Query psy6084
Match_columns 106
No_of_seqs 131 out of 927
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 17:13:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6084.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6084hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01302 CAP_GLY: CAP-Gly doma 100.0 1.1E-28 2.4E-33 158.1 8.5 67 18-84 1-69 (69)
2 KOG3206|consensus 99.9 4.4E-24 9.5E-29 162.0 7.0 72 14-85 147-221 (234)
3 KOG0971|consensus 99.9 1.6E-21 3.4E-26 170.5 8.5 73 12-84 2-74 (1243)
4 COG5244 NIP100 Dynactin comple 99.8 1.7E-20 3.6E-25 156.3 7.4 67 15-83 3-69 (669)
5 KOG3207|consensus 99.8 1.6E-18 3.5E-23 143.4 7.3 72 15-88 2-75 (505)
6 KOG4568|consensus 99.7 2.1E-17 4.6E-22 141.9 4.6 80 8-88 10-89 (664)
7 KOG3556|consensus 99.3 2.1E-12 4.6E-17 109.1 7.1 80 14-93 234-322 (724)
8 KOG0241|consensus 99.3 1.1E-12 2.4E-17 116.5 4.4 76 8-88 1623-1698(1714)
9 KOG4568|consensus 99.2 2.7E-12 5.9E-17 110.7 0.8 75 11-86 150-224 (664)
10 PTZ00243 ABC transporter; Prov 95.8 0.012 2.6E-07 55.5 4.4 55 17-71 126-197 (1560)
11 PF10781 DSRB: Dextransucrase 94.8 0.17 3.6E-06 31.8 6.0 56 16-81 1-61 (62)
12 PRK10708 hypothetical protein; 94.6 0.21 4.7E-06 31.3 6.0 55 16-80 1-60 (62)
13 PF09926 DUF2158: Uncharacteri 91.1 1.1 2.4E-05 27.2 5.5 47 16-62 1-47 (53)
14 COG3350 Uncharacterized conser 67.9 2.3 4.9E-05 26.1 0.5 30 45-74 6-35 (53)
15 PF02211 NHase_beta: Nitrile h 66.1 1.9 4.2E-05 33.2 -0.0 24 3-26 122-145 (222)
16 PF14001 YdfZ: YdfZ protein 55.3 16 0.00035 23.2 2.8 22 15-36 9-30 (64)
17 PF13403 Hint_2: Hint domain 53.3 12 0.00026 26.6 2.2 29 12-41 17-45 (147)
18 PF00924 MS_channel: Mechanose 53.0 11 0.00024 27.0 2.1 24 14-39 59-82 (206)
19 CHL00141 rpl24 ribosomal prote 50.9 31 0.00066 22.6 3.7 27 10-36 3-32 (83)
20 TIGR02266 gmx_TIGR02266 Myxoco 49.9 49 0.0011 20.7 4.6 42 13-54 34-83 (96)
21 PF07238 PilZ: PilZ domain; I 46.5 57 0.0012 19.8 4.4 38 14-53 43-87 (102)
22 PRK12281 rplX 50S ribosomal pr 45.0 41 0.00089 21.6 3.6 24 14-37 5-31 (76)
23 smart00739 KOW KOW (Kyprides, 43.6 30 0.00065 16.9 2.3 11 16-26 2-12 (28)
24 TIGR03318 YdfZ_fam putative se 43.1 23 0.0005 22.5 2.1 22 15-36 10-31 (65)
25 PRK05886 yajC preprotein trans 41.9 42 0.0009 23.2 3.4 35 11-52 34-68 (109)
26 PRK00321 rdgC recombination as 41.7 87 0.0019 25.1 5.7 60 10-69 182-256 (303)
27 PF13437 HlyD_3: HlyD family s 40.4 72 0.0016 20.3 4.3 32 10-41 44-81 (105)
28 TIGR00739 yajC preprotein tran 39.3 19 0.00042 23.5 1.4 26 11-37 33-58 (84)
29 PF15290 Syntaphilin: Golgi-lo 38.7 14 0.0003 29.9 0.7 21 57-77 22-52 (305)
30 PF04945 YHS: YHS domain; Int 34.8 16 0.00034 20.9 0.4 14 60-73 18-31 (47)
31 PRK05585 yajC preprotein trans 34.4 62 0.0013 22.0 3.3 35 11-52 48-82 (106)
32 PRK00004 rplX 50S ribosomal pr 33.2 79 0.0017 21.4 3.7 23 14-36 3-28 (105)
33 PRK10334 mechanosensitive chan 32.2 57 0.0012 25.7 3.2 25 13-39 127-151 (286)
34 PF01176 eIF-1a: Translation i 31.2 63 0.0014 19.7 2.7 22 14-35 40-64 (65)
35 TIGR01079 rplX_bact ribosomal 29.9 88 0.0019 21.2 3.5 22 15-36 3-27 (104)
36 PF02699 YajC: Preprotein tran 29.8 18 0.0004 23.3 0.1 26 10-36 31-56 (82)
37 PRK06531 yajC preprotein trans 29.4 34 0.00074 23.8 1.4 26 11-37 32-57 (113)
38 cd03698 eRF3_II_like eRF3_II_l 27.4 1.6E+02 0.0035 18.3 5.5 39 15-53 26-69 (83)
39 KOG2045|consensus 27.4 72 0.0016 30.4 3.4 42 15-58 1129-1178(1493)
40 TIGR00523 eIF-1A eukaryotic/ar 26.6 77 0.0017 21.4 2.7 24 13-36 55-82 (99)
41 COG4841 Uncharacterized protei 26.4 2E+02 0.0044 19.5 4.7 49 16-71 19-68 (95)
42 PF07154 DUF1392: Protein of u 26.3 1.1E+02 0.0024 22.5 3.6 43 13-55 85-128 (150)
43 CHL00010 infA translation init 26.1 1E+02 0.0023 19.6 3.2 23 14-36 45-70 (78)
44 cd05793 S1_IF1A S1_IF1A: Trans 25.8 1E+02 0.0022 19.8 3.0 23 14-36 37-62 (77)
45 TIGR01955 RfaH transcriptional 25.7 1.6E+02 0.0034 20.4 4.3 24 12-35 105-131 (159)
46 PRK14533 groES co-chaperonin G 25.4 67 0.0014 21.3 2.2 11 14-24 52-62 (91)
47 PF12700 HlyD_2: HlyD family s 25.2 2.5E+02 0.0054 21.1 5.7 74 10-85 204-284 (328)
48 cd04451 S1_IF1 S1_IF1: Transla 24.9 1.1E+02 0.0024 18.2 3.0 11 15-25 40-50 (64)
49 PRK00276 infA translation init 24.8 1.1E+02 0.0024 19.0 3.1 21 15-35 46-69 (72)
50 PF14801 GCD14_N: tRNA methylt 24.5 94 0.002 19.1 2.6 43 15-62 5-52 (54)
51 cd04486 YhcR_OBF_like YhcR_OBF 23.4 97 0.0021 19.6 2.6 22 13-39 42-64 (78)
52 COG4831 Roadblock/LC7 domain [ 23.2 29 0.00064 24.0 0.2 41 46-89 62-103 (109)
53 PRK05609 nusG transcription an 23.1 2.5E+02 0.0054 19.9 5.0 24 13-36 124-150 (181)
54 smart00652 eIF1a eukaryotic tr 23.1 1.2E+02 0.0026 19.7 3.0 23 14-36 42-67 (83)
55 PF02298 Cu_bind_like: Plastoc 23.1 48 0.001 21.4 1.2 13 13-25 16-28 (85)
56 PF10220 DUF2146: Uncharacteri 22.9 1.3E+02 0.0028 27.9 4.2 34 44-85 746-779 (895)
57 PTZ00414 10 kDa heat shock pro 22.6 68 0.0015 21.8 1.8 13 13-25 60-72 (100)
58 cd04456 S1_IF1A_like S1_IF1A_l 22.0 1.3E+02 0.0027 19.4 3.0 23 14-36 37-63 (78)
59 KOG4792|consensus 21.8 74 0.0016 25.4 2.1 39 13-53 245-285 (293)
60 smart00266 CAD Domains present 20.9 43 0.00092 21.8 0.6 24 58-81 45-69 (74)
61 PF04381 RdgC: Putative exonuc 20.9 91 0.002 24.8 2.5 59 11-69 183-256 (301)
62 KOG1641|consensus 20.8 1E+02 0.0022 21.3 2.4 21 5-25 56-76 (104)
63 COG5466 Predicted small metal- 20.6 83 0.0018 19.7 1.8 19 64-82 2-23 (59)
64 cd04496 SSB_OBF SSB_OBF: A sub 20.1 2.3E+02 0.005 17.5 4.6 33 14-51 60-92 (100)
No 1
>PF01302 CAP_GLY: CAP-Gly domain; InterPro: IPR000938 Cytoskeleton-associated proteins (CAP) are made of three distinct parts, an N-terminal section that is most probably globular and contains the CAP-Gly domain, a large central region predicted to be in an alpha-helical coiled-coil conformation and, finally, a short C-terminal globular domain. The CAP-Gly domain is a conserved, glycine-rich domain of about 42 residues found in some CAPs []. Proteins known to contain this domain include restin (also known as cytoplasmic linker protein-170 or CLIP-170), a 160 kDa protein associated with intermediate filaments and that links endocytic vesicles to microtubules; vertebrate dynactin (150 kDa dynein-associated polypeptide; DAP) and Drosophila glued, a major component of activator I; yeast protein BIK1, which seems to be required for the formation or stabilisation of microtubules during mitosis and for spindle pole body fusion during conjugation; yeast protein NIP100 (NIP80); human protein CKAP1/TFCB; Schizosaccharomyces pombe protein alp11 and Caenorhabditis elegans hypothetical protein F53F4.3. The latter proteins contain a N-terminal ubiquitin domain and a C-terminal CAP-Gly domain. The crystal structure of the CAP-Gly domain of C. elegans F53F4.3 protein, solved by single wavelength sulphur-anomalous phasing, revealed a novel protein fold containing three beta-sheets. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. Residues in the groove are highly conserved as measured from the information content of the aligned sequences. The C-terminal tail of another molecule in the crystal is bound in this groove []. ; PDB: 2CP6_A 2E4H_A 2E3H_A 3E2U_B 2HL3_B 3TQ7_Q 2HKQ_B 2HQH_A 2HKN_B 2HL5_C ....
Probab=99.96 E-value=1.1e-28 Score=158.05 Aligned_cols=67 Identities=57% Similarity=1.086 Sum_probs=59.7
Q ss_pred ccCeEEEe-CCCceEEEEEEeecC-CCCCeEEEEEEcCCCCCCCcEECCEEeeEeCCCCeeEEecCCcc
Q psy6084 18 LGESVLIR-PYNSSGVIAYIGPTE-FAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIFVRADKLI 84 (106)
Q Consensus 18 vG~rV~v~-~~~~~GtVRyiG~~~-~~~g~~vGVElde~~Gk~dGt~~G~rYF~c~p~~GiFv~~~kv~ 84 (106)
|||||.|. .....|||||+|+++ ...|+|+|||||++.|+|||+++|+|||+|+|+||+||++++|.
T Consensus 1 VG~rV~v~~~~~~~G~vryiG~~~~~~~g~~vGVEld~~~G~~dGt~~G~rYF~c~~~~G~Fv~~~~v~ 69 (69)
T PF01302_consen 1 VGDRVRVDDPGGRRGTVRYIGPVPGFKSGIWVGVELDEPRGKNDGTVKGKRYFECPPNHGIFVRPSKVE 69 (69)
T ss_dssp TTSEEEESSTTTEEEEEEEEEE-SSSSSSEEEEEEESSSTSSBSSEETTEESS-SSTTTEEEEEGGGE-
T ss_pred CCCEEEEeeCCCCEEEEEEEeeCCCCCCCEEEEEEEcCCCCCCCcEECCEEEeeeCCCCEEEecHHHCC
Confidence 79999992 347999999999999 67789999999999999999999999999999999999999874
No 2
>KOG3206|consensus
Probab=99.90 E-value=4.4e-24 Score=161.99 Aligned_cols=72 Identities=44% Similarity=0.861 Sum_probs=67.4
Q ss_pred CcccccCeEEEe-CC--CceEEEEEEeecCCCCCeEEEEEEcCCCCCCCcEECCEEeeEeCCCCeeEEecCCccc
Q psy6084 14 EWVCLGESVLIR-PY--NSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIFVRADKLIQ 85 (106)
Q Consensus 14 ~~l~vG~rV~v~-~~--~~~GtVRyiG~~~~~~g~~vGVElde~~Gk~dGt~~G~rYF~c~p~~GiFv~~~kv~~ 85 (106)
..+.||+||+|+ +. ..+|+|||+|++++.+|+|+|||+|||.|||||+++|++||+|+|+||.||+|..|..
T Consensus 147 ~~i~vG~rCeVtv~G~~~Rrg~vrYvG~~~~k~G~wiGVeydEplGKnDGsv~G~ryF~c~p~yGgfVrP~~V~V 221 (234)
T KOG3206|consen 147 ATIAVGRRCEVTVPGQAPRRGTVRYVGPLEFKPGYWIGVEYDEPLGKNDGSVNGKRYFECAPKYGGFVRPRAVTV 221 (234)
T ss_pred hccccCCeeEEecCCCCCcceEEEEecccCCCCceEEEEecCCccccCCCcccceEeeecCCccCCccccceeee
Confidence 348999999998 43 4899999999999999999999999999999999999999999999999999999985
No 3
>KOG0971|consensus
Probab=99.85 E-value=1.6e-21 Score=170.45 Aligned_cols=73 Identities=45% Similarity=0.848 Sum_probs=69.9
Q ss_pred CCCcccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEEcCCCCCCCcEECCEEeeEeCCCCeeEEecCCcc
Q psy6084 12 LPEWVCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIFVRADKLI 84 (106)
Q Consensus 12 ~~~~l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVElde~~Gk~dGt~~G~rYF~c~p~~GiFv~~~kv~ 84 (106)
.+..|+||.||.|.+++..|+|.|+|.+.|..|.||||-||+|.||||||++|++||+|++|||+||+.+.|.
T Consensus 2 s~r~lkvG~RVevtgknl~G~VayvG~T~FA~G~WvGVvLDep~GKNnGsVqg~qYF~Cd~ncG~FVr~sq~r 74 (1243)
T KOG0971|consen 2 SPRSLKVGTRVEVTGKNLQGTVAYVGQTQFAEGKWVGVVLDEPKGKNNGSVQGVQYFECDENCGVFVRSSQVR 74 (1243)
T ss_pred CCccccccceEEeccCCccceEEEecccccccCceEEEEeccccCCCCCcccceeeEecCCCcceEeehhhhH
Confidence 3678999999999988999999999999999999999999999999999999999999999999999999965
No 4
>COG5244 NIP100 Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell division and chromosome partitioning]
Probab=99.82 E-value=1.7e-20 Score=156.28 Aligned_cols=67 Identities=45% Similarity=0.969 Sum_probs=62.6
Q ss_pred cccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEEcCCCCCCCcEECCEEeeEeCCCCeeEEecCCc
Q psy6084 15 WVCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIFVRADKL 83 (106)
Q Consensus 15 ~l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVElde~~Gk~dGt~~G~rYF~c~p~~GiFv~~~kv 83 (106)
-|.+||+|.+. ...|+|||+|.+.+..|+|+|||||+|.|+|||+++|+|||.|+.+||+|+++..=
T Consensus 3 ~lSv~D~Vll~--~~~g~VrfiG~t~f~~GiW~GlELd~p~GkNDGSvnGvRYF~Ckk~~giFir~~~~ 69 (669)
T COG5244 3 LLSVNDRVLLG--DKFGTVRFIGKTKFKDGIWIGLELDDPVGKNDGSVNGVRYFHCKKRHGIFIRPDDD 69 (669)
T ss_pred eeecCCEEEec--cccceEEEeeecccccceEEEEEecCCCCCCCCccCceEEEEecCCcceEEecCch
Confidence 36799999997 67899999999999999999999999999999999999999999999999997654
No 5
>KOG3207|consensus
Probab=99.75 E-value=1.6e-18 Score=143.40 Aligned_cols=72 Identities=36% Similarity=0.674 Sum_probs=67.0
Q ss_pred cccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEEcCCC-CCCCcEECCEEeeEeC-CCCeeEEecCCccccCC
Q psy6084 15 WVCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPT-GKNDGTVQGTRYFESR-PKHGIFVRADKLIQDRR 88 (106)
Q Consensus 15 ~l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVElde~~-Gk~dGt~~G~rYF~c~-p~~GiFv~~~kv~~~~~ 88 (106)
.+.||+||.|. ...+||||+|.+++..+.|+|||||++. |||||+++|++||.|. |+.|+|+++.+|.+.+.
T Consensus 2 ~~~IG~RvkI~--~~~~Tvr~iG~V~g~~~~w~GvEWDd~~RGKH~G~vdgk~YF~~q~P~GGSFik~~kV~~p~d 75 (505)
T KOG3207|consen 2 TMEIGTRVKIG--GEIATVRYIGEVEGNNSKWYGVEWDDPVRGKHDGIVDGKRYFQTQHPNGGSFIKPGKVKFPTD 75 (505)
T ss_pred ceeccceEEEc--CEEEEEEEEEEEcCCCCcceeeEecCCCccccCceecceeeeeeecCCCccccCCccCCCCcc
Confidence 46899999997 6889999999999999999999999996 9999999999999998 99999999999987543
No 6
>KOG4568|consensus
Probab=99.68 E-value=2.1e-17 Score=141.95 Aligned_cols=80 Identities=39% Similarity=0.716 Sum_probs=71.2
Q ss_pred CCCCCCCcccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEEcCCCCCCCcEECCEEeeEeCCCCeeEEecCCccccC
Q psy6084 8 DDVTLPEWVCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIFVRADKLIQDR 87 (106)
Q Consensus 8 ~~~~~~~~l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVElde~~Gk~dGt~~G~rYF~c~p~~GiFv~~~kv~~~~ 87 (106)
.+...-..+.||++|+|.. +..|.|||+|++++..|+|+||+|++|.|||||+|+|++||.|.+.+|+|++..+.....
T Consensus 10 ~q~~~~~~~~ig~~v~v~~-~~~G~v~y~G~t~f~~G~w~GveL~~p~GKNdGsv~G~rYF~ce~~kgif~~~~~~t~~~ 88 (664)
T KOG4568|consen 10 VQLDDLGQFIIGRRVWVNN-VELGFVRYAGETDFAKGIWAGVELLEPKGKNDGSVHGKRYFQCEPKKGIFFRQGRGTASK 88 (664)
T ss_pred chhhhhhhhhhcceEEecC-CcceeeeeccCcccccceeeceeeccccCCCCcccchhhhhccccccceeeccccccccc
Confidence 3455567789999999973 688999999999999999999999999999999999999999999999999888777543
Q ss_pred C
Q psy6084 88 R 88 (106)
Q Consensus 88 ~ 88 (106)
.
T Consensus 89 ~ 89 (664)
T KOG4568|consen 89 N 89 (664)
T ss_pred c
Confidence 3
No 7
>KOG3556|consensus
Probab=99.34 E-value=2.1e-12 Score=109.11 Aligned_cols=80 Identities=25% Similarity=0.347 Sum_probs=72.3
Q ss_pred CcccccCeEEEeCC----CceEEEEEEeecCCCCCeEEEEEEcCC-----CCCCCcEECCEEeeEeCCCCeeEEecCCcc
Q psy6084 14 EWVCLGESVLIRPY----NSSGVIAYIGPTEFAAGTWVGVELDAP-----TGKNDGTVQGTRYFESRPKHGIFVRADKLI 84 (106)
Q Consensus 14 ~~l~vG~rV~v~~~----~~~GtVRyiG~~~~~~g~~vGVElde~-----~Gk~dGt~~G~rYF~c~p~~GiFv~~~kv~ 84 (106)
..|+||+.|.|... .+.|+|||||.-|...++|+|||+++. .+..||++.|.|||+|-.+..+||+...+.
T Consensus 234 ~~L~IGslveV~np~~~~~~ygvVrWIG~pP~~~~Vl~gve~edet~~~~~~~~dgs~~g~Rlftc~d~~a~Fv~~~scs 313 (724)
T KOG3556|consen 234 LNLKIGSLVEVENPETMRRVYGVVRWIGEPPEASGVLYGVEFEDETSQWPSSNQDGSSSGDRLFTCFDTNANFVMSGSCS 313 (724)
T ss_pred ccceecceEEecCCccccccceeeEecccCCcccCceEeeeecCccccCccccccCcccCceeeeeccccceeeEcCCCC
Confidence 45899999999732 588999999999999999999999976 378999999999999999999999999999
Q ss_pred ccCCCcccc
Q psy6084 85 QDRRGRAMR 93 (106)
Q Consensus 85 ~~~~~~~~~ 93 (106)
.|+++....
T Consensus 314 ~d~rfa~l~ 322 (724)
T KOG3556|consen 314 VDPRFARLY 322 (724)
T ss_pred cCcccchhc
Confidence 999998764
No 8
>KOG0241|consensus
Probab=99.32 E-value=1.1e-12 Score=116.53 Aligned_cols=76 Identities=38% Similarity=0.643 Sum_probs=69.0
Q ss_pred CCCCCCCcccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEEcCCCCCCCcEECCEEeeEeCCCCeeEEecCCccccC
Q psy6084 8 DDVTLPEWVCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIFVRADKLIQDR 87 (106)
Q Consensus 8 ~~~~~~~~l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVElde~~Gk~dGt~~G~rYF~c~p~~GiFv~~~kv~~~~ 87 (106)
+...+|+|+..|.+|.+.. ..+++|||+|..++.. |||||.|.|+|||+..|++||.|.|++|.||+++++..++
T Consensus 1623 ~~~~~pew~~~ge~v~~~~-h~t~v~r~vg~tefq~----gveld~p~gkndgs~gg~qyfrc~p~~g~~vr~s~~~~~~ 1697 (1714)
T KOG0241|consen 1623 PSKISPEWRGFGERVVTVE-HTTNVLRDVGFTEFQG----GVELDDPDGKNDGSAGGLQYFRCLPNKGGGVRVSDGLHHP 1697 (1714)
T ss_pred hhhcCchhhhcCceeEEee-cccceeeecchhhccC----cccccCCCCCcCccccceeEEeecCCCCCcccchhhccCc
Confidence 3567899999999998874 5678999999998865 9999999999999999999999999999999999999876
Q ss_pred C
Q psy6084 88 R 88 (106)
Q Consensus 88 ~ 88 (106)
+
T Consensus 1698 ~ 1698 (1714)
T KOG0241|consen 1698 S 1698 (1714)
T ss_pred H
Confidence 5
No 9
>KOG4568|consensus
Probab=99.21 E-value=2.7e-12 Score=110.68 Aligned_cols=75 Identities=44% Similarity=0.775 Sum_probs=69.4
Q ss_pred CCCCcccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEEcCCCCCCCcEECCEEeeEeCCCCeeEEecCCcccc
Q psy6084 11 TLPEWVCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIFVRADKLIQD 86 (106)
Q Consensus 11 ~~~~~l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVElde~~Gk~dGt~~G~rYF~c~p~~GiFv~~~kv~~~ 86 (106)
.....+.+||||.+. .+..|++||.|...+..|-|+|||||+|.|++||++.+++||.|+|.+|+|.+..++...
T Consensus 150 ~~~~~l~v~dr~l~~-gq~~~~~r~~~~t~fa~g~w~~~elde~~~~~d~sv~k~~~~~~k~ky~~f~~v~kv~~~ 224 (664)
T KOG4568|consen 150 TSMLGLRVGDRVLVG-GQKSGTLRYSGHTKFASGSWLGVELDEPVGKNDGSVGKVRYFQCKPKYGKFAPVQKVFKI 224 (664)
T ss_pred cCccccccccceeec-CcccchhhhhccccccCCcccchhcccccccccccccccccccCcchhcchhHHHHHhhc
Confidence 345678999999997 478899999999999999999999999999999999999999999999999999999864
No 10
>PTZ00243 ABC transporter; Provisional
Probab=95.78 E-value=0.012 Score=55.53 Aligned_cols=55 Identities=24% Similarity=0.398 Sum_probs=44.1
Q ss_pred cccCeEEEeC-CCceEEEEEEeecC--CCCCeEEEEEEcCC-----------C---CCCCcEECCEEeeEeC
Q psy6084 17 CLGESVLIRP-YNSSGVIAYIGPTE--FAAGTWVGVELDAP-----------T---GKNDGTVQGTRYFESR 71 (106)
Q Consensus 17 ~vG~rV~v~~-~~~~GtVRyiG~~~--~~~g~~vGVElde~-----------~---Gk~dGt~~G~rYF~c~ 71 (106)
-||.+|-+.. ..-.|++||+|.+. +.++.++||||.-| . +-|||.++|.++|.-.
T Consensus 126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 197 (1560)
T PTZ00243 126 MVGAEVVSTLDASSRGVLRWVGVPQQGGYTRMMAGVEWSVPPALRTAARSDDSGASPFFNGVAHGEHLFTPE 197 (1560)
T ss_pred ccccEEEeeccccccceEEeecccccCCCcceeeeeeeccCchhhhcccCCCCCCccccccccccccccCcc
Confidence 5788988862 35779999999996 35679999999954 1 2589999999999854
No 11
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=94.83 E-value=0.17 Score=31.77 Aligned_cols=56 Identities=27% Similarity=0.497 Sum_probs=41.0
Q ss_pred ccccCeEEEeC---CCceEEEEEEeecCCCCCeEEEEEEcC-CCCCCCcEECCEEeeE-eCCCCeeEEecC
Q psy6084 16 VCLGESVLIRP---YNSSGVIAYIGPTEFAAGTWVGVELDA-PTGKNDGTVQGTRYFE-SRPKHGIFVRAD 81 (106)
Q Consensus 16 l~vG~rV~v~~---~~~~GtVRyiG~~~~~~g~~vGVElde-~~Gk~dGt~~G~rYF~-c~p~~GiFv~~~ 81 (106)
++|.|||.|.. ..+.|+|.-+ =++..|+++-|.|++ |.| +-||. ....-|+||.+.
T Consensus 1 MkvnD~VtVKTDG~~rR~G~ilav--E~F~EG~MYLvaL~dYP~G--------iWFFNE~~~~dG~FVep~ 61 (62)
T PF10781_consen 1 MKVNDRVTVKTDGGPRREGVILAV--EPFNEGTMYLVALEDYPAG--------IWFFNEKDSPDGTFVEPR 61 (62)
T ss_pred CccccEEEEecCCcccccceEEEE--eeccCcEEEEEEcCcCCcc--------eEEEecCCCCCcEEeeec
Confidence 37899999973 2466888766 356789999999997 445 33676 457789999764
No 12
>PRK10708 hypothetical protein; Provisional
Probab=94.58 E-value=0.21 Score=31.28 Aligned_cols=55 Identities=29% Similarity=0.555 Sum_probs=40.7
Q ss_pred ccccCeEEEeC---CCceEEEEEEeecCCCCCeEEEEEEcC-CCCCCCcEECCEEeeE-eCCCCeeEEec
Q psy6084 16 VCLGESVLIRP---YNSSGVIAYIGPTEFAAGTWVGVELDA-PTGKNDGTVQGTRYFE-SRPKHGIFVRA 80 (106)
Q Consensus 16 l~vG~rV~v~~---~~~~GtVRyiG~~~~~~g~~vGVElde-~~Gk~dGt~~G~rYF~-c~p~~GiFv~~ 80 (106)
++|.|||.|.. ..+.|+|.-+ =++..|+++-|.|++ |.| +-||. ....-|+||.+
T Consensus 1 MkvnD~VtVKTDG~~rR~G~iLav--E~F~EG~MyLvaL~dYP~G--------iWFFNE~~~~~G~FVep 60 (62)
T PRK10708 1 MKVNDRVTVKTDGGPRRPGVVLAV--EEFSEGTMYLVSLEDYPLG--------IWFFNEAGHQDGIFVEK 60 (62)
T ss_pred CccccEEEEecCCCccccceEEEE--eeccCcEEEEEEcCcCCCc--------eEEEeccCCCCceEecc
Confidence 37899999973 2466888776 356789999999997 445 34776 44778999965
No 13
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=91.08 E-value=1.1 Score=27.24 Aligned_cols=47 Identities=21% Similarity=0.377 Sum_probs=37.4
Q ss_pred ccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEEcCCCCCCCcEE
Q psy6084 16 VCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGKNDGTV 62 (106)
Q Consensus 16 l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVElde~~Gk~dGt~ 62 (106)
+++||.|++.+++..=||.++|+.....+.|+=-.|-+..+...++|
T Consensus 1 f~~GDvV~LKSGGp~MTV~~v~~~~~~~~~~v~C~WFd~~~~~~~~F 47 (53)
T PF09926_consen 1 FKIGDVVQLKSGGPRMTVTEVGPNAGASGGWVECQWFDGHGEQRETF 47 (53)
T ss_pred CCCCCEEEEccCCCCeEEEEccccccCCCCeEEEEeCCCCCcccccc
Confidence 57899999987666779999999877778888888888776654443
No 14
>COG3350 Uncharacterized conserved protein [Function unknown]
Probab=67.88 E-value=2.3 Score=26.14 Aligned_cols=30 Identities=13% Similarity=0.318 Sum_probs=22.7
Q ss_pred eEEEEEEcCCCCCCCcEECCEEeeEeCCCC
Q psy6084 45 TWVGVELDAPTGKNDGTVQGTRYFESRPKH 74 (106)
Q Consensus 45 ~~vGVElde~~Gk~dGt~~G~rYF~c~p~~ 74 (106)
..+|-.+|...-..-=+++|+.||.|.+.+
T Consensus 6 PVcgm~v~~~~a~~k~~Y~GktYYFcse~~ 35 (53)
T COG3350 6 PVCGMKVDNENAEYKSSYGGKTYYFCSEEC 35 (53)
T ss_pred CCcCccccccccceeEEeCCEEEEEeCHHH
Confidence 346677776666666789999999998654
No 15
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=66.09 E-value=1.9 Score=33.18 Aligned_cols=24 Identities=29% Similarity=0.473 Sum_probs=13.2
Q ss_pred CCCCCCCCCCCCcccccCeEEEeC
Q psy6084 3 GDQSFDDVTLPEWVCLGESVLIRP 26 (106)
Q Consensus 3 ~~~~~~~~~~~~~l~vG~rV~v~~ 26 (106)
|+++..+...+..|++||+|.|..
T Consensus 122 G~p~~r~~~~~~~F~vGd~Vrv~~ 145 (222)
T PF02211_consen 122 GDPADRPVDAPPRFAVGDRVRVRN 145 (222)
T ss_dssp ----EETTSSS-SS-TT-EEEE--
T ss_pred CCCccCCCCCCCCCCCCCEEEECC
Confidence 455666778889999999999973
No 16
>PF14001 YdfZ: YdfZ protein
Probab=55.30 E-value=16 Score=23.20 Aligned_cols=22 Identities=32% Similarity=0.437 Sum_probs=18.8
Q ss_pred cccccCeEEEeCCCceEEEEEE
Q psy6084 15 WVCLGESVLIRPYNSSGVIAYI 36 (106)
Q Consensus 15 ~l~vG~rV~v~~~~~~GtVRyi 36 (106)
.|..|+||.+...+..|+|+-|
T Consensus 9 ~i~~G~rVMiagtG~~gvikAi 30 (64)
T PF14001_consen 9 AITTGSRVMIAGTGATGVIKAI 30 (64)
T ss_pred cCCCCCEEEEcCCCcccEEeee
Confidence 4678999999877888999877
No 17
>PF13403 Hint_2: Hint domain
Probab=53.26 E-value=12 Score=26.65 Aligned_cols=29 Identities=24% Similarity=0.264 Sum_probs=22.1
Q ss_pred CCCcccccCeEEEeCCCceEEEEEEeecCC
Q psy6084 12 LPEWVCLGESVLIRPYNSSGVIAYIGPTEF 41 (106)
Q Consensus 12 ~~~~l~vG~rV~v~~~~~~GtVRyiG~~~~ 41 (106)
.-++|++||+|.-.. +..=.|+|+|....
T Consensus 17 ~Ve~L~~GD~V~T~d-gg~~~V~wig~~~~ 45 (147)
T PF13403_consen 17 PVEDLRPGDRVLTRD-GGFQPVRWIGRRTV 45 (147)
T ss_pred EeeccCCCCEEEecC-CCEEEEEEEEEEEe
Confidence 346789999998764 55678999997643
No 18
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=53.03 E-value=11 Score=27.02 Aligned_cols=24 Identities=21% Similarity=0.274 Sum_probs=16.8
Q ss_pred CcccccCeEEEeCCCceEEEEEEeec
Q psy6084 14 EWVCLGESVLIRPYNSSGVIAYIGPT 39 (106)
Q Consensus 14 ~~l~vG~rV~v~~~~~~GtVRyiG~~ 39 (106)
..+++||+|.+. +..|.|.-+|..
T Consensus 59 ~pf~vGD~I~i~--~~~G~V~~I~l~ 82 (206)
T PF00924_consen 59 RPFKVGDRIEIG--GVEGRVEEIGLR 82 (206)
T ss_dssp -SS-TT-EEESS--S-EEEEEEE-SS
T ss_pred CCccCCCEEEEE--EeehHHHhcCcc
Confidence 468999999997 789999999876
No 19
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=50.88 E-value=31 Score=22.57 Aligned_cols=27 Identities=22% Similarity=0.193 Sum_probs=20.0
Q ss_pred CCCCCcccccCeEEEeC---CCceEEEEEE
Q psy6084 10 VTLPEWVCLGESVLIRP---YNSSGVIAYI 36 (106)
Q Consensus 10 ~~~~~~l~vG~rV~v~~---~~~~GtVRyi 36 (106)
++....|..||+|.|.. .+..|+|..+
T Consensus 3 ~~~~~~I~~GD~V~Vi~G~dKGK~G~V~~V 32 (83)
T CHL00141 3 KKKKMHVKIGDTVKIISGSDKGKIGEVLKI 32 (83)
T ss_pred cceeCcccCCCEEEEeEcCCCCcEEEEEEE
Confidence 34456789999999963 4677888777
No 20
>TIGR02266 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266. This domain is related to Type IV pilus assembly protein PilZ (Pfam model pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622.
Probab=49.89 E-value=49 Score=20.73 Aligned_cols=42 Identities=21% Similarity=0.392 Sum_probs=25.5
Q ss_pred CCcccccCeEEEe---CC-----CceEEEEEEeecCCCCCeEEEEEEcCC
Q psy6084 13 PEWVCLGESVLIR---PY-----NSSGVIAYIGPTEFAAGTWVGVELDAP 54 (106)
Q Consensus 13 ~~~l~vG~rV~v~---~~-----~~~GtVRyiG~~~~~~g~~vGVElde~ 54 (106)
...+.+|++|.+. +. ...|.|.|+-........++||++.+.
T Consensus 34 ~~~~~~g~~v~l~l~l~~~~~~i~~~g~Vv~~~~~~~~~~~~~Gv~F~~~ 83 (96)
T TIGR02266 34 RKPLAVGTRVELKLTLPGGERPVELKGVVAWVRPAADGGPPGMGVRFEDL 83 (96)
T ss_pred CCCcCCCCEEEEEEEcCCCCeEEEEEEEEEEeCCCCCCCCCeeEEEeccC
Confidence 4567889988775 21 245777777432221125789998754
No 21
>PF07238 PilZ: PilZ domain; InterPro: IPR009875 The ubiquitous bacterial second messenger cyclic-di-GMP (c-di-GMP) is associated with the regulation of biofilm formation, the control of exopolysaccharide synthesis, flagellar- and pili-based motility, gene expression, interactions of bacteria with eukaryotic hosts and multicellular behaviour in diverse bacteria. With the exception of bacterial cellulose synthases, the identities of c-di-GMP receptors and end targets of the proteins having one or more PilZ domains are mostly uncharacterised. However it was suggested that the PilZ domains present in the BcsA subunits of bacterial cellulose synthases function in c-di-GMP binding []. More recently YcgR (see IPR023787 from INTERPRO) was found to bind c-di-GMP tightly and specifically; also isolated PilZ domains from YcgR and BcsA bound c-di-GMP indicating that the PilZ domain was sufficient for binding of c-di-GMP and significantly that site-directed mutagenesis performed on YcgR implicated the most conserved residues in the PilZ domain directly in c-di-GMP binding []. It was suggested that c-di-GMP binding to PilZ brings about conformational changes in the protein that stabilise the bound ligand and probability initiates the downstream signal transduction cascade. In the case of YcgR, c-di-GMP binding regulates flagellum-based motility in a c-di-GMP-dependent manner (see IPR023787 from INTERPRO) []. The association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development. Binding and mutagenesis studies of several PilZ domain proteins have confirmed this observation and demonstrated that c-di-GMP binding depends on residues in RxxxR and D/NxSxxG sequence motifs. The crystal structure, at 1.7 A, of a PilZ domain::c-di-GMP complex from Vibrio cholerae shows c-di-GMP contacting seven of nine strongly conserved residues. Binding of c-di-GMP causes a conformational switch whereby the C- and N-terminal domains are brought into close opposition forming a new allosteric interaction surface that spans these domains and the c-di-GMP at their interface []. ; GO: 0035438 cyclic-di-GMP binding; PDB: 2RDE_B 1YLN_A 3KYG_A 3DSG_B 2GJG_A 3KYF_A 1YWU_A 2L74_A 2L1T_A 3CNR_A ....
Probab=46.53 E-value=57 Score=19.81 Aligned_cols=38 Identities=24% Similarity=0.250 Sum_probs=25.0
Q ss_pred CcccccCeEEEe--C--CC---ceEEEEEEeecCCCCCeEEEEEEcC
Q psy6084 14 EWVCLGESVLIR--P--YN---SSGVIAYIGPTEFAAGTWVGVELDA 53 (106)
Q Consensus 14 ~~l~vG~rV~v~--~--~~---~~GtVRyiG~~~~~~g~~vGVElde 53 (106)
..+.+|+.|.+. . .. ..|.|+++-+. ....++|+++++
T Consensus 43 ~~~~~~~~v~l~~~~~~~~~~~~~~~V~~~~~~--~~~~~~g~~f~~ 87 (102)
T PF07238_consen 43 KPLEPGDRVRLSFSLPGGGFPIVTGRVVRIQKD--SDGYRVGVEFVD 87 (102)
T ss_dssp TG--TTSEEEEEEECTTTSCEEEEEEEEEEEEE--SSEEEEEEEECH
T ss_pred CCCCCCCEEEEEEEeCCCCeeEEEEEEEEEECC--CCceEEEEEEee
Confidence 367888877665 1 12 67888888666 556799999854
No 22
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=44.98 E-value=41 Score=21.64 Aligned_cols=24 Identities=17% Similarity=0.080 Sum_probs=18.5
Q ss_pred CcccccCeEEEeC---CCceEEEEEEe
Q psy6084 14 EWVCLGESVLIRP---YNSSGVIAYIG 37 (106)
Q Consensus 14 ~~l~vG~rV~v~~---~~~~GtVRyiG 37 (106)
..|..||+|.|.. .+..|+|..+-
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~ 31 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVL 31 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEE
Confidence 4789999999963 46778888773
No 23
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=43.61 E-value=30 Score=16.91 Aligned_cols=11 Identities=18% Similarity=0.362 Sum_probs=9.1
Q ss_pred ccccCeEEEeC
Q psy6084 16 VCLGESVLIRP 26 (106)
Q Consensus 16 l~vG~rV~v~~ 26 (106)
+++|+.|.|..
T Consensus 2 ~~~G~~V~I~~ 12 (28)
T smart00739 2 FEVGDTVRVIA 12 (28)
T ss_pred CCCCCEEEEeE
Confidence 57899999974
No 24
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=43.08 E-value=23 Score=22.53 Aligned_cols=22 Identities=32% Similarity=0.418 Sum_probs=18.4
Q ss_pred cccccCeEEEeCCCceEEEEEE
Q psy6084 15 WVCLGESVLIRPYNSSGVIAYI 36 (106)
Q Consensus 15 ~l~vG~rV~v~~~~~~GtVRyi 36 (106)
.|..|+||.|...+..|+++-|
T Consensus 10 ait~G~rVMia~tG~tgvikaI 31 (65)
T TIGR03318 10 AITTGSRVMIAGTGHTGVIKAI 31 (65)
T ss_pred ccCCCcEEEEecCCccceeehh
Confidence 4678999999877888888866
No 25
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=41.90 E-value=42 Score=23.23 Aligned_cols=35 Identities=23% Similarity=0.168 Sum_probs=25.6
Q ss_pred CCCCcccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEEc
Q psy6084 11 TLPEWVCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELD 52 (106)
Q Consensus 11 ~~~~~l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVEld 52 (106)
++...|++||+|.-. ++..|+|.-+.. .++-||+.
T Consensus 34 ~m~~~Lk~GD~VvT~-gGi~G~V~~I~d------~~v~leia 68 (109)
T PRK05886 34 DLHESLQPGDRVHTT-SGLQATIVGITD------DTVDLEIA 68 (109)
T ss_pred HHHHhcCCCCEEEEC-CCeEEEEEEEeC------CEEEEEEC
Confidence 455789999999776 489999988752 25556654
No 26
>PRK00321 rdgC recombination associated protein; Reviewed
Probab=41.73 E-value=87 Score=25.11 Aligned_cols=60 Identities=13% Similarity=0.174 Sum_probs=43.0
Q ss_pred CCCCCcccccCeEEEeC-CCceEEEEEEeecCC--------CCC---eEEEEEEcCCC---CCCCcEECCEEeeE
Q psy6084 10 VTLPEWVCLGESVLIRP-YNSSGVIAYIGPTEF--------AAG---TWVGVELDAPT---GKNDGTVQGTRYFE 69 (106)
Q Consensus 10 ~~~~~~l~vG~rV~v~~-~~~~GtVRyiG~~~~--------~~g---~~vGVElde~~---Gk~dGt~~G~rYF~ 69 (106)
.++|..|.+|+.|.+.. ....|+|||.+.--. ..| +-.++.|++.. =..|++++..+|-.
T Consensus 182 ~~~P~~f~l~~~~eL~~~~e~~~~vr~k~~~L~~~Ei~~hl~~Gk~vtkLaL~w~~~isFvL~~~~~iKrlkf~d 256 (303)
T PRK00321 182 GEAPAGFTLDDECELKSALEDGAVVRCKRQDLDSDEIRQHIEAGKQVTKLALTWQDRLSFVLTDDLTIKRLKFLD 256 (303)
T ss_pred CCCCCCcEecceeEEecCCCCccEEEEeCCCCCcHHHHHHHHCCCEEEEEEEEEcCceEEEEcCCceEeeeecch
Confidence 47899999999999974 345579999984311 234 35788998764 35678887777655
No 27
>PF13437 HlyD_3: HlyD family secretion protein
Probab=40.36 E-value=72 Score=20.27 Aligned_cols=32 Identities=19% Similarity=0.174 Sum_probs=20.1
Q ss_pred CCCCCccc-ccCeEEEeC-----CCceEEEEEEeecCC
Q psy6084 10 VTLPEWVC-LGESVLIRP-----YNSSGVIAYIGPTEF 41 (106)
Q Consensus 10 ~~~~~~l~-vG~rV~v~~-----~~~~GtVRyiG~~~~ 41 (106)
.+....|+ .|+.|.+.. ....|+|.++.+...
T Consensus 44 ~~~~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~~~~ 81 (105)
T PF13437_consen 44 EKDIARIKDPGQKVTVRLDPGPEKTIEGKVSSISPSPD 81 (105)
T ss_pred hHhhcceEeCCCEEEEEECCCCCcEEEEEEEEEeCccc
Confidence 34445666 788777752 245788888877543
No 28
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=39.33 E-value=19 Score=23.49 Aligned_cols=26 Identities=27% Similarity=0.233 Sum_probs=21.2
Q ss_pred CCCCcccccCeEEEeCCCceEEEEEEe
Q psy6084 11 TLPEWVCLGESVLIRPYNSSGVIAYIG 37 (106)
Q Consensus 11 ~~~~~l~vG~rV~v~~~~~~GtVRyiG 37 (106)
++.+.|++||+|.-. ++..|+|.-++
T Consensus 33 ~m~~~L~~Gd~VvT~-gGi~G~V~~i~ 58 (84)
T TIGR00739 33 KLIESLKKGDKVLTI-GGIIGTVTKIA 58 (84)
T ss_pred HHHHhCCCCCEEEEC-CCeEEEEEEEe
Confidence 456789999999776 47999998775
No 29
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=38.71 E-value=14 Score=29.93 Aligned_cols=21 Identities=38% Similarity=0.735 Sum_probs=16.1
Q ss_pred CCCcEECC----------EEeeEeCCCCeeE
Q psy6084 57 KNDGTVQG----------TRYFESRPKHGIF 77 (106)
Q Consensus 57 k~dGt~~G----------~rYF~c~p~~GiF 77 (106)
.|.|+++| .||-.|.+||||=
T Consensus 22 snSgS~KgSd~Sp~~rr~~rY~~C~dNHGik 52 (305)
T PF15290_consen 22 SNSGSCKGSDSSPTMRRSGRYMSCGDNHGIK 52 (305)
T ss_pred CCCccccCCCCCCCCCCCCceeecccCCCCC
Confidence 35566665 6899999999974
No 30
>PF04945 YHS: YHS domain; InterPro: IPR007029 This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterised membrane proteins including Q9CNI0 from SWISSPROT. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases.; PDB: 3U52_B 2INN_A 2INP_B 1T0Q_A 2RDB_A 1T0R_A 2IND_A 1T0S_A 2INC_A 3DHI_A ....
Probab=34.82 E-value=16 Score=20.89 Aligned_cols=14 Identities=14% Similarity=0.233 Sum_probs=11.2
Q ss_pred cEECCEEeeEeCCC
Q psy6084 60 GTVQGTRYFESRPK 73 (106)
Q Consensus 60 Gt~~G~rYF~c~p~ 73 (106)
-.++|+.|+.|.+.
T Consensus 18 ~~y~G~~Y~FCS~~ 31 (47)
T PF04945_consen 18 VEYNGRTYYFCSEG 31 (47)
T ss_dssp EEETTEEEEESSHH
T ss_pred EEECCEEEEEcCHH
Confidence 35899999999754
No 31
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=34.41 E-value=62 Score=22.05 Aligned_cols=35 Identities=17% Similarity=0.285 Sum_probs=25.0
Q ss_pred CCCCcccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEEc
Q psy6084 11 TLPEWVCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELD 52 (106)
Q Consensus 11 ~~~~~l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVEld 52 (106)
++.+.|++||+|.-. ++..|+|.-+.. ..+-||..
T Consensus 48 ~~~~~Lk~Gd~VvT~-gGi~G~Vv~i~~------~~v~lei~ 82 (106)
T PRK05585 48 KMLSSLAKGDEVVTN-GGIIGKVTKVSE------DFVIIELN 82 (106)
T ss_pred HHHHhcCCCCEEEEC-CCeEEEEEEEeC------CEEEEEEC
Confidence 456789999999776 488999987743 24555553
No 32
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=33.21 E-value=79 Score=21.43 Aligned_cols=23 Identities=13% Similarity=0.244 Sum_probs=18.1
Q ss_pred CcccccCeEEEeC---CCceEEEEEE
Q psy6084 14 EWVCLGESVLIRP---YNSSGVIAYI 36 (106)
Q Consensus 14 ~~l~vG~rV~v~~---~~~~GtVRyi 36 (106)
..|..||+|+|.. .+..|+|..+
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V 28 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKV 28 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEE
Confidence 3688999999963 4677888877
No 33
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=32.18 E-value=57 Score=25.69 Aligned_cols=25 Identities=16% Similarity=0.032 Sum_probs=20.6
Q ss_pred CCcccccCeEEEeCCCceEEEEEEeec
Q psy6084 13 PEWVCLGESVLIRPYNSSGVIAYIGPT 39 (106)
Q Consensus 13 ~~~l~vG~rV~v~~~~~~GtVRyiG~~ 39 (106)
...+++||.|.+. +..|+|.-+|..
T Consensus 127 ~rpf~vGD~I~i~--~~~G~V~~I~~r 151 (286)
T PRK10334 127 FRPFRAGEYVDLG--GVAGTVLSVQIF 151 (286)
T ss_pred cCCCCCCCEEEEC--CEEEEEEEEEeE
Confidence 3568999999996 688999988755
No 34
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=31.15 E-value=63 Score=19.74 Aligned_cols=22 Identities=36% Similarity=0.717 Sum_probs=13.3
Q ss_pred CcccccCeEEEeC---CCceEEEEE
Q psy6084 14 EWVCLGESVLIRP---YNSSGVIAY 35 (106)
Q Consensus 14 ~~l~vG~rV~v~~---~~~~GtVRy 35 (106)
-|+..||.|.|.. ....|.|-|
T Consensus 40 iwI~~GD~V~V~~~~~d~~kG~Ii~ 64 (65)
T PF01176_consen 40 IWIKRGDFVLVEPSPYDKVKGRIIY 64 (65)
T ss_dssp C---TTEEEEEEESTTCTTEEEEEE
T ss_pred EecCCCCEEEEEecccCCCeEEEEE
Confidence 4788899998873 246677765
No 35
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=29.86 E-value=88 Score=21.23 Aligned_cols=22 Identities=14% Similarity=0.213 Sum_probs=17.6
Q ss_pred cccccCeEEEeC---CCceEEEEEE
Q psy6084 15 WVCLGESVLIRP---YNSSGVIAYI 36 (106)
Q Consensus 15 ~l~vG~rV~v~~---~~~~GtVRyi 36 (106)
.|..||+|+|.. .+..|+|..+
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V 27 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKV 27 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEE
Confidence 578999999963 4677888877
No 36
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=29.84 E-value=18 Score=23.33 Aligned_cols=26 Identities=15% Similarity=0.102 Sum_probs=3.2
Q ss_pred CCCCCcccccCeEEEeCCCceEEEEEE
Q psy6084 10 VTLPEWVCLGESVLIRPYNSSGVIAYI 36 (106)
Q Consensus 10 ~~~~~~l~vG~rV~v~~~~~~GtVRyi 36 (106)
.++.+.|++||+|... ++..|+|.-+
T Consensus 31 ~~m~~~Lk~Gd~VvT~-gGi~G~V~~i 56 (82)
T PF02699_consen 31 QEMLASLKPGDEVVTI-GGIYGTVVEI 56 (82)
T ss_dssp TTGGG----------------------
T ss_pred HHHHHcCCCCCEEEEC-CcEEEEEEEE
Confidence 4567889999999776 4788888765
No 37
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=29.35 E-value=34 Score=23.79 Aligned_cols=26 Identities=12% Similarity=0.086 Sum_probs=20.8
Q ss_pred CCCCcccccCeEEEeCCCceEEEEEEe
Q psy6084 11 TLPEWVCLGESVLIRPYNSSGVIAYIG 37 (106)
Q Consensus 11 ~~~~~l~vG~rV~v~~~~~~GtVRyiG 37 (106)
++.+.|+.||+|.-. ++..|+|.-+.
T Consensus 32 em~~sLk~GD~VvT~-GGi~G~V~~I~ 57 (113)
T PRK06531 32 NQLNAIQKGDEVVTI-GGLYGTVDEVD 57 (113)
T ss_pred HHHHhcCCCCEEEEC-CCcEEEEEEEe
Confidence 455689999999765 58999998775
No 38
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=27.45 E-value=1.6e+02 Score=18.28 Aligned_cols=39 Identities=23% Similarity=0.277 Sum_probs=25.5
Q ss_pred cccccCeEEEeCCCceEEEEEEeecC-----CCCCeEEEEEEcC
Q psy6084 15 WVCLGESVLIRPYNSSGVIAYIGPTE-----FAAGTWVGVELDA 53 (106)
Q Consensus 15 ~l~vG~rV~v~~~~~~GtVRyiG~~~-----~~~g~~vGVElde 53 (106)
.+++||.|.+.+.+...+|+=+-.-. ...|.-+++.|.+
T Consensus 26 ~i~~Gd~v~i~P~~~~~~V~si~~~~~~~~~a~aGd~v~~~l~~ 69 (83)
T cd03698 26 SIQKGDTLLVMPSKESVEVKSIYVDDEEVDYAVAGENVRLKLKG 69 (83)
T ss_pred EEeCCCEEEEeCCCcEEEEEEEEECCeECCEECCCCEEEEEECC
Confidence 46788888888766777777553221 1456677777753
No 39
>KOG2045|consensus
Probab=27.44 E-value=72 Score=30.42 Aligned_cols=42 Identities=26% Similarity=0.458 Sum_probs=29.3
Q ss_pred cccccCeEEEeC------CCceEEEEEEeecCCCCCeEEEEEEcCCC--CCC
Q psy6084 15 WVCLGESVLIRP------YNSSGVIAYIGPTEFAAGTWVGVELDAPT--GKN 58 (106)
Q Consensus 15 ~l~vG~rV~v~~------~~~~GtVRyiG~~~~~~g~~vGVElde~~--Gk~ 58 (106)
.+..||||.... ..-.||| +|........+++|-+|-|. |.|
T Consensus 1129 ~f~lgdrVvyvqdsgkvPv~~kGTV--vG~m~~~~~~~~~vlFd~~~~ngnn 1178 (1493)
T KOG2045|consen 1129 PFRLGDRVVYVQDSGKVPVGTKGTV--VGIMPVTDDTFCKVLFDSPVPNGNN 1178 (1493)
T ss_pred cccccceEEEeeccCccccccccce--EEEEecccccccceeecccccCCCc
Confidence 467899987642 2345777 56566666889999999886 544
No 40
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=26.60 E-value=77 Score=21.38 Aligned_cols=24 Identities=21% Similarity=0.617 Sum_probs=14.7
Q ss_pred CCcccccCeEEEeCC----CceEEEEEE
Q psy6084 13 PEWVCLGESVLIRPY----NSSGVIAYI 36 (106)
Q Consensus 13 ~~~l~vG~rV~v~~~----~~~GtVRyi 36 (106)
--|+..||.|.|.+. ...|.|-|.
T Consensus 55 ~iwI~~GD~VlVsp~d~~~~~kg~Iv~r 82 (99)
T TIGR00523 55 RIWIREGDVVIVKPWEFQGDDKCDIVWR 82 (99)
T ss_pred cEEecCCCEEEEEEccCCCCccEEEEEE
Confidence 346777888888532 234666665
No 41
>COG4841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.36 E-value=2e+02 Score=19.51 Aligned_cols=49 Identities=20% Similarity=0.340 Sum_probs=33.0
Q ss_pred ccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEEcCCCCC-CCcEECCEEeeEeC
Q psy6084 16 VCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVELDAPTGK-NDGTVQGTRYFESR 71 (106)
Q Consensus 16 l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVElde~~Gk-~dGt~~G~rYF~c~ 71 (106)
|+-|+.|+. -|||-|.-....|.-+||.-+.|.-. ---.++|..+|--.
T Consensus 19 l~~g~~vrf-------fvRyGG~~~~~~GFS~gv~~e~PkE~g~~q~~Dgltffiee 68 (95)
T COG4841 19 LEEGNKVRF-------FVRYGGCSSLQQGFSLGVAKEVPKEIGYKQEYDGLTFFIEE 68 (95)
T ss_pred CCCCCEEEE-------EEEEcCcccccCCcceeeeccCchhhchheeecCeEEEEec
Confidence 344555554 48999977677899999999977521 12246777777654
No 42
>PF07154 DUF1392: Protein of unknown function (DUF1392); InterPro: IPR009824 This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length, which seem to be specific to Anabaena species. The function of this family is unknown.
Probab=26.26 E-value=1.1e+02 Score=22.50 Aligned_cols=43 Identities=23% Similarity=0.191 Sum_probs=26.0
Q ss_pred CCcccccCeEEEeCCCceEEEEEEeec-CCCCCeEEEEEEcCCC
Q psy6084 13 PEWVCLGESVLIRPYNSSGVIAYIGPT-EFAAGTWVGVELDAPT 55 (106)
Q Consensus 13 ~~~l~vG~rV~v~~~~~~GtVRyiG~~-~~~~g~~vGVElde~~ 55 (106)
...|.+||+|.+...+.--..|-|--+ -....-++.|||--|.
T Consensus 85 kp~F~LGd~V~~~f~~~~pkqRlIlGv~lv~~~W~Y~VE~~SPt 128 (150)
T PF07154_consen 85 KPAFRLGDRVEFRFYSDGPKQRLILGVFLVNNSWFYAVEWRSPT 128 (150)
T ss_pred CCceecCCEEEEEecCCCCceEEEEEEEEecCceEEEEEEeCCc
Confidence 345789999999732222233433222 2234557899999886
No 43
>CHL00010 infA translation initiation factor 1
Probab=26.10 E-value=1e+02 Score=19.57 Aligned_cols=23 Identities=26% Similarity=0.371 Sum_probs=14.4
Q ss_pred CcccccCeEEEe--C-CCceEEEEEE
Q psy6084 14 EWVCLGESVLIR--P-YNSSGVIAYI 36 (106)
Q Consensus 14 ~~l~vG~rV~v~--~-~~~~GtVRyi 36 (106)
.++.+||+|.+. + ....|.|-|-
T Consensus 45 i~~~vGD~V~ve~~~~~~~~g~Ii~r 70 (78)
T CHL00010 45 IRILPGDRVKVELSPYDLTKGRIIYR 70 (78)
T ss_pred cccCCCCEEEEEEcccCCCeEEEEEE
Confidence 345789999887 2 2334666553
No 44
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=25.84 E-value=1e+02 Score=19.77 Aligned_cols=23 Identities=30% Similarity=0.629 Sum_probs=15.3
Q ss_pred CcccccCeEEEeC---CCceEEEEEE
Q psy6084 14 EWVCLGESVLIRP---YNSSGVIAYI 36 (106)
Q Consensus 14 ~~l~vG~rV~v~~---~~~~GtVRyi 36 (106)
-|+..||.|.|.. ....|.|-|.
T Consensus 37 iwI~~GD~V~Ve~~~~d~~kg~Iv~r 62 (77)
T cd05793 37 VWINEGDIVLVAPWDFQDDKADIIYK 62 (77)
T ss_pred EEEcCCCEEEEEeccccCCEEEEEEE
Confidence 5778888888863 2456666665
No 45
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=25.73 E-value=1.6e+02 Score=20.42 Aligned_cols=24 Identities=13% Similarity=0.029 Sum_probs=16.2
Q ss_pred CCCcccccCeEEEeCC---CceEEEEE
Q psy6084 12 LPEWVCLGESVLIRPY---NSSGVIAY 35 (106)
Q Consensus 12 ~~~~l~vG~rV~v~~~---~~~GtVRy 35 (106)
....++.||+|.|..+ +..|.|.-
T Consensus 105 ~~~~~~~G~~V~V~~GPf~g~~g~v~~ 131 (159)
T TIGR01955 105 ATTLPYKGDKVRITDGAFAGFEAIFLE 131 (159)
T ss_pred cccCCCCCCEEEEeccCCCCcEEEEEE
Confidence 3456889999999743 45555544
No 46
>PRK14533 groES co-chaperonin GroES; Provisional
Probab=25.40 E-value=67 Score=21.35 Aligned_cols=11 Identities=18% Similarity=0.293 Sum_probs=4.9
Q ss_pred CcccccCeEEE
Q psy6084 14 EWVCLGESVLI 24 (106)
Q Consensus 14 ~~l~vG~rV~v 24 (106)
..+++||+|.+
T Consensus 52 ~~Vk~GD~Vl~ 62 (91)
T PRK14533 52 FDIKVGDKVIF 62 (91)
T ss_pred ccccCCCEEEE
Confidence 33444444444
No 47
>PF12700 HlyD_2: HlyD family secretion protein; PDB: 3LNN_B 4DK0_A 4DK1_C 3FPP_B 2K32_A 2K33_A 3OW7_B 3OOC_A 3T53_B 4DNT_C ....
Probab=25.25 E-value=2.5e+02 Score=21.12 Aligned_cols=74 Identities=20% Similarity=0.309 Sum_probs=46.1
Q ss_pred CCCCCcccccCeEEE--eC----CCceEEEEEEeecCCCCCeEEEEEEcCCCCC-CCcEECCEEeeEeCCCCeeEEecCC
Q psy6084 10 VTLPEWVCLGESVLI--RP----YNSSGVIAYIGPTEFAAGTWVGVELDAPTGK-NDGTVQGTRYFESRPKHGIFVRADK 82 (106)
Q Consensus 10 ~~~~~~l~vG~rV~v--~~----~~~~GtVRyiG~~~~~~g~~vGVElde~~Gk-~dGt~~G~rYF~c~p~~GiFv~~~k 82 (106)
......+++|+.|.| .. ....|+|.++.+.. ..-..+=++++++.+. ..|..--... ......++.||.+-
T Consensus 204 e~~~~~i~~g~~~~v~~~~~~~~~~~~g~v~~i~~~~-~~~~~v~~~~~~~~~~l~~g~~v~v~i-~~~~~~~~~VP~~A 281 (328)
T PF12700_consen 204 ESDASKIKVGQKVEVTIDAPDNGKSFTGKVSSISPSA-SRTFKVRVSLDNPNGNLRPGMFVEVSI-ILGSENGLVVPKSA 281 (328)
T ss_dssp CCGTTTHTTTGEEEEEETTSS-SSEEEEEEEEEESSE-TTEEEEEEEEE-SSS-S-TT-EEEEEE-ESEESCEEEEEGGG
T ss_pred HHHHHhccCCcEEEEEEEeecCCCceeeEEeecCCcc-ceeeEEEEEeccccchhhhccccccee-ccccccEEEEcChh
Confidence 445677899999555 31 24789999998776 2223566888887532 4555433333 33348889999888
Q ss_pred ccc
Q psy6084 83 LIQ 85 (106)
Q Consensus 83 v~~ 85 (106)
|..
T Consensus 282 i~~ 284 (328)
T PF12700_consen 282 IIE 284 (328)
T ss_dssp EEE
T ss_pred hcc
Confidence 875
No 48
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=24.91 E-value=1.1e+02 Score=18.22 Aligned_cols=11 Identities=18% Similarity=0.353 Sum_probs=8.8
Q ss_pred cccccCeEEEe
Q psy6084 15 WVCLGESVLIR 25 (106)
Q Consensus 15 ~l~vG~rV~v~ 25 (106)
++.+||+|.+.
T Consensus 40 ~~~vGD~V~~~ 50 (64)
T cd04451 40 RILPGDRVKVE 50 (64)
T ss_pred ccCCCCEEEEE
Confidence 36789999887
No 49
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=24.81 E-value=1.1e+02 Score=18.98 Aligned_cols=21 Identities=29% Similarity=0.526 Sum_probs=12.4
Q ss_pred cccccCeEEEe--C-CCceEEEEE
Q psy6084 15 WVCLGESVLIR--P-YNSSGVIAY 35 (106)
Q Consensus 15 ~l~vG~rV~v~--~-~~~~GtVRy 35 (106)
++.+||+|.+. + ....|.|-|
T Consensus 46 ~i~vGD~V~ve~~~~~~~~g~Iv~ 69 (72)
T PRK00276 46 RILPGDKVTVELSPYDLTKGRITY 69 (72)
T ss_pred ccCCCCEEEEEEcccCCCeEEEEE
Confidence 35778888887 2 223455544
No 50
>PF14801 GCD14_N: tRNA methyltransferase complex GCD14 subunit N-term; PDB: 1I9G_A.
Probab=24.48 E-value=94 Score=19.08 Aligned_cols=43 Identities=21% Similarity=0.255 Sum_probs=19.5
Q ss_pred cccccCeEEEeC-CCceEEEEEEeecCCCCCe----EEEEEEcCCCCCCCcEE
Q psy6084 15 WVCLGESVLIRP-YNSSGVIAYIGPTEFAAGT----WVGVELDAPTGKNDGTV 62 (106)
Q Consensus 15 ~l~vG~rV~v~~-~~~~GtVRyiG~~~~~~g~----~vGVElde~~Gk~dGt~ 62 (106)
.|..||||++.. ++..=|+. +.. .+. +=.|.-|+-.|..+|++
T Consensus 5 pf~~GdrVQlTD~Kgr~~Ti~----L~~-G~~fhThrG~i~HDdlIG~~eGsV 52 (54)
T PF14801_consen 5 PFRAGDRVQLTDPKGRKHTIT----LEP-GGEFHTHRGAIRHDDLIGRPEGSV 52 (54)
T ss_dssp S--TT-EEEEEETT--EEEEE------T-T-EEEETTEEEEHHHHTT--TTEE
T ss_pred CCCCCCEEEEccCCCCeeeEE----ECC-CCeEEcCccccchhheecCCCcEE
Confidence 478899999973 44444443 211 111 12356666678888875
No 51
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=23.38 E-value=97 Score=19.63 Aligned_cols=22 Identities=32% Similarity=0.522 Sum_probs=15.3
Q ss_pred CCcccccCeEEEeCCCceEEEE-EEeec
Q psy6084 13 PEWVCLGESVLIRPYNSSGVIA-YIGPT 39 (106)
Q Consensus 13 ~~~l~vG~rV~v~~~~~~GtVR-yiG~~ 39 (106)
+..+++||+|+|. |+|. |-|.+
T Consensus 42 ~~~~~~Gd~V~vt-----G~v~ey~g~t 64 (78)
T cd04486 42 GADVAVGDLVRVT-----GTVTEYYGLT 64 (78)
T ss_pred CCCCCCCCEEEEE-----EEEEeeCCeE
Confidence 5677899999997 4554 55533
No 52
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=23.21 E-value=29 Score=23.98 Aligned_cols=41 Identities=24% Similarity=0.305 Sum_probs=28.1
Q ss_pred EEEEEEcCCCCCCCcEECCEEeeEeC-CCCeeEEecCCccccCCC
Q psy6084 46 WVGVELDAPTGKNDGTVQGTRYFESR-PKHGIFVRADKLIQDRRG 89 (106)
Q Consensus 46 ~vGVElde~~Gk~dGt~~G~rYF~c~-p~~GiFv~~~kv~~~~~~ 89 (106)
+.|-+|-...| =.+-|-+|=-|- .|.|+||+.++...+.-+
T Consensus 62 ~sg~~w~P~~g---wa~agg~yavci~Gn~GVFVe~~kadf~kIf 103 (109)
T COG4831 62 LSGMNWTPQNG---WAVAGGKYAVCIMGNVGVFVELDKADFNKIF 103 (109)
T ss_pred hhcCccccccc---eEEecCceEEEEecceeEEEEcchhhHHHHH
Confidence 34445443333 246677888997 899999999998765443
No 53
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=23.10 E-value=2.5e+02 Score=19.85 Aligned_cols=24 Identities=17% Similarity=0.133 Sum_probs=17.0
Q ss_pred CCcccccCeEEEeC---CCceEEEEEE
Q psy6084 13 PEWVCLGESVLIRP---YNSSGVIAYI 36 (106)
Q Consensus 13 ~~~l~vG~rV~v~~---~~~~GtVRyi 36 (106)
...+++||+|.|.. .+..|+|.-+
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~g~v~~i 150 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFNGTVEEV 150 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCEEEEEEE
Confidence 45688999999974 3566666554
No 54
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=23.08 E-value=1.2e+02 Score=19.69 Aligned_cols=23 Identities=30% Similarity=0.615 Sum_probs=14.7
Q ss_pred CcccccCeEEEeC---CCceEEEEEE
Q psy6084 14 EWVCLGESVLIRP---YNSSGVIAYI 36 (106)
Q Consensus 14 ~~l~vG~rV~v~~---~~~~GtVRyi 36 (106)
-|+..||.|.|.. ....|.|-|+
T Consensus 42 iwI~~GD~VlVe~~~~~~~kg~Iv~r 67 (83)
T smart00652 42 VWIRRGDIVLVDPWDFQDVKADIIYK 67 (83)
T ss_pred EEEcCCCEEEEEecCCCCCEEEEEEE
Confidence 4677788888863 2355666655
No 55
>PF02298 Cu_bind_like: Plastocyanin-like domain; InterPro: IPR003245 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. This domain is found in a variety of plant cyanins and pollern allergen. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Amb a 3.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1JER_A 1WS7_A 1WS8_D 1F56_B 1X9R_B 1X9U_A 2CBP_A.
Probab=23.05 E-value=48 Score=21.36 Aligned_cols=13 Identities=8% Similarity=0.297 Sum_probs=8.8
Q ss_pred CCcccccCeEEEe
Q psy6084 13 PEWVCLGESVLIR 25 (106)
Q Consensus 13 ~~~l~vG~rV~v~ 25 (106)
...+.+||-+...
T Consensus 16 ~~~F~vGD~LvF~ 28 (85)
T PF02298_consen 16 GKTFRVGDTLVFN 28 (85)
T ss_dssp TS-BETTEEEEEE
T ss_pred CCcEeCCCEEEEE
Confidence 3468899977665
No 56
>PF10220 DUF2146: Uncharacterized conserved protein (DUF2146); InterPro: IPR019354 Smg8 and Smg9 are two subunits of the Smg-1 complex. They suppress Smg-1 kinase activity in the isolated Smg-1 complex, and are involved in nonsense-mediated mRNA decay (NMD) in both mammals and nematodes []. NMD is a surveillance mechanism that detects and degrades mRNAs containing premature translation termination codons.
Probab=22.91 E-value=1.3e+02 Score=27.92 Aligned_cols=34 Identities=26% Similarity=0.583 Sum_probs=25.8
Q ss_pred CeEEEEEEcCCCCCCCcEECCEEeeEeCCCCeeEEecCCccc
Q psy6084 44 GTWVGVELDAPTGKNDGTVQGTRYFESRPKHGIFVRADKLIQ 85 (106)
Q Consensus 44 g~~vGVElde~~Gk~dGt~~G~rYF~c~p~~GiFv~~~kv~~ 85 (106)
-.|||+|...+.| +|||.|.|..-+++.-+.+..
T Consensus 746 k~fvG~EYEc~rG--------hRF~~~~pd~~~~~~~s~~~k 779 (895)
T PF10220_consen 746 KVFVGFEYECPRG--------HRFMMSGPDKVVKVTGSGIVK 779 (895)
T ss_pred EEEEEEEEecCCC--------ceeeeeCCCceEEecCCCCcc
Confidence 3589999998876 789999998888774444443
No 57
>PTZ00414 10 kDa heat shock protein; Provisional
Probab=22.62 E-value=68 Score=21.85 Aligned_cols=13 Identities=31% Similarity=0.478 Sum_probs=6.4
Q ss_pred CCcccccCeEEEe
Q psy6084 13 PEWVCLGESVLIR 25 (106)
Q Consensus 13 ~~~l~vG~rV~v~ 25 (106)
+..+++||+|.+.
T Consensus 60 ~~~Vk~GD~Vl~~ 72 (100)
T PTZ00414 60 TPTVKVGDTVLLP 72 (100)
T ss_pred cceecCCCEEEEc
Confidence 3345555555543
No 58
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=22.04 E-value=1.3e+02 Score=19.36 Aligned_cols=23 Identities=17% Similarity=0.562 Sum_probs=15.4
Q ss_pred CcccccCeEEEeC----CCceEEEEEE
Q psy6084 14 EWVCLGESVLIRP----YNSSGVIAYI 36 (106)
Q Consensus 14 ~~l~vG~rV~v~~----~~~~GtVRyi 36 (106)
-|+..||.|.|.+ ....|.|-|.
T Consensus 37 iwI~~GD~VlV~~~~~~~~~kg~Iv~r 63 (78)
T cd04456 37 IWIKRGDFLIVDPIEEGEDVKADIIFV 63 (78)
T ss_pred EEEcCCCEEEEEecccCCCceEEEEEE
Confidence 5678888888863 2456666665
No 59
>KOG4792|consensus
Probab=21.79 E-value=74 Score=25.42 Aligned_cols=39 Identities=18% Similarity=0.237 Sum_probs=23.5
Q ss_pred CCcccccCeEEEeCCCceEEEEEEeecCCCCCe--EEEEEEcC
Q psy6084 13 PEWVCLGESVLIRPYNSSGVIAYIGPTEFAAGT--WVGVELDA 53 (106)
Q Consensus 13 ~~~l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~--~vGVElde 53 (106)
+-.|++||.|.|+..+..| .|-|.+.+..|. +-=|++-+
T Consensus 245 aL~levGdiVkVTk~ninG--qwegElnGk~G~fPfThvrf~d 285 (293)
T KOG4792|consen 245 ALALEVGDIVKVTKKNING--QWEGELNGKIGHFPFTHVRFTD 285 (293)
T ss_pred hhhhhcCcEEEEEeeccCc--eeeeeecCccccccceeEEeec
Confidence 4457889988887433333 377777766664 33444443
No 60
>smart00266 CAD Domains present in proteins implicated in post-mortem DNA fragmentation.
Probab=20.93 E-value=43 Score=21.75 Aligned_cols=24 Identities=29% Similarity=0.628 Sum_probs=19.3
Q ss_pred CCcE-ECCEEeeEeCCCCeeEEecC
Q psy6084 58 NDGT-VQGTRYFESRPKHGIFVRAD 81 (106)
Q Consensus 58 ~dGt-~~G~rYF~c~p~~GiFv~~~ 81 (106)
.||| ++-..||.|=|..-.|+-+.
T Consensus 45 eDGT~VddEeyF~tLp~nt~l~~L~ 69 (74)
T smart00266 45 EDGTIVDDEEYFQTLPDNTELMALE 69 (74)
T ss_pred cCCcEEccHHHHhcCCCCcEEEEEc
Confidence 4888 67889999998888887543
No 61
>PF04381 RdgC: Putative exonuclease, RdgC; InterPro: IPR007476 Members of the RdgC family may have exonuclease activity. RdgC is required for efficient pilin variation in Neisseria gonorrhoeae, suggesting that it may be involved in recombination reactions []. In Escherichia coli, RdgC is required for growth in recombination-deficient exonuclease-depleted strains. Under these conditions, RdgC may act as an exonuclease to remove collapsed replication forks, in the absence of the normal repair mechanisms [].; GO: 0006310 DNA recombination; PDB: 2OWY_A 2OWL_A.
Probab=20.86 E-value=91 Score=24.77 Aligned_cols=59 Identities=17% Similarity=0.309 Sum_probs=36.9
Q ss_pred CCCCcccccCeEEEeC-CCceEEEEEEeecCC--------CCCe---EEEEEEcCCC---CCCCcEECCEEeeE
Q psy6084 11 TLPEWVCLGESVLIRP-YNSSGVIAYIGPTEF--------AAGT---WVGVELDAPT---GKNDGTVQGTRYFE 69 (106)
Q Consensus 11 ~~~~~l~vG~rV~v~~-~~~~GtVRyiG~~~~--------~~g~---~vGVElde~~---Gk~dGt~~G~rYF~ 69 (106)
++|+.|.+|+.|.+.. ....++|||.+.--. ..|. -++++|++.. =..|.++...+|-.
T Consensus 183 ~~p~~f~lg~~~eL~~~~e~~~~Vr~~~~dL~~dEi~~hl~~Gk~v~kLaL~w~d~isFvL~~dl~ikrikf~d 256 (301)
T PF04381_consen 183 ELPDGFTLGDECELKSPGEEGAVVRYKRQDLDSDEIKQHLEAGKQVTKLALTWDDRISFVLTDDLSIKRIKFLD 256 (301)
T ss_dssp --STTEEEEEEEEEEESSTTS-EEEEES--TTSHHHHHHHHTTEEEEEEEEEETTTEEEEEETTS-EEEEEE-H
T ss_pred CCCCCcccCCeEEEccCCCCCcEEEEecccCChHHHHHHHHCCCEEEEEEeeeCCcEEEEEcCCccEEeeeecc
Confidence 7889999999999973 356799999984321 2343 4788888764 24666776666653
No 62
>KOG1641|consensus
Probab=20.85 E-value=1e+02 Score=21.35 Aligned_cols=21 Identities=24% Similarity=0.341 Sum_probs=15.3
Q ss_pred CCCCCCCCCCcccccCeEEEe
Q psy6084 5 QSFDDVTLPEWVCLGESVLIR 25 (106)
Q Consensus 5 ~~~~~~~~~~~l~vG~rV~v~ 25 (106)
-.+-....|.++++||||++.
T Consensus 56 ~~~~G~~v~~~Vk~Gd~VLlp 76 (104)
T KOG1641|consen 56 RDKGGEIVPVSVKVGDRVLLP 76 (104)
T ss_pred ccCCCCCcCccccCCCEEEee
Confidence 344556677788889998885
No 63
>COG5466 Predicted small metal-binding protein [Function unknown]
Probab=20.63 E-value=83 Score=19.66 Aligned_cols=19 Identities=26% Similarity=0.287 Sum_probs=14.3
Q ss_pred CEEeeEeC---CCCeeEEecCC
Q psy6084 64 GTRYFESR---PKHGIFVRADK 82 (106)
Q Consensus 64 G~rYF~c~---p~~GiFv~~~k 82 (106)
+.+||.|. ++||--++.+.
T Consensus 2 ~m~~f~C~slg~~C~f~~~a~~ 23 (59)
T COG5466 2 AMYLFKCGSLGMGCGFEARADS 23 (59)
T ss_pred CceEEEccccCCCCcceeccCc
Confidence 57899997 78887766543
No 64
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=20.09 E-value=2.3e+02 Score=17.46 Aligned_cols=33 Identities=15% Similarity=0.225 Sum_probs=18.1
Q ss_pred CcccccCeEEEeCCCceEEEEEEeecCCCCCeEEEEEE
Q psy6084 14 EWVCLGESVLIRPYNSSGVIAYIGPTEFAAGTWVGVEL 51 (106)
Q Consensus 14 ~~l~vG~rV~v~~~~~~GtVRyiG~~~~~~g~~vGVEl 51 (106)
..++.||+|.|. |.++..-..+........+++
T Consensus 60 ~~~~kG~~V~v~-----G~l~~~~~~~~~g~~~~~~~i 92 (100)
T cd04496 60 KYLKKGDLVYVE-----GRLRTRSWEDKDGQKRYGTEV 92 (100)
T ss_pred HHhCCCCEEEEE-----EEEEeceeECCCCCEEEEEEE
Confidence 357888988887 555544333322333444443
Done!