.9
Q ss_pred CCCCHHHHHHHHhcCCCcEEEEeeCC
Q 020955 250 PPLTVSEAIEQLENVDHDFYGFRNEE 275 (319)
Q Consensus 250 kPMSveEAV~QMEllghdF~vF~N~e 275 (319)
.-+++.+++.+|...++.+++..|.+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~v~~~~ 32 (49)
T smart00116 7 PDTTLEEALELLREHGIRRLPVVDEE 32 (49)
T ss_pred CCCcHHHHHHHHHHhCCCcccEECCC
Confidence 35788999999988888888777753
No 41
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=23.50 E-value=2.4e+02 Score=21.80 Aligned_cols=24 Identities=21% Similarity=0.108 Sum_probs=11.4
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHhH
Q 020955 175 ETVYASIDLVSSIIQRKLRKIKEK 198 (319)
Q Consensus 175 ~D~YaAID~A~dKLeRQLrK~KeK 198 (319)
+.+-..|-.|+....++.++...+
T Consensus 58 ~~L~~~I~~A~n~A~~~a~~~~~~ 81 (93)
T PF02575_consen 58 EELEDLIVEAVNDAQKKAREKAQE 81 (93)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555555555555444433
No 42
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=23.25 E-value=64 Score=27.64 Aligned_cols=45 Identities=38% Similarity=0.588 Sum_probs=29.3
Q ss_pred CCCcEEEEeeCCCCceeEEEEecCCcEEE-EEeC----CCCcccc-ccccccc
Q 020955 264 VDHDFYGFRNEETGEINIVYKRKAGGYGV-IIPK----GNGKAKK-LEPLEVE 310 (319)
Q Consensus 264 lghdF~vF~N~eTg~vnVVYRRkDG~YGL-IeP~----~~~~~~~-~~~~~~~ 310 (319)
+|++-|+|+|. ||.+.|---.+.+ .|+ |.|. ..||.+| |.+..++
T Consensus 70 l~~d~Y~F~D~-TG~I~VeId~~~w-~G~~v~p~d~V~I~GeVDk~~~~~~Id 120 (126)
T TIGR00156 70 IGDDRYVFRDK-SGEINVVIPAAVW-NGREVQPKDMVNISGSLDKKSAPAEVD 120 (126)
T ss_pred eCCceEEEECC-CCCEEEEECHHHc-CCCcCCCCCEEEEEEEECCCCCCeEEE
Confidence 58899999997 9999998766665 443 4443 2255544 4444443
No 43
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=23.10 E-value=1.9e+02 Score=23.50 Aligned_cols=45 Identities=13% Similarity=0.127 Sum_probs=32.7
Q ss_pred ceEEEeeeccCCCCCHHHHHHHHhc-CCCcEEEEeeCCCCceeEEEEecC
Q 020955 239 DEIVRMKFFEMPPLTVSEAIEQLEN-VDHDFYGFRNEETGEINIVYKRKA 287 (319)
Q Consensus 239 ~~IVr~K~f~lkPMSveEAV~QMEl-lghdF~vF~N~eTg~vnVVYRRkD 287 (319)
.++|+.|-..--+.+..|++.++.- .|-.+.=-+ |.+-|+||+..
T Consensus 42 hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~i----G~~~vlYR~~~ 87 (95)
T TIGR00253 42 RELIKVKVATEDREDKTLIAEALVKETGACNVQVI----GKTIVLYRPTK 87 (95)
T ss_pred CCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEEE----ccEEEEEecCC
Confidence 3578888766678888999999944 444444333 89999999854
No 44
>TIGR02889 spore_YpeB germination protein YpeB. Members of this family are YpeB, a protein usually encoded with the putative spore-cortex-lytic enzyme SleB and required, together with SleB, for normal germination. This family is retricted to endospore-forming species in the Firmicutes lineage of bacteria, and found in all such species to date except Clostridium perfringens. The matching phenotypes of mutants in SleB (called a lytic transglycosylase) and YpeB suggests that YpeB is necessary to allow SleB to function.
Probab=22.99 E-value=96 Score=31.86 Aligned_cols=17 Identities=29% Similarity=0.383 Sum_probs=14.2
Q ss_pred eeccCCCCCHHHHHHHH
Q 020955 245 KFFEMPPLTVSEAIEQL 261 (319)
Q Consensus 245 K~f~lkPMSveEAV~QM 261 (319)
+.++-+.+|.+||-..+
T Consensus 366 R~ip~pkls~eeAr~~v 382 (435)
T TIGR02889 366 RTLPKPKLTEEEARSKV 382 (435)
T ss_pred ccCCCCcCCHHHHHHhh
Confidence 46778899999999874
No 45
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. 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=22.20 E-value=3.8e+02 Score=20.83 Aligned_cols=42 Identities=14% Similarity=0.215 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEE
Q 020955 113 TVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAE 171 (319)
Q Consensus 113 aLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~~g~~IrAe 171 (319)
.+++|+++++.+ ..+. +|.+.... ..++|+|++..-+.+.+.
T Consensus 6 ~Ire~l~k~~~~------agis--~IeI~Rt~---------~~i~I~I~tarPg~vIG~ 47 (81)
T cd02413 6 ELNEFLTRELAE------DGYS--GVEVRVTP---------TRTEIIIRATRTQNVLGE 47 (81)
T ss_pred HHHHHHHHHHHh------CCee--eEEEEEcC---------CeEEEEEEeCCCceEECC
Confidence 467777766544 2344 44444322 258888888643444443
No 46
>PRK00296 minE cell division topological specificity factor MinE; Reviewed
Probab=22.07 E-value=3.5e+02 Score=21.48 Aligned_cols=45 Identities=16% Similarity=0.169 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHhhhCC-CceEEEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020955 112 DTVKNHVEEKVGKAVLKHSH-LVREVDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (319)
Q Consensus 112 daLreyIeeKl~K~L~Ky~~-~i~~a~V~Ls~e~~~~~kg~~~~~vEItV~~~ 163 (319)
+.+-+.+.+-|-.++.||++ ....++|.+..++ ..-.-|++|.+|
T Consensus 36 p~~l~~lk~dIl~VIsKY~~Id~~~v~i~l~~~~-------~~~~Le~nI~lp 81 (86)
T PRK00296 36 PDYLPQLRKEILEVIAKYVQIDPDKVSVQLDKDG-------DISTLELNVTLP 81 (86)
T ss_pred HHHHHHHHHHHHHHHHHheecChhhEEEEEEeCC-------CeEEEEEEEEcC
Confidence 44556666777777888987 3345666666433 235677777776
No 47
>cd04593 CBS_pair_EriC_assoc_bac_arch This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in bacteria and archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS d
Probab=22.05 E-value=1.6e+02 Score=22.45 Aligned_cols=34 Identities=24% Similarity=0.261 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHHhcCCCcEEEEeeCCCCceeEEE
Q 020955 250 PPLTVSEAIEQLENVDHDFYGFRNEETGEINIVY 283 (319)
Q Consensus 250 kPMSveEAV~QMEllghdF~vF~N~eTg~vnVVY 283 (319)
.-+++.+|+..|...++.+++..|.+..-+.+|-
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~V~d~~~~~~G~v~ 41 (115)
T cd04593 8 ATTPLREAAEQLIESKHGSALVVDRDGGVVGIIT 41 (115)
T ss_pred CCCCHHHHHHHHHhCCCcEEEEEcCCCCEEEEEE
Confidence 4689999999998888888888886433344554
No 48
>PF09313 DUF1971: Domain of unknown function (DUF1971); InterPro: IPR015392 This uncharacterised domain is predominantly found in bacterial Tellurite resistance proteins. ; PDB: 3BB6_C 3M70_A 3DL3_I.
Probab=21.80 E-value=1.1e+02 Score=24.17 Aligned_cols=30 Identities=27% Similarity=0.042 Sum_probs=19.4
Q ss_pred EEEeeCCCCceeEEEEecCCcEEEEEeCCC
Q 020955 269 YGFRNEETGEINIVYKRKAGGYGVIIPKGN 298 (319)
Q Consensus 269 ~vF~N~eTg~vnVVYRRkDG~YGLIeP~~~ 298 (319)
|.|.|.+.+.+.--.--..|+.|+|+|..-
T Consensus 38 f~~~~~~~~~~~~~~~~~~~~~~~i~Pq~w 67 (82)
T PF09313_consen 38 FYGLDEEGEEPEEEVFIPAGQPPVIEPQQW 67 (82)
T ss_dssp EEEESSTT-SESEEEEEETTEEEEE-TT-E
T ss_pred EEEECCCCCceeEEEEeCCCCCceeCCCce
Confidence 445555556666666668999999999874
No 49
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=21.69 E-value=1.9e+02 Score=26.42 Aligned_cols=53 Identities=17% Similarity=0.179 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHhhhCCCceEEEEEEEeecC-cCCCCCceeEEEEEEEcCCCce
Q 020955 114 VKNHVEEKVGKAVLKHSHLVREVDVRLSVRGG-EFGKGPRIRRCEVTLFTKKHGV 167 (319)
Q Consensus 114 LreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~-~~~kg~~~~~vEItV~~~~g~~ 167 (319)
.+-.++..|++.|..+ +.|..|+|+|..... .+......-.+-|.|.+.+|..
T Consensus 112 ~~~ale~eL~~tI~~i-~gV~~A~V~l~~Pe~~~f~~~~~~~sASV~l~~~~g~~ 165 (206)
T PF01514_consen 112 YQRALEGELERTIESI-DGVESARVHLVLPERSVFGENQQPPSASVVLKLKPGSE 165 (206)
T ss_dssp HHHHHHHHHHHHHTTS-TTEEEEEEEEEE----BTTB----EEEEEEEEE-TTS-
T ss_pred HHHHHHHHHHHHHHcC-CCeeEEEEEEecCCccccccCCCCCeEEEEEEECCCCC
Confidence 4456677777766665 789999999987542 2222222357778787765543
No 50
>PLN03014 carbonic anhydrase
Probab=21.43 E-value=75 Score=31.76 Aligned_cols=13 Identities=15% Similarity=0.388 Sum_probs=7.4
Q ss_pred EEeeCCCCceeEE
Q 020955 270 GFRNEETGEINIV 282 (319)
Q Consensus 270 vF~N~eTg~vnVV 282 (319)
.|+|-+||++.++
T Consensus 312 ~~YDi~TG~V~~l 324 (347)
T PLN03014 312 GYYDFVKGAFELW 324 (347)
T ss_pred EEEECCCceEEEe
Confidence 3556666666543
No 51
>COG2098 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.17 E-value=4.9e+02 Score=22.02 Aligned_cols=65 Identities=12% Similarity=0.129 Sum_probs=41.7
Q ss_pred eeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCC--------CceeEEEEEEEcCCCceEEEEe
Q 020955 105 GKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKG--------PRIRRCEVTLFTKKHGVVRAEE 172 (319)
Q Consensus 105 gRnvelTdaLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~~~kg--------~~~~~vEItV~~~~g~~IrAee 172 (319)
+-+.-++..-.+.+++.|+. --+..+-+.+++|.+..++.. ..+ +.-..|+|+|..+ +..+.|.=
T Consensus 29 f~GtPvs~~~a~~le~aI~e-si~~QP~v~daeV~Id~~~~K-~~~~~gYt~LsG~mLdV~l~v~~g-~~~v~a~l 101 (116)
T COG2098 29 FVGTPVSPGTAESLEKAIEE-SIKVQPFVEDAEVKIDRDKEK-LDGEFGYTELSGEMLDVRLKVRYG-GTVVVARL 101 (116)
T ss_pred hcCCcCCccchHHHHHHHHH-HHhcCCceeeEEEEecccccc-cccccceEEeccccEEEEEEEEEC-CEEEEEEE
Confidence 44556777777888888877 335556788899998865321 111 1224688888876 56666653
No 52
>COG1724 Predicted RNA binding protein (dsRBD-like fold), HicA family [General function prediction only]
Probab=20.91 E-value=2e+02 Score=22.07 Aligned_cols=40 Identities=25% Similarity=0.370 Sum_probs=29.0
Q ss_pred CCCCCHHHHHHHHhcCCCcEEEEeeCCCCceeEEEEecCCcEEEE
Q 020955 249 MPPLTVSEAIEQLENVDHDFYGFRNEETGEINIVYKRKAGGYGVI 293 (319)
Q Consensus 249 lkPMSveEAV~QMEllghdF~vF~N~eTg~vnVVYRRkDG~YGLI 293 (319)
+.+|+..|++..||..|-. +-+- -.=-+.|+..||++-.+
T Consensus 4 lp~~~~ke~ik~Le~~Gf~--~vrq---kGSH~q~kHp~~~~vtV 43 (66)
T COG1724 4 LPRMKAKEVIKALEKDGFQ--LVRQ---KGSHRQYKHPDGGRVTV 43 (66)
T ss_pred CCcCCHHHHHHHHHhCCcE--EEEe---ecceeEEEcCCCCEEEe
Confidence 6899999999999998843 3332 34457888888666544
No 53
>PRK15463 cold shock-like protein CspF; Provisional
Probab=20.81 E-value=1.2e+02 Score=23.05 Aligned_cols=20 Identities=20% Similarity=0.260 Sum_probs=15.9
Q ss_pred eEEEEecCCcEEEEEeCCCC
Q 020955 280 NIVYKRKAGGYGVIIPKGNG 299 (319)
Q Consensus 280 nVVYRRkDG~YGLIeP~~~~ 299 (319)
.|.+--.+-+||.|+|..++
T Consensus 8 ~Vk~fn~~kGfGFI~~~~g~ 27 (70)
T PRK15463 8 IVKTFDGKSGKGLITPSDGR 27 (70)
T ss_pred EEEEEeCCCceEEEecCCCC
Confidence 56667788999999997654
No 54
>PF06933 SSP160: Special lobe-specific silk protein SSP160; InterPro: IPR009701 This family consists of several special lobe-specific silk protein SSP160 sequences which appear to be specific to Chironomus (Midge) species.
Probab=20.40 E-value=91 Score=32.11 Aligned_cols=12 Identities=8% Similarity=0.096 Sum_probs=5.5
Q ss_pred CCCceEEEEEee
Q 020955 95 PLSSVKLIIQGK 106 (319)
Q Consensus 95 ~~~~MkI~ItgR 106 (319)
.....+|.|.+-
T Consensus 222 ai~yiniti~fi 233 (756)
T PF06933_consen 222 AIAYINITIYFI 233 (756)
T ss_pred eeeEEEEEEEEE
Confidence 333455555443
No 55
>COG1539 FolB Dihydroneopterin aldolase [Coenzyme metabolism]
Probab=20.36 E-value=2.2e+02 Score=23.93 Aligned_cols=40 Identities=18% Similarity=0.388 Sum_probs=26.8
Q ss_pred EEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCc
Q 020955 103 IQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGE 146 (319)
Q Consensus 103 ItgRnvelTdaLreyIeeKl~K~L~Ky~~~i~~a~V~Ls~e~~~ 146 (319)
|.|+++.|=+.+-+.|-+.+ +.+| +.+..++|.+++.+-+
T Consensus 65 v~~~~~~LiE~lA~~ia~~l---~~~~-~~v~~~~v~v~KP~ap 104 (121)
T COG1539 65 VEGKRFALIETLAEEIADLL---LARF-PRVELVEVKVTKPKAP 104 (121)
T ss_pred HhCCccchHHHHHHHHHHHH---HhhC-CccEEEEEEEECCCCC
Confidence 45666666555555554444 4455 8889999999998754
No 56
>PF03714 PUD: Bacterial pullanase-associated domain; InterPro: IPR005323 Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C-termini of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrate binding function.; GO: 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process; PDB: 2J43_A 2J44_A 2YA1_A 2FHC_A 2FHB_A 2FHF_A 2J73_B 2J72_A 2J71_A.
Probab=20.21 E-value=57 Score=26.19 Aligned_cols=14 Identities=29% Similarity=0.750 Sum_probs=11.4
Q ss_pred CceeEEEEecCCcE
Q 020955 277 GEINIVYKRKAGGY 290 (319)
Q Consensus 277 g~vnVVYRRkDG~Y 290 (319)
+.+.|-|+|.||+|
T Consensus 2 ~~v~vhY~r~d~~Y 15 (103)
T PF03714_consen 2 NTVRVHYHRPDGDY 15 (103)
T ss_dssp TEEEEEEESTTS-G
T ss_pred CEEEEEEECCCCCC
Confidence 46889999999987
No 57
>PF07118 DUF1374: Protein of unknown function (DUF1374); InterPro: IPR009804 This family consists of several hypothetical Sulfolobus virus proteins of around 100 residues in length. The function of this family is unknown.; PDB: 3DJW_B 3DF6_D 2H36_X.
Probab=20.15 E-value=1.6e+02 Score=23.90 Aligned_cols=30 Identities=13% Similarity=0.159 Sum_probs=24.1
Q ss_pred CCcEEEEeeCCCCc--eeEEEEecCCcEEEEE
Q 020955 265 DHDFYGFRNEETGE--INIVYKRKAGGYGVII 294 (319)
Q Consensus 265 ghdF~vF~N~eTg~--vnVVYRRkDG~YGLIe 294 (319)
--|+|+|.+....- +.+.|.++|..+.+.+
T Consensus 55 ~~d~f~y~e~~n~~vKl~i~Y~k~~~KI~I~e 86 (92)
T PF07118_consen 55 IIDEFEYYENDNIYVKLEIDYYKKDNKIYILE 86 (92)
T ss_dssp EEEEEEEE-SSSEEEEEEEEEEECTTEEEEEE
T ss_pred EEEEEEEEcCCCeEEEEEEEEEecCCEEEEEE
Confidence 35899999987664 7899999999999876
No 58
>PF07466 DUF1517: Protein of unknown function (DUF1517); InterPro: IPR010903 This family consists of several hypothetical glycine rich plant and bacterial proteins of around 300 residues in length. The function of this family is unknown.
Probab=20.06 E-value=94 Score=30.11 Aligned_cols=11 Identities=27% Similarity=0.591 Sum_probs=6.3
Q ss_pred HHHHHHHHhcC
Q 020955 254 VSEAIEQLENV 264 (319)
Q Consensus 254 veEAV~QMEll 264 (319)
+.+|+.+|-.+
T Consensus 243 l~~aL~~l~~~ 253 (289)
T PF07466_consen 243 LREALRKLGSI 253 (289)
T ss_pred HHHHHHHHhCC
Confidence 45666666543
Done!