Query 045364
Match_columns 97
No_of_seqs 104 out of 261
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 12:33:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045364.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045364hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01900 RNase_P_Rpp14: Rpp14/ 100.0 5.3E-30 1.2E-34 166.3 6.6 92 1-97 3-94 (107)
2 PRK03717 ribonuclease P protei 99.9 1.8E-27 3.8E-32 159.0 10.2 85 1-97 19-103 (120)
3 KOG4639 RNase P/RNase MRP subu 99.9 3.2E-27 6.9E-32 161.5 9.4 92 1-97 9-100 (154)
4 COG1369 POP5 RNase P/RNase MRP 99.8 4.6E-20 9.9E-25 123.4 9.4 77 19-97 27-103 (124)
5 PF09345 DUF1987: Domain of un 67.3 7.1 0.00015 25.1 2.8 40 21-61 21-60 (99)
6 PF08777 RRM_3: RNA binding mo 67.1 31 0.00066 22.1 6.1 56 31-94 15-77 (105)
7 cd03485 MutL_Trans_hPMS_1_like 64.9 8.1 0.00018 25.5 2.9 31 4-39 101-132 (132)
8 cd00559 Cyanase_C Cyanase C-te 58.3 24 0.00052 21.5 3.7 38 28-65 20-58 (69)
9 cd06407 PB1_NLP A PB1 domain i 55.2 44 0.00095 20.5 4.8 57 27-91 22-78 (82)
10 PF14199 DUF4317: Domain of un 49.4 25 0.00055 27.8 3.6 71 16-92 275-359 (371)
11 cd03484 MutL_Trans_hPMS_2_like 45.1 32 0.0007 23.0 3.3 32 3-38 110-141 (142)
12 PF11429 Colicin_D: Colicin D; 43.5 31 0.00066 22.1 2.7 31 37-71 42-72 (92)
13 PF02560 Cyanate_lyase: Cyanat 42.4 47 0.001 20.4 3.3 35 29-63 25-60 (73)
14 PF00564 PB1: PB1 domain; Int 42.3 71 0.0015 18.7 5.8 64 21-93 18-81 (84)
15 PF11537 DUF3227: Protein of u 42.2 13 0.00028 24.3 0.8 17 29-45 48-64 (102)
16 PF14552 Tautomerase_2: Tautom 39.8 29 0.00063 21.4 2.2 31 2-39 31-61 (82)
17 PRK02866 cyanate hydratase; Va 39.6 55 0.0012 22.6 3.7 37 29-65 99-136 (147)
18 PF11918 DUF3436: Domain of un 39.4 64 0.0014 18.8 3.4 31 5-35 19-52 (55)
19 cd01735 LSm12_N LSm12 belongs 39.2 43 0.00092 19.7 2.7 18 52-69 23-40 (61)
20 PRK00745 4-oxalocrotonate taut 38.9 61 0.0013 18.0 3.4 32 2-40 3-34 (62)
21 PF10850 DUF2653: Protein of u 38.6 45 0.00098 21.3 2.9 50 2-54 30-84 (91)
22 cd06396 PB1_NBR1 The PB1 domai 38.5 98 0.0021 19.2 4.5 42 27-75 24-65 (81)
23 cd05992 PB1 The PB1 domain is 38.2 82 0.0018 18.2 6.5 57 26-91 22-78 (81)
24 TIGR00673 cynS cyanate hydrata 37.4 64 0.0014 22.4 3.8 37 29-65 102-139 (150)
25 PF01119 DNA_mis_repair: DNA m 37.3 42 0.00091 21.5 2.8 31 4-38 88-118 (119)
26 PRK02220 4-oxalocrotonate taut 35.8 72 0.0016 17.6 3.3 32 2-40 3-34 (61)
27 cd00782 MutL_Trans MutL_Trans: 35.6 63 0.0014 20.4 3.4 31 3-38 91-122 (122)
28 smart00200 SEA Domain found in 35.2 78 0.0017 20.6 3.8 51 5-59 19-69 (121)
29 cd00491 4Oxalocrotonate_Tautom 35.2 77 0.0017 17.1 3.3 31 3-40 3-33 (58)
30 PF09559 Cas6: Cas6 Crispr; I 34.6 1.1E+02 0.0024 22.1 4.7 65 23-91 17-91 (195)
31 smart00666 PB1 PB1 domain. Pho 34.3 98 0.0021 18.0 7.2 52 27-87 23-74 (81)
32 COG2302 Uncharacterized conser 33.8 1.9E+02 0.004 21.9 6.0 69 2-94 89-159 (257)
33 PF14350 Beta_protein: Beta pr 33.7 1.2E+02 0.0026 22.9 5.2 48 17-65 213-273 (347)
34 TIGR02807 cas6_var CRISPR-asso 33.3 1.8E+02 0.0038 21.0 5.6 66 2-76 3-77 (190)
35 PF14730 DUF4468: Domain of un 31.4 1.3E+02 0.0028 18.4 5.6 40 20-66 9-48 (91)
36 PF10184 DUF2358: Uncharacteri 31.2 1.4E+02 0.0031 18.9 5.1 53 25-83 2-55 (113)
37 PRK01964 4-oxalocrotonate taut 31.2 87 0.0019 17.6 3.2 32 2-40 3-34 (64)
38 KOG4048 Uncharacterized conser 31.2 28 0.00062 24.9 1.2 23 22-44 67-89 (201)
39 PF08265 YL1_C: YL1 nuclear pr 31.1 19 0.00042 18.2 0.3 14 48-61 6-19 (30)
40 COG1513 CynS Cyanate lyase [In 29.8 92 0.002 21.5 3.5 36 29-64 102-139 (151)
41 PRK02289 4-oxalocrotonate taut 29.1 1.1E+02 0.0023 17.2 3.3 32 2-40 3-34 (60)
42 TIGR02520 pilus_B_mal_scr type 29.1 1.9E+02 0.0041 23.5 5.8 61 23-92 204-264 (497)
43 PF14500 MMS19_N: Dos2-interac 28.4 99 0.0021 23.0 3.8 29 16-44 181-211 (262)
44 PF05265 DUF723: Protein of un 28.2 1.3E+02 0.0029 17.7 4.3 35 30-73 8-42 (60)
45 cd06401 PB1_TFG The PB1 domain 26.9 1.5E+02 0.0033 18.5 3.8 37 27-66 23-60 (81)
46 cd01814 NTGP5 Ubiquitin-like N 24.9 2.1E+02 0.0046 18.9 4.9 49 3-55 5-58 (113)
47 cd03483 MutL_Trans_MLH1 MutL_T 24.6 1E+02 0.0022 20.1 3.0 30 4-38 96-126 (127)
48 PF00313 CSD: 'Cold-shock' DNA 24.5 1.4E+02 0.003 16.8 3.3 43 52-94 5-52 (66)
49 COG1270 CbiB Cobalamin biosynt 24.0 87 0.0019 24.3 2.9 25 17-41 132-156 (320)
50 PRK06163 hypothetical protein; 23.9 2.1E+02 0.0046 20.2 4.7 30 2-34 167-196 (202)
51 cd04458 CSP_CDS Cold-Shock Pro 23.8 1.5E+02 0.0032 16.6 4.0 20 51-70 4-23 (65)
52 PF08865 DUF1830: Domain of un 23.8 85 0.0018 18.9 2.3 16 53-68 2-17 (68)
53 KOG1434 Meiotic recombination 23.7 49 0.0011 25.6 1.4 21 32-52 115-135 (335)
54 PF10302 DUF2407: DUF2407 ubiq 23.4 1.6E+02 0.0034 18.7 3.6 32 17-55 20-51 (97)
55 PF07317 YcgR: Flagellar regul 23.1 1.5E+02 0.0032 18.8 3.5 71 22-95 6-85 (108)
56 PF09929 DUF2161: Uncharacteri 22.3 2.5E+02 0.0053 18.8 4.4 59 2-78 10-68 (118)
57 COG4737 Uncharacterized protei 21.9 54 0.0012 22.0 1.2 34 17-50 14-48 (123)
58 PRK10509 bacterioferritin-asso 21.5 89 0.0019 18.2 2.0 26 20-45 8-37 (64)
59 KOG0876 Manganese superoxide d 21.4 2.3E+02 0.0049 21.2 4.5 27 50-76 155-181 (234)
60 PLN02355 probable galactinol-- 21.0 1.4E+02 0.0031 25.9 3.8 51 24-76 414-465 (758)
61 PF03958 Secretin_N: Bacterial 20.5 1.4E+02 0.0031 17.2 2.8 30 49-79 45-74 (82)
62 PF15513 DUF4651: Domain of un 20.1 1.6E+02 0.0035 17.4 2.9 24 29-58 6-29 (62)
No 1
>PF01900 RNase_P_Rpp14: Rpp14/Pop5 family; InterPro: IPR002759 This family contains proteins found in some eukaryotes and archaebacteria that are related to yeast ribonuclease P. This enzyme is essential for tRNA processing generating 5'-termini of mature tRNA molecules []. tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40 [].; GO: 0004540 ribonuclease activity, 0008033 tRNA processing; PDB: 2CZV_D 2AV5_B.
Probab=99.96 E-value=5.3e-30 Score=166.29 Aligned_cols=92 Identities=33% Similarity=0.502 Sum_probs=76.1
Q ss_pred CEEEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHh
Q 045364 1 MIVEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITM 80 (97)
Q Consensus 1 ~l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtl 80 (97)
|+|||+++|+. .+..++++++.++|+++++++|||+|+|.+..++.|+|||+.|+.+||||+|++++++|+|||+
T Consensus 3 i~~~i~~~~~~-----~~~~~~~~~l~~~I~~a~~~l~G~~G~~~~~~~l~v~~~~~~t~~~IiR~~r~~~~~v~~aL~~ 77 (107)
T PF01900_consen 3 IVFEIISEDPS-----DPAELSPSDLKKAIREAVKELFGDFGAAAISPSLQVKYFNPKTGIGIIRCRREYYKKVWSALTL 77 (107)
T ss_dssp EEEEEEES----------S---HHHHHHHHHHHHHHHCHHHHHHHH--EEE--EEETTTTEEEEEEEGGGHHHHHHHHHT
T ss_pred EEEEEEEcccc-----ccCcCCHHHHHHHHHHHHHHHcChhhhhhcccccceeeEcCCCCEEEEEEcchhhhHHHHHHHH
Confidence 58999999976 3567999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCeeeEEEEEeeC
Q 045364 81 VRSIGNCLVLFNALDLS 97 (97)
Q Consensus 81 it~i~~~~~~~rvl~vS 97 (97)
+++++|.||.|+|++||
T Consensus 78 i~~i~~~~~~~~vl~vS 94 (107)
T PF01900_consen 78 ITSINGRPCSIRVLHVS 94 (107)
T ss_dssp --EETTEEEEEEEEEEE
T ss_pred HhccCCceEEEEEEEEC
Confidence 99999999999999997
No 2
>PRK03717 ribonuclease P protein component 2; Provisional
Probab=99.95 E-value=1.8e-27 Score=159.05 Aligned_cols=85 Identities=20% Similarity=0.210 Sum_probs=79.2
Q ss_pred CEEEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHh
Q 045364 1 MIVEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITM 80 (97)
Q Consensus 1 ~l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtl 80 (97)
|+|||++++ ++++++|.++||++++++|||+|+|.+. +++.|||+.|+.+||||.|++++.+|+||++
T Consensus 19 i~~ei~~~~----------~~~~~~l~~~Ir~av~~~fGd~G~~~~~--~~li~f~~~t~~gIlRc~R~~~~~v~aAL~l 86 (120)
T PRK03717 19 IAFQVIGER----------PFTKDEIKKAIWEASLSTLGELGTARAK--PWFIKFDEKTQTGIVRCDRKHVEELRFALTL 86 (120)
T ss_pred EEEEEEeCC----------CCCHHHHHHHHHHHHHHHcChhhhcccc--ceEEEEeCCCCEEEEEcCchhHHHHHHHHHH
Confidence 589999854 2689999999999999999999999975 6778999999999999999999999999999
Q ss_pred hhhcCCeeeEEEEEeeC
Q 045364 81 VRSIGNCLVLFNALDLS 97 (97)
Q Consensus 81 it~i~~~~~~~rvl~vS 97 (97)
|++++|.||.|++++||
T Consensus 87 i~~i~~~~v~ir~l~vS 103 (120)
T PRK03717 87 VTEINGSKAIIRTLGVS 103 (120)
T ss_pred HHhCCCeeEEEEEeecc
Confidence 99999999999999998
No 3
>KOG4639 consensus RNase P/RNase MRP subunit POP5 [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=3.2e-27 Score=161.54 Aligned_cols=92 Identities=23% Similarity=0.434 Sum_probs=86.3
Q ss_pred CEEEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHh
Q 045364 1 MIVEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITM 80 (97)
Q Consensus 1 ~l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtl 80 (97)
+|||+++++.. .+..++.+.|...+|+.+.++|||||+|.+.++|.|||+|+.|+++||||.|+.++.+|+||++
T Consensus 9 ilvel~~~~p~-----~~~~~~~siL~~iir~~v~~~~Gd~G~a~~~s~l~VkYl~~~T~v~ilRc~~~~~k~v~~aLpl 83 (154)
T KOG4639|consen 9 ILVELLFPDPP-----PDLSLKDSILQSIIRSRVSENYGDFGLAKVKSLLSVKYLNENTSVAILRCAREGCKLVWAALPL 83 (154)
T ss_pred EEEEEecCCCC-----CCCCcchHHHHHHHHHHHHHHhhhHHHHHhhcceEEEEeCCCCcEEEEEEccccchhHHHHHhH
Confidence 58999999543 4567899999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCeeeEEEEEeeC
Q 045364 81 VRSIGNCLVLFNALDLS 97 (97)
Q Consensus 81 it~i~~~~~~~rvl~vS 97 (97)
|+++++.||.|++|+||
T Consensus 84 I~~i~d~~~~~~tl~Vg 100 (154)
T KOG4639|consen 84 ITKIGDVPCIFRTLFVG 100 (154)
T ss_pred HHhhcCcceEEEEEEEh
Confidence 99999999999999997
No 4
>COG1369 POP5 RNase P/RNase MRP subunit POP5 [Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=4.6e-20 Score=123.41 Aligned_cols=77 Identities=17% Similarity=0.178 Sum_probs=72.5
Q ss_pred cccCHHHHHHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHhhhhcCCeeeEEEEEeeC
Q 045364 19 IILTQFNELKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITMVRSIGNCLVLFNALDLS 97 (97)
Q Consensus 19 ~~l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtlit~i~~~~~~~rvl~vS 97 (97)
..++.+++.++||+++.++|||+|+|.+ ++++.+|++.|+.+||||.|++++.+|+||+++++++|.|+.+++++||
T Consensus 27 ~~i~~~~l~~~I~~s~l~llG~~gta~~--~~~lv~~~~~t~~GIvrc~R~~~~~v~aAL~l~~~~~g~rv~I~~lgvS 103 (124)
T COG1369 27 EEITRGELVRLIRRSLLSLLGDVGTAKA--NPRLVKYYFSTGTGIVRCRREYVDLVRAALMLAREVNGKRVIIVVLGVS 103 (124)
T ss_pred ccCChhHHHHHHHHHHHHHcCccccccc--ceeEEEEeccCCceEEEEechhHHHHHHHHHHHHHhCCceEEEEEeecc
Confidence 3579999999999999999999999986 5888888888999999999999999999999999999999999999998
No 5
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=67.33 E-value=7.1 Score=25.12 Aligned_cols=40 Identities=18% Similarity=0.171 Sum_probs=33.3
Q ss_pred cCHHHHHHHHHHHHHhhcCcccccccCCceeEEEeCCCCce
Q 045364 21 LTQFNELKAIRDNILVNFSECGLASSLRSFQVKYVNPITKL 61 (97)
Q Consensus 21 l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~ 61 (97)
=+..++++-|.+-+.....+ ..+.+...+++.|||..+..
T Consensus 21 En~~~Fy~Pi~~wl~~Yl~~-~~~~i~~~~~L~YfNTSSsk 60 (99)
T PF09345_consen 21 ENAFAFYQPILDWLEAYLAE-PNKPITFNFKLSYFNTSSSK 60 (99)
T ss_pred cCHHHHHHHHHHHHHHHHhC-CCCcEEEEEEEEEEecHhHH
Confidence 37789999999999998888 77778889999999965543
No 6
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=67.10 E-value=31 Score=22.12 Aligned_cols=56 Identities=23% Similarity=0.259 Sum_probs=32.9
Q ss_pred HHHHHhhcCcccccccCCceeEEEe--CCCCceEEEEeCCC-ChhhhHhHHHhh----hhcCCeeeEEEEE
Q 045364 31 RDNILVNFSECGLASSLRSFQVKYV--NPITKLCIIKTSMK-DFQKVWSTITMV----RSIGNCLVLFNAL 94 (97)
Q Consensus 31 ~~~v~~lfGd~G~~~~~~~l~Vky~--~~~t~~~IlRc~r~-~~~~v~saLtli----t~i~~~~~~~rvl 94 (97)
|+.+.+.|.++| .|+|. ..-...|.||+.-. ..+.++.+++.. -.+++..+.+++|
T Consensus 15 re~iK~~f~~~g--------~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~~~~~~~~~i~~~~~~~~vL 77 (105)
T PF08777_consen 15 REDIKEAFSQFG--------EVAYVDFSRGDTEGYVRFKTPEAAQKALEKLKEANDGKLKIKGKEVTLEVL 77 (105)
T ss_dssp HHHHHHHT-SS----------EEEEE--TT-SEEEEEESS---HHHHHHHHHHTTTS-B-TTSSSEEEE--
T ss_pred HHHHHHHHHhcC--------CcceEEecCCCCEEEEEECCcchHHHHHHHHHhccCCceEEcCceEEEEEC
Confidence 667777788877 24443 44456899999986 467777777766 3456777777776
No 7
>cd03485 MutL_Trans_hPMS_1_like MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2. hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. PMS1 forms a heterodimer with MLH1. The MLH1-PMS1 complex functions in meiosis. Loss of yMLH2 results in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies. A role for hMLH1-hPMS1 in DNA mismatch repair has not been established. Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families, however there is no convincing evidence to support hPMS1 having a role in HNPCC predisposition.
Probab=64.92 E-value=8.1 Score=25.46 Aligned_cols=31 Identities=23% Similarity=0.468 Sum_probs=22.2
Q ss_pred EEEeCCCCCCCCCCCccc-CHHHHHHHHHHHHHhhcC
Q 045364 4 EVFLDPNKELPMDDPIIL-TQFNELKAIRDNILVNFS 39 (97)
Q Consensus 4 ei~~~~~~~~~~~~~~~l-~~~~l~~aI~~~v~~lfG 39 (97)
.|..+|.+ ....+ +++.++++|++++.+.|+
T Consensus 101 DVNVhP~K-----~eV~f~~e~~v~~~i~~~v~~~~~ 132 (132)
T cd03485 101 DVNIEPDK-----DDVLLQNKEAVLQAVENLLESLYG 132 (132)
T ss_pred eeccCCcc-----CEEEEcChHHHHHHHHHHHHHHcC
Confidence 34445554 23344 689999999999999986
No 8
>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=58.29 E-value=24 Score=21.46 Aligned_cols=38 Identities=16% Similarity=0.184 Sum_probs=29.1
Q ss_pred HHHHHHHHhhcCcccccccCCceeEEEe-CCCCceEEEE
Q 045364 28 KAIRDNILVNFSECGLASSLRSFQVKYV-NPITKLCIIK 65 (97)
Q Consensus 28 ~aI~~~v~~lfGd~G~~~~~~~l~Vky~-~~~t~~~IlR 65 (97)
.++++-+.+.|||==++++.++++|... ||....++|.
T Consensus 20 ~~~K~li~E~FGDGIMSAIdF~~~v~k~~dp~gdRvvit 58 (69)
T cd00559 20 PTLKALIHEKFGDGIMSAIDFKLDVDKVEDPGGDRVVIT 58 (69)
T ss_pred HHHHHHHHHHcCCceeeeEEeeeeEEeccCCCCCEEEEE
Confidence 3788999999999888998888888876 5544555544
No 9
>cd06407 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-inte
Probab=55.24 E-value=44 Score=20.54 Aligned_cols=57 Identities=16% Similarity=0.298 Sum_probs=35.9
Q ss_pred HHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHhhhhcCCeeeEE
Q 045364 27 LKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITMVRSIGNCLVLF 91 (97)
Q Consensus 27 ~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtlit~i~~~~~~~ 91 (97)
++.+++.+.+.|+--. ...+.+||.|...-.+-|.|..+- .-|+.+-..-+...+.+
T Consensus 22 ~~~L~~~i~~r~~~~~----~~~f~LkY~Ddegd~v~ltsd~DL----~eai~i~~~~~~~~v~l 78 (82)
T cd06407 22 FTELKQEIAKRFKLDD----MSAFDLKYLDDDEEWVLLTCDADL----EECIDVYRSSGSHTIRL 78 (82)
T ss_pred HHHHHHHHHHHhCCCC----CCeeEEEEECCCCCeEEeecHHHH----HHHHHHHHHCCCCeEEE
Confidence 5556666666666421 135999999999999999887553 44444444444444444
No 10
>PF14199 DUF4317: Domain of unknown function (DUF4317)
Probab=49.41 E-value=25 Score=27.76 Aligned_cols=71 Identities=18% Similarity=0.186 Sum_probs=51.5
Q ss_pred CCCcccCHHHHHHHHHHH-HHh------------hcCcccccccCCcee-EEEeCCCCceEEEEeCCCChhhhHhHHHhh
Q 045364 16 DDPIILTQFNELKAIRDN-ILV------------NFSECGLASSLRSFQ-VKYVNPITKLCIIKTSMKDFQKVWSTITMV 81 (97)
Q Consensus 16 ~~~~~l~~~~l~~aI~~~-v~~------------lfGd~G~~~~~~~l~-Vky~~~~t~~~IlRc~r~~~~~v~saLtli 81 (97)
+.|..|+.+++.+.++++ +.+ .+|+ ...-.+.++. -|.+.-.|.-+.|++.-+..+.|.+
T Consensus 275 ~Ep~~L~~~~v~~iL~~sGv~~e~~e~~e~~y~~~~g~-~~~~~a~ni~~~K~~~i~t~~v~I~V~P~~~~~V~t----- 348 (371)
T PF14199_consen 275 PEPPTLDKKDVKRILEESGVEEEKLEKFEKAYEEVFGE-DYELKASNIVDSKSIKIKTPDVVIKVNPEDLDLVKT----- 348 (371)
T ss_pred CCCcccCHHHHHHHHHHcCCchHHHHHHHHHHHHHhCC-CCccchhhccccceEEecCCCEEEEEChhhhcceeE-----
Confidence 477889999999988877 443 5665 3333334443 4666667888999999998888876
Q ss_pred hhcCCeeeEEE
Q 045364 82 RSIGNCLVLFN 92 (97)
Q Consensus 82 t~i~~~~~~~r 92 (97)
..|+|++|.+-
T Consensus 349 ~~idGrkcLvI 359 (371)
T PF14199_consen 349 RVIDGRKCLVI 359 (371)
T ss_pred EEECCEEEEEE
Confidence 44789998764
No 11
>cd03484 MutL_Trans_hPMS_2_like MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2). hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to yeast PMS1. The yeast MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a role in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Cells lacking hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome.
Probab=45.14 E-value=32 Score=22.97 Aligned_cols=32 Identities=13% Similarity=0.281 Sum_probs=21.6
Q ss_pred EEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhc
Q 045364 3 VEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNF 38 (97)
Q Consensus 3 ~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lf 38 (97)
+++..+|.+. +-.-.+++.++++|++++++.|
T Consensus 110 vDvNVhP~K~----eV~f~~e~~i~~~i~~~v~~~~ 141 (142)
T cd03484 110 YDVNVTPDKR----TVLLHDEDRLIDTLKTSLSELF 141 (142)
T ss_pred eeeeeCCccC----EEEEcChHHHHHHHHHHHHHHh
Confidence 3444556553 2222368899999999999876
No 12
>PF11429 Colicin_D: Colicin D; InterPro: IPR024440 Colicin D is a bacteriocin that kills target cells by cleaving tRNA(Arg). This entry represents a domain found in the C terminus of colicin D, which is responsible for its catalytic activity []. The domain is also found in some S-type pyocins, which are also bacteriocins.; GO: 0004540 ribonuclease activity; PDB: 1TFO_A 1V74_A 1TFK_A.
Probab=43.53 E-value=31 Score=22.09 Aligned_cols=31 Identities=19% Similarity=0.157 Sum_probs=18.0
Q ss_pred hcCcccccccCCceeEEEeCCCCceEEEEeCCCCh
Q 045364 37 NFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDF 71 (97)
Q Consensus 37 lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~ 71 (97)
.-|.|+-.. -.-.||||.|+.+++.-.-+.+
T Consensus 42 ~~GtYr~~~----~skV~~N~~T~~~Vi~d~~G~F 72 (92)
T PF11429_consen 42 EKGTYRRVK----DSKVYFNPKTNNVVIIDKDGNF 72 (92)
T ss_dssp E--BETTST----T-EEEEETTTTEEEEE-TTS-E
T ss_pred eccceecCC----CcEEEEeCCCCeEEEEcCCCCE
Confidence 456665432 2367889999999987655543
No 13
>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=42.40 E-value=47 Score=20.38 Aligned_cols=35 Identities=20% Similarity=0.220 Sum_probs=25.0
Q ss_pred HHHHHHHhhcCcccccccCCceeEEEe-CCCCceEE
Q 045364 29 AIRDNILVNFSECGLASSLRSFQVKYV-NPITKLCI 63 (97)
Q Consensus 29 aI~~~v~~lfGd~G~~~~~~~l~Vky~-~~~t~~~I 63 (97)
++++-+.+-|||==++++.++++|... ||..-..+
T Consensus 25 ~~K~li~E~FGDGIMSAIdF~~~v~k~~d~~GdRv~ 60 (73)
T PF02560_consen 25 AIKALIHEKFGDGIMSAIDFKMDVEKVEDPKGDRVV 60 (73)
T ss_dssp HHHHHHHHHT-SEEEEEEEEEEEEEEEE-TTSEEEE
T ss_pred HHHHHHHHhhCcceEEEeeEEEEEEEeeCCCCCEEE
Confidence 567999999999888898888888776 44443333
No 14
>PF00564 PB1: PB1 domain; InterPro: IPR000270 The Phox and Bem1p domain, is present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.; GO: 0005515 protein binding; PDB: 1IPG_A 1IP9_A 2KFK_A 1WMH_A 1VD2_A 1WI0_A 1OEY_C 1PQS_A 1Q1O_A 1TZ1_A ....
Probab=42.25 E-value=71 Score=18.67 Aligned_cols=64 Identities=19% Similarity=0.238 Sum_probs=42.2
Q ss_pred cCHHHHHHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHhhhhcCCeeeEEEE
Q 045364 21 LTQFNELKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITMVRSIGNCLVLFNA 93 (97)
Q Consensus 21 l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtlit~i~~~~~~~rv 93 (97)
+.+..-+..+++.+.+.||.- ...+.++|-|...-..-|.+. ..+.-|+....+.++.+..+.|
T Consensus 18 ~~~~~s~~~L~~~i~~~~~~~-----~~~~~l~Y~D~dgD~V~i~sd----~Dl~~a~~~~~~~~~~~lrl~v 81 (84)
T PF00564_consen 18 LPSDVSFDDLRSKIREKFGLL-----DEDFQLKYKDEDGDLVTISSD----EDLQEAIEQAKESGSKTLRLFV 81 (84)
T ss_dssp ECSTSHHHHHHHHHHHHHTTS-----TSSEEEEEEETTSSEEEESSH----HHHHHHHHHHHHCTTSCEEEEE
T ss_pred cCCCCCHHHHHHHHHHHhCCC-----CccEEEEeeCCCCCEEEeCCH----HHHHHHHHHHHhcCCCcEEEEE
Confidence 334446777888888888886 345999999987766655544 4455566666655666665554
No 15
>PF11537 DUF3227: Protein of unknown function (DUF3227); InterPro: IPR021609 This archaeal family of proteins has no known function. ; PDB: 2P9X_C.
Probab=42.20 E-value=13 Score=24.26 Aligned_cols=17 Identities=12% Similarity=0.090 Sum_probs=12.1
Q ss_pred HHHHHHHhhcCcccccc
Q 045364 29 AIRDNILVNFSECGLAS 45 (97)
Q Consensus 29 aI~~~v~~lfGd~G~~~ 45 (97)
-+++++.++||++++-.
T Consensus 48 ~F~~avsklfGe~sA~l 64 (102)
T PF11537_consen 48 KFYEAVSKLFGEYSARL 64 (102)
T ss_dssp HHHHHHHHHH-HHHHHH
T ss_pred HHHHHHHHHHHHhHHHH
Confidence 46778899999996543
No 16
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=39.83 E-value=29 Score=21.37 Aligned_cols=31 Identities=6% Similarity=0.184 Sum_probs=18.9
Q ss_pred EEEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcC
Q 045364 2 IVEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNFS 39 (97)
Q Consensus 2 l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfG 39 (97)
++||...+++. . =.++.|+++|.+.+.+..|
T Consensus 31 ~I~It~~~gRs-----~--e~K~~ly~~l~~~L~~~~g 61 (82)
T PF14552_consen 31 IIQITSGAGRS-----T--EQKKALYRALAERLAEKLG 61 (82)
T ss_dssp EEEEEECS--------H--HHHHHHHHHHHHHHHHHH-
T ss_pred EEEEEECCCCC-----H--HHHHHHHHHHHHHHHHHcC
Confidence 56666666552 1 1578888888888877655
No 17
>PRK02866 cyanate hydratase; Validated
Probab=39.63 E-value=55 Score=22.63 Aligned_cols=37 Identities=16% Similarity=0.215 Sum_probs=29.4
Q ss_pred HHHHHHHhhcCcccccccCCceeEEEe-CCCCceEEEE
Q 045364 29 AIRDNILVNFSECGLASSLRSFQVKYV-NPITKLCIIK 65 (97)
Q Consensus 29 aI~~~v~~lfGd~G~~~~~~~l~Vky~-~~~t~~~IlR 65 (97)
+|++-+.+-|||==++++.++++|..- ||.....+|-
T Consensus 99 ~~K~~i~E~FGDGIMSAIdf~~~v~k~~dp~Gdrv~it 136 (147)
T PRK02866 99 TLKALIHEKFGDGIMSAIDFKLDVDKVEDPKGDRVVIT 136 (147)
T ss_pred HHHHHHHHHhCCceeeeeeeceeeeeccCCCCCEEEEE
Confidence 678999999999888999889998876 5665555554
No 18
>PF11918 DUF3436: Domain of unknown function (DUF3436); InterPro: IPR024591 This uncharacterised N-terminal domain is associated with the interphotoreceptor retinol-binding protein family. It is about 50 amino acids in length and has two conserved sequence motifs: DPRL and SYEP.
Probab=39.37 E-value=64 Score=18.76 Aligned_cols=31 Identities=19% Similarity=0.180 Sum_probs=21.3
Q ss_pred EEeCCCCC-CCCC--CCcccCHHHHHHHHHHHHH
Q 045364 5 VFLDPNKE-LPMD--DPIILTQFNELKAIRDNIL 35 (97)
Q Consensus 5 i~~~~~~~-~~~~--~~~~l~~~~l~~aI~~~v~ 35 (97)
|-|+|+-- .|+. ....|++.+|...|+.+++
T Consensus 19 ISYEP~~~eaP~~~p~~~~Lt~EqLla~lq~~ik 52 (55)
T PF11918_consen 19 ISYEPSYVEAPQQPPALPNLTPEQLLAMLQKSIK 52 (55)
T ss_pred EEeCCCCCCCCCCCCCCCCcCHHHHHHHHHhhee
Confidence 56777732 2322 3346899999999998874
No 19
>cd01735 LSm12_N LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain.
Probab=39.22 E-value=43 Score=19.74 Aligned_cols=18 Identities=22% Similarity=0.200 Sum_probs=15.7
Q ss_pred EEEeCCCCceEEEEeCCC
Q 045364 52 VKYVNPITKLCIIKTSMK 69 (97)
Q Consensus 52 Vky~~~~t~~~IlRc~r~ 69 (97)
|.-||..|++.||+|+..
T Consensus 23 V~afD~~tk~lIlk~~s~ 40 (61)
T cd01735 23 VVAFDYPSKMLILKCPSS 40 (61)
T ss_pred EEEecCCCcEEEEECccc
Confidence 667899999999999884
No 20
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=38.92 E-value=61 Score=17.96 Aligned_cols=32 Identities=6% Similarity=-0.035 Sum_probs=24.0
Q ss_pred EEEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCc
Q 045364 2 IVEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNFSE 40 (97)
Q Consensus 2 l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd 40 (97)
+++|.+.++++ +. ..+.|.++|-+++.+.||-
T Consensus 3 ~i~I~~~~grs-----~e--qk~~l~~~it~~l~~~~~~ 34 (62)
T PRK00745 3 TFHIELFEGRT-----VE--QKRKLVEEITRVTVETLGC 34 (62)
T ss_pred EEEEEEcCCCC-----HH--HHHHHHHHHHHHHHHHcCC
Confidence 46677677652 22 6789999999999999983
No 21
>PF10850 DUF2653: Protein of unknown function (DUF2653); InterPro: IPR020516 This entry contains proteins with no known function.
Probab=38.56 E-value=45 Score=21.31 Aligned_cols=50 Identities=16% Similarity=0.244 Sum_probs=33.1
Q ss_pred EEEEEeCCCCCCCCC-----CCcccCHHHHHHHHHHHHHhhcCcccccccCCceeEEE
Q 045364 2 IVEVFLDPNKELPMD-----DPIILTQFNELKAIRDNILVNFSECGLASSLRSFQVKY 54 (97)
Q Consensus 2 l~ei~~~~~~~~~~~-----~~~~l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky 54 (97)
.||+.|+++.-+... +.-.|....+.+|||.=+.+.++-=--+ .++++++
T Consensus 30 eVeL~yDdd~GFsAEv~~ngr~q~l~~~nlieAIr~~l~~~~~~~p~~---~~i~L~l 84 (91)
T PF10850_consen 30 EVELMYDDDYGFSAEVWVNGRSQYLIEANLIEAIRQYLEEEYNMDPFR---AGIELEL 84 (91)
T ss_pred EEEEEEecCCCeeEEEEECCeEEEEchhhHHHHHHHHHHHHhCCCcch---hheEEEE
Confidence 467888876543211 3346789999999999999988753222 2356664
No 22
>cd06396 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain.
Probab=38.48 E-value=98 Score=19.23 Aligned_cols=42 Identities=14% Similarity=0.185 Sum_probs=31.6
Q ss_pred HHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhH
Q 045364 27 LKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVW 75 (97)
Q Consensus 27 ~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~ 75 (97)
+..+.+.++..||=- .+++||.|...--+.|-|.-+..+-++
T Consensus 24 ~~~L~~ev~~rf~l~-------~f~lKYlDde~e~v~lssd~eLeE~~r 65 (81)
T cd06396 24 WASVEAMVKVSFGLN-------DIQIKYVDEENEEVSVNSQGEYEEALK 65 (81)
T ss_pred HHHHHHHHHHHhCCC-------cceeEEEcCCCCEEEEEchhhHHHHHH
Confidence 555666667777643 489999999999999999776666554
No 23
>cd05992 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.
Probab=38.18 E-value=82 Score=18.24 Aligned_cols=57 Identities=21% Similarity=0.302 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHhhhhcCCeeeEE
Q 045364 26 ELKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITMVRSIGNCLVLF 91 (97)
Q Consensus 26 l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtlit~i~~~~~~~ 91 (97)
=+..+++.+.+.||... ..+.++|-|+..-...|... ..+.-|+.....-+.....+
T Consensus 22 s~~~L~~~i~~~~~~~~-----~~~~l~y~D~e~d~v~l~sd----~Dl~~a~~~~~~~~~~~l~l 78 (81)
T cd05992 22 SFEDLRSKIAEKFGLDA-----VSFKLKYPDEDGDLVTISSD----EDLEEAIEEARRSGSKKLRL 78 (81)
T ss_pred CHHHHHHHHHHHhCCCC-----CcEEEEeeCCCCCEEEeCCH----HHHHHHHHHHhhcCCccEEE
Confidence 35667777777787643 35899999998866666653 34445555554433333333
No 24
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=37.43 E-value=64 Score=22.38 Aligned_cols=37 Identities=14% Similarity=0.210 Sum_probs=29.3
Q ss_pred HHHHHHHhhcCcccccccCCceeEEEe-CCCCceEEEE
Q 045364 29 AIRDNILVNFSECGLASSLRSFQVKYV-NPITKLCIIK 65 (97)
Q Consensus 29 aI~~~v~~lfGd~G~~~~~~~l~Vky~-~~~t~~~IlR 65 (97)
++++-+.+-|||==++++-++++|..- ||...+.+|.
T Consensus 102 ~~K~~i~E~FGDGIMSAIdF~~~v~k~~dp~Gdrv~it 139 (150)
T TIGR00673 102 TLKAVVHEKFGDGIMSAIDFKLDVEKVADPGGERAVIT 139 (150)
T ss_pred HHHHHHHHHhCcceeeeeeeceeeeeecCCCCCEEEEE
Confidence 688999999999888999889998875 6655555554
No 25
>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL. This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....
Probab=37.27 E-value=42 Score=21.50 Aligned_cols=31 Identities=19% Similarity=0.225 Sum_probs=20.4
Q ss_pred EEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhc
Q 045364 4 EVFLDPNKELPMDDPIILTQFNELKAIRDNILVNF 38 (97)
Q Consensus 4 ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lf 38 (97)
.+..+|.+. +-.-.+++.+.++|++++.+.+
T Consensus 88 DVNvhP~K~----eV~f~~e~~i~~~i~~~i~~~L 118 (119)
T PF01119_consen 88 DVNVHPAKR----EVRFRDEDEILNLIEEAIREAL 118 (119)
T ss_dssp EETSSTTTT-----EEETTHHHHHHHHHHHHHHHH
T ss_pred cccccccce----EEEecCHHHHHHHHHHHHHHHh
Confidence 445556653 3333378999999999988753
No 26
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=35.75 E-value=72 Score=17.59 Aligned_cols=32 Identities=13% Similarity=0.030 Sum_probs=23.5
Q ss_pred EEEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCc
Q 045364 2 IVEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNFSE 40 (97)
Q Consensus 2 l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd 40 (97)
+++|..-+|+. + =..+.|+++|.+++.+.+|-
T Consensus 3 ~i~i~~~~Grs-----~--eqk~~l~~~it~~l~~~~~~ 34 (61)
T PRK02220 3 YVHIKLIEGRT-----E--EQLKALVKDVTAAVSKNTGA 34 (61)
T ss_pred EEEEEEcCCCC-----H--HHHHHHHHHHHHHHHHHhCc
Confidence 35565566652 2 26889999999999999985
No 27
>cd00782 MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot synd
Probab=35.58 E-value=63 Score=20.43 Aligned_cols=31 Identities=23% Similarity=0.385 Sum_probs=21.1
Q ss_pred EEEEeCCCCCCCCCCCccc-CHHHHHHHHHHHHHhhc
Q 045364 3 VEVFLDPNKELPMDDPIIL-TQFNELKAIRDNILVNF 38 (97)
Q Consensus 3 ~ei~~~~~~~~~~~~~~~l-~~~~l~~aI~~~v~~lf 38 (97)
+++..+|.+. ...+ +++.+.++|++++.+.+
T Consensus 91 ~DvNvhP~K~-----eV~f~~~~~i~~~i~~~v~~~l 122 (122)
T cd00782 91 VDVNVHPTKR-----EVRFSDEEEVLELIREALRSAL 122 (122)
T ss_pred eeeeeCCCCC-----EEEecCHHHHHHHHHHHHHHhC
Confidence 3455666653 3334 68899999999988753
No 28
>smart00200 SEA Domain found in sea urchin sperm protein, enterokinase, agrin. Proposed function of regulating or binding carbohydrate sidechains.
Probab=35.18 E-value=78 Score=20.64 Aligned_cols=51 Identities=12% Similarity=0.107 Sum_probs=36.0
Q ss_pred EEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCcccccccCCceeEEEeCCCC
Q 045364 5 VFLDPNKELPMDDPIILTQFNELKAIRDNILVNFSECGLASSLRSFQVKYVNPIT 59 (97)
Q Consensus 5 i~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t 59 (97)
+-|.|+.+ +|..-.-++|.+.|.+.+.+.|+.--.+.-=.+..|+++.+..
T Consensus 19 i~ys~~L~----d~sS~~f~eL~~~ie~~l~~~f~~s~l~~~f~~~~V~~~~~gs 69 (121)
T smart00200 19 LQYSPSLE----DPSSEEYQELVRDVEKLLEQIYGKTDLKPDFVGTEVIEFRNGS 69 (121)
T ss_pred eeeChhhC----CcccHHHHHHHHHHHHHHHHHHhcCccccceeEEEEEEEcCCc
Confidence 56777766 5665667899999999999999875332222356788887744
No 29
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=35.15 E-value=77 Score=17.15 Aligned_cols=31 Identities=3% Similarity=0.163 Sum_probs=22.7
Q ss_pred EEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCc
Q 045364 3 VEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNFSE 40 (97)
Q Consensus 3 ~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd 40 (97)
++|-+.++++ +. ..+.|.++|.+++.+.+|-
T Consensus 3 i~i~~~~grt-----~e--qk~~l~~~i~~~l~~~~g~ 33 (58)
T cd00491 3 VQIYILEGRT-----DE--QKRELIERVTEAVSEILGA 33 (58)
T ss_pred EEEEEcCCCC-----HH--HHHHHHHHHHHHHHHHhCc
Confidence 4555566552 22 5788999999999999886
No 30
>PF09559 Cas6: Cas6 Crispr; InterPro: IPR014174 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. Members of this entry resemble the Cas6 proteins described by IPR010156 from INTERPRO in having a C-terminal motif GXGXXXXXGXG, where the single X of each GXG is hydrophobic and the spacer XXXXX has at least one Lys or Arg. Examples are found in cas gene operons of CRISPR regions in Anabaena variabilis (strain ATCC 29413/PCC 7937), Leptospira interrogans, Gemmata obscuriglobus UQM 2246, and twice in Myxococcus xanthus (strain DK 1622). Oddly, an orphan member is found in Thiobacillus denitrificans (strain ATCC 25259), whose genome does not seem to contain other evidence of CRISPR repeats or cas genes.
Probab=34.55 E-value=1.1e+02 Score=22.11 Aligned_cols=65 Identities=14% Similarity=0.154 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHhhcCcccccc-------cCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHhhh---hcCCeeeEE
Q 045364 23 QFNELKAIRDNILVNFSECGLAS-------SLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITMVR---SIGNCLVLF 91 (97)
Q Consensus 23 ~~~l~~aI~~~v~~lfGd~G~~~-------~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtlit---~i~~~~~~~ 91 (97)
...|+.||...+-.++.+=+.|. .+.+=+..|.+..| ...|||+++....+. ++.. +++|+++.+
T Consensus 17 ~y~L~sAl~~~~P~l~e~~~~gI~~I~g~~~~~g~~~l~Ls~rs-rL~lR~P~~~v~~~~---~L~G~~l~l~gh~l~l 91 (195)
T PF09559_consen 17 AYALYSALCRLLPWLHEEPGLGIHPIHGAPSGNGDQLLYLSRRS-RLRLRVPRDRVDDVY---ALAGKTLDLGGHPLRL 91 (195)
T ss_pred HHHHHHHHHHhCccccCCCCcceEEeecCcCCCCceEEEeCCCc-eEEEECCHHHhhHHH---hcCCCEEEECCeEEEe
Confidence 67899999999988888776551 11111267777655 567999999888654 2333 246666654
No 31
>smart00666 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.
Probab=34.32 E-value=98 Score=18.02 Aligned_cols=52 Identities=19% Similarity=0.297 Sum_probs=34.3
Q ss_pred HHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHhhhhcCCe
Q 045364 27 LKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITMVRSIGNC 87 (97)
Q Consensus 27 ~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtlit~i~~~ 87 (97)
+..+++.+.+.|+.-+ .++.++|-|+..-..-|.+ -..+..|+.+...-++.
T Consensus 23 ~~dL~~~i~~~~~~~~-----~~~~l~Y~Dedgd~v~l~s----d~Dl~~a~~~~~~~~~~ 74 (81)
T smart00666 23 FEDLRSKVAKRFGLDN-----QSFTLKYQDEDGDLVSLTS----DEDLEEAIEEYDSLGSK 74 (81)
T ss_pred HHHHHHHHHHHhCCCC-----CCeEEEEECCCCCEEEecC----HHHHHHHHHHHHHcCCc
Confidence 6667777778887543 3588999998876666665 34555566666554433
No 32
>COG2302 Uncharacterized conserved protein, contains S4-like domain [Function unknown]
Probab=33.84 E-value=1.9e+02 Score=21.94 Aligned_cols=69 Identities=13% Similarity=0.116 Sum_probs=43.3
Q ss_pred EEEEEeCCCCCCCCCCCcccCHHHHHHHHHHH--HHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHH
Q 045364 2 IVEVFLDPNKELPMDDPIILTQFNELKAIRDN--ILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTIT 79 (97)
Q Consensus 2 l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~--v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLt 79 (97)
|+||.|++.- .+++.++++.+++.- -++.|||.=...- .-++. +.. ++.-..+.
T Consensus 89 l~eI~y~~kF-------~~l~H~~~LGtll~lGikRe~~GDIiv~~~--~aQli------------v~~---~~~~f~~~ 144 (257)
T COG2302 89 LLEISYASKF-------VSLTHRDILGTLLSLGIKREKFGDIIVEGE--GAQLI------------VAT---ELADFFLL 144 (257)
T ss_pred EEEEEccccc-------ccccHHHHHHHHHhccCcHHhhccEEEeCC--eeEEE------------Eeh---hHHHHHHH
Confidence 6788888754 468999999999882 3688999632211 11111 222 23333444
Q ss_pred hhhhcCCeeeEEEEE
Q 045364 80 MVRSIGNCLVLFNAL 94 (97)
Q Consensus 80 lit~i~~~~~~~rvl 94 (97)
=++++++.||.+.-+
T Consensus 145 ~Ltkig~~~V~l~ei 159 (257)
T COG2302 145 HLTKIGKAPVKLEEI 159 (257)
T ss_pred HHHhhcCcceEEEEc
Confidence 578888888887654
No 33
>PF14350 Beta_protein: Beta protein
Probab=33.72 E-value=1.2e+02 Score=22.92 Aligned_cols=48 Identities=19% Similarity=0.260 Sum_probs=36.1
Q ss_pred CCcccCHHHHHHHHHH---HHHhhcCcccccccCCc----------eeEEEeCCCCceEEEE
Q 045364 17 DPIILTQFNELKAIRD---NILVNFSECGLASSLRS----------FQVKYVNPITKLCIIK 65 (97)
Q Consensus 17 ~~~~l~~~~l~~aI~~---~v~~lfGd~G~~~~~~~----------l~Vky~~~~t~~~IlR 65 (97)
...+..+..+++.|++ ...-.|||||....... .+|.|-- .+..-+.|
T Consensus 213 ~~i~r~E~~l~~~i~~~~~~~~~~yGDYg~~~p~~~~~~~~~~~~~~~I~Yt~-~~~w~~~R 273 (347)
T PF14350_consen 213 GEIPRHEWDLWKAIRSQNNDRRPIYGDYGSIHPDYSDPDGGGGRPNPRIRYTT-DDKWYVVR 273 (347)
T ss_pred CceeeHHHHHHHHHhhhcCCCCcccCCCCCCCcccccCCccCCCCCeEEEEEC-CCcEEEEE
Confidence 4455679999999999 88889999998754433 4677755 45678888
No 34
>TIGR02807 cas6_var CRISPR-associated protein, Cas6-related. Members of this protein family resemble the Cas6 proteins described by TIGR01877 in having a C-terminal motif GXGXXXXXGXG, where the single X of each GXG is hydrophobic and the spacer XXXXX has at least one Lys or Arg. Examples are found in cas gene operons of CRISPR regions in Anabaena variabilis ATCC 29413, Leptospira interrogans, Gemmata obscuriglobus UQM 2246, and twice in Myxococcus xanthus DK 1622. Oddly, an orphan member is found in Thiobacillus denitrificans ATCC 25259, whose genome does not seem to contain other evidence of CRISPR repeats or cas genes.
Probab=33.27 E-value=1.8e+02 Score=21.01 Aligned_cols=66 Identities=8% Similarity=0.058 Sum_probs=42.2
Q ss_pred EEEEEeC-CCCCCCCCCCcccC-HHHHHHHHHHHHHhhcCcccccc--c-----CCceeEEEeCCCCceEEEEeCCCChh
Q 045364 2 IVEVFLD-PNKELPMDDPIILT-QFNELKAIRDNILVNFSECGLAS--S-----LRSFQVKYVNPITKLCIIKTSMKDFQ 72 (97)
Q Consensus 2 l~ei~~~-~~~~~~~~~~~~l~-~~~l~~aI~~~v~~lfGd~G~~~--~-----~~~l~Vky~~~~t~~~IlRc~r~~~~ 72 (97)
++++.|+ .++. .+++ ...|+.||...+-.++.+-++|. + ..+ +.|.++. +...+||+++...
T Consensus 3 ~vDl~F~v~g~~------lP~DHay~L~sAl~~~~P~l~~~~~~gI~~i~g~~~~~G--~l~l~~r-s~L~iRvp~~~v~ 73 (190)
T TIGR02807 3 LIDLLFPVRGGT------VPADHAYMLFSALCGVLPALHERDDLGIQTLRGVPDNSG--VLNLTRR-SRLRIRIPVEQVP 73 (190)
T ss_pred cEEEEeEecCcc------ccccchHHHHHHHHhhCcccccCCCcceEEeccCCCCCc--eEeeCCc-ceEEEEcCHHHhH
Confidence 3566666 3333 3333 57888999888887776665552 1 122 6777764 4678999998877
Q ss_pred hhHh
Q 045364 73 KVWS 76 (97)
Q Consensus 73 ~v~s 76 (97)
.+..
T Consensus 74 ~~~~ 77 (190)
T TIGR02807 74 LVLP 77 (190)
T ss_pred HHHH
Confidence 6443
No 35
>PF14730 DUF4468: Domain of unknown function (DUF4468) with TBP-like fold
Probab=31.44 E-value=1.3e+02 Score=18.43 Aligned_cols=40 Identities=13% Similarity=0.115 Sum_probs=33.4
Q ss_pred ccCHHHHHHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEe
Q 045364 20 ILTQFNELKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKT 66 (97)
Q Consensus 20 ~l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc 66 (97)
..+..+|++..++-+.+.|.+. +-.|.+-|...|..+.+.
T Consensus 9 g~sk~~ly~~~~~W~~~~~~~~-------~s~I~~~dke~g~I~~~g 48 (91)
T PF14730_consen 9 GMSKDQLYDRAKKWLAKNFKSA-------NSVIQYSDKEEGTIIAKG 48 (91)
T ss_pred CCCHHHHHHHHHHHHHHhcccc-------cceEEEEcCCCCEEEEEE
Confidence 3589999999999999999992 234888899998887776
No 36
>PF10184 DUF2358: Uncharacterized conserved protein (DUF2358); InterPro: IPR018790 This entry represents a family of conserved proteins. The function is unknown.
Probab=31.23 E-value=1.4e+02 Score=18.94 Aligned_cols=53 Identities=9% Similarity=0.303 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHhhc-CcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHhhhh
Q 045364 25 NELKAIRDNILVNF-SECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITMVRS 83 (97)
Q Consensus 25 ~l~~aI~~~v~~lf-Gd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtlit~ 83 (97)
++.+.+|+-+...| |+.-.+. ..-+|.+-||.++.-= ++.|+...+++.++..
T Consensus 2 ~~~~~Lr~D~~~~f~~~~~~~i--Y~~dv~F~Dp~~~f~g----~~~Y~~~~~~l~~l~~ 55 (113)
T PF10184_consen 2 DVIRTLREDLPRFFTGDLDYSI--YDEDVVFIDPIVSFKG----LDRYKRNLWALRFLGR 55 (113)
T ss_pred hHHHHHHHHHHHHhcCCCChhh--cCCCeEEECCCCceec----HHHHHHHHHHHHHHHh
Confidence 46788999999988 4544443 4577999999765432 6667777667777777
No 37
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=31.22 E-value=87 Score=17.61 Aligned_cols=32 Identities=16% Similarity=0.191 Sum_probs=23.2
Q ss_pred EEEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCc
Q 045364 2 IVEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNFSE 40 (97)
Q Consensus 2 l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd 40 (97)
+++|.+.++++ + =..+.|+++|-+++.+.+|-
T Consensus 3 ~v~i~l~~grt-----~--eqk~~l~~~it~~l~~~lg~ 34 (64)
T PRK01964 3 IVQIQLLEGRP-----E--EKIKNLIREVTEAISATLDV 34 (64)
T ss_pred EEEEEEeCCCC-----H--HHHHHHHHHHHHHHHHHhCc
Confidence 35666666652 2 26788999999999998875
No 38
>KOG4048 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.20 E-value=28 Score=24.86 Aligned_cols=23 Identities=17% Similarity=0.176 Sum_probs=19.5
Q ss_pred CHHHHHHHHHHHHHhhcCccccc
Q 045364 22 TQFNELKAIRDNILVNFSECGLA 44 (97)
Q Consensus 22 ~~~~l~~aI~~~v~~lfGd~G~~ 44 (97)
-++.+.++||+.+++.||+=-.|
T Consensus 67 Ge~Nf~~CiR~gLe~HyG~Kivg 89 (201)
T KOG4048|consen 67 GEKNFTNCIRDGLEEHYGKKIVG 89 (201)
T ss_pred ccchHHHHHHHHHHHhcCccccc
Confidence 47899999999999999995333
No 39
>PF08265 YL1_C: YL1 nuclear protein C-terminal domain; InterPro: IPR013272 This domain is found at the C terminus in proteins of the YL1 family []. These proteins have been shown to be DNA-binding and may be transcription factors []. This domain is also found in proteins that do not belong to the YL1 family.
Probab=31.06 E-value=19 Score=18.25 Aligned_cols=14 Identities=29% Similarity=0.565 Sum_probs=11.0
Q ss_pred CceeEEEeCCCCce
Q 045364 48 RSFQVKYVNPITKL 61 (97)
Q Consensus 48 ~~l~Vky~~~~t~~ 61 (97)
.++--+|.||.|++
T Consensus 6 TglpA~Y~DP~T~l 19 (30)
T PF08265_consen 6 TGLPARYRDPKTGL 19 (30)
T ss_pred cCCCccccCCCCCC
Confidence 35678999999975
No 40
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=29.81 E-value=92 Score=21.47 Aligned_cols=36 Identities=17% Similarity=0.228 Sum_probs=28.2
Q ss_pred HHHHHHHhhcCcccccccCCceeEEEe-CCCC-ceEEE
Q 045364 29 AIRDNILVNFSECGLASSLRSFQVKYV-NPIT-KLCII 64 (97)
Q Consensus 29 aI~~~v~~lfGd~G~~~~~~~l~Vky~-~~~t-~~~Il 64 (97)
.+++-+.+.|||==.+++.++++|++. ||+. .++.|
T Consensus 102 ~lK~lihE~FGDGImSAIdf~ld~ek~~dpeG~~R~~i 139 (151)
T COG1513 102 TLKALIHEKFGDGIMSAIDFKLDVEKVADPEGGERVVI 139 (151)
T ss_pred hHHHHHHHHhccchhhheeeeeeeeeccCCCCCceEEE
Confidence 478889999999889999999999887 5555 34444
No 41
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=29.14 E-value=1.1e+02 Score=17.16 Aligned_cols=32 Identities=6% Similarity=-0.029 Sum_probs=23.5
Q ss_pred EEEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCc
Q 045364 2 IVEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNFSE 40 (97)
Q Consensus 2 l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd 40 (97)
++.|-+.+|++ +. ..+.|.++|-+++.+.||.
T Consensus 3 ~i~i~~~~Grs-----~E--qK~~L~~~it~a~~~~~~~ 34 (60)
T PRK02289 3 FVRIDLFEGRS-----QE--QKNALAREVTEVVSRIAKA 34 (60)
T ss_pred EEEEEECCCCC-----HH--HHHHHHHHHHHHHHHHhCc
Confidence 35566666653 22 5788999999999999886
No 42
>TIGR02520 pilus_B_mal_scr type IVB pilus formation outer membrane protein, R64 PilN family. Several related protein families encode outer membrane pore proteins for type II secretion, type III secretion, and type IV pilus formation. This protein family appears to encode a secretin for pilus formation, although it is quite different from PilQ. Members include the PilN lipoprotein of the plasmid R64 thin pilus, a type IV pilus. Scoring between the trusted and noise cutoffs are examples of bundle-forming pilus B (bfpB).
Probab=29.12 E-value=1.9e+02 Score=23.48 Aligned_cols=61 Identities=20% Similarity=0.103 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHHHhhhhcCCeeeEEE
Q 045364 23 QFNELKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTITMVRSIGNCLVLFN 92 (97)
Q Consensus 23 ~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saLtlit~i~~~~~~~r 92 (97)
+.++.+.|.+.++.+-+.-| . ...|+.++..++|-..+.++.+..-|.-+..--.+.|.+.
T Consensus 204 ~~d~w~~l~~~i~~~Ls~~G--~-------v~~~~~tg~l~Vt~tp~~l~~V~~~i~~l~~~l~rQV~Ie 264 (497)
T TIGR02520 204 ESSVHNDIQQSIKSMLSSSG--S-------WHLSGSTGSLVVTDVPEVLDRVASYIDSQNRRLTRQVLLN 264 (497)
T ss_pred cchHHHHHHHHHHHHhCCCC--c-------EEEcCCCCEEEEEeCHHHHHHHHHHHHHHHhhhcceEEEE
Confidence 56788999999999888733 2 2359999999999999888888875555544223345444
No 43
>PF14500 MMS19_N: Dos2-interacting transcription regulator of RNA-Pol-II
Probab=28.43 E-value=99 Score=22.95 Aligned_cols=29 Identities=21% Similarity=0.323 Sum_probs=23.9
Q ss_pred CCCcccCHHHHHHHHHHHHH--hhcCccccc
Q 045364 16 DDPIILTQFNELKAIRDNIL--VNFSECGLA 44 (97)
Q Consensus 16 ~~~~~l~~~~l~~aI~~~v~--~lfGd~G~~ 44 (97)
++|..+|+.+|..++++.+. ..|+++-..
T Consensus 181 ~dp~~IT~edLk~~L~~cl~s~~~fa~~~~p 211 (262)
T PF14500_consen 181 NDPYGITREDLKRALRNCLSSTPLFAPFAFP 211 (262)
T ss_pred CCCCCCCHHHHHHHHHHHhcCcHhhHHHHHH
Confidence 37889999999999999997 477776544
No 44
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=28.21 E-value=1.3e+02 Score=17.68 Aligned_cols=35 Identities=6% Similarity=0.075 Sum_probs=21.8
Q ss_pred HHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhh
Q 045364 30 IRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQK 73 (97)
Q Consensus 30 I~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~ 73 (97)
.....++.||| +++.-|+....-..|||+--....
T Consensus 8 ~~~r~~e~Fp~---------~slvef~g~~~PvtI~CP~HG~~~ 42 (60)
T PF05265_consen 8 AASRFEEKFPH---------YSLVEFSGVATPVTIRCPKHGNFT 42 (60)
T ss_pred HHHHHHHHCCC---------ceEEEEeCCCCceEEECCCCCcEE
Confidence 34557889999 334444445556788998644433
No 45
>cd06401 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown.
Probab=26.87 E-value=1.5e+02 Score=18.47 Aligned_cols=37 Identities=16% Similarity=0.116 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhcCcc-cccccCCceeEEEeCCCCceEEEEe
Q 045364 27 LKAIRDNILVNFSEC-GLASSLRSFQVKYVNPITKLCIIKT 66 (97)
Q Consensus 27 ~~aI~~~v~~lfGd~-G~~~~~~~l~Vky~~~~t~~~IlRc 66 (97)
+.-+++.++..|.+- +... ++-|||-|+..-..-|-+
T Consensus 23 ~~~L~~~v~~~F~~~~~~~~---~flIKYkD~dGDlVTIts 60 (81)
T cd06401 23 YDELLLMMQRVFRGKLGSSD---DVLIKYKDEDGDLITIFD 60 (81)
T ss_pred HHHHHHHHHHHhccccCCcc---cEEEEEECCCCCEEEecc
Confidence 445666777777643 3222 488999999766555544
No 46
>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and ATGP4 are plant-specific isoprenylated GTP-binding proteins with a single fold that resembles ubiquitin. The function of these proteins is unknown.
Probab=24.93 E-value=2.1e+02 Score=18.91 Aligned_cols=49 Identities=6% Similarity=0.219 Sum_probs=33.7
Q ss_pred EEEE--eCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCccc---ccccCCceeEEEe
Q 045364 3 VEVF--LDPNKELPMDDPIILTQFNELKAIRDNILVNFSECG---LASSLRSFQVKYV 55 (97)
Q Consensus 3 ~ei~--~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd~G---~~~~~~~l~Vky~ 55 (97)
+||- ++||.|. .|..+++++-...+++.|.+.+|+ + .-......+++|-
T Consensus 5 ~e~kfrl~dg~di---gp~~~~~sdTV~~lKekI~~~~p~-~ke~~P~~~~~qKLIys 58 (113)
T cd01814 5 IEIKFRLYDGSDI---GPKRYPAATTVDFLKERVVSQWPK-DKEVGPKTVNEVKLISA 58 (113)
T ss_pred EEEEEEccCCCcc---CccccChhhHHHHHHHHHHHhccc-ccccCCCCHHHeEEEeC
Confidence 4544 4577664 577889999999999999999986 2 1111223667774
No 47
>cd03483 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.
Probab=24.56 E-value=1e+02 Score=20.09 Aligned_cols=30 Identities=13% Similarity=0.243 Sum_probs=20.7
Q ss_pred EEEeCCCCCCCCCCCccc-CHHHHHHHHHHHHHhhc
Q 045364 4 EVFLDPNKELPMDDPIIL-TQFNELKAIRDNILVNF 38 (97)
Q Consensus 4 ei~~~~~~~~~~~~~~~l-~~~~l~~aI~~~v~~lf 38 (97)
.+..+|.+ ....+ +++.+.++|++++.+.+
T Consensus 96 DVNVHP~K-----~eV~f~~e~~i~~~i~~~v~~~L 126 (127)
T cd03483 96 DVNVHPTK-----REVHFLNEEEIIERIQKLVEDKL 126 (127)
T ss_pred eeccCCCc-----cEEEecCHHHHHHHHHHHHHHHh
Confidence 44455655 33444 68899999999998754
No 48
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=24.50 E-value=1.4e+02 Score=16.81 Aligned_cols=43 Identities=16% Similarity=0.062 Sum_probs=27.8
Q ss_pred EEEeCCCCceEEEEeCCCChhhh--HhHHHhhh--hc-CCeeeEEEEE
Q 045364 52 VKYVNPITKLCIIKTSMKDFQKV--WSTITMVR--SI-GNCLVLFNAL 94 (97)
Q Consensus 52 Vky~~~~t~~~IlRc~r~~~~~v--~saLtlit--~i-~~~~~~~rvl 94 (97)
|+.||+..+.+.|++..+..+.. .+++.--. .+ .|.+|.|.+.
T Consensus 5 V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G~~V~F~~~ 52 (66)
T PF00313_consen 5 VKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEGDRVEFEVE 52 (66)
T ss_dssp EEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TTSEEEEEEE
T ss_pred EEEEECCCCceEEEEcccceeEEeccccccccccccCCCCCEEEEEEE
Confidence 89999999999999998773222 23333222 22 4667777664
No 49
>COG1270 CbiB Cobalamin biosynthesis protein CobD/CbiB [Coenzyme metabolism]
Probab=23.99 E-value=87 Score=24.34 Aligned_cols=25 Identities=16% Similarity=0.147 Sum_probs=22.6
Q ss_pred CCcccCHHHHHHHHHHHHHhhcCcc
Q 045364 17 DPIILTQFNELKAIRDNILVNFSEC 41 (97)
Q Consensus 17 ~~~~l~~~~l~~aI~~~v~~lfGd~ 41 (97)
++..+++.++.+|--|++.+++.|-
T Consensus 132 Dts~L~~~~i~~AaIES~aEN~~Dg 156 (320)
T COG1270 132 DTSKLSEAEIASAAIESLAENLVDG 156 (320)
T ss_pred CcccCCHHHHHHHHHHHHHHhcccc
Confidence 5668999999999999999999983
No 50
>PRK06163 hypothetical protein; Provisional
Probab=23.88 E-value=2.1e+02 Score=20.24 Aligned_cols=30 Identities=7% Similarity=0.038 Sum_probs=22.6
Q ss_pred EEEEEeCCCCCCCCCCCcccCHHHHHHHHHHHH
Q 045364 2 IVEVFLDPNKELPMDDPIILTQFNELKAIRDNI 34 (97)
Q Consensus 2 l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v 34 (97)
|+|+..++....+ .| +-++.++.+.+++++
T Consensus 167 lIeV~i~~~~~~~--~~-~~~~~~~~~~~~~~~ 196 (202)
T PRK06163 167 FIAVRIDDKPGVG--TT-ERDPAQIRERFMQGL 196 (202)
T ss_pred EEEEEecCCCCCC--CC-CCCHHHHHHHHHHHh
Confidence 7899888765433 33 368999999999976
No 51
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=23.80 E-value=1.5e+02 Score=16.63 Aligned_cols=20 Identities=15% Similarity=0.174 Sum_probs=17.0
Q ss_pred eEEEeCCCCceEEEEeCCCC
Q 045364 51 QVKYVNPITKLCIIKTSMKD 70 (97)
Q Consensus 51 ~Vky~~~~t~~~IlRc~r~~ 70 (97)
.||.||+..+.+.|++....
T Consensus 4 ~Vk~~~~~kGfGFI~~~~~g 23 (65)
T cd04458 4 TVKWFDDEKGFGFITPDDGG 23 (65)
T ss_pred EEEEEECCCCeEEEecCCCC
Confidence 48899999999999998733
No 52
>PF08865 DUF1830: Domain of unknown function (DUF1830); InterPro: IPR014964 This group of short proteins is functionally uncharacterised.
Probab=23.80 E-value=85 Score=18.87 Aligned_cols=16 Identities=25% Similarity=0.401 Sum_probs=13.6
Q ss_pred EEeCCCCceEEEEeCC
Q 045364 53 KYVNPITKLCIIKTSM 68 (97)
Q Consensus 53 ky~~~~t~~~IlRc~r 68 (97)
-|.|..+++-|+||.-
T Consensus 2 ~Y~N~T~~~qI~Ri~~ 17 (68)
T PF08865_consen 2 CYVNDTSQMQILRIIN 17 (68)
T ss_pred eEECCCCcEEEEEEeC
Confidence 3889999999999974
No 53
>KOG1434 consensus Meiotic recombination protein Dmc1 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=23.67 E-value=49 Score=25.57 Aligned_cols=21 Identities=19% Similarity=0.094 Sum_probs=17.4
Q ss_pred HHHHhhcCcccccccCCceeE
Q 045364 32 DNILVNFSECGLASSLRSFQV 52 (97)
Q Consensus 32 ~~v~~lfGd~G~~~~~~~l~V 52 (97)
-++.+.||++|.|..+.+.++
T Consensus 115 m~iTEifGefr~GKTQlshtL 135 (335)
T KOG1434|consen 115 MSITEIFGEFRCGKTQLSHTL 135 (335)
T ss_pred hhhHHHcCCCCcCccceeeEE
Confidence 468899999999999877653
No 54
>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi. They contain a characteristic GFDRL sequence motif.
Probab=23.40 E-value=1.6e+02 Score=18.66 Aligned_cols=32 Identities=22% Similarity=0.215 Sum_probs=23.2
Q ss_pred CCcccCHHHHHHHHHHHHHhhcCcccccccCCceeEEEe
Q 045364 17 DPIILTQFNELKAIRDNILVNFSECGLASSLRSFQVKYV 55 (97)
Q Consensus 17 ~~~~l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~ 55 (97)
.|...|-.+|.+.||+.+ +.......|+++|-
T Consensus 20 ~~~~~Tv~~LK~lIR~~~-------p~~~s~~rLRlI~~ 51 (97)
T PF10302_consen 20 SPNTTTVAWLKQLIRERL-------PPEPSRRRLRLIYA 51 (97)
T ss_pred CCCcccHHHHHHHHHhhc-------CCCCccccEEeeec
Confidence 556688999999999888 33344456888873
No 55
>PF07317 YcgR: Flagellar regulator YcgR; InterPro: IPR009926 This entry represents the N-terminal domain of YcgR proteins. The function of this domain is not known, but it is known to interact with the C-terminal which has cyclic-di-GMP bound []. YcgR is involved in the flagellar motor function and is a member of the flagellar regulon [, ].; PDB: 2GJG_A 3KYF_A.
Probab=23.11 E-value=1.5e+02 Score=18.83 Aligned_cols=71 Identities=13% Similarity=0.113 Sum_probs=42.9
Q ss_pred CHHHHHHHHHHHHHh-----hcCcccccccCCceeEEEeCCCCceEEEEeCCCChhh--hHh--HHHhhhhcCCeeeEEE
Q 045364 22 TQFNELKAIRDNILV-----NFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQK--VWS--TITMVRSIGNCLVLFN 92 (97)
Q Consensus 22 ~~~~l~~aI~~~v~~-----lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~--v~s--aLtlit~i~~~~~~~r 92 (97)
++.+|...+++-+++ .+-+-|-. . -=.+...|+..+..++-+..+.... +.. .+++++..+|.++.|.
T Consensus 6 ~p~eI~~~Lr~L~~~~~~l~v~~~~g~~-f--~T~iL~VD~~~~~l~lD~~~~~~~n~~~l~a~~~~~~a~~~gVkI~F~ 82 (108)
T PF07317_consen 6 NPREILAVLRDLAKQRSPLTVRHPRGQS-F--ITSILAVDPDRGTLVLDEGSDEEENQRLLNAEELTFVAELDGVKIQFT 82 (108)
T ss_dssp SHHHHHHHHHHHHHTT--EEEETT-SSE-E--EE-EEEEETTTTEEEEE--BSGGGHHHHHTT--EEEEEEETTEEEEEE
T ss_pred CHHHHHHHHHHHHhCCCeEEEEeCCCCE-E--EEEEEEEeCCCCEEEEEcCCChHHHHHHhcCCcEEEEEEeCCeEEEEE
Confidence 455666666654443 23221221 2 1338889999999999999866533 333 5888899999999998
Q ss_pred EEe
Q 045364 93 ALD 95 (97)
Q Consensus 93 vl~ 95 (97)
+-.
T Consensus 83 ~~~ 85 (108)
T PF07317_consen 83 LGQ 85 (108)
T ss_dssp E-S
T ss_pred cCC
Confidence 743
No 56
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=22.32 E-value=2.5e+02 Score=18.78 Aligned_cols=59 Identities=17% Similarity=0.174 Sum_probs=33.9
Q ss_pred EEEEEeCCCCCCCCCCCcccCHHHHHHHHHHHHHhhcCcccccccCCceeEEEeCCCCceEEEEeCCCChhhhHhHH
Q 045364 2 IVEVFLDPNKELPMDDPIILTQFNELKAIRDNILVNFSECGLASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWSTI 78 (97)
Q Consensus 2 l~ei~~~~~~~~~~~~~~~l~~~~l~~aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~saL 78 (97)
.|||+++|+.-.| .. + +.=...+....+..-||...|-. |...|+--.|+..=.+.++|
T Consensus 10 ~VeV~~dP~~~~p--Rk---~-~krr~rLl~Ef~rR~GDpn~GGs------------Tr~~imTAYRQ~Al~~A~~L 68 (118)
T PF09929_consen 10 RVEVLCDPGPYAP--RK---N-KKRRSRLLREFQRRSGDPNVGGS------------TRHKIMTAYRQDALRCAAAL 68 (118)
T ss_pred EEEEEeCCCCCCC--CC---C-HHHHHHHHHHHHHhcCCCCCCCc------------cCCccchhhHHHHHHHHHHH
Confidence 5899999986422 22 2 22233445556778999988764 44455555555443333333
No 57
>COG4737 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.87 E-value=54 Score=22.01 Aligned_cols=34 Identities=6% Similarity=-0.001 Sum_probs=28.7
Q ss_pred CCcccCHHHHHHHHHHHHHhhcC-cccccccCCce
Q 045364 17 DPIILTQFNELKAIRDNILVNFS-ECGLASSLRSF 50 (97)
Q Consensus 17 ~~~~l~~~~l~~aI~~~v~~lfG-d~G~~~~~~~l 50 (97)
.+..++..+|.+|+++..+-++- |.|.|..+..+
T Consensus 14 rk~~I~D~eL~~Av~e~~qGl~DadLGGGV~KkRl 48 (123)
T COG4737 14 RKHGIKDAELCEAVEEAMQGLIDADLGGGVIKKRL 48 (123)
T ss_pred HHccCChHHHHHHHHHHhcCcchhccCcchHHhhc
Confidence 34568999999999999999999 99999766554
No 58
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=21.51 E-value=89 Score=18.24 Aligned_cols=26 Identities=8% Similarity=-0.058 Sum_probs=18.2
Q ss_pred ccCHHHHHHHHHH----HHHhhcCcccccc
Q 045364 20 ILTQFNELKAIRD----NILVNFSECGLAS 45 (97)
Q Consensus 20 ~l~~~~l~~aI~~----~v~~lfGd~G~~~ 45 (97)
.+|+++|.++|++ ++.++....|+|.
T Consensus 8 ~Vtd~~I~~ai~~~g~~s~~~l~~~~~~g~ 37 (64)
T PRK10509 8 GVSDKKIRQAVRQFHPQSFQQLRKFVPVGN 37 (64)
T ss_pred CCCHHHHHHHHHHcCCCCHHHHHHhcCCCC
Confidence 4689999999986 4666665555553
No 59
>KOG0876 consensus Manganese superoxide dismutase [Inorganic ion transport and metabolism]
Probab=21.37 E-value=2.3e+02 Score=21.18 Aligned_cols=27 Identities=26% Similarity=0.395 Sum_probs=17.4
Q ss_pred eeEEEeCCCCceEEEEeCCCChhhhHh
Q 045364 50 FQVKYVNPITKLCIIKTSMKDFQKVWS 76 (97)
Q Consensus 50 l~Vky~~~~t~~~IlRc~r~~~~~v~s 76 (97)
+|+.|-+...++.|++|.-..--.+|+
T Consensus 155 ~WLv~~~~~~kL~i~~T~Na~~P~~~~ 181 (234)
T KOG0876|consen 155 LWLVYNKELKKLFILTTYNAGDPLVWT 181 (234)
T ss_pred EEEEEcCCCCeEEEEecCCCCCCeecc
Confidence 567765555678888887664445554
No 60
>PLN02355 probable galactinol--sucrose galactosyltransferase 1
Probab=21.00 E-value=1.4e+02 Score=25.92 Aligned_cols=51 Identities=16% Similarity=0.207 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHhhcCccc-ccccCCceeEEEeCCCCceEEEEeCCCChhhhHh
Q 045364 24 FNELKAIRDNILVNFSECG-LASSLRSFQVKYVNPITKLCIIKTSMKDFQKVWS 76 (97)
Q Consensus 24 ~~l~~aI~~~v~~lfGd~G-~~~~~~~l~Vky~~~~t~~~IlRc~r~~~~~v~s 76 (97)
+..++|+..++.++|++-| .++...+.+-.| +. ...++.|++-|++-..-+
T Consensus 414 ~~y~~ALe~S~~r~F~~ngvI~CMs~~~d~i~-~~-k~sav~R~SDDF~P~dP~ 465 (758)
T PLN02355 414 RKYHQALEASIARNFPDNGIISCMSHNTDGLY-SA-KRTAVIRASDDFWPRDPA 465 (758)
T ss_pred HHHHHHHHHHHHHhCCCCceEEecccCchhhc-cc-ccceeeeeccccccCCCc
Confidence 4567889999999999988 333333344444 33 456899999888754433
No 61
>PF03958 Secretin_N: Bacterial type II/III secretion system short domain; InterPro: IPR005644 This is a group of NolW-like proteins, which are closely related to bacterial type II and III secretion system protein (IPR004846 from INTERPRO).; PDB: 3EZJ_C 2Y3M_A 3OSS_D.
Probab=20.50 E-value=1.4e+02 Score=17.22 Aligned_cols=30 Identities=17% Similarity=0.251 Sum_probs=22.2
Q ss_pred ceeEEEeCCCCceEEEEeCCCChhhhHhHHH
Q 045364 49 SFQVKYVNPITKLCIIKTSMKDFQKVWSTIT 79 (97)
Q Consensus 49 ~l~Vky~~~~t~~~IlRc~r~~~~~v~saLt 79 (97)
+++|. .|+.|+..|++-..+.++.+...+.
T Consensus 45 ~~~i~-~d~~tNsliv~g~~~~~~~i~~li~ 74 (82)
T PF03958_consen 45 SGRIV-ADERTNSLIVRGTPEDLEQIRELIK 74 (82)
T ss_dssp TTEEE-EECTTTEEEEEEEHHHHHHHHHHHH
T ss_pred CeEEE-EECCCCEEEEEeCHHHHHHHHHHHH
Confidence 35444 5888999999988888777766443
No 62
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=20.14 E-value=1.6e+02 Score=17.42 Aligned_cols=24 Identities=42% Similarity=0.540 Sum_probs=15.5
Q ss_pred HHHHHHHhhcCcccccccCCceeEEEeCCC
Q 045364 29 AIRDNILVNFSECGLASSLRSFQVKYVNPI 58 (97)
Q Consensus 29 aI~~~v~~lfGd~G~~~~~~~l~Vky~~~~ 58 (97)
.|.+.|++.|-++|- +.|.|+|+.
T Consensus 6 ~i~~~iR~~fs~lG~------I~vLYvn~~ 29 (62)
T PF15513_consen 6 EITAEIRQFFSQLGE------IAVLYVNPY 29 (62)
T ss_pred HHHHHHHHHHHhcCc------EEEEEEccc
Confidence 344555666666663 679999873
Done!