Query 020905
Match_columns 320
No_of_seqs 253 out of 1412
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:04:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020905.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020905hhsearch_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 8.3E-27 1.8E-31 193.2 13.1 99 99-204 1-99 (110)
2 PRK10324 translation inhibitor 99.9 2.1E-26 4.5E-31 191.6 14.6 98 99-205 1-98 (113)
3 PRK10470 ribosome hibernation 99.9 2.1E-26 4.6E-31 185.0 14.0 95 99-202 1-95 (95)
4 TIGR00741 yfiA ribosomal subun 99.9 1.4E-24 3E-29 173.3 14.0 95 99-202 1-95 (95)
5 PF02482 Ribosomal_S30AE: Sigm 99.9 2.3E-23 5E-28 166.3 12.8 97 100-202 1-97 (97)
6 cd00552 RaiA RaiA ("ribosome-a 99.9 5.9E-22 1.3E-26 157.4 12.8 93 100-198 1-93 (93)
7 PF10500 SR-25: Nuclear RNA-sp 79.9 1.1 2.3E-05 41.9 1.8 37 247-289 154-190 (225)
8 PHA03308 transcriptional regul 79.4 1.2 2.6E-05 48.0 2.2 6 126-131 1365-1370(1463)
9 PHA03309 transcriptional regul 77.7 1.7 3.7E-05 47.7 2.8 12 39-50 1833-1844(2033)
10 PHA03308 transcriptional regul 67.5 4.5 9.8E-05 43.9 3.0 12 105-117 1297-1308(1463)
11 COG3111 Periplasmic protein wi 64.1 5.3 0.00011 34.2 2.2 46 265-311 70-120 (128)
12 PF05717 TnpB_IS66: IS66 Orf2 60.7 9.5 0.00021 31.5 3.2 37 260-297 28-64 (107)
13 PF13031 DUF3892: Protein of u 60.5 43 0.00093 26.1 6.7 64 242-308 17-84 (85)
14 KOG1711 Mitochondrial/chloropl 60.0 4.6 0.0001 37.5 1.3 18 250-267 93-110 (218)
15 PF11419 DUF3194: Protein of u 54.1 31 0.00068 27.8 4.9 15 131-145 33-47 (87)
16 PF03776 MinE: Septum formatio 53.4 70 0.0015 24.4 6.6 58 99-163 9-69 (70)
17 PF04370 DUF508: Domain of unk 45.9 15 0.00033 32.1 2.1 9 99-107 53-61 (156)
18 TIGR03357 VI_zyme type VI secr 45.2 90 0.0019 26.1 6.8 58 103-163 56-113 (133)
19 PF04965 GPW_gp25: Gene 25-lik 44.8 76 0.0017 24.8 6.0 40 103-144 36-75 (99)
20 PLN03014 carbonic anhydrase 37.4 31 0.00067 34.4 3.1 15 283-297 313-327 (347)
21 PF14671 DSPn: Dual specificit 34.6 26 0.00057 30.5 1.9 29 251-279 96-124 (141)
22 PRK10053 hypothetical protein; 33.2 32 0.0007 29.6 2.2 46 265-311 74-124 (130)
23 cd02418 Peptidase_C39B A sub-f 33.2 1E+02 0.0022 24.8 5.2 37 260-296 70-108 (136)
24 PF06933 SSP160: Special lobe- 32.9 35 0.00076 35.0 2.7 10 98-107 225-234 (756)
25 PRK14128 iraD DNA replication/ 29.8 2.5E+02 0.0055 21.3 7.5 47 113-163 7-53 (69)
26 cd04623 CBS_pair_10 The CBS do 27.8 98 0.0021 23.3 4.0 33 253-285 10-42 (113)
27 PF02120 Flg_hook: Flagellar h 26.5 1.5E+02 0.0033 22.3 4.8 55 132-193 11-65 (85)
28 cd04619 CBS_pair_6 The CBS dom 25.9 1.2E+02 0.0025 23.5 4.1 35 251-285 8-42 (114)
29 cd02423 Peptidase_C39G A sub-f 25.5 1.8E+02 0.0038 23.1 5.3 39 260-298 69-108 (129)
30 PF07218 RAP1: Rhoptry-associa 25.4 85 0.0019 33.5 4.0 15 247-261 460-474 (782)
31 TIGR01215 minE cell division t 24.9 2.8E+02 0.0061 21.7 6.1 49 108-163 31-80 (81)
32 TIGR00156 conserved hypothetic 24.8 58 0.0012 27.9 2.3 45 265-311 70-120 (126)
33 PF14492 EFG_II: Elongation Fa 24.5 78 0.0017 24.1 2.8 28 255-282 21-48 (75)
34 PRK15463 cold shock-like prote 23.7 95 0.0021 23.6 3.1 20 281-300 8-27 (70)
35 TIGR02889 spore_YpeB germinati 23.1 99 0.0022 31.8 4.0 59 246-305 366-432 (435)
36 cd02413 40S_S3_KH K homology R 22.5 3.8E+02 0.0082 20.9 7.0 41 113-170 6-46 (81)
37 PF06918 DUF1280: Protein of u 22.4 5.9E+02 0.013 23.8 8.7 80 113-196 133-222 (224)
38 PF02560 Cyanate_lyase: Cyanat 22.1 1.3E+02 0.0029 23.4 3.6 41 112-162 24-65 (73)
39 COG1539 FolB Dihydroneopterin 21.8 2E+02 0.0043 24.3 5.0 40 103-146 65-104 (121)
40 smart00116 CBS Domain in cysta 21.6 1.3E+02 0.0027 18.4 3.0 26 251-276 7-32 (49)
41 PF02575 YbaB_DNA_bd: YbaB/Ebf 21.3 2.7E+02 0.0059 21.5 5.4 23 176-198 59-81 (93)
42 PLN03078 Putative tRNA pseudou 21.2 99 0.0021 32.5 3.6 16 82-97 69-84 (513)
43 PRK00296 minE cell division to 21.0 3.8E+02 0.0083 21.3 6.2 45 112-163 36-81 (86)
44 cd04593 CBS_pair_EriC_assoc_ba 20.9 1.8E+02 0.0039 22.2 4.3 34 251-284 8-41 (115)
45 cd00559 Cyanase_C Cyanase C-te 20.3 2.2E+02 0.0047 22.1 4.3 43 111-163 19-62 (69)
No 1
>COG1544 Ribosome-associated protein Y (PSrp-1) [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=8.3e-27 Score=193.17 Aligned_cols=99 Identities=40% Similarity=0.559 Sum_probs=92.2
Q ss_pred eEEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHH
Q 020905 99 VKLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVY 178 (320)
Q Consensus 99 MkI~ItgRnvelTdaLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~~g~~IrAee~~~D~Y 178 (320)
|+++|+|+|+++||+||+||++||+| |++|+.+++.++|+|.+++. +..+.|||+|++++ ++|+|++.++|||
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 89998888899999999974 13489999999995 5999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhhccC
Q 020905 179 ASIDLVSSIIQRKLRKIKEKESDHGR 204 (320)
Q Consensus 179 aAID~A~dKLeRQLrK~KeKlk~~~r 204 (320)
+|||.|+|||||||||+|+|+++|++
T Consensus 74 aAID~a~dKLerqlrK~K~K~~~~~~ 99 (110)
T COG1544 74 AAIDLAIDKLERQLRKHKEKLKDHRR 99 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhc
Confidence 99999999999999999999999873
No 2
>PRK10324 translation inhibitor protein RaiA; Provisional
Probab=99.94 E-value=2.1e-26 Score=191.61 Aligned_cols=98 Identities=22% Similarity=0.342 Sum_probs=92.3
Q ss_pred eEEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHH
Q 020905 99 VKLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVY 178 (320)
Q Consensus 99 MkI~ItgRnvelTdaLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~~g~~IrAee~~~D~Y 178 (320)
|+|+|+|||+++||+|++||++|++| |+||++++.+|+|+|+.+++ .++|||+|+++ |..|+|++.++|||
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-LEKWQTHLINPHIILSKEPQ-------GFVADATINTP-NGVLVASGKHEDMY 71 (113)
T ss_pred CEEEEEEEcCcCCHHHHHHHHHHHHH-HHHhcCCCceEEEEEEEcCC-------CeEEEEEEECC-CCeEEEEEecCCHH
Confidence 89999999999999999999999999 99999999999999998864 27899999998 67899999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhhccCC
Q 020905 179 ASIDLVSSIIQRKLRKIKEKESDHGRH 205 (320)
Q Consensus 179 aAID~A~dKLeRQLrK~KeKlk~~~r~ 205 (320)
+|||.|+++|+|||+|+|+|+.+|+.+
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=2.1e-26 Score=184.99 Aligned_cols=95 Identities=28% Similarity=0.417 Sum_probs=89.8
Q ss_pred eEEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHH
Q 020905 99 VKLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVY 178 (320)
Q Consensus 99 MkI~ItgRnvelTdaLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~~g~~IrAee~~~D~Y 178 (320)
|+|+|+|||+++|++|++||++|+++ |+||+++|..|+|+|+.+++. +.|||+++++ |..++|++.++|||
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 67999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhhc
Q 020905 179 ASIDLVSSIIQRKLRKIKEKESDH 202 (320)
Q Consensus 179 aAID~A~dKLeRQLrK~KeKlk~~ 202 (320)
+|||.|+++|+|||+|+|+|+++|
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=1.4e-24 Score=173.33 Aligned_cols=95 Identities=38% Similarity=0.608 Sum_probs=89.9
Q ss_pred eEEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHH
Q 020905 99 VKLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVY 178 (320)
Q Consensus 99 MkI~ItgRnvelTdaLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~~g~~IrAee~~~D~Y 178 (320)
|+|+|+|+|+++|++|++||++|+++ |+||++.+..|+|+|+.+++. ++|+|+|+++ |+.++|++.++|+|
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 89999999999999999999999999 999999999999999988642 8999999999 56999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhHhhhc
Q 020905 179 ASIDLVSSIIQRKLRKIKEKESDH 202 (320)
Q Consensus 179 aAID~A~dKLeRQLrK~KeKlk~~ 202 (320)
+|||.|+++|+|||+|+|+|+++|
T Consensus 72 ~Aid~a~~klerql~k~k~k~~~~ 95 (95)
T TIGR00741 72 AAIDLAIDKLERQLRKLKEKRKEH 95 (95)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhcC
Confidence 999999999999999999998764
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=2.3e-23 Score=166.26 Aligned_cols=97 Identities=38% Similarity=0.499 Sum_probs=85.0
Q ss_pred EEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHHH
Q 020905 100 KLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVYA 179 (320)
Q Consensus 100 kI~ItgRnvelTdaLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~~g~~IrAee~~~D~Ya 179 (320)
||+|+|||+++|++|++||++||++ |++|++++..++|+|+.++ .++..++|+|+|.++ |..|+|++.++|+|+
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 679999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhHhhhc
Q 020905 180 SIDLVSSIIQRKLRKIKEKESDH 202 (320)
Q Consensus 180 AID~A~dKLeRQLrK~KeKlk~~ 202 (320)
|||.|+++|+|||+|+|+|+++|
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=5.9e-22 Score=157.35 Aligned_cols=93 Identities=42% Similarity=0.580 Sum_probs=86.7
Q ss_pred EEEEEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHHH
Q 020905 100 KLIIQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVYA 179 (320)
Q Consensus 100 kI~ItgRnvelTdaLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~~g~~IrAee~~~D~Ya 179 (320)
+|+|+|||+++|++|++||++++++ |.||++++..|+|+|+.++++ +..++|+|+|+++ |..|+|++.++|+|+
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 5899999999999999999999999 999999999999999988752 3358999999999 789999999999999
Q ss_pred HHHHHHHHHHHHHHHHHhH
Q 020905 180 SIDLVSSIIQRKLRKIKEK 198 (320)
Q Consensus 180 AID~A~dKLeRQLrK~KeK 198 (320)
|||.|+++|+|||+|+|+|
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
>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=79.91 E-value=1.1 Score=41.85 Aligned_cols=37 Identities=22% Similarity=0.355 Sum_probs=25.5
Q ss_pred eccCCCCCHHHHHHHHhcCCCcEEEEeeCCCCceeEEEEecCC
Q 020905 247 FFEMPPLTVSEAIEQLENVDHDFYGFRNEETGEINIVYKRKAG 289 (320)
Q Consensus 247 ~~~lkPMsveEAV~QMEllghdF~vF~N~eTg~vnVVYRRkDG 289 (320)
.-.|.|||-||=-.+=-.+- =-+|+|||+..+| ++||
T Consensus 154 ~~am~PmTkEEyearQSvIR----rVvDpETGRtRLI--kGdG 190 (225)
T PF10500_consen 154 IQAMAPMTKEEYEARQSVIR----RVVDPETGRTRLI--KGDG 190 (225)
T ss_pred hhhcCCCCHHHHHHHHhhhe----eeecCCCCceeee--cccc
Confidence 35689999998655444333 3458899998887 5555
No 8
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=79.35 E-value=1.2 Score=47.99 Aligned_cols=6 Identities=0% Similarity=-0.202 Sum_probs=2.4
Q ss_pred HhhhCC
Q 020905 126 VLKHSH 131 (320)
Q Consensus 126 L~Ky~d 131 (320)
+..|+.
T Consensus 1365 isdyyp 1370 (1463)
T PHA03308 1365 ISDYYP 1370 (1463)
T ss_pred HhhhCC
Confidence 333443
No 9
>PHA03309 transcriptional regulator ICP4; Provisional
Probab=77.73 E-value=1.7 Score=47.74 Aligned_cols=12 Identities=33% Similarity=0.454 Sum_probs=5.3
Q ss_pred CCCCCCCCCccc
Q 020905 39 SSSSSSVSPFVT 50 (320)
Q Consensus 39 ~~~~~~~~~~~~ 50 (320)
+-.|+++.|.-+
T Consensus 1833 srpsrsatpsls 1844 (2033)
T PHA03309 1833 SRPSRSATPSLS 1844 (2033)
T ss_pred CCCcccCCCCCC
Confidence 333444444443
No 10
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=67.54 E-value=4.5 Score=43.85 Aligned_cols=12 Identities=17% Similarity=0.166 Sum_probs=7.9
Q ss_pred eeecccCHHHHHH
Q 020905 105 GKNLELTDTVKNH 117 (320)
Q Consensus 105 gRnvelTdaLkey 117 (320)
||. .|...+|.|
T Consensus 1297 GRK-~LPpe~Ka~ 1308 (1463)
T PHA03308 1297 GRQ-RLPIRDRVY 1308 (1463)
T ss_pred CCC-CCChHHhhh
Confidence 555 566667766
No 11
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=64.10 E-value=5.3 Score=34.22 Aligned_cols=46 Identities=30% Similarity=0.510 Sum_probs=33.9
Q ss_pred CCCcEEEEeeCCCCceeEEEEecCCcEEEEEeC----CCCcccc-ccccccc
Q 020905 265 VDHDFYGFRNEETGEINIVYKRKAGGYGVIIPK----GNGKAKK-LEPLEVE 311 (320)
Q Consensus 265 lghdF~vF~N~eTg~vnVVYRRkDG~YGLIeP~----~~~~~~~-~~~~~~~ 311 (320)
+|+|-|+|+|. ||++||.--.+.++=-=|.|. ..||.+| |...+++
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 69999999998 999999988777766667775 3366544 4554443
No 12
>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=60.73 E-value=9.5 Score=31.55 Aligned_cols=37 Identities=22% Similarity=0.405 Sum_probs=27.7
Q ss_pred HHHhcCCCcEEEEeeCCCCceeEEEEecCCcEEEEEeC
Q 020905 260 EQLENVDHDFYGFRNEETGEINIVYKRKAGGYGVIIPK 297 (320)
Q Consensus 260 ~QMEllghdF~vF~N~eTg~vnVVYRRkDG~YGLIeP~ 297 (320)
+.++..+.+.|||.|..-..+.|+|.- +++|-|+.-.
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 456667788999999999999999984 4455555443
No 13
>PF13031 DUF3892: Protein of unknown function (DUF3892)
Probab=60.54 E-value=43 Score=26.05 Aligned_cols=64 Identities=25% Similarity=0.284 Sum_probs=42.4
Q ss_pred eeEeeeccCCCC---CHHHHHHHHhcCCCcEEEEeeCCCCceeEEEEecCCcEEEEEeCCCC-cccccccc
Q 020905 242 IVRMKFFEMPPL---TVSEAIEQLENVDHDFYGFRNEETGEINIVYKRKAGGYGVIIPKGNG-KAKKLEPL 308 (320)
Q Consensus 242 IVr~K~~~lkPM---sveEAV~QMEllghdF~vF~N~eTg~vnVVYRRkDG~YGLIeP~~~~-~~~~~~~~ 308 (320)
|+..+.-.-... +.++||..+|.-.+.||+= +...-.+.|+ +-.+| ---|....|| +..-|..|
T Consensus 17 I~~v~~~~g~~~~~~s~~~~i~~ie~g~~~~yv~-~~~~~~V~V~-~~~~G-~kYirT~~Dg~~~dNLl~L 84 (85)
T PF13031_consen 17 ITHVKLNNGGVPWKYSREEAIAWIENGKWSFYVE-GGWIAGVNVV-TSRNG-EKYIRTDADGTESDNLLSL 84 (85)
T ss_pred eEEEECCCCCccccccHHHHHHHHHcCCceEEeC-CCCCccEEEE-ECCCC-CeeEeeCCCCCCCchhhcc
Confidence 555554444555 9999999999977899988 7666777777 33444 4456766665 33444433
No 14
>KOG1711 consensus Mitochondrial/chloroplast ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=60.05 E-value=4.6 Score=37.55 Aligned_cols=18 Identities=39% Similarity=0.486 Sum_probs=15.3
Q ss_pred CCCCCHHHHHHHHhcCCC
Q 020905 250 MPPLTVSEAIEQLENVDH 267 (320)
Q Consensus 250 lkPMsveEAV~QMEllgh 267 (320)
+.-|++|||++||++.+.
T Consensus 93 irgm~v~~AL~Ql~~s~k 110 (218)
T KOG1711|consen 93 IRGMSVEEALMQLEFSDK 110 (218)
T ss_pred HcCCCHHHHHHHhhcchH
Confidence 356999999999999864
No 15
>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=54.12 E-value=31 Score=27.79 Aligned_cols=15 Identities=27% Similarity=0.450 Sum_probs=11.1
Q ss_pred CCceEEEEEEEeecC
Q 020905 131 HLVREVDVRLSVRGG 145 (320)
Q Consensus 131 d~I~~a~V~Ls~e~~ 145 (320)
..+...+|++..+.+
T Consensus 33 sEV~DlDVtv~~~~~ 47 (87)
T PF11419_consen 33 SEVKDLDVTVRFEYG 47 (87)
T ss_dssp TTEEEEEEEEEEEES
T ss_pred hhcccceeEEEEecC
Confidence 357888888888754
No 16
>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=53.43 E-value=70 Score=24.36 Aligned_cols=58 Identities=16% Similarity=0.178 Sum_probs=37.6
Q ss_pred eEEEEEeeecccCH--HHHHHHHHHHHHHHhhhCC-CceEEEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020905 99 VKLIIQGKNLELTD--TVKNHVEEKVGKAVLKHSH-LVREVDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (320)
Q Consensus 99 MkI~ItgRnvelTd--aLkeyIeeKl~K~L~Ky~d-~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~ 163 (320)
+++.+.......++ .+-+.+.+-|-.++.||.+ ....++|.++.+++ .-..+++|.++
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 7777788888888999986 23566777764432 24566666554
No 17
>PF04370 DUF508: Domain of unknown function (DUF508) ; InterPro: IPR007465 This is a family of uncharacterised proteins from Caenorhabditis elegans.
Probab=45.87 E-value=15 Score=32.07 Aligned_cols=9 Identities=11% Similarity=-0.090 Sum_probs=4.1
Q ss_pred eEEEEEeee
Q 020905 99 VKLIIQGKN 107 (320)
Q Consensus 99 MkI~ItgRn 107 (320)
.++....-|
T Consensus 53 VhVKFilLh 61 (156)
T PF04370_consen 53 VHVKFILLH 61 (156)
T ss_pred EEEEEEEEe
Confidence 344444444
No 18
>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=45.21 E-value=90 Score=26.14 Aligned_cols=58 Identities=12% Similarity=0.084 Sum_probs=38.3
Q ss_pred EEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020905 103 IQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (320)
Q Consensus 103 ItgRnvelTdaLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~ 163 (320)
+.+..+. +...+..|...|.+++.+|-+++..++|.+..+... .+.-.+.++.++...
T Consensus 56 ~~~~~~~-~~~~~~~i~~~I~~aI~r~EPRl~~~~V~~~~~~~~--~~~l~f~I~~~l~~~ 113 (133)
T TIGR03357 56 LNDLSLS-SADDRRRIRRAIEQAIERYEPRLSSVRVTALEDEED--PLALRFRIEAELDVD 113 (133)
T ss_pred ccccccc-CHHHHHHHHHHHHHHHHhcCCCcCceEEEEecCCCC--ccEEEEEEEEEEEeC
Confidence 3343433 367778888899888999999999888888743221 122235666666655
No 19
>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=44.77 E-value=76 Score=24.84 Aligned_cols=40 Identities=8% Similarity=0.204 Sum_probs=28.5
Q ss_pred EEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeec
Q 020905 103 IQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRG 144 (320)
Q Consensus 103 ItgRnvelTdaLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~ 144 (320)
+.+.++ ++.....+...|..+|.+|-+++...+|.+....
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 445554 8899999999999999999999999999888744
No 20
>PLN03014 carbonic anhydrase
Probab=37.37 E-value=31 Score=34.42 Aligned_cols=15 Identities=13% Similarity=0.173 Sum_probs=7.4
Q ss_pred EEEecCCcEEEEEeC
Q 020905 283 VYKRKAGGYGVIIPK 297 (320)
Q Consensus 283 VYRRkDG~YGLIeP~ 297 (320)
+|-=.+|.+-++++.
T Consensus 313 ~YDi~TG~V~~l~~~ 327 (347)
T PLN03014 313 YYDFVKGAFELWGLE 327 (347)
T ss_pred EEECCCceEEEeccc
Confidence 344455555555543
No 21
>PF14671 DSPn: Dual specificity protein phosphatase, N-terminal half; PDB: 1OHD_A 1OHE_A 1OHC_A.
Probab=34.57 E-value=26 Score=30.53 Aligned_cols=29 Identities=24% Similarity=0.411 Sum_probs=16.4
Q ss_pred CCCCHHHHHHHHhcCCCcEEEEeeCCCCc
Q 020905 251 PPLTVSEAIEQLENVDHDFYGFRNEETGE 279 (320)
Q Consensus 251 kPMsveEAV~QMEllghdF~vF~N~eTg~ 279 (320)
.-||+|||...+...+-+|.-|||+-.|.
T Consensus 96 l~~spe~A~~~l~~~~p~~~pFRDAs~g~ 124 (141)
T PF14671_consen 96 LGMSPEEAYKPLASIQPPFMPFRDASYGP 124 (141)
T ss_dssp S---HHHHHHHHTTTT-----B--SSSSS
T ss_pred cCCCHHHHHHHHHhcCCCCCCCCCCCCCC
Confidence 45899999999999999999999997664
No 22
>PRK10053 hypothetical protein; Provisional
Probab=33.22 E-value=32 Score=29.61 Aligned_cols=46 Identities=30% Similarity=0.395 Sum_probs=29.9
Q ss_pred CCCcEEEEeeCCCCceeEEEEecCCcEEEEEeC----CCCcccc-ccccccc
Q 020905 265 VDHDFYGFRNEETGEINIVYKRKAGGYGVIIPK----GNGKAKK-LEPLEVE 311 (320)
Q Consensus 265 lghdF~vF~N~eTg~vnVVYRRkDG~YGLIeP~----~~~~~~~-~~~~~~~ 311 (320)
+|++-|+|+|. ||+++|---.+.++=--|.|. ..||.+| |.|..++
T Consensus 74 lg~d~Y~F~D~-tG~I~VeID~~~w~G~~v~p~~kV~I~GevDk~~~~~~Id 124 (130)
T PRK10053 74 KGDDRYVFRDK-SGEINVIIPAAVFDGREVQPDQMININGSLDKKSAPPVVR 124 (130)
T ss_pred eCCceEEEECC-CCcEEEEeCHHHcCCCcCCCCCEEEEEEEECCCCCCeEEE
Confidence 69999999997 999999877666632235554 2255543 4444443
No 23
>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=33.18 E-value=1e+02 Score=24.79 Aligned_cols=37 Identities=19% Similarity=0.156 Sum_probs=30.1
Q ss_pred HHHhcCCCcEEEEee--CCCCceeEEEEecCCcEEEEEe
Q 020905 260 EQLENVDHDFYGFRN--EETGEINIVYKRKAGGYGVIIP 296 (320)
Q Consensus 260 ~QMEllghdF~vF~N--~eTg~vnVVYRRkDG~YGLIeP 296 (320)
.++.-+..+++++.+ ...|...||++.+++.+-+.+|
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 24
>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=32.87 E-value=35 Score=35.01 Aligned_cols=10 Identities=20% Similarity=0.102 Sum_probs=5.0
Q ss_pred ceEEEEEeee
Q 020905 98 SVKLIIQGKN 107 (320)
Q Consensus 98 ~MkI~ItgRn 107 (320)
.++|.|.+.+
T Consensus 225 yiniti~fi~ 234 (756)
T PF06933_consen 225 YINITIYFIN 234 (756)
T ss_pred EEEEEEEEEe
Confidence 3555555443
No 25
>PRK14128 iraD DNA replication/recombination/repair protein; Provisional
Probab=29.83 E-value=2.5e+02 Score=21.34 Aligned_cols=47 Identities=15% Similarity=0.131 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020905 113 TVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (320)
Q Consensus 113 aLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~ 163 (320)
.-+..|++.|..++.+|-+++..++|.+....+ ++-.|.++..|...
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 347788999999999999999998888764332 23446677777643
No 26
>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=27.81 E-value=98 Score=23.34 Aligned_cols=33 Identities=15% Similarity=0.105 Sum_probs=25.1
Q ss_pred CCHHHHHHHHhcCCCcEEEEeeCCCCceeEEEE
Q 020905 253 LTVSEAIEQLENVDHDFYGFRNEETGEINIVYK 285 (320)
Q Consensus 253 MsveEAV~QMEllghdF~vF~N~eTg~vnVVYR 285 (320)
++++||+.+|...++..++-.|.+..-+.+++.
T Consensus 10 ~~~~~~~~~~~~~~~~~~~V~~~~~~~~Giv~~ 42 (113)
T cd04623 10 ATVAEAAKLMAEKNIGAVVVVDDGGRLVGIFSE 42 (113)
T ss_pred CcHHHHHHHHHHcCCCeEEEECCCCCEEEEEeh
Confidence 689999999988888777777765445666765
No 27
>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=26.52 E-value=1.5e+02 Score=22.31 Aligned_cols=55 Identities=11% Similarity=0.046 Sum_probs=27.4
Q ss_pred CceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEEEeeccCHHHHHHHHHHHHHHHHH
Q 020905 132 LVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRAEEDAETVYASIDLVSSIIQRKLR 193 (320)
Q Consensus 132 ~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~~g~~IrAee~~~D~YaAID~A~dKLeRQLr 193 (320)
....+.+.|..+.- | ...|.|.+... +..++.....++.+..|....+.|...|.
T Consensus 11 ~~~~~~l~L~p~~L----G--~v~v~l~~~~~-~l~v~~~~~~~~~~~~L~~~~~~L~~~L~ 65 (85)
T PF02120_consen 11 GSWELSLQLDPPEL----G--SVEVKLRLQGG-NLSVQFTAENPETKELLRQNLPELKERLQ 65 (85)
T ss_dssp T--EEEE--SSGGG--------EEEEEEEETT-EEEEEEE--SSHHHHHHHHTHHHHHHHHH
T ss_pred CceEEEEEEccccc----C--cEEEEEEEeCC-EEEEEEEECCHHHHHHHHHHHHHHHHHHH
Confidence 34455555555442 1 13344444432 34667777777787777777776666665
No 28
>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=25.94 E-value=1.2e+02 Score=23.53 Aligned_cols=35 Identities=14% Similarity=0.052 Sum_probs=27.6
Q ss_pred CCCCHHHHHHHHhcCCCcEEEEeeCCCCceeEEEE
Q 020905 251 PPLTVSEAIEQLENVDHDFYGFRNEETGEINIVYK 285 (320)
Q Consensus 251 kPMsveEAV~QMEllghdF~vF~N~eTg~vnVVYR 285 (320)
.-+++.||+..|...++.+++..|.+..-+.+|.+
T Consensus 8 ~~~~l~~a~~~~~~~~~~~~~Vvd~~g~~~G~vt~ 42 (114)
T cd04619 8 VNATLQRAAKILGEPGIDLVVVCDPHGKLAGVLTK 42 (114)
T ss_pred CCCcHHHHHHHHHhcCCCEEEEECCCCCEEEEEeh
Confidence 45889999999988888998888875555666664
No 29
>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=25.47 E-value=1.8e+02 Score=23.13 Aligned_cols=39 Identities=13% Similarity=0.050 Sum_probs=30.5
Q ss_pred HHHhcCCCcEEEEeeC-CCCceeEEEEecCCcEEEEEeCC
Q 020905 260 EQLENVDHDFYGFRNE-ETGEINIVYKRKAGGYGVIIPKG 298 (320)
Q Consensus 260 ~QMEllghdF~vF~N~-eTg~vnVVYRRkDG~YGLIeP~~ 298 (320)
.+|.-+..+|+++.+. ..+...||++..++.+-+.+|..
T Consensus 69 ~~L~~~~lP~i~~~~~~~~~~~vvl~~~~~~~~~i~dp~~ 108 (129)
T cd02423 69 DKLNALQIPVIVLVNNGGYGHFVVIKGIDGDRVLVGDPAL 108 (129)
T ss_pred HHHhhCCCCEEEEEecCCCceEEEEEEEeCCEEEEECCCC
Confidence 3455667899999853 36799999998888888888854
No 30
>PF07218 RAP1: Rhoptry-associated protein 1 (RAP-1); InterPro: IPR009864 This family consists of several rhoptry-associated protein 1 (RAP-1) sequences which appear to be specific to Plasmodium falciparum [].
Probab=25.41 E-value=85 Score=33.52 Aligned_cols=15 Identities=20% Similarity=0.439 Sum_probs=8.6
Q ss_pred eccCCCCCHHHHHHH
Q 020905 247 FFEMPPLTVSEAIEQ 261 (320)
Q Consensus 247 ~~~lkPMsveEAV~Q 261 (320)
-.-|.|-++|+-+-+
T Consensus 460 fCLLnPktLE~fLKk 474 (782)
T PF07218_consen 460 FCLLNPKTLEKFLKK 474 (782)
T ss_pred eeecCHHHHHHHHhH
Confidence 344566666666544
No 31
>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=24.87 E-value=2.8e+02 Score=21.74 Aligned_cols=49 Identities=14% Similarity=0.161 Sum_probs=30.8
Q ss_pred cccCHHHHHHHHHHHHHHHhhhCC-CceEEEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020905 108 LELTDTVKNHVEEKVGKAVLKHSH-LVREVDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (320)
Q Consensus 108 velTdaLkeyIeeKl~K~L~Ky~d-~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~ 163 (320)
..+++..-+.+.+-|-.++.||.+ ....++|.++.+++ .-..+++|.++
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 346777778888888888999986 23445555554322 24566666554
No 32
>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=24.81 E-value=58 Score=27.95 Aligned_cols=45 Identities=38% Similarity=0.588 Sum_probs=30.5
Q ss_pred CCCcEEEEeeCCCCceeEEEEecCCcEEE-EEeC----CCCcccc-ccccccc
Q 020905 265 VDHDFYGFRNEETGEINIVYKRKAGGYGV-IIPK----GNGKAKK-LEPLEVE 311 (320)
Q Consensus 265 lghdF~vF~N~eTg~vnVVYRRkDG~YGL-IeP~----~~~~~~~-~~~~~~~ 311 (320)
+|++-|+|+|. ||++.|---.+.+ .|+ |.|. ..||.+| |.+..++
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 68999999997 9999998876666 443 4453 2266654 4444443
No 33
>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=24.54 E-value=78 Score=24.06 Aligned_cols=28 Identities=39% Similarity=0.547 Sum_probs=23.8
Q ss_pred HHHHHHHHhcCCCcEEEEeeCCCCceeE
Q 020905 255 VSEAIEQLENVDHDFYGFRNEETGEINI 282 (320)
Q Consensus 255 veEAV~QMEllghdF~vF~N~eTg~vnV 282 (320)
+.+|+.+|..-|--|-+.+|.+||++-|
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 34
>PRK15463 cold shock-like protein CspF; Provisional
Probab=23.67 E-value=95 Score=23.59 Aligned_cols=20 Identities=20% Similarity=0.260 Sum_probs=15.8
Q ss_pred eEEEEecCCcEEEEEeCCCC
Q 020905 281 NIVYKRKAGGYGVIIPKGNG 300 (320)
Q Consensus 281 nVVYRRkDG~YGLIeP~~~~ 300 (320)
.|.+--.+-+||.|+|..++
T Consensus 8 ~Vk~fn~~kGfGFI~~~~g~ 27 (70)
T PRK15463 8 IVKTFDGKSGKGLITPSDGR 27 (70)
T ss_pred EEEEEeCCCceEEEecCCCC
Confidence 45666778999999998664
No 35
>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=23.10 E-value=99 Score=31.78 Aligned_cols=59 Identities=22% Similarity=0.269 Sum_probs=32.8
Q ss_pred eeccCCCCCHHHHHHHH----hcCCCcEEEEeeCCCCceeEEEE----ecCCcEEEEEeCCCCccccc
Q 020905 246 KFFEMPPLTVSEAIEQL----ENVDHDFYGFRNEETGEINIVYK----RKAGGYGVIIPKGNGKAKKL 305 (320)
Q Consensus 246 K~~~lkPMsveEAV~QM----EllghdF~vF~N~eTg~vnVVYR----RkDG~YGLIeP~~~~~~~~~ 305 (320)
+.++-+.+|.|||-..+ +..+..--+-.|. .|+=-+.|- .+|..|-+..-..+|+-||+
T Consensus 366 R~ip~pkls~eeAr~~vnp~l~v~~~rLalIp~~-~~~EvLcYEF~G~~~~~~y~vYINA~tG~EE~I 432 (435)
T TIGR02889 366 RTLPKPKLTEEEARSKVNKHLKILSTRLAVIPNE-TNQEVLTYEFLGTYLGETFLVYINAETGYEEKI 432 (435)
T ss_pred ccCCCCcCCHHHHHHhhCCCceeccceeEEEECC-CCcEEEEEEEEEEeCCCEEEEEEECCCCCeeEE
Confidence 56777899999999874 3333333333332 333323332 45556666666666655544
No 36
>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=22.49 E-value=3.8e+02 Score=20.87 Aligned_cols=41 Identities=12% Similarity=0.190 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCcCCCCCceeEEEEEEEcCCCceEEE
Q 020905 113 TVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGEFGKGPRIRRCEVTLFTKKHGVVRA 170 (320)
Q Consensus 113 aLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~~g~~IrA 170 (320)
.+++|+++++.+ ..+. +|.+.... ..++|+|++..-+.+..
T Consensus 6 ~Ire~l~k~~~~------agis--~IeI~Rt~---------~~i~I~I~tarPg~vIG 46 (81)
T cd02413 6 ELNEFLTRELAE------DGYS--GVEVRVTP---------TRTEIIIRATRTQNVLG 46 (81)
T ss_pred HHHHHHHHHHHh------CCee--eEEEEEcC---------CeEEEEEEeCCCceEEC
Confidence 467777765544 2344 44444322 25889998864344444
No 37
>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=22.40 E-value=5.9e+02 Score=23.76 Aligned_cols=80 Identities=11% Similarity=0.160 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHHHHhhh----CCCceEEEEEEEeecCcCCCCCceeE-EEEEEEc-----CCCceEEEEeeccCHHHHHH
Q 020905 113 TVKNHVEEKVGKAVLKH----SHLVREVDVRLSVRGGEFGKGPRIRR-CEVTLFT-----KKHGVVRAEEDAETVYASID 182 (320)
Q Consensus 113 aLkeyIeeKl~K~L~Ky----~d~I~~a~V~Ls~e~~~~~kg~~~~~-vEVtV~~-----~~g~~IrAee~~~D~YaAID 182 (320)
.+++.+..||+. |.+. ++..+.-+|.|..-+. +|+..++ |-+..++ +.+..+.+=-.++|-|..|.
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 578888888888 6633 3333345677776543 3444444 3333333 23346778889999999999
Q ss_pred HHHHHHHHHHHHHH
Q 020905 183 LVSSIIQRKLRKIK 196 (320)
Q Consensus 183 ~A~dKLeRQLrK~K 196 (320)
..+..+-.||..++
T Consensus 209 ~~~~~v~~qln~L~ 222 (224)
T PF06918_consen 209 KYLGPVFEQLNNLT 222 (224)
T ss_pred HHHHHHHHHHhccc
Confidence 99999999987654
No 38
>PF02560 Cyanate_lyase: Cyanate lyase C-terminal domain; InterPro: IPR003712 Some bacteria can overcome the toxicity of environmental cyanate by hydrolysis of cyanate. This reaction is catalyzed by cyanate lyase (also known as cyanase) []. Cyanate lyase is found in bacteria and plants and catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. The cyanate lyase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer []. ; GO: 0008824 cyanate hydratase activity, 0009439 cyanate metabolic process; PDB: 2IV1_B 2IUO_A 2IVQ_B 1DW9_A 1DWK_E 2IVG_G 2IU7_J 2IVB_A.
Probab=22.12 E-value=1.3e+02 Score=23.44 Aligned_cols=41 Identities=24% Similarity=0.392 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHhhhCCCceE-EEEEEEeecCcCCCCCceeEEEEEEEc
Q 020905 112 DTVKNHVEEKVGKAVLKHSHLVRE-VDVRLSVRGGEFGKGPRIRRCEVTLFT 162 (320)
Q Consensus 112 daLkeyIeeKl~K~L~Ky~d~I~~-a~V~Ls~e~~~~~kg~~~~~vEVtV~~ 162 (320)
++||+-|+++++ |.|++ ++..+++++.. ++..-+|.||+..
T Consensus 24 ~~~K~li~E~FG-------DGIMSAIdF~~~v~k~~---d~~GdRv~it~~G 65 (73)
T PF02560_consen 24 PAIKALIHEKFG-------DGIMSAIDFKMDVEKVE---DPKGDRVVITMNG 65 (73)
T ss_dssp HHHHHHHHHHT--------SEEEEEEEEEEEEEEEE----TTSEEEEEEEEE
T ss_pred HHHHHHHHHhhC-------cceEEEeeEEEEEEEee---CCCCCEEEEEEec
Confidence 566777766664 45644 45555554432 2233588888874
No 39
>COG1539 FolB Dihydroneopterin aldolase [Coenzyme metabolism]
Probab=21.83 E-value=2e+02 Score=24.26 Aligned_cols=40 Identities=18% Similarity=0.388 Sum_probs=25.9
Q ss_pred EEeeecccCHHHHHHHHHHHHHHHhhhCCCceEEEEEEEeecCc
Q 020905 103 IQGKNLELTDTVKNHVEEKVGKAVLKHSHLVREVDVRLSVRGGE 146 (320)
Q Consensus 103 ItgRnvelTdaLkeyIeeKl~K~L~Ky~d~I~~a~V~Ls~e~~~ 146 (320)
|.|+++.+=+.+-+.|-+.+ +.+| +.+..++|.+++++.+
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 44555555555555444443 3455 8889999999998765
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=21.62 E-value=1.3e+02 Score=18.35 Aligned_cols=26 Identities=31% Similarity=0.316 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHhcCCCcEEEEeeCC
Q 020905 251 PPLTVSEAIEQLENVDHDFYGFRNEE 276 (320)
Q Consensus 251 kPMsveEAV~QMEllghdF~vF~N~e 276 (320)
.-+++.+++.+|..-++.+++..|.+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~v~~~~ 32 (49)
T smart00116 7 PDTTLEEALELLREHGIRRLPVVDEE 32 (49)
T ss_pred CCCcHHHHHHHHHHhCCCcccEECCC
Confidence 34688999999988888888777753
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=21.31 E-value=2.7e+02 Score=21.52 Aligned_cols=23 Identities=17% Similarity=0.060 Sum_probs=10.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHhH
Q 020905 176 TVYASIDLVSSIIQRKLRKIKEK 198 (320)
Q Consensus 176 D~YaAID~A~dKLeRQLrK~KeK 198 (320)
.+-..|-.|+....++.++...+
T Consensus 59 ~L~~~I~~A~n~A~~~a~~~~~~ 81 (93)
T PF02575_consen 59 ELEDLIVEAVNDAQKKAREKAQE 81 (93)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444554444444444333
No 42
>PLN03078 Putative tRNA pseudouridine synthase; Provisional
Probab=21.24 E-value=99 Score=32.54 Aligned_cols=16 Identities=19% Similarity=0.289 Sum_probs=12.4
Q ss_pred cCCCcceeeecCCCCC
Q 020905 82 HTKPLPVRMSWDGPLS 97 (320)
Q Consensus 82 ~~~~~~~~~~~~~~~~ 97 (320)
++..+.+++.|+|..+
T Consensus 69 ~krrvaL~IaYdGt~Y 84 (513)
T PLN03078 69 RKKKVVLRVGYVGTDY 84 (513)
T ss_pred cceEEEEEEEEcCCCc
Confidence 3456789999999876
No 43
>PRK00296 minE cell division topological specificity factor MinE; Reviewed
Probab=20.97 E-value=3.8e+02 Score=21.28 Aligned_cols=45 Identities=16% Similarity=0.169 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHhhhCC-CceEEEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020905 112 DTVKNHVEEKVGKAVLKHSH-LVREVDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (320)
Q Consensus 112 daLkeyIeeKl~K~L~Ky~d-~I~~a~V~Ls~e~~~~~kg~~~~~vEVtV~~~ 163 (320)
+.+-+.+.+-|-.++.||.+ ....++|.++.++ ....-|++|.+|
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 44556666666677888987 3345666665432 235678888776
No 44
>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=20.85 E-value=1.8e+02 Score=22.24 Aligned_cols=34 Identities=24% Similarity=0.261 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHHhcCCCcEEEEeeCCCCceeEEE
Q 020905 251 PPLTVSEAIEQLENVDHDFYGFRNEETGEINIVY 284 (320)
Q Consensus 251 kPMsveEAV~QMEllghdF~vF~N~eTg~vnVVY 284 (320)
.-+++.+|+..|...++.+++..|.+..-+.+|-
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~V~d~~~~~~G~v~ 41 (115)
T cd04593 8 ATTPLREAAEQLIESKHGSALVVDRDGGVVGIIT 41 (115)
T ss_pred CCCCHHHHHHHHHhCCCcEEEEEcCCCCEEEEEE
Confidence 4578999999998888888888876433344444
No 45
>cd00559 Cyanase_C Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain.
Probab=20.34 E-value=2.2e+02 Score=22.06 Aligned_cols=43 Identities=33% Similarity=0.369 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHHHHHHhhhCCCceE-EEEEEEeecCcCCCCCceeEEEEEEEcC
Q 020905 111 TDTVKNHVEEKVGKAVLKHSHLVRE-VDVRLSVRGGEFGKGPRIRRCEVTLFTK 163 (320)
Q Consensus 111 TdaLkeyIeeKl~K~L~Ky~d~I~~-a~V~Ls~e~~~~~kg~~~~~vEVtV~~~ 163 (320)
.+++|+-|.++++ |.|.+ ++..+++++.. ++..-+|.||+..+
T Consensus 19 G~~~K~li~E~FG-------DGIMSAIdF~~~v~k~~---dp~gdRvvit~~GK 62 (69)
T cd00559 19 GPTLKALIHEKFG-------DGIMSAIDFKLDVDKVE---DPGGDRVVITLDGK 62 (69)
T ss_pred hHHHHHHHHHHcC-------CceeeeEEeeeeEEecc---CCCCCEEEEEEcce
Confidence 4677887777765 45654 44555555432 22335788887643
Done!