Query 029220
Match_columns 197
No_of_seqs 75 out of 77
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 09:25:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029220.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029220hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03703 bPH_2: Bacterial PH d 98.9 4.1E-09 8.9E-14 71.6 5.3 69 110-179 4-80 (80)
2 PF14470 bPH_3: Bacterial PH d 97.4 0.00086 1.9E-08 47.1 7.5 68 111-181 25-96 (96)
3 COG3428 Predicted membrane pro 94.6 0.034 7.4E-07 53.6 3.6 95 87-185 47-148 (494)
4 PF08512 Rtt106: Histone chape 90.3 1.2 2.7E-05 33.2 6.2 54 128-182 28-88 (95)
5 PF08000 bPH_1: Bacterial PH d 90.2 2.8 6.1E-05 33.5 8.6 73 111-183 43-123 (124)
6 PF10882 bPH_5: Bacterial PH d 89.7 0.45 9.8E-06 34.4 3.5 34 110-146 1-34 (100)
7 COG3402 Uncharacterized conser 89.1 3.5 7.5E-05 35.2 8.7 74 104-180 71-151 (161)
8 PF06713 bPH_4: Bacterial PH d 87.7 4.5 9.7E-05 28.9 7.4 67 111-184 2-72 (74)
9 PF12462 Helicase_IV_N: DNA he 87.3 1.5 3.2E-05 35.9 5.3 56 111-171 19-75 (166)
10 PF10756 bPH_6: Bacterial PH d 80.1 5.4 0.00012 27.9 5.0 52 111-169 3-54 (73)
11 COG5554 NifU Nitrogen fixation 58.2 7.4 0.00016 29.2 1.9 24 148-172 31-54 (69)
12 PRK11054 helD DNA helicase IV; 58.1 26 0.00056 34.8 6.0 58 111-173 19-76 (684)
13 TIGR02186 alph_Pro_TM conserve 58.0 22 0.00047 32.1 5.1 38 93-130 5-50 (261)
14 PF12068 DUF3548: Domain of un 57.2 11 0.00024 32.8 3.0 33 131-164 114-146 (213)
15 PF13349 DUF4097: Domain of un 55.2 74 0.0016 24.1 6.9 74 90-168 8-82 (166)
16 PF14373 Imm_superinfect: Supe 54.6 9.3 0.0002 26.0 1.7 14 83-96 20-33 (43)
17 PF08608 Wyosine_form: Wyosine 51.3 11 0.00024 27.0 1.8 24 162-185 20-43 (62)
18 PRK00665 petG cytochrome b6-f 46.2 11 0.00024 25.5 1.0 29 87-115 4-32 (37)
19 PF02893 GRAM: GRAM domain; I 45.3 47 0.001 22.4 4.1 37 108-144 30-68 (69)
20 COG2511 GatE Archaeal Glu-tRNA 44.7 26 0.00056 35.3 3.7 38 143-180 216-254 (631)
21 cd01770 p47_UBX p47-like ubiqu 44.0 51 0.0011 24.0 4.3 30 154-183 7-38 (79)
22 PF01679 Pmp3: Proteolipid mem 42.7 21 0.00045 24.9 2.0 35 73-113 17-51 (51)
23 CHL00008 petG cytochrome b6/f 42.4 13 0.00029 25.1 1.0 30 87-116 4-33 (37)
24 PF02824 TGS: TGS domain; Int 40.8 45 0.00098 22.8 3.5 34 154-187 1-34 (60)
25 CHL00114 psbX photosystem II p 40.5 29 0.00063 23.6 2.4 24 79-102 3-26 (39)
26 PF03799 FtsQ: Cell division p 38.3 96 0.0021 21.9 5.0 44 135-184 58-101 (117)
27 PF07481 DUF1521: Domain of Un 35.5 29 0.00064 30.0 2.2 24 148-171 58-81 (171)
28 COG2268 Uncharacterized protei 35.1 2.2E+02 0.0047 28.6 8.3 32 154-185 93-130 (548)
29 smart00568 GRAM domain in gluc 35.1 73 0.0016 21.0 3.7 37 108-144 22-60 (61)
30 KOG4737 ATPase membrane sector 33.8 66 0.0014 30.2 4.4 37 83-120 280-324 (326)
31 PF00789 UBX: UBX domain; Int 32.3 1.3E+02 0.0028 20.8 4.8 33 154-186 9-43 (82)
32 cd01774 Faf1_like2_UBX Faf1 ik 30.4 1E+02 0.0022 22.8 4.2 29 154-182 7-37 (85)
33 PF11808 DUF3329: Domain of un 30.4 20 0.00042 26.7 0.3 23 144-183 63-85 (90)
34 PRK10879 proline aminopeptidas 29.5 66 0.0014 29.8 3.6 40 146-185 397-438 (438)
35 PLN00091 photosystem I reactio 28.5 34 0.00075 29.2 1.5 36 1-47 1-36 (160)
36 PF07787 DUF1625: Protein of u 28.3 59 0.0013 27.7 2.9 6 108-113 242-247 (248)
37 PF14317 YcxB: YcxB-like prote 27.6 84 0.0018 19.8 2.9 30 116-148 3-32 (62)
38 PF02529 PetG: Cytochrome B6-F 27.4 41 0.00089 22.8 1.4 28 86-113 3-30 (37)
39 PF09191 CD4-extracel: CD4, ex 27.0 92 0.002 25.3 3.6 53 106-162 42-99 (108)
40 PF03658 Ub-RnfH: RnfH family 26.9 29 0.00062 26.5 0.7 19 148-166 49-70 (84)
41 PF06173 DUF986: Protein of un 25.2 59 0.0013 27.4 2.3 44 132-181 102-147 (149)
42 TIGR00134 gatE_arch glutamyl-t 24.1 1E+02 0.0022 30.9 4.1 37 144-180 214-251 (620)
43 PRK04028 glutamyl-tRNA(Gln) am 22.9 97 0.0021 31.2 3.7 29 152-180 226-254 (630)
44 PF06385 Baculo_LEF-11: Baculo 22.8 86 0.0019 24.6 2.6 25 170-194 34-58 (94)
45 smart00683 DM16 Repeats in sea 22.8 2E+02 0.0044 20.5 4.3 33 111-143 22-54 (55)
46 COG0401 Uncharacterized homolo 21.4 1.3E+02 0.0028 22.0 3.1 35 73-113 20-55 (56)
47 PF10459 Peptidase_S46: Peptid 21.2 89 0.0019 31.6 3.1 36 116-151 148-186 (698)
48 PF00085 Thioredoxin: Thioredo 20.4 2.1E+02 0.0046 19.2 4.0 28 155-182 75-103 (103)
49 smart00166 UBX Domain present 20.4 3.2E+02 0.0068 19.2 5.0 30 154-183 7-38 (80)
No 1
>PF03703 bPH_2: Bacterial PH domain; InterPro: IPR005182 A domain that is found in uncharacterised family of membrane proteins. 1-3 copies found in each protein, with each copy flanked by transmembrane helices.
Probab=98.87 E-value=4.1e-09 Score=71.57 Aligned_cols=69 Identities=23% Similarity=0.376 Sum_probs=63.9
Q ss_pred eEeEEeeeEEEEeeccCCcccceeeeceeeeeEE----eeccccceeeEEEEecCCc----eEEeecccchHHHHHHH
Q 029220 110 LRYRFTNLRVTVISGWTGEDRSDFSYKVIKDVQV----VPRFIGDWGDIIITLKDGT----KVDLRSVPKFREIAKYC 179 (197)
Q Consensus 110 lRYrITnRRIsV~sGw~GrdrtdIvY~eI~dV~~----VpRG~G~WGDmVvtLkDGs----rLEmRslP~Frei~~yI 179 (197)
.+|.|||++|.+.+|+.++....+.|+.|.+|.. +-|.+|+ |++.+...+|+ .+.++++|++++++++|
T Consensus 4 ~~y~i~~~~l~i~~G~~~~~~~~i~~~~Iq~v~~~q~~~~r~~g~-~~i~i~~~~~~~~~~~i~~~~~~~a~~i~~~i 80 (80)
T PF03703_consen 4 TGYTITDDRLIIRSGLFSKRTTIIPLDRIQSVSIKQNPLQRLFGL-GTIKIDTAGGSGEKIEIPFLSIEDAEEIYDWI 80 (80)
T ss_pred EEEEEECCEEEEEECeEEEEEEEEEhhHeEEEEEEcCHHHHhCcc-EEEEEEECCCCCceeEEecCCHHHHHHHHhhC
Confidence 4799999999999999999999999999999999 4477888 99999999999 69999999999999875
No 2
>PF14470 bPH_3: Bacterial PH domain
Probab=97.45 E-value=0.00086 Score=47.15 Aligned_cols=68 Identities=24% Similarity=0.329 Sum_probs=54.4
Q ss_pred EeEEeeeEEEEeecc--CCcccceeeeceeeeeEEeeccccceeeEEEEecCCceEEeeccc--chHHHHHHHHh
Q 029220 111 RYRFTNLRVTVISGW--TGEDRSDFSYKVIKDVQVVPRFIGDWGDIIITLKDGTKVDLRSVP--KFREIAKYCVS 181 (197)
Q Consensus 111 RYrITnRRIsV~sGw--~GrdrtdIvY~eI~dV~~VpRG~G~WGDmVvtLkDGsrLEmRslP--~Frei~~yI~~ 181 (197)
-+-+||+||-..+-- .+.+..+|.|++|.+|..- .|+.. +.+.+.. +|.++++.+++ +.+++++||++
T Consensus 25 ~l~~TnkRlif~~~~~~~~~~~~~i~y~~I~~v~~~-~g~~~-~~i~i~~-~~~~~~i~~i~k~~~~~~~~~i~~ 96 (96)
T PF14470_consen 25 VLVLTNKRLIFYSKGMFGGKKFESIPYDDITSVSFK-KGILG-GKITIET-NGEKIKIDNIQKGDVKEFYEYIKE 96 (96)
T ss_pred EEEEeCCEEEEEEcccCCCceEEEEEhhheEEEEEE-ccccc-cEEEEEE-CCEEEEEEEcCHHHHHHHHHHHhC
Confidence 467999999887554 3788999999999999995 67644 7788888 99999999886 46677777653
No 3
>COG3428 Predicted membrane protein [Function unknown]
Probab=94.57 E-value=0.034 Score=53.60 Aligned_cols=95 Identities=18% Similarity=0.221 Sum_probs=63.4
Q ss_pred HHHHHhHHHHHHHHHHHHhHhceeEeEEeeeEEEEeeccCCcccceeeeceeeeeEE----eeccccceeeEEEEec-CC
Q 029220 87 NLLLGFTLFWLPLTLAAVSRAFNLRYRFTNLRVTVISGWTGEDRSDFSYKVIKDVQV----VPRFIGDWGDIIITLK-DG 161 (197)
Q Consensus 87 nlllg~TlI~lPltiaAi~RalWlRYrITnRRIsV~sGw~GrdrtdIvY~eI~dV~~----VpRG~G~WGDmVvtLk-DG 161 (197)
-+++++++||+.+. +.+=.-.+|||+|.-+.+..|..-|++..|.|++|..|.+ +-|-||+ -++=|.+. ||
T Consensus 47 ~~~~vv~vi~~i~~---ii~w~~~~Yried~~~~l~~Gi~~rk~r~i~~~RIQsVd~t~~lv~rlfgl-~~l~IeTaGg~ 122 (494)
T COG3428 47 GAALVVLVIFLILQ---IIKWITFTYRIEDEEVRLQTGIFSRKKRYIPIDRIQSVDTTAGLVARLFGL-VVLRIETAGGG 122 (494)
T ss_pred eehhhHHHHHHHHh---hhEEEEEEEEEecceEEEEeeEEeecceecchHhhhhhHHHHHHHHHhhcc-EEEEEEcCCCC
Confidence 34667778887776 4443347999999999999999999999999999999988 3444677 45555555 22
Q ss_pred --ceEEeecccchHHHHHHHHhhhcC
Q 029220 162 --TKVDLRSVPKFREIAKYCVSMAEQ 185 (197)
Q Consensus 162 --srLEmRslP~Frei~~yI~~~~e~ 185 (197)
+..|+-+.+==.+.....+|..-+
T Consensus 123 ~eae~~~~~~~i~~~~~~~~~e~~~k 148 (494)
T COG3428 123 GEAEAELVEREIAFELAALVREARVK 148 (494)
T ss_pred CccceeeehhhhhHHHHHHHHHhhcc
Confidence 344443333333334444444433
No 4
>PF08512 Rtt106: Histone chaperone Rttp106-like; InterPro: IPR013719 This is a domain of unknown function that is associated with a number of different protein families. It is found in Rtt106p, which is a histone chaperone involved in heterochromatin-mediated silencing []. It is also found in genes annotated as transcription factors/regulators. This domain is the C-terminal domain of yeast Spt16p P32558 from SWISSPROT, which is a subunit of the heterodimeric yeast FACT complex (Spt16p-Pob3p, IPR000969 from INTERPRO) []. In addition Spt16p and its relatives, in this entry, are described as non-peptidase homologues belonging to the MEROPS peptidase family M24. The FACT complex facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [, ]. ; PDB: 3TW1_A 3GYO_A 3TO1_A 3FSS_A 3TVV_B 3GYP_A 2GCJ_D 2GCL_A.
Probab=90.25 E-value=1.2 Score=33.18 Aligned_cols=54 Identities=19% Similarity=0.306 Sum_probs=40.0
Q ss_pred cccceeeeceeeeeEEeecc---ccceeeEEEEecC--CceEEeecccc--hHHHHHHHHhh
Q 029220 128 EDRSDFSYKVIKDVQVVPRF---IGDWGDIIITLKD--GTKVDLRSVPK--FREIAKYCVSM 182 (197)
Q Consensus 128 rdrtdIvY~eI~dV~~VpRG---~G~WGDmVvtLkD--GsrLEmRslP~--Frei~~yI~~~ 182 (197)
|--.=|.|+||..|..- |- -+..=||++++|| |..+++.++|+ +..+.+|+.++
T Consensus 28 kP~~~i~~~dI~~v~fe-Rv~~~~~ktFDl~v~~k~~~~~~~~fs~I~~~e~~~l~~~l~~~ 88 (95)
T PF08512_consen 28 KPPFVIPLDDIESVEFE-RVSSFSSKTFDLVVILKDYEGPPHEFSSIDREEYDNLKDFLKSK 88 (95)
T ss_dssp SS-EEEEGGGEEEEEEE---ESSSSSEEEEEEEETT-TS-EEEEEEEEGGGHHHHHHHHHHC
T ss_pred CCeEEEEhhHeeEEEEE-ecccCcceEEEEEEEEecCCCCcEEEeeECHHHHHHHHHHHHHC
Confidence 45566889999888873 53 2444699999999 88999999885 78888998764
No 5
>PF08000 bPH_1: Bacterial PH domain; InterPro: IPR012544 This family contains many bacterial hypothetical proteins.; PDB: 3DCX_E 3HSA_C 3B77_D.
Probab=90.20 E-value=2.8 Score=33.50 Aligned_cols=73 Identities=19% Similarity=0.274 Sum_probs=54.3
Q ss_pred EeEEeeeEEEEee--ccCCccc--ceeeeceeeeeEEeeccccce-eeEEEEecCCc-eE--EeecccchHHHHHHHHhh
Q 029220 111 RYRFTNLRVTVIS--GWTGEDR--SDFSYKVIKDVQVVPRFIGDW-GDIIITLKDGT-KV--DLRSVPKFREIAKYCVSM 182 (197)
Q Consensus 111 RYrITnRRIsV~s--Gw~Grdr--tdIvY~eI~dV~~VpRG~G~W-GDmVvtLkDGs-rL--EmRslP~Frei~~yI~~~ 182 (197)
-+-||||||-..- |.+|+.+ ..|+|+.|..+..-.=|.... .++=+....+. .+ |++.--+.+++++.+.++
T Consensus 43 ~~vFTnkRlI~vD~QG~TGkK~~~~siPY~~I~~~siETAG~~DlD~Elki~i~~~~~~i~~~f~k~~di~~i~k~L~~~ 122 (124)
T PF08000_consen 43 EIVFTNKRLILVDKQGITGKKVEYKSIPYSSITHFSIETAGTFDLDSELKIWISGQGFPIEFEFKKKTDIYEIYKALAEY 122 (124)
T ss_dssp EEEEESSEEEEEEEESSSSSEEEEEEEEGGGEEEEEEEECSSTTSEEEEEEEETTESSEEEEEEGTTSHHHHHHHHHHHH
T ss_pred eEEEecChheEEecccCccceEEEEEEehhhccEEEEEeCCcccCcccEEEEECCCcEEEEEecCCCCCHHHHHHHHHHH
Confidence 3569999987665 7888654 589999999999977776543 56666666544 34 488888888888888776
Q ss_pred h
Q 029220 183 A 183 (197)
Q Consensus 183 ~ 183 (197)
+
T Consensus 123 v 123 (124)
T PF08000_consen 123 V 123 (124)
T ss_dssp H
T ss_pred h
Confidence 4
No 6
>PF10882 bPH_5: Bacterial PH domain; InterPro: IPR020482 This entry contains membrane proteins with no known function.
Probab=89.75 E-value=0.45 Score=34.41 Aligned_cols=34 Identities=18% Similarity=0.283 Sum_probs=28.2
Q ss_pred eEeEEeeeEEEEeeccCCcccceeeeceeeeeEEeec
Q 029220 110 LRYRFTNLRVTVISGWTGEDRSDFSYKVIKDVQVVPR 146 (197)
Q Consensus 110 lRYrITnRRIsV~sGw~GrdrtdIvY~eI~dV~~VpR 146 (197)
|+|.+++..|.|..++. +..|.|++|.+|.....
T Consensus 1 l~y~v~~~~l~I~~~~~---~~~Ip~~~I~~v~~~~~ 34 (100)
T PF10882_consen 1 LRYEVDDDGLIIRWPFG---KITIPLAEIESVELVDD 34 (100)
T ss_pred CEEEEECCEEEEEEccc---cEEEEHHHcEEEEeccc
Confidence 68999999999966654 78899999999987543
No 7
>COG3402 Uncharacterized conserved protein [Function unknown]
Probab=89.09 E-value=3.5 Score=35.17 Aligned_cols=74 Identities=14% Similarity=0.175 Sum_probs=55.2
Q ss_pred HhHhceeEeEEeeeEEEEeeccCCcccceeeeceeeeeEEeecc-----ccceeeEEEEecCCceEEeeccc--chHHHH
Q 029220 104 VSRAFNLRYRFTNLRVTVISGWTGEDRSDFSYKVIKDVQVVPRF-----IGDWGDIIITLKDGTKVDLRSVP--KFREIA 176 (197)
Q Consensus 104 i~RalWlRYrITnRRIsV~sGw~GrdrtdIvY~eI~dV~~VpRG-----~G~WGDmVvtLkDGsrLEmRslP--~Frei~ 176 (197)
++|-.=-||.|-..-+-+..||+=++|+=|+|..|.-|-+ .|| +|+ +.+.|++..+ ..++.+++ .=.++-
T Consensus 71 ~~Ryr~wry~v~~~el~iq~GiLv~~r~viP~~RVQhVDt-~~GPL~R~~~L-a~vti~TAss-~~~IeaL~~~eAdrlr 147 (161)
T COG3402 71 LVRYRVWRYEVEEDELDIQHGILVRTRTVIPYVRVQHVDT-EQGPLLRRYGL-ATVTITTASS-DHTIEALDREEADRLR 147 (161)
T ss_pred HHhhhhheeecccceEEeeccEEEEEEEEeeEEEEEeeec-ccChHHHHhCc-ceEEEEeccc-cceecccCHHHHHHHH
Confidence 3443334899988999999999999999999999999887 466 898 9999998866 45555554 333444
Q ss_pred HHHH
Q 029220 177 KYCV 180 (197)
Q Consensus 177 ~yI~ 180 (197)
+.|.
T Consensus 148 ~~l~ 151 (161)
T COG3402 148 ERLA 151 (161)
T ss_pred HHHH
Confidence 4443
No 8
>PF06713 bPH_4: Bacterial PH domain; InterPro: IPR009589 This entry is represented by Bacteriophage SP-beta, YolF. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical proteins specific to Oceanobacillus and Bacillus species. Members of this family are typically around 130 residues in length. The function of this family is unknown.
Probab=87.72 E-value=4.5 Score=28.90 Aligned_cols=67 Identities=10% Similarity=0.172 Sum_probs=42.1
Q ss_pred EeEEeeeEEEEeeccCCcccceeeeceeeeeEEee----ccccceeeEEEEecCCceEEeecccchHHHHHHHHhhhc
Q 029220 111 RYRFTNLRVTVISGWTGEDRSDFSYKVIKDVQVVP----RFIGDWGDIIITLKDGTKVDLRSVPKFREIAKYCVSMAE 184 (197)
Q Consensus 111 RYrITnRRIsV~sGw~GrdrtdIvY~eI~dV~~Vp----RG~G~WGDmVvtLkDGsrLEmRslP~Frei~~yI~~~~e 184 (197)
+|.|+|..+.|..|+. +.+ |.|.+|++|+... +-.+.---+.|..+++.. -+- -|+ +-++||.+..+
T Consensus 2 ~Y~i~~~~L~I~~G~~-~~~--I~i~~I~~I~~~~~~~~~~a~S~~rl~I~y~~~~~-i~I-sP~--~~~~FI~~L~k 72 (74)
T PF06713_consen 2 KYIIEDDYLIIKCGFF-KKK--IPIEDIRSIRPTKNPLSSPALSLDRLEIYYGKYKS-ILI-SPK--DKEEFIAELQK 72 (74)
T ss_pred EEEEeCCEEEEEECCc-ccE--EEhHHccEEEecCCccccccccccEEEEEECCCCE-EEE-ECC--CHHHHHHHHHh
Confidence 7999999999999944 444 9999999999862 122222344455443333 222 243 44566665543
No 9
>PF12462 Helicase_IV_N: DNA helicase IV / RNA helicase N terminal; InterPro: IPR022161 This domain family is found in bacteria and eukaryotes, and is approximately 170 amino acids in length. The family is found in association with PF00580 from PFAM. Nucleolin unwinds nucleic acid strands in the 5' to 3' direction with respect to the bound strand. It can unwind RNA-RNA duplexes, as well as DNA-DNA and DNA-RNA duplexes. Nucleolin is modulated by phosphorylation of serine and threonine residues in its N-terminal region.
Probab=87.28 E-value=1.5 Score=35.91 Aligned_cols=56 Identities=23% Similarity=0.399 Sum_probs=48.0
Q ss_pred EeEEeeeEEEEeeccCCcccceeeeceee-eeEEeeccccceeeEEEEecCCceEEeecccc
Q 029220 111 RYRFTNLRVTVISGWTGEDRSDFSYKVIK-DVQVVPRFIGDWGDIIITLKDGTKVDLRSVPK 171 (197)
Q Consensus 111 RYrITnRRIsV~sGw~GrdrtdIvY~eI~-dV~~VpRG~G~WGDmVvtLkDGsrLEmRslP~ 171 (197)
+-++-|-.|.|.++ +....|.++++. .|++ .||+ .||.+.+++.|+.-+-|+++|.
T Consensus 19 ~v~L~~~~l~ls~~---~~~~~Ipf~~~~g~i~~-krGl-~Wg~L~f~~~~~~~v~l~Gl~w 75 (166)
T PF12462_consen 19 RVELDNAGLELSSD---GHEYRIPFNQLSGSIQV-KRGL-FWGELEFFLPDQKVVRLHGLPW 75 (166)
T ss_pred eEEEcCCEEEEEeC---CeEEEecHHHhccceee-ecce-eEEEEEEEcCCCcEEEEcCCcc
Confidence 55677788877776 777889999999 6665 7999 8999999999999999999996
No 10
>PF10756 bPH_6: Bacterial PH domain; InterPro: IPR019692 Proteins in this entry are conserved in the Actinomycetales. Although several members are annotated as RbiX homologues, RbiX being a putative regulator of riboflavin biosynthesis, the function could not be confirmed. This entry also includes low molecular weight protein antigen 6.
Probab=80.13 E-value=5.4 Score=27.87 Aligned_cols=52 Identities=23% Similarity=0.327 Sum_probs=40.8
Q ss_pred EeEEeeeEEEEeeccCCcccceeeeceeeeeEEeeccccceeeEEEEecCCceEEeecc
Q 029220 111 RYRFTNLRVTVISGWTGEDRSDFSYKVIKDVQVVPRFIGDWGDIIITLKDGTKVDLRSV 169 (197)
Q Consensus 111 RYrITnRRIsV~sGw~GrdrtdIvY~eI~dV~~VpRG~G~WGDmVvtLkDGsrLEmRsl 169 (197)
|-.+++..|.|.+.+ .+..+.++||.+|+. +.-+-| +.+.+.||..+-|.++
T Consensus 3 rv~v~~~Gl~vr~~~---rt~~vpW~~I~~v~~--~~~~~~--v~~~~~dg~~~~l~~~ 54 (73)
T PF10756_consen 3 RVEVDPDGLRVRNLF---RTRRVPWSEIAGVRF--RRGRRW--VRLDLRDGRLVPLPAV 54 (73)
T ss_pred eEEEcCCcEEEEcCc---eeEEEChHHeEEEEc--cCCceE--EEEECCCCCEEEEeeE
Confidence 456788889999887 466799999999995 233445 8999999998877654
No 11
>COG5554 NifU Nitrogen fixation protein [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=58.22 E-value=7.4 Score=29.16 Aligned_cols=24 Identities=29% Similarity=0.609 Sum_probs=20.3
Q ss_pred ccceeeEEEEecCCceEEeecccch
Q 029220 148 IGDWGDIIITLKDGTKVDLRSVPKF 172 (197)
Q Consensus 148 ~G~WGDmVvtLkDGsrLEmRslP~F 172 (197)
--+||--++ |+||=|||++.+|+-
T Consensus 31 edlwGG~il-L~NGWrL~lp~lP~d 54 (69)
T COG5554 31 EDLWGGKIL-LANGWRLELPELPDD 54 (69)
T ss_pred cccccceEE-eccceEEEcccCCCc
Confidence 457887776 999999999999974
No 12
>PRK11054 helD DNA helicase IV; Provisional
Probab=58.13 E-value=26 Score=34.79 Aligned_cols=58 Identities=19% Similarity=0.238 Sum_probs=49.5
Q ss_pred EeEEeeeEEEEeeccCCcccceeeeceeeeeEEeeccccceeeEEEEecCCceEEeecccchH
Q 029220 111 RYRFTNLRVTVISGWTGEDRSDFSYKVIKDVQVVPRFIGDWGDIIITLKDGTKVDLRSVPKFR 173 (197)
Q Consensus 111 RYrITnRRIsV~sGw~GrdrtdIvY~eI~dV~~VpRG~G~WGDmVvtLkDGsrLEmRslP~Fr 173 (197)
+-++.+-.|.|.+. +...-|.+.++.. ..+.||+ .||.+.+.+.|+..+.++++|...
T Consensus 19 ~~~l~~~~~~~~~~---~~~~~i~~~~~~~-~~~~~g~-~~~~l~~~~~~~~~~~~~g~~~~~ 76 (684)
T PRK11054 19 RVELLNAGVKVSGD---KHEYLIPFNQLLA-IHCKRGL-VWGELEFVLPDQKVVRLHGTEWQE 76 (684)
T ss_pred eEEEeCCEEEEecC---CeEEEeehhhccc-eEEEecc-EEEEEEEEECCCcEEEEcCCChHH
Confidence 56788888888776 6777899999999 6678998 899999999998888999999754
No 13
>TIGR02186 alph_Pro_TM conserved hypothetical protein. This family consists of predicted transmembrane proteins of about 270 amino acids. Members are found, so far, only among the Alphaproteobacteria and only once in each genome.
Probab=58.01 E-value=22 Score=32.07 Aligned_cols=38 Identities=21% Similarity=0.273 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhHhce--------eEeEEeeeEEEEeeccCCccc
Q 029220 93 TLFWLPLTLAAVSRAFN--------LRYRFTNLRVTVISGWTGEDR 130 (197)
Q Consensus 93 TlI~lPltiaAi~RalW--------lRYrITnRRIsV~sGw~Grdr 130 (197)
-.+|+.+.+++..+-.| +---.++.||.|++++.|.|-
T Consensus 5 l~~~~~~~~~~~~~~~~~~~~~~e~lv~~lS~~~V~Its~F~G~el 50 (261)
T TIGR02186 5 LAIVLVLLLGAAATVAQAQNPAAERLEIGVSTEEIAITSNFRGADL 50 (261)
T ss_pred HHHHHHHHhcCcccccccccccCCCEEEEccCceEEEecCccCcEE
Confidence 35667777777777666 788899999999999999764
No 14
>PF12068 DUF3548: Domain of unknown function (DUF3548); InterPro: IPR021935 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes and is typically between 184 to 216 amino acids in length. The domain is found associated with PF00566 from PFAM and at the N terminus of GYP7 proteins.
Probab=57.16 E-value=11 Score=32.75 Aligned_cols=33 Identities=27% Similarity=0.488 Sum_probs=27.5
Q ss_pred ceeeeceeeeeEEeeccccceeeEEEEecCCceE
Q 029220 131 SDFSYKVIKDVQVVPRFIGDWGDIIITLKDGTKV 164 (197)
Q Consensus 131 tdIvY~eI~dV~~VpRG~G~WGDmVvtLkDGsrL 164 (197)
--|..+||+.|+.-+.++|-|= ||+++|||..+
T Consensus 114 Fsv~lsdl~Si~~~~p~~G~~~-lv~~~kdG~~~ 146 (213)
T PF12068_consen 114 FSVPLSDLKSIRVSKPSLGWWY-LVFILKDGTSL 146 (213)
T ss_pred EEEEhhheeeEEecCCCCCceE-EEEEecCCCcc
Confidence 3467889999999999998654 99999999754
No 15
>PF13349 DUF4097: Domain of unknown function (DUF4097)
Probab=55.21 E-value=74 Score=24.08 Aligned_cols=74 Identities=18% Similarity=0.153 Sum_probs=36.7
Q ss_pred HHhHHHHHHHHHHHHhHhceeEeEEeeeEEEEeeccCCcccceeee-ceeeeeEEeeccccceeeEEEEecCCceEEeec
Q 029220 90 LGFTLFWLPLTLAAVSRAFNLRYRFTNLRVTVISGWTGEDRSDFSY-KVIKDVQVVPRFIGDWGDIIITLKDGTKVDLRS 168 (197)
Q Consensus 90 lg~TlI~lPltiaAi~RalWlRYrITnRRIsV~sGw~GrdrtdIvY-~eI~dV~~VpRG~G~WGDmVvtLkDGsrLEmRs 168 (197)
+.+.++|+.++++++.-.---.+.+ ++.-.+...+.-.+..+..| .+|+++.. -.+. ||+.|.--|+.++++..
T Consensus 8 ~~l~viG~il~~~g~~~~~~~~~~~-~~~~~i~~~~~~~~~~~~~~~~~i~~i~i---~~~~-~~V~I~~~~~~~i~v~~ 82 (166)
T PF13349_consen 8 LILIVIGIILIGIGFFSGGFKSINF-DNGSPIENKETNEKTYEKSFKENIKKIDI---DTDN-GDVEIKPSDDDKIKVEY 82 (166)
T ss_pred HHHHHHHHHHHHHHHhhCCcceeEe-cCCcccccccccceeeeeeccCCCCEEEE---EcCc-eeEEEEEcCCccEEEEE
Confidence 3445666665555443333111111 22223333332233344554 77777766 1222 77777777777776665
No 16
>PF14373 Imm_superinfect: Superinfection immunity protein
Probab=54.63 E-value=9.3 Score=26.02 Aligned_cols=14 Identities=50% Similarity=0.527 Sum_probs=11.9
Q ss_pred hHHHHHHHHhHHHH
Q 029220 83 DLLANLLLGFTLFW 96 (197)
Q Consensus 83 DLI~nlllg~TlI~ 96 (197)
=+++|+++|+|+||
T Consensus 20 I~~~Nl~lGWT~iG 33 (43)
T PF14373_consen 20 IFLLNLLLGWTGIG 33 (43)
T ss_pred hHhHHHHHHhHHHH
Confidence 35899999999885
No 17
>PF08608 Wyosine_form: Wyosine base formation; InterPro: IPR013917 The proteins in this entry appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that it participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW []. ; PDB: 2YX0_A 2Z2U_A.
Probab=51.29 E-value=11 Score=26.97 Aligned_cols=24 Identities=17% Similarity=0.429 Sum_probs=16.6
Q ss_pred ceEEeecccchHHHHHHHHhhhcC
Q 029220 162 TKVDLRSVPKFREIAKYCVSMAEQ 185 (197)
Q Consensus 162 srLEmRslP~Frei~~yI~~~~e~ 185 (197)
.||.|-.+|...|+.+|+++.++.
T Consensus 20 ~rLt~~nmp~h~eV~~F~~~l~~~ 43 (62)
T PF08608_consen 20 NRLTMGNMPWHEEVLDFAEELAEL 43 (62)
T ss_dssp ----GGGS--HHHHHHHHHHHHTT
T ss_pred CccccCCCCcHHHHHHHHHHHHhh
Confidence 579999999999999999988875
No 18
>PRK00665 petG cytochrome b6-f complex subunit PetG; Reviewed
Probab=46.18 E-value=11 Score=25.47 Aligned_cols=29 Identities=34% Similarity=0.359 Sum_probs=23.6
Q ss_pred HHHHHhHHHHHHHHHHHHhHhceeEeEEe
Q 029220 87 NLLLGFTLFWLPLTLAAVSRAFNLRYRFT 115 (197)
Q Consensus 87 nlllg~TlI~lPltiaAi~RalWlRYrIT 115 (197)
++|+|+-+=.+|.|++.+.=+.|+.||=-
T Consensus 4 plL~GiVLGlipiTl~GlfvaAylQYrRg 32 (37)
T PRK00665 4 PLLCGIVLGLIPVTLAGLFVAAWNQYKRG 32 (37)
T ss_pred hhhhhHHHHhHHHHHHHHHHHHHHHHhcc
Confidence 56778877788999999888999999743
No 19
>PF02893 GRAM: GRAM domain; InterPro: IPR004182 The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. It is normally about 70 amino acids in length. It is thought to be an intracellular protein-binding or lipid-binding signalling domain, which has an important function in membrane-associated processes. Mutations in the GRAM domain of myotubularins cause a muscle disease, which suggests that the domain is essential for the full function of the enzyme []. Myotubularin-related proteins are a large subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids [].; PDB: 1M7R_B 1LW3_A 1ZVR_A 1ZSQ_A.
Probab=45.32 E-value=47 Score=22.44 Aligned_cols=37 Identities=19% Similarity=0.103 Sum_probs=30.1
Q ss_pred ceeEeEEeeeEEEEeeccCCcc--cceeeeceeeeeEEe
Q 029220 108 FNLRYRFTNLRVTVISGWTGED--RSDFSYKVIKDVQVV 144 (197)
Q Consensus 108 lWlRYrITnRRIsV~sGw~Grd--rtdIvY~eI~dV~~V 144 (197)
..-+--||+.||.-.+-..+.. +..|.+++|.+|...
T Consensus 30 ~~G~LyiT~~~lcF~s~~~~~~~~~~~ipl~~I~~i~k~ 68 (69)
T PF02893_consen 30 VQGRLYITNNYLCFYSNKFGSKTCKFVIPLSDIKSIEKE 68 (69)
T ss_dssp EEEEEEEESSEEEEEESSSSS-E-EEEEEGGGEEEEEEE
T ss_pred eeeEEEECCCEEEEEECCCCCceEEEEEEhHheeEEEEe
Confidence 4567789999999999776654 699999999999764
No 20
>COG2511 GatE Archaeal Glu-tRNAGln amidotransferase subunit E (contains GAD domain) [Translation, ribosomal structure and biogenesis]
Probab=44.68 E-value=26 Score=35.33 Aligned_cols=38 Identities=24% Similarity=0.433 Sum_probs=32.0
Q ss_pred Eeeccccce-eeEEEEecCCceEEeecccchHHHHHHHH
Q 029220 143 VVPRFIGDW-GDIIITLKDGTKVDLRSVPKFREIAKYCV 180 (197)
Q Consensus 143 ~VpRG~G~W-GDmVvtLkDGsrLEmRslP~Frei~~yI~ 180 (197)
.|.||+|.- -|+-+-.+||+|+|+.++++.--|-+-++
T Consensus 216 kvKrglgTIRQDvNvSI~~GarvEIKGVq~LdlI~~vv~ 254 (631)
T COG2511 216 KVKRGLGTIRQDVNVSIKGGARVEIKGVQDLDLIPDVVE 254 (631)
T ss_pred cccccCcceeeeeeeeecCCceEEecCcchhhhHHHHHH
Confidence 378999876 79999999999999999998876655544
No 21
>cd01770 p47_UBX p47-like ubiquitin domain. p47_UBX p47 is an adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is to regulate membrane fusion events. Mono-ubiquitin recognition by p47 is crucial for p97-p47-mediated Golgi membrane fusion events. p47 has carboxy-terminal SEP and UBX domains. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=43.96 E-value=51 Score=23.95 Aligned_cols=30 Identities=20% Similarity=0.366 Sum_probs=23.1
Q ss_pred EEEEecCCceEEeecc--cchHHHHHHHHhhh
Q 029220 154 IIITLKDGTKVDLRSV--PKFREIAKYCVSMA 183 (197)
Q Consensus 154 mVvtLkDGsrLEmRsl--P~Frei~~yI~~~~ 183 (197)
+.|-|.||+|++-|=- -..+++++||..+.
T Consensus 7 iqiRlpdG~r~~~rF~~~~tv~~l~~~v~~~~ 38 (79)
T cd01770 7 IQIRLADGKRLVQKFNSSHRVSDVRDFIVNAR 38 (79)
T ss_pred EEEECCCCCEEEEEeCCCCcHHHHHHHHHHhC
Confidence 5677889999976533 46789999999765
No 22
>PF01679 Pmp3: Proteolipid membrane potential modulator; InterPro: IPR000612 Proteolipid membrane potential modulator is an evolutionarily conserved proteolipid in the plasma membrane which, in S. pombe, is transcriptionally regulated by the Spc1 stress MAPK (mitogen-activated protein kinases) pathway. It functions to modulate the membrane potential, particularly to resist high cellular cation concentration. In eukaryotic organisms, stress-activated mitogen-activated protein kinases play crucial roles in transmitting environmental signals that will regulate gene expression for allowing the cell to adapt to cellular stress. Pmp3-like proteins are highly conserved in bacteria, yeast, nematode and plants. Proteins in this entry include the PMP3 as well as several other proteins that have been shown [] to be evolutionary related. These are small proteins of from 52 to 140 amino-acid resiudes that contain two transmembrane domains and belong to the UPF0057 (PMP3) protein family.; GO: 0016021 integral to membrane
Probab=42.67 E-value=21 Score=24.86 Aligned_cols=35 Identities=37% Similarity=0.679 Sum_probs=22.8
Q ss_pred EEeeCCCCchhHHHHHHHHhHHHHHHHHHHHHhHhceeEeE
Q 029220 73 VFFDGGAHYGDLLANLLLGFTLFWLPLTLAAVSRAFNLRYR 113 (197)
Q Consensus 73 VfyEGgPh~gDLI~nlllg~TlI~lPltiaAi~RalWlRYr 113 (197)
|+...| -.+|+.+|+++-+ +-|+|-.+ =|+|+-|+
T Consensus 17 V~~~~g-~~~~~~inl~Ltl-~g~iPg~i----hA~y~i~~ 51 (51)
T PF01679_consen 17 VFLKKG-CSKDFWINLLLTL-LGWIPGVI----HALYVIYK 51 (51)
T ss_pred HHHHcC-CchhhHHHHHHHH-HHHHHHHH----HeeEEEeC
Confidence 344455 7889999998732 34677444 56787663
No 23
>CHL00008 petG cytochrome b6/f complex subunit V
Probab=42.40 E-value=13 Score=25.06 Aligned_cols=30 Identities=37% Similarity=0.511 Sum_probs=23.7
Q ss_pred HHHHHhHHHHHHHHHHHHhHhceeEeEEee
Q 029220 87 NLLLGFTLFWLPLTLAAVSRAFNLRYRFTN 116 (197)
Q Consensus 87 nlllg~TlI~lPltiaAi~RalWlRYrITn 116 (197)
++|+|+-+=.+|.|++.+.=+.|+.||=-|
T Consensus 4 ~lL~GiVLGlipvTl~GlfvaAylQYrRg~ 33 (37)
T CHL00008 4 VLLFGIVLGLIPITLAGLFVTAYLQYRRGD 33 (37)
T ss_pred hhhhhHHHHhHHHHHHHHHHHHHHHHhhcc
Confidence 567777777789999988888999997433
No 24
>PF02824 TGS: TGS domain; InterPro: IPR004095 The TGS domain is present in a number of enzymes, for example, in threonyl-tRNA synthetase (ThrRS), GTPase, and guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (SpoT) []. The TGS domain is also present at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organism, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role []. ; PDB: 1WXQ_A 1NYR_B 1NYQ_B 2KMM_A 1WWT_A 1TKE_A 1TKG_A 1TJE_A 1QF6_A 1TKY_A ....
Probab=40.83 E-value=45 Score=22.83 Aligned_cols=34 Identities=21% Similarity=0.176 Sum_probs=25.5
Q ss_pred EEEEecCCceEEeecccchHHHHHHHHhhhcCCe
Q 029220 154 IIITLKDGTKVDLRSVPKFREIAKYCVSMAEQPV 187 (197)
Q Consensus 154 mVvtLkDGsrLEmRslP~Frei~~yI~~~~e~~~ 187 (197)
|.|+|.||+..|+..=--..+++..|-+...+.+
T Consensus 1 I~v~lpdG~~~~~~~g~T~~d~A~~I~~~l~~~~ 34 (60)
T PF02824_consen 1 IRVYLPDGSIKELPEGSTVLDVAYSIHSSLAKRA 34 (60)
T ss_dssp EEEEETTSCEEEEETTBBHHHHHHHHSHHHHHCE
T ss_pred CEEECCCCCeeeCCCCCCHHHHHHHHCHHHHhhe
Confidence 5788999999998777777777777765554443
No 25
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=40.50 E-value=29 Score=23.65 Aligned_cols=24 Identities=33% Similarity=0.607 Sum_probs=20.2
Q ss_pred CCchhHHHHHHHHhHHHHHHHHHH
Q 029220 79 AHYGDLLANLLLGFTLFWLPLTLA 102 (197)
Q Consensus 79 Ph~gDLI~nlllg~TlI~lPltia 102 (197)
|+-..++..++.|.-++.+|.++|
T Consensus 3 pSLsnF~~SL~~Ga~ivvipi~~a 26 (39)
T CHL00114 3 PSLSAFINSLLLGAIIVVIPITLA 26 (39)
T ss_pred hhHHHHHHHHHHHHHHhHHHhhhh
Confidence 566778888999999999999885
No 26
>PF03799 FtsQ: Cell division protein FtsQ; InterPro: IPR005548 FtsQ is one of several cell division proteins. FtsQ interacts with other Fts proteins, reviewed in []. The precise function of FtsQ is unknown.; PDB: 2VH1_B 2VH2_B 2ALJ_A 1YR1_A.
Probab=38.30 E-value=96 Score=21.89 Aligned_cols=44 Identities=23% Similarity=0.260 Sum_probs=29.2
Q ss_pred eceeeeeEEeeccccceeeEEEEecCCceEEeecccchHHHHHHHHhhhc
Q 029220 135 YKVIKDVQVVPRFIGDWGDIIITLKDGTKVDLRSVPKFREIAKYCVSMAE 184 (197)
Q Consensus 135 Y~eI~dV~~VpRG~G~WGDmVvtLkDGsrLEmRslP~Frei~~yI~~~~e 184 (197)
..+|++|..-+|+- +.+.|+||.+|.+-.- ++.+-+++..+...
T Consensus 58 ~~~i~~i~~~~~~~-----~~l~l~dg~~V~lg~~-~~~~kl~~~~~i~~ 101 (117)
T PF03799_consen 58 RSQISEISYDPRGS-----WTLYLDDGVEVKLGRS-DLAEKLQRLVKILP 101 (117)
T ss_dssp THS-SEEEEETTSC-----EEEE-SSS-EEEEESS-THHHHHHHHHHHHH
T ss_pred hceeeEEEECCCCe-----EEEEECCCcEEEEcCc-CHHHHHHHHHHHHH
Confidence 45677787776643 8999999999998776 47776666554443
No 27
>PF07481 DUF1521: Domain of Unknown Function (DUF1521); InterPro: IPR011086 This domain of unknown function is found in a limited set of Bradyrhizobium proteins. There appears to be a periodic -DG- motif in the domain.
Probab=35.50 E-value=29 Score=29.98 Aligned_cols=24 Identities=38% Similarity=0.590 Sum_probs=21.1
Q ss_pred ccceeeEEEEecCCceEEeecccc
Q 029220 148 IGDWGDIIITLKDGTKVDLRSVPK 171 (197)
Q Consensus 148 ~G~WGDmVvtLkDGsrLEmRslP~ 171 (197)
|-+||||-+.|-||+||-+--.|-
T Consensus 58 fDFk~~~tf~L~DGTKItV~T~p~ 81 (171)
T PF07481_consen 58 FDFKGDMTFQLDDGTKITVDTVPW 81 (171)
T ss_pred eeecCceEEEeCCCCEEEEeeeec
Confidence 458999999999999999887774
No 28
>COG2268 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.11 E-value=2.2e+02 Score=28.57 Aligned_cols=32 Identities=22% Similarity=0.349 Sum_probs=24.8
Q ss_pred EEEEecCCceEEeecc------cchHHHHHHHHhhhcC
Q 029220 154 IIITLKDGTKVDLRSV------PKFREIAKYCVSMAEQ 185 (197)
Q Consensus 154 mVvtLkDGsrLEmRsl------P~Frei~~yI~~~~e~ 185 (197)
-.+..+||.++-++.+ |+|.++..|+..--++
T Consensus 93 ~~v~t~Dg~p~~v~~~a~v~i~~~~~dI~~aae~~g~K 130 (548)
T COG2268 93 DNVYTKDGMPLNVEAVAYVKIGDTFQDIATAAERFGGK 130 (548)
T ss_pred eeeEecCCCccceeEEEEEEecCCHHHHHHHHHHhccc
Confidence 4577899999988776 7888888887765554
No 29
>smart00568 GRAM domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins.
Probab=35.09 E-value=73 Score=20.97 Aligned_cols=37 Identities=16% Similarity=0.161 Sum_probs=30.6
Q ss_pred ceeEeEEeeeEEEEeeccCCcc--cceeeeceeeeeEEe
Q 029220 108 FNLRYRFTNLRVTVISGWTGED--RSDFSYKVIKDVQVV 144 (197)
Q Consensus 108 lWlRYrITnRRIsV~sGw~Grd--rtdIvY~eI~dV~~V 144 (197)
++-|--||+.++.-.+...|.. ...|.+++|.+|..+
T Consensus 22 ~~G~lyiT~~~l~F~S~~~~~~~~~~~ipl~~I~~i~k~ 60 (61)
T smart00568 22 VQGRLYISNYRLCFRSDLPGKLTPKVVIPLADITRIEKS 60 (61)
T ss_pred ccEEEEEECCEEEEEccCCCCeeEEEEEEHHHeeEEEEC
Confidence 5677789999999999887754 488899999998764
No 30
>KOG4737 consensus ATPase membrane sector associated protein [Energy production and conversion]
Probab=33.84 E-value=66 Score=30.22 Aligned_cols=37 Identities=24% Similarity=0.432 Sum_probs=28.0
Q ss_pred hHHHHHHHHhHHHHHHHHHHHHhHhce--------eEeEEeeeEEE
Q 029220 83 DLLANLLLGFTLFWLPLTLAAVSRAFN--------LRYRFTNLRVT 120 (197)
Q Consensus 83 DLI~nlllg~TlI~lPltiaAi~RalW--------lRYrITnRRIs 120 (197)
-.|+|++|++-++ +.+++-+++=++| +-||.|+.||.
T Consensus 280 pviFni~Lw~mvi-l~lali~i~y~ia~mDPg~DSIIYRMTttrik 324 (326)
T KOG4737|consen 280 PVIFNIFLWLMVI-LVLALIYIVYGIASMDPGKDSIIYRMTTTRIK 324 (326)
T ss_pred cHHHHHHHHHHHH-HHHHHHHHHhhhhccCCCcceeEEEeccceec
Confidence 4789998877544 4566667777888 58999999984
No 31
>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast. The function of the UBX domain is not known although the fragment of avian FAF-1 containing the UBX domain causes apoptosis of transfected cells.; GO: 0005515 protein binding; PDB: 3QX1_A 1H8C_A 3QCA_B 3QQ8_B 3QC8_B 3R3M_A 3QWZ_B 1S3S_H 1JRU_A 1I42_A ....
Probab=32.34 E-value=1.3e+02 Score=20.84 Aligned_cols=33 Identities=21% Similarity=0.388 Sum_probs=24.1
Q ss_pred EEEEecCCceEEeecc--cchHHHHHHHHhhhcCC
Q 029220 154 IIITLKDGTKVDLRSV--PKFREIAKYCVSMAEQP 186 (197)
Q Consensus 154 mVvtLkDGsrLEmRsl--P~Frei~~yI~~~~e~~ 186 (197)
+.|-|.||++++-+=- -..+.+++||..+...+
T Consensus 9 I~vRlpdG~~l~~~F~~~~tl~~l~~~v~~~~~~~ 43 (82)
T PF00789_consen 9 IQVRLPDGSRLQRRFPKSDTLQDLYDFVESQLFSP 43 (82)
T ss_dssp EEEEETTSTEEEEEEETTSBHHHHHHHHHHHHHCT
T ss_pred EEEECCCCCEEEEEECCcchHHHHHHHHHHhcCCC
Confidence 4566779998876544 46899999998765544
No 32
>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 is a protein of unknown function with a domain architecture that includes the UAS (ubiquitin-associated) and UBX (ubiquitin-like) domains. This protein is related to other UBA/UBX-containing proteins like Faf1, p47, and SAKS1 and may serve as an adaptor molecule that shuttles proteins to the proteasome for degradation. The UBX domain has a beta-grasp fold similar to that of ubiquitin however, UBX lacks the c-terminal double glycine motif and is thus unlikely to be conjugated to other proteins.
Probab=30.44 E-value=1e+02 Score=22.76 Aligned_cols=29 Identities=31% Similarity=0.579 Sum_probs=22.7
Q ss_pred EEEEecCCceEEeecc--cchHHHHHHHHhh
Q 029220 154 IIITLKDGTKVDLRSV--PKFREIAKYCVSM 182 (197)
Q Consensus 154 mVvtLkDGsrLEmRsl--P~Frei~~yI~~~ 182 (197)
+.|-|-||+|++-|=. -..+++++|+..+
T Consensus 7 I~iRlp~G~Rl~rrF~~~~tl~~l~~fv~~~ 37 (85)
T cd01774 7 IVFKLPNGTRVERRFLFTQSLRVIHDFLFSL 37 (85)
T ss_pred EEEECCCCCEEEEEeCCCCcHHHHHHHHHhC
Confidence 4667789999987755 4578999999644
No 33
>PF11808 DUF3329: Domain of unknown function (DUF3329); InterPro: IPR021766 This family of proteins are functionally uncharacterised. This family is only found in bacteria. ; GO: 0004673 protein histidine kinase activity
Probab=30.43 E-value=20 Score=26.66 Aligned_cols=23 Identities=26% Similarity=0.472 Sum_probs=17.5
Q ss_pred eeccccceeeEEEEecCCceEEeecccchHHHHHHHHhhh
Q 029220 144 VPRFIGDWGDIIITLKDGTKVDLRSVPKFREIAKYCVSMA 183 (197)
Q Consensus 144 VpRG~G~WGDmVvtLkDGsrLEmRslP~Frei~~yI~~~~ 183 (197)
.|.|.|.|||+ |..+|.+-+++.
T Consensus 63 pP~~~G~W~~i-----------------f~~Lyr~qrr~r 85 (90)
T PF11808_consen 63 PPEGSGIWGEI-----------------FDRLYRLQRRNR 85 (90)
T ss_pred CCCCCCcHHHH-----------------HHHHHHHHHHHH
Confidence 59999999998 677776655443
No 34
>PRK10879 proline aminopeptidase P II; Provisional
Probab=29.48 E-value=66 Score=29.80 Aligned_cols=40 Identities=30% Similarity=0.208 Sum_probs=30.8
Q ss_pred ccccc-eeeEEEEecCCceEEeecccc-hHHHHHHHHhhhcC
Q 029220 146 RFIGD-WGDIIITLKDGTKVDLRSVPK-FREIAKYCVSMAEQ 185 (197)
Q Consensus 146 RG~G~-WGDmVvtLkDGsrLEmRslP~-Frei~~yI~~~~e~ 185 (197)
||+|. +-|.|++..||..+=-..+|+ ..||++++..++++
T Consensus 397 ~~~GiRiED~VlVT~~G~e~LT~~~pk~~~~iE~~m~~~~~~ 438 (438)
T PRK10879 397 RGIGIRIEDDIVITETGNENLTASVVKKPDEIEALMAAARQQ 438 (438)
T ss_pred CccEEEeccEEEECCCcCeEcCccCCCCHHHHHHHHHhhhcC
Confidence 45665 389999999999876667886 77888888776653
No 35
>PLN00091 photosystem I reaction center subunit V (PsaG); Provisional
Probab=28.48 E-value=34 Score=29.22 Aligned_cols=36 Identities=33% Similarity=0.445 Sum_probs=22.9
Q ss_pred CCcccccCcccceeeeeeeeeeeccCCCCCCCCCCCccccCCCceee
Q 029220 1 MASTRILSPTAAAAVGITHKSIYLFSKPPSPSSFPTFTVTHNRPITK 47 (197)
Q Consensus 1 ma~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~ 47 (197)
||+++.+++++.. ..+.||.+..+.. +|. --||++|
T Consensus 1 ma~~~~~~~p~~~-~~~~~~~~~~~~~-----sF~-----GLRpl~~ 36 (160)
T PLN00091 1 MATSALLSTPTFS-KAIHHHNLTPSSI-----SFQ-----GLRPLSK 36 (160)
T ss_pred CcccccccCCccc-hhhhhhccCCCcc-----ccc-----ccccccc
Confidence 8888888877776 5556665433322 565 4577777
No 36
>PF07787 DUF1625: Protein of unknown function (DUF1625); InterPro: IPR012430 Sequences making up this family are derived from hypothetical proteins expressed by both prokaryotic and eukaryotic species. The region in question is approximately 250 residues long.
Probab=28.26 E-value=59 Score=27.71 Aligned_cols=6 Identities=50% Similarity=0.412 Sum_probs=4.5
Q ss_pred ceeEeE
Q 029220 108 FNLRYR 113 (197)
Q Consensus 108 lWlRYr 113 (197)
.|+.||
T Consensus 242 aW~~yR 247 (248)
T PF07787_consen 242 AWLFYR 247 (248)
T ss_pred hheeeC
Confidence 388887
No 37
>PF14317 YcxB: YcxB-like protein
Probab=27.56 E-value=84 Score=19.75 Aligned_cols=30 Identities=20% Similarity=0.289 Sum_probs=23.4
Q ss_pred eeEEEEeeccCCcccceeeeceeeeeEEeeccc
Q 029220 116 NLRVTVISGWTGEDRSDFSYKVIKDVQVVPRFI 148 (197)
Q Consensus 116 nRRIsV~sGw~GrdrtdIvY~eI~dV~~VpRG~ 148 (197)
+.-|.+.+ +.....+.|++|.+|.--++.+
T Consensus 3 ~~gi~~~~---~~~~~~~~w~~i~~v~e~~~~~ 32 (62)
T PF14317_consen 3 EDGIIIES---GNGSSRIPWSDIKKVVETKDYF 32 (62)
T ss_pred CCEEEEEE---CCeEEEEEchheEEEEEeCCEE
Confidence 34455655 6889999999999999987664
No 38
>PF02529 PetG: Cytochrome B6-F complex subunit 5; InterPro: IPR003683 This family consists of cytochrome b6/f complex subunit 5 (PetG). The cytochrome bf complex, found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase []. The purified complex from the unicellular alga Chlamydomonas reinhardtii contains seven subunits; namely four high molecular weight subunits (cytochrome f, Rieske iron-sulphur protein, cytochrome b6, and subunit IV) and three approximately miniproteins (PetG, PetL, and PetX) []. Stoichiometry measurements are consistent with every subunit being present as two copies per b6/f dimer. The absence of PetG affects either the assembly or stability of the cytochrome bf complex in C. reinhardtii [].; GO: 0009512 cytochrome b6f complex; PDB: 1Q90_G 2ZT9_G 1VF5_G 2D2C_G 2E74_G 2E75_G 2E76_G.
Probab=27.44 E-value=41 Score=22.76 Aligned_cols=28 Identities=43% Similarity=0.548 Sum_probs=21.6
Q ss_pred HHHHHHhHHHHHHHHHHHHhHhceeEeE
Q 029220 86 ANLLLGFTLFWLPLTLAAVSRAFNLRYR 113 (197)
Q Consensus 86 ~nlllg~TlI~lPltiaAi~RalWlRYr 113 (197)
=++++|+-+=.+|.+++.+.=+.|+.||
T Consensus 3 EplL~GiVlGli~vtl~Glfv~Ay~QY~ 30 (37)
T PF02529_consen 3 EPLLSGIVLGLIPVTLAGLFVAAYLQYR 30 (37)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred chhhhhHHHHhHHHHHHHHHHHHHHHHh
Confidence 3567788777888888888878888876
No 39
>PF09191 CD4-extracel: CD4, extracellular; InterPro: IPR015274 This domain adopts an immunoglobulin-like beta-sandwich with seven strands in 2 beta sheets, in a Greek key topology. It is predominantly found in the extracellular portion of CD4 proteins, where it enables interaction with major histocompatibility complex class II antigens []. ; PDB: 1WIQ_B 1WIP_B 1WIO_A 3T0E_E 1CID_A.
Probab=26.98 E-value=92 Score=25.28 Aligned_cols=53 Identities=19% Similarity=0.397 Sum_probs=33.2
Q ss_pred HhceeEeEEeeeEEEEeeccCC-c----ccceeeeceeeeeEEeeccccceeeEEEEecCCc
Q 029220 106 RAFNLRYRFTNLRVTVISGWTG-E----DRSDFSYKVIKDVQVVPRFIGDWGDIIITLKDGT 162 (197)
Q Consensus 106 RalWlRYrITnRRIsV~sGw~G-r----drtdIvY~eI~dV~~VpRG~G~WGDmVvtLkDGs 162 (197)
-+.|+.|...||.++|..+..- | +..-+ .++=-+..|+--|- |++-++|..|.
T Consensus 42 ~q~WitFsl~n~kvsv~~~~~~~Klqm~e~lPL---~ltL~q~l~q~AGS-GnltL~L~~G~ 99 (108)
T PF09191_consen 42 SQSWITFSLKNKKVSVQKVTQDPKLQMKEKLPL---TLTLPQALPQYAGS-GNLTLTLDKGK 99 (108)
T ss_dssp S--EEEEEEETTEEEEECEETSST-EE-SCTT----EEEESSB-GGG-EE-EEEEEEBTTSE
T ss_pred CCCcEEEEEeCCeEEEeecCCCcccccccCCce---EEEccccChhhcCC-ceEEEEecCCc
Confidence 3679999999999999977631 1 11111 11222335777788 99999999886
No 40
>PF03658 Ub-RnfH: RnfH family Ubiquitin; InterPro: IPR005346 This is a small family of proteins of unknown function.; PDB: 2HJ1_B.
Probab=26.88 E-value=29 Score=26.49 Aligned_cols=19 Identities=32% Similarity=0.903 Sum_probs=11.4
Q ss_pred ccceeeEE---EEecCCceEEe
Q 029220 148 IGDWGDII---ITLKDGTKVDL 166 (197)
Q Consensus 148 ~G~WGDmV---vtLkDGsrLEm 166 (197)
+|.||-.| =.|+||.|||+
T Consensus 49 vGIfGk~~~~d~~L~~GDRVEI 70 (84)
T PF03658_consen 49 VGIFGKLVKLDTVLRDGDRVEI 70 (84)
T ss_dssp EEEEE-S--TT-B--TT-EEEE
T ss_pred eeeeeeEcCCCCcCCCCCEEEE
Confidence 68999877 37899999997
No 41
>PF06173 DUF986: Protein of unknown function (DUF986); InterPro: IPR009328 This family consists of several bacterial putative membrane proteins of unknown function.
Probab=25.23 E-value=59 Score=27.38 Aligned_cols=44 Identities=20% Similarity=0.465 Sum_probs=32.8
Q ss_pred eeeeceeeeeEEeeccccceeeEEEEecCCceEEee--cccchHHHHHHHHh
Q 029220 132 DFSYKVIKDVQVVPRFIGDWGDIIITLKDGTKVDLR--SVPKFREIAKYCVS 181 (197)
Q Consensus 132 dIvY~eI~dV~~VpRG~G~WGDmVvtLkDGsrLEmR--slP~Frei~~yI~~ 181 (197)
=+.|++|+++... +=|=+|+.| +|.|+.++ .+.+-+++++++.+
T Consensus 102 fi~Y~~Ik~mNLs-----EDgILVi~L-~~rrLli~v~~~dDlEki~~f~~~ 147 (149)
T PF06173_consen 102 FIPYSRIKAMNLS-----EDGILVIDL-EGRRLLIRVKNLDDLEKIYQFFIG 147 (149)
T ss_pred eeeHHHHHhcccC-----cCcEEEEEe-CCcEEEEEecCHHHHHHHHHHHhc
Confidence 4789999999876 346799999 99998765 45566666666543
No 42
>TIGR00134 gatE_arch glutamyl-tRNA(Gln) amidotransferase, subunit E. The Archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp--tRNA ligase, but the genes have not been identified. It is likely that this protein replaces gatB in Asp-tRNA(Asn) amidotransferase but that both enzymes share gatA.
Probab=24.15 E-value=1e+02 Score=30.87 Aligned_cols=37 Identities=30% Similarity=0.521 Sum_probs=29.7
Q ss_pred eeccccce-eeEEEEecCCceEEeecccchHHHHHHHH
Q 029220 144 VPRFIGDW-GDIIITLKDGTKVDLRSVPKFREIAKYCV 180 (197)
Q Consensus 144 VpRG~G~W-GDmVvtLkDGsrLEmRslP~Frei~~yI~ 180 (197)
+.||.|.- =|+=|-++.|+|+|+..|..|+-+.+-|+
T Consensus 214 ~~~~~GsiR~DvNvSi~~G~rvEIKnvns~~~i~~ai~ 251 (620)
T TIGR00134 214 VKRGLGTIRQDLNISIRDGARVEVKGVQDLDLIPKIVE 251 (620)
T ss_pred CCcCCCCeeeeEEEeccCCceeeecCCCcHHHHHHHHH
Confidence 34565543 68888889999999999999998887654
No 43
>PRK04028 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated
Probab=22.91 E-value=97 Score=31.15 Aligned_cols=29 Identities=24% Similarity=0.493 Sum_probs=25.5
Q ss_pred eeEEEEecCCceEEeecccchHHHHHHHH
Q 029220 152 GDIIITLKDGTKVDLRSVPKFREIAKYCV 180 (197)
Q Consensus 152 GDmVvtLkDGsrLEmRslP~Frei~~yI~ 180 (197)
=|+=|-++.|+|+|+..|..|+.+.+-|.
T Consensus 226 ~DvNvSv~~g~rvEiKnlns~~~v~~ai~ 254 (630)
T PRK04028 226 QDVNVSIAGGARVEIKGVQKLDLIPKVVE 254 (630)
T ss_pred EEEEEeccCCceeeecCCCcHHHHHHHHH
Confidence 57788889999999999999999887754
No 44
>PF06385 Baculo_LEF-11: Baculovirus LEF-11 protein; InterPro: IPR009429 This family consists of several Baculovirus LEF-11 proteins. The exact function of this family is unknown although it has been shown that LEF-11 is required for viral DNA replication during the infection cycle [] and plays a role in late/very late gene activation.; GO: 0006355 regulation of transcription, DNA-dependent, 0019058 viral infectious cycle
Probab=22.80 E-value=86 Score=24.62 Aligned_cols=25 Identities=20% Similarity=0.401 Sum_probs=20.8
Q ss_pred cchHHHHHHHHhhhcCCeecccCCC
Q 029220 170 PKFREIAKYCVSMAEQPVVFKETGP 194 (197)
Q Consensus 170 P~Frei~~yI~~~~e~~~vlk~~~~ 194 (197)
|.|.++-+||++.+++..++-..+.
T Consensus 34 ~~F~~~~~yIr~nl~~~~I~~~d~~ 58 (94)
T PF06385_consen 34 PGFEEIKDYIRENLDKAFIIHGDCS 58 (94)
T ss_pred cchHHHHHHHHHhhcccEEEeCCCC
Confidence 8899999999999999877654443
No 45
>smart00683 DM16 Repeats in sea squirt COS41.4, worm R01H10.6, fly CG1126 etc.
Probab=22.80 E-value=2e+02 Score=20.47 Aligned_cols=33 Identities=27% Similarity=0.243 Sum_probs=25.6
Q ss_pred EeEEeeeEEEEeeccCCcccceeeeceeeeeEE
Q 029220 111 RYRFTNLRVTVISGWTGEDRSDFSYKVIKDVQV 143 (197)
Q Consensus 111 RYrITnRRIsV~sGw~GrdrtdIvY~eI~dV~~ 143 (197)
++.+||-|+.=-+--.-+=-..|.|.+|..++.
T Consensus 22 ~l~VTNlRiiW~s~~~~~~NlSIgy~~i~~i~~ 54 (55)
T smart00683 22 VFFVTNLRLVWHSDTNPRFNISVGYLQITNVRV 54 (55)
T ss_pred EEEEEeeEEEEEeCCCCceEEEEcceeEEEEEe
Confidence 688999999766665556667789999988864
No 46
>COG0401 Uncharacterized homolog of Blt101 [Function unknown]
Probab=21.42 E-value=1.3e+02 Score=21.98 Aligned_cols=35 Identities=37% Similarity=0.590 Sum_probs=22.4
Q ss_pred EEeeCCCCchhHHHHHHHHhHHH-HHHHHHHHHhHhceeEeE
Q 029220 73 VFFDGGAHYGDLLANLLLGFTLF-WLPLTLAAVSRAFNLRYR 113 (197)
Q Consensus 73 VfyEGgPh~gDLI~nlllg~TlI-~lPltiaAi~RalWlRYr 113 (197)
||-+-|.--.|+++|+++ |++ |+|-.+ -|+|+-+|
T Consensus 20 VfL~~G~~~~df~iNiLL--tlLg~~PGii----HA~yvi~~ 55 (56)
T COG0401 20 VFLRRGFGGKDFLINILL--TLLGYIPGII----HALYVILR 55 (56)
T ss_pred hhhhccCCcHHHHHHHHH--HHHHhhhhhH----hheEEEEe
Confidence 344455566799999876 333 577655 67787543
No 47
>PF10459 Peptidase_S46: Peptidase S46; InterPro: IPR019500 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This entry represents S46 peptidases, where dipeptidyl-peptidase 7 (DPP-7) is the best-characterised member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains.
Probab=21.23 E-value=89 Score=31.61 Aligned_cols=36 Identities=36% Similarity=0.588 Sum_probs=32.1
Q ss_pred eeEEEEeeccCCcccceeeeceeeeeEEe---eccccce
Q 029220 116 NLRVTVISGWTGEDRSDFSYKVIKDVQVV---PRFIGDW 151 (197)
Q Consensus 116 nRRIsV~sGw~GrdrtdIvY~eI~dV~~V---pRG~G~W 151 (197)
+.|..|.+=+.|..-.=+.|.+++|||.| |+.+|.+
T Consensus 148 ~~~~~V~~fy~G~~Y~L~~y~~y~DVRLV~APp~siG~F 186 (698)
T PF10459_consen 148 GYRCQVVSFYGGNQYYLFVYRRYKDVRLVYAPPSSIGKF 186 (698)
T ss_pred CeEEEEEEecCCceEEEEEEEEecceEEecCChHHhccc
Confidence 88999999999999999999999999997 5666665
No 48
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=20.37 E-value=2.1e+02 Score=19.17 Aligned_cols=28 Identities=18% Similarity=0.262 Sum_probs=20.3
Q ss_pred EEEecCCceEEee-cccchHHHHHHHHhh
Q 029220 155 IITLKDGTKVDLR-SVPKFREIAKYCVSM 182 (197)
Q Consensus 155 VvtLkDGsrLEmR-slP~Frei~~yI~~~ 182 (197)
++.++||..+.-. +.-+-.++.++|+++
T Consensus 75 ~~~~~~g~~~~~~~g~~~~~~l~~~i~~~ 103 (103)
T PF00085_consen 75 IIFFKNGKEVKRYNGPRNAESLIEFIEKH 103 (103)
T ss_dssp EEEEETTEEEEEEESSSSHHHHHHHHHHH
T ss_pred EEEEECCcEEEEEECCCCHHHHHHHHHcC
Confidence 5577999888544 444888888888875
No 49
>smart00166 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p.
Probab=20.37 E-value=3.2e+02 Score=19.20 Aligned_cols=30 Identities=20% Similarity=0.364 Sum_probs=22.0
Q ss_pred EEEEecCCceEEeec--ccchHHHHHHHHhhh
Q 029220 154 IIITLKDGTKVDLRS--VPKFREIAKYCVSMA 183 (197)
Q Consensus 154 mVvtLkDGsrLEmRs--lP~Frei~~yI~~~~ 183 (197)
+.|-|-||+|++-+= =-..+++++|+.++.
T Consensus 7 I~iRlPdG~ri~~~F~~~~tl~~v~~~v~~~~ 38 (80)
T smart00166 7 LQIRLPDGSRLVRRFPSSDTLRTVYEFVSAAL 38 (80)
T ss_pred EEEEcCCCCEEEEEeCCCCcHHHHHHHHHHcc
Confidence 556777999987653 345789999996544
Done!