Query 031764
Match_columns 153
No_of_seqs 124 out of 177
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 05:01:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031764.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031764hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00059 PsbP domain-containin 100.0 7.1E-30 1.5E-34 216.3 11.7 107 43-150 71-181 (286)
2 PLN00042 photosystem II oxygen 99.9 1.6E-27 3.6E-32 201.0 10.5 103 45-149 46-165 (260)
3 PF01789 PsbP: PsbP; InterPro 99.9 4.2E-22 9.1E-27 156.8 6.9 73 79-151 21-94 (175)
4 PLN00067 PsbP domain-containin 99.8 2.6E-18 5.5E-23 145.4 9.2 100 46-149 40-184 (263)
5 PLN00066 PsbP domain-containin 99.7 1.3E-16 2.8E-21 135.2 10.0 100 49-149 45-186 (262)
6 PLN03152 hypothetical protein; 99.1 4.2E-10 9.1E-15 94.3 7.9 101 46-149 28-168 (241)
7 PF12712 DUF3805: Domain of un 89.7 0.42 9E-06 38.2 3.5 45 82-126 2-46 (153)
8 PF08006 DUF1700: Protein of u 67.8 3.1 6.6E-05 32.7 1.4 21 130-150 44-64 (181)
9 TIGR02811 formate_TAT formate 57.9 8.7 0.00019 26.5 2.1 15 46-60 6-20 (66)
10 PF10518 TAT_signal: TAT (twin 55.2 18 0.00039 20.5 2.8 20 48-67 1-20 (26)
11 COG1797 CobB Cobyrinic acid a, 49.5 8 0.00017 35.9 1.0 64 80-151 245-311 (451)
12 PF07174 FAP: Fibronectin-atta 46.9 12 0.00027 32.9 1.7 31 82-112 110-144 (297)
13 PF05984 Cytomega_UL20A: Cytom 46.1 18 0.00039 26.9 2.2 20 49-68 1-20 (100)
14 PRK10943 cold shock-like prote 33.3 51 0.0011 22.4 2.8 27 80-112 6-32 (69)
15 COG4709 Predicted membrane pro 31.0 30 0.00064 28.9 1.5 19 131-149 45-63 (195)
16 cd04458 CSP_CDS Cold-Shock Pro 28.3 76 0.0017 20.5 2.9 25 83-113 6-30 (65)
17 PRK09890 cold shock protein Cs 28.1 67 0.0014 21.9 2.7 28 79-112 6-33 (70)
18 PF06570 DUF1129: Protein of u 28.1 34 0.00074 27.5 1.4 17 136-152 52-68 (206)
19 PF12559 Inhibitor_I10: Serine 27.5 25 0.00055 23.8 0.5 12 90-101 44-55 (56)
20 cd03130 GATase1_CobB Type 1 gl 27.1 25 0.00055 28.0 0.5 42 88-129 6-49 (198)
21 PRK15464 cold shock-like prote 25.9 70 0.0015 22.0 2.5 27 80-112 7-33 (70)
22 PF12318 FAD-SLDH: Membrane bo 25.2 66 0.0014 25.6 2.5 8 48-55 1-8 (168)
23 PRK09937 stationary phase/star 24.1 96 0.0021 21.5 2.9 43 80-128 4-55 (74)
24 TIGR02381 cspD cold shock doma 24.1 99 0.0021 20.8 2.9 27 80-112 4-30 (68)
25 COG5014 Predicted Fe-S oxidore 23.3 70 0.0015 27.0 2.4 23 131-153 68-90 (228)
26 PRK09507 cspE cold shock prote 22.8 1E+02 0.0022 20.9 2.8 27 80-112 6-32 (69)
27 PRK15463 cold shock-like prote 22.6 1E+02 0.0023 21.0 2.8 27 80-112 7-33 (70)
28 PF14326 DUF4384: Domain of un 22.6 2.5E+02 0.0055 19.1 4.8 34 81-114 22-57 (83)
29 PRK14998 cold shock-like prote 22.0 1.1E+02 0.0025 21.0 2.9 27 80-112 4-30 (73)
30 TIGR03741 PRTRC_E PRTRC system 21.7 1.9E+02 0.0042 21.6 4.3 30 119-148 24-62 (104)
31 PF08338 DUF1731: Domain of un 20.7 37 0.00079 21.8 0.2 10 88-97 30-39 (48)
32 COG3355 Predicted transcriptio 20.5 41 0.00089 26.1 0.5 18 87-104 80-98 (126)
33 PRK10354 RNA chaperone/anti-te 20.1 1.2E+02 0.0025 20.6 2.6 27 80-112 7-33 (70)
34 PF00313 CSD: 'Cold-shock' DNA 20.1 1.2E+02 0.0026 19.6 2.7 25 82-112 5-29 (66)
No 1
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=99.96 E-value=7.1e-30 Score=216.31 Aligned_cols=107 Identities=20% Similarity=0.345 Sum_probs=91.1
Q ss_pred hhhhccchhHHHHH-HHHHHHHhhhcCCCCCCCCccccCceeeecCCCceEEecCCCCccccccCccEEeecCCCCCcee
Q 031764 43 ELSSLRLSKRELCL-SSFVLILNGLYPKLSKASLPEEMELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFEEANKGTNNL 121 (153)
Q Consensus 43 ~~~~~~~~RR~~ll-~i~~~~~t~~l~~~s~~~~A~~~gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D~~~~~eNV 121 (153)
....|.+.||.+|+ ++++..+..+..+ .+.++|+..||++|+|+.|||+|+||.||++|++.|+||+|||+++.+|||
T Consensus 71 ~~~~~~~~rr~~~~~~l~~~~~~~s~~~-~~~a~a~~~~l~~y~D~~DGY~FlYP~GWi~V~~~G~DVvFrD~Ie~~ENV 149 (286)
T PLN00059 71 AKQVCAVGRRKSMMMGLLMSGLIVSEAN-LPTAFASIPVFREYIDTFDGYSFKYPQNWIQVRGAGADIFFRDPVVLDENL 149 (286)
T ss_pred hhhhhhhhhhhhhHHHHHHHHHHHHhhc-CchhhcCCcccceeEcCCCCeEEeCCCCCeEeccCCCceEEeccCccccce
Confidence 44468889999854 4444444444333 335788888999999999999999999999999999999999999999999
Q ss_pred EEEEeeCC---CCCcccCCCHHHHHHHHHHHH
Q 031764 122 GVVVNPVR---VASLGEFGTPQFVADKLIQAE 150 (153)
Q Consensus 122 sV~VsPv~---~~sL~dfGsPeeVg~~L~~ae 150 (153)
||+|+|++ +++|+|||+|+||||+|+++.
T Consensus 150 SV~ISs~sss~~~sLeDLGsP~eVgerLlkqv 181 (286)
T PLN00059 150 SVEFSSPSSSKYTSLEDLGSPEEVGKRVLRQY 181 (286)
T ss_pred EEEEecCCcccCCChHHcCCHHHHHHHHHHHH
Confidence 99999885 899999999999999999864
No 2
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=99.95 E-value=1.6e-27 Score=200.96 Aligned_cols=103 Identities=26% Similarity=0.372 Sum_probs=80.8
Q ss_pred hhccchhHHHHHHHHHHHHhhhcCCCCCCCCccc----------cCceeeecCCCceEEecCCCCcccc---ccCccEEe
Q 031764 45 SSLRLSKRELCLSSFVLILNGLYPKLSKASLPEE----------MELQRYTDSNEGFTLLRPSSWIKVD---KAGATVLF 111 (153)
Q Consensus 45 ~~~~~~RR~~ll~i~~~~~t~~l~~~s~~~~A~~----------~gf~~y~D~~dGYsflyP~gW~~v~---~~G~dv~F 111 (153)
....++||++|+.++..++.+..++....+++++ .||.+|. +|||+|+||++|++++ .+|+|++|
T Consensus 46 ~~~~~srr~~l~~~~ga~a~~~~~~pa~aay~~~anvfg~~k~~~gF~~y~--~dgY~FlyP~~W~~~ke~~~~G~dv~f 123 (260)
T PLN00042 46 DNSAVSRRAALALLAGAAAAGAKVSPANAAYGESANVFGKPKTNTGFLPYN--GDGFKLLVPSKWNPSKEREFPGQVLRF 123 (260)
T ss_pred ccccccHHHHHHHHHHHHHhhcccCchhhhhcchhhccCCCCCCCCCeEee--CCCeEEecCCCCccccccccCCceEEe
Confidence 4566788888765543322223333233355444 6999996 5999999999999776 56999999
Q ss_pred ecCCCCCceeEEEEeeCCCCCcccCCCHHH----HHHHHHHH
Q 031764 112 EEANKGTNNLGVVVNPVRVASLGEFGTPQF----VADKLIQA 149 (153)
Q Consensus 112 ~D~~~~~eNVsV~VsPv~~~sL~dfGsPee----Vg~~L~~a 149 (153)
+|+++++|||+|+|+|+++++|+|||+||| |++.|.++
T Consensus 124 ~D~~~~~eNVSV~Ispt~k~sI~dlGsPee~l~~vgylL~kq 165 (260)
T PLN00042 124 EDNFDATSNLSVMVTPTDKKSITDYGSPEEFLSKVSYLLGKQ 165 (260)
T ss_pred eccccccccEEEEEecCCcCCHhhcCCHHHHHHHHHHHHHhh
Confidence 999999999999999999999999999999 88888774
No 3
>PF01789 PsbP: PsbP; InterPro: IPR002683 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbP. Both PsbP and PsbQ (IPR008797 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. PsbP increases the affinity of the water oxidation site for chloride ions and provides the conditions required for high affinity binding of calcium ions [, ]. The crystal structure of PsbP from Nicotiana tabacum (Common tobacco) revealed a two-domain structure, where domain 1 may play a role in the ion retention activity in PSII, the N-terminal residues being essential for calcium and chloride ion retention activity []. PsbP is encoded in the nuclear genome in plants.; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 2VU4_A 1V2B_A 2LNJ_A 2XB3_A.
Probab=99.86 E-value=4.2e-22 Score=156.77 Aligned_cols=73 Identities=41% Similarity=0.756 Sum_probs=67.7
Q ss_pred cCceeeecCCCceEEecCCCCccccccCccEEeecCCCCCceeEEEEeeCCCC-CcccCCCHHHHHHHHHHHHh
Q 031764 79 MELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFEEANKGTNNLGVVVNPVRVA-SLGEFGTPQFVADKLIQAEK 151 (153)
Q Consensus 79 ~gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D~~~~~eNVsV~VsPv~~~-sL~dfGsPeeVg~~L~~ae~ 151 (153)
.||++|.|+.+||+|.||+||+++++.|+|++|+|+++.++||+|+|+|+... +|+|||+|+|||++|++++.
T Consensus 21 ~~~~~y~d~~~~y~f~~P~gW~~~~~~G~~v~f~d~~~~~~nvsV~v~p~~~~~sl~~lGs~~~va~~l~~~~~ 94 (175)
T PF01789_consen 21 TGFQPYTDSDDGYSFLYPSGWEEVDVSGADVVFRDPIDADENVSVVVSPVPKDFSLEDLGSPEEVAERLLNGEL 94 (175)
T ss_dssp SSEEEEEECTTTEEEEEETTEEEEESTTEEEEEEETTETTSEEEEEEEE-STS-SGGGG-SHHHHHHHHHHHCC
T ss_pred CCceEEEcCCCCEEEECCCCCeecCCCCeEEEEECcccccceEEEEEEecCCcCchhhcCCHHHHHHHHhhhhc
Confidence 69999999999999999999999999999999999999999999999999855 99999999999999998753
No 4
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=99.76 E-value=2.6e-18 Score=145.41 Aligned_cols=100 Identities=22% Similarity=0.366 Sum_probs=75.6
Q ss_pred hccchhHHHHHHHHHHHHhhhcCCCCCCCCccc-------------cCceeeec-----------CCCceEEecCCCCcc
Q 031764 46 SLRLSKRELCLSSFVLILNGLYPKLSKASLPEE-------------MELQRYTD-----------SNEGFTLLRPSSWIK 101 (153)
Q Consensus 46 ~~~~~RR~~ll~i~~~~~t~~l~~~s~~~~A~~-------------~gf~~y~D-----------~~dGYsflyP~gW~~ 101 (153)
.....||++|+|+...++. +++... .+-|.| .||.-|.- ...||+|+||.||++
T Consensus 40 ~~~~~rr~~~~~~~~~~~~-~~~~~~-~~~~~~~~v~~~lp~~~~~~~~~~f~~~~~~tpalra~~i~gY~FlyP~gW~~ 117 (263)
T PLN00067 40 AVVIHRRELLLGLALAPLI-LIAPEP-PAEAREVEVGSYLPPSPSDPSFVLFKASPKDTPALRAGNVQPYQFILPPTWKQ 117 (263)
T ss_pred cchhHHHHHHhhhhhhhhh-hccCCc-hhhhheehhhcccCCCCCCCceEEEecCCCCCcccccCCcccceEeCCCCCcC
Confidence 4457899999998754332 222222 233544 36766642 357999999999999
Q ss_pred cccc----C-----------ccEEeecCCCCCceeEEEEeeC------CCCCcccCCCHHHHHHHHHHH
Q 031764 102 VDKA----G-----------ATVLFEEANKGTNNLGVVVNPV------RVASLGEFGTPQFVADKLIQA 149 (153)
Q Consensus 102 v~~~----G-----------~dv~F~D~~~~~eNVsV~VsPv------~~~sL~dfGsPeeVg~~L~~a 149 (153)
++++ | +|++|+|+ .++||+|+|+|+ ++++|+|||+|+||+++|.+.
T Consensus 118 v~Vs~~~sGnycqp~c~~p~~dv~F~D~--~dgnVSVIVSPV~r~t~k~~~sIeDlGsPeeVl~~Lg~~ 184 (263)
T PLN00067 118 TRVANILSGNYCQPKCAEPWVEVKFEDE--KQGKVQVVASPLIRLTNKPNATIEEIGSPEKLIASLGPF 184 (263)
T ss_pred ccccccccCccccccccCCCceEEEeCC--CCCCEEEEEecccccccCCCCChHHccCHHHHHHHhhHH
Confidence 9986 4 89999994 477999999998 468999999999999999654
No 5
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=99.69 E-value=1.3e-16 Score=135.23 Aligned_cols=100 Identities=22% Similarity=0.306 Sum_probs=77.9
Q ss_pred chhHHHHHHHHHHHHhhhcCCCCCCCCcc----------------ccCceeeecCC-------------CceEEecCCCC
Q 031764 49 LSKRELCLSSFVLILNGLYPKLSKASLPE----------------EMELQRYTDSN-------------EGFTLLRPSSW 99 (153)
Q Consensus 49 ~~RR~~ll~i~~~~~t~~l~~~s~~~~A~----------------~~gf~~y~D~~-------------dGYsflyP~gW 99 (153)
++||.+|.+.++++.. ..++.+..++|. +.||+.|..+. ..|+|+||.||
T Consensus 45 ~~rr~~~~s~~~~~~~-~~~~~~~~~~a~~~g~~ag~~~~~s~~~~~g~~~~~rp~~~~Gg~G~~~~~i~~Y~F~yP~GW 123 (262)
T PLN00066 45 VSRRSALASGAAAASS-AVLAFPGEGLAVKQGLLAGRVPGLSEPDENGWRTYRRPEGKSGGHGVGWSEITPYSFKVPQGW 123 (262)
T ss_pred hhHHHHHHHHHHHHhh-hhhcCCcchhhhhhcccccCCCCCCCccccceEEEecCccccCcCCCCccccCCeEEECCCCC
Confidence 6999999876654222 222333333322 25899998652 57999999999
Q ss_pred cccccc-----CccEEeecCCCCCceeEEEEeeC--------CCCCcccCCCHHHHHHHHHHH
Q 031764 100 IKVDKA-----GATVLFEEANKGTNNLGVVVNPV--------RVASLGEFGTPQFVADKLIQA 149 (153)
Q Consensus 100 ~~v~~~-----G~dv~F~D~~~~~eNVsV~VsPv--------~~~sL~dfGsPeeVg~~L~~a 149 (153)
.++.++ |+++.|++.++.++||+|+|+|+ ++++|+|||+||+|++.|.++
T Consensus 124 ~ev~VS~~d~gg~~vd~Rf~~~~~~nvsVvVspv~rla~~~~~~~sI~dLGspeeVi~~l~~~ 186 (262)
T PLN00066 124 EEVPVSIADLGGTEIDLRFASDKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEKVISGFGPE 186 (262)
T ss_pred eEeecccccCCCCceEEEeccCCCccEEEEEeccccccccccCCCChHHcCCHHHHHHHHHHH
Confidence 999986 77788888889999999999998 589999999999999999864
No 6
>PLN03152 hypothetical protein; Provisional
Probab=99.07 E-value=4.2e-10 Score=94.26 Aligned_cols=101 Identities=20% Similarity=0.350 Sum_probs=67.6
Q ss_pred hccchhHHHHHHHHHHHHhhhcC-CCCCCCCc--------------cccCceeeecCCCceEEecCCCCcccccc-----
Q 031764 46 SLRLSKRELCLSSFVLILNGLYP-KLSKASLP--------------EEMELQRYTDSNEGFTLLRPSSWIKVDKA----- 105 (153)
Q Consensus 46 ~~~~~RR~~ll~i~~~~~t~~l~-~~s~~~~A--------------~~~gf~~y~D~~dGYsflyP~gW~~v~~~----- 105 (153)
.|+.+||+.++-...+.+..+.. +..+.++| ++..+-.| .++||+.-||..+..+-.+
T Consensus 28 ~~~~~~r~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nt~~w~~~--~g~gf~~~~pp~f~di~e~~~~~~ 105 (241)
T PLN03152 28 RCGASRRDFILHTASLCASSLAAQNPLPPSLADPSKPSKPLLSGIANTKSWFQF--YGDGFSIRVPPSFEDIMEPEDYNA 105 (241)
T ss_pred cccccccceeeehhHHHHhhhhcCCCCCccccCCCCCCCchheeeecchhhhhh--hCCceEEeCCCChhhhcChhhccc
Confidence 58889999877433222221111 11112333 33334444 4899999999999887632
Q ss_pred C------------ccEEeecCCCCCceeEEEEeeC--------CCCCcccCCCHHHHHHHHHHH
Q 031764 106 G------------ATVLFEEANKGTNNLGVVVNPV--------RVASLGEFGTPQFVADKLIQA 149 (153)
Q Consensus 106 G------------~dv~F~D~~~~~eNVsV~VsPv--------~~~sL~dfGsPeeVg~~L~~a 149 (153)
| -.++|..+ |.+|||||+|+|+ +.++|+|||+|+|||+.++-.
T Consensus 106 g~~~yg~~akp~~~~aRf~s~-D~sEnVSVVIspv~~LK~tfle~kDLtDLGsp~EVgkv~vP~ 168 (241)
T PLN03152 106 GLSLYGDKAKPRTFAARFASP-DGSEVLSVVIRPSNQLKITFLEAKDITDLGSLKEAAKIFVPG 168 (241)
T ss_pred ccceecCCCCCcceeeeecCC-CCCceEEEEEecCccccccccccCChhHcCCHHHHHHhhCCC
Confidence 1 23556554 5999999999997 589999999999999887644
No 7
>PF12712 DUF3805: Domain of unknown function (DUF3805); InterPro: IPR024315 This entry represents an N-terminal domain found in a family of bacterial proteins, whose function is unknown. In two related Bacteroides species, the gene for members of this family lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1tui, also of unknown function. The domain carries four conserved tryptophan residues.; PDB: 3HLZ_A.
Probab=89.69 E-value=0.42 Score=38.19 Aligned_cols=45 Identities=16% Similarity=0.426 Sum_probs=28.1
Q ss_pred eeeecCCCceEEecCCCCccccccCccEEeecCCCCCceeEEEEe
Q 031764 82 QRYTDSNEGFTLLRPSSWIKVDKAGATVLFEEANKGTNNLGVVVN 126 (153)
Q Consensus 82 ~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D~~~~~eNVsV~Vs 126 (153)
.-|..++.=|++.||.+|.+........+|=||..=+-|..+..-
T Consensus 2 kKfiSpg~WFS~~YP~~W~EfED~E~sflFYnp~~WTGNfRISay 46 (153)
T PF12712_consen 2 KKFISPGAWFSMEYPADWNEFEDGEGSFLFYNPDQWTGNFRISAY 46 (153)
T ss_dssp EEEE-GGG-EEEEE-TT-EEE---TTEEEEE-SSS---EEEEEEE
T ss_pred CcccCCCceEEEecCCCcchhccCCcceEEEChHHhcCceEEEEE
Confidence 457888888999999999999977777889999999999965543
No 8
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=67.84 E-value=3.1 Score=32.71 Aligned_cols=21 Identities=19% Similarity=0.439 Sum_probs=17.0
Q ss_pred CCCcccCCCHHHHHHHHHHHH
Q 031764 130 VASLGEFGTPQFVADKLIQAE 150 (153)
Q Consensus 130 ~~sL~dfGsPeeVg~~L~~ae 150 (153)
.+=+++||+|+|+|..++.+.
T Consensus 44 eeii~~LG~P~~iA~~i~~~~ 64 (181)
T PF08006_consen 44 EEIIAELGSPKEIAREILAEY 64 (181)
T ss_pred HHHHHHcCCHHHHHHHHHHhh
Confidence 344789999999999988654
No 9
>TIGR02811 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein.
Probab=57.90 E-value=8.7 Score=26.50 Aligned_cols=15 Identities=27% Similarity=0.124 Sum_probs=11.4
Q ss_pred hccchhHHHHHHHHH
Q 031764 46 SLRLSKRELCLSSFV 60 (153)
Q Consensus 46 ~~~~~RR~~ll~i~~ 60 (153)
+...+||++|.+++.
T Consensus 6 ~~~~sRR~Flk~lg~ 20 (66)
T TIGR02811 6 KADPSRRDLLKGLGV 20 (66)
T ss_pred cCCccHHHHHHHHHH
Confidence 456799999987764
No 10
>PF10518 TAT_signal: TAT (twin-arginine translocation) pathway signal sequence; InterPro: IPR019546 The twin-arginine translocation (Tat) pathway serves the role of transporting folded proteins across energy-transducing membranes []. Homologues of the genes that encode the transport apparatus occur in archaea, bacteria, chloroplasts, and plant mitochondria []. In bacteria, the Tat pathway catalyses the export of proteins from the cytoplasm across the inner/cytoplasmic membrane. In chloroplasts, the Tat components are found in the thylakoid membrane and direct the import of proteins from the stroma. The Tat pathway acts separately from the general secretory (Sec) pathway, which transports proteins in an unfolded state []. It is generally accepted that the primary role of the Tat system is to translocate fully folded proteins across membranes. An example of proteins that need to be exported in their 3D conformation are redox proteins that have acquired complex multi-atom cofactors in the bacterial cytoplasm (or the chloroplast stroma or mitochondrial matrix). They include hydrogenases, formate dehydrogenases, nitrate reductases, trimethylamine N-oxide (TMAO) reductases and dimethyl sulphoxide (DMSO) reductases [, ]. The Tat system can also export whole heteroligomeric complexes in which some proteins have no Tat signal. This is the case of the DMSO reductase or formate dehydrogenase complexes. But there are also other cases where the physiological rationale for targeting a protein to the Tat signal is less obvious. Indeed, there are examples of homologous proteins that are in some cases targeted to the Tat pathway and in other cases to the Sec apparatus. Some examples are: copper nitrite reductases, flavin domains of flavocytochrome c and N-acetylmuramoyl-L-alanine amidases []. In halophilic archaea such as Halobacterium almost all secreted proteins appear to be Tat targeted. It has been proposed to be a response to the difficulties these organisms would otherwise face in successfully folding proteins extracellularly at high ionic strength []. The Tat signal peptide consists of three motifs: the positively charged N-terminal motif, the hydrophobic region and the C-terminal region that generally ends with a consensus short motif (A-x-A) specifying cleavage by signal peptidase. Sequence analysis revealed that signal peptides capable of targeting the Tat protein contain the consensus sequence [ST]-R-R-x-F-L-K. The nearly invariant twin-arginine gave rise to the pathway's name. In addition the h-region of Tat signal peptides is typically less hydrophobic than that of Sec-specific signal peptides [, ].
Probab=55.18 E-value=18 Score=20.52 Aligned_cols=20 Identities=15% Similarity=0.142 Sum_probs=13.7
Q ss_pred cchhHHHHHHHHHHHHhhhc
Q 031764 48 RLSKRELCLSSFVLILNGLY 67 (153)
Q Consensus 48 ~~~RR~~ll~i~~~~~t~~l 67 (153)
+++||+.|-+.+..+....+
T Consensus 1 ~~sRR~fLk~~~a~~a~~~~ 20 (26)
T PF10518_consen 1 NLSRRQFLKGGAAAAAAAAL 20 (26)
T ss_pred CCcHHHHHHHHHHHHHHHHh
Confidence 36899999877655555443
No 11
>COG1797 CobB Cobyrinic acid a,c-diamide synthase [Coenzyme metabolism]
Probab=49.52 E-value=8 Score=35.89 Aligned_cols=64 Identities=19% Similarity=0.284 Sum_probs=43.0
Q ss_pred CceeeecCCCceEEecCCCCccccccCccEEeecCCCCCc---eeEEEEeeCCCCCcccCCCHHHHHHHHHHHHh
Q 031764 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFEEANKGTN---NLGVVVNPVRVASLGEFGTPQFVADKLIQAEK 151 (153)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D~~~~~e---NVsV~VsPv~~~sL~dfGsPeeVg~~L~~ae~ 151 (153)
|.+-=+-.+.-|.|+||.+...-...|+.++|=+|-.-.+ .+-.+..| =|=||-.++.|-+++.
T Consensus 245 ~~rIAVA~D~AF~FyY~~nl~~Lr~~GAelv~FSPL~D~~lP~~~D~vYlg--------GGYPElfA~~L~~n~~ 311 (451)
T COG1797 245 GVRIAVARDAAFNFYYPENLELLREAGAELVFFSPLADEELPPDVDAVYLG--------GGYPELFAEELSANES 311 (451)
T ss_pred CceEEEEecchhccccHHHHHHHHHCCCEEEEeCCcCCCCCCCCCCEEEeC--------CCChHHHHHHHhhCHH
Confidence 4444444578999999999999999999988866652111 12111111 1349999999998874
No 12
>PF07174 FAP: Fibronectin-attachment protein (FAP); InterPro: IPR010801 This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix [].; GO: 0050840 extracellular matrix binding, 0005576 extracellular region
Probab=46.90 E-value=12 Score=32.89 Aligned_cols=31 Identities=26% Similarity=0.691 Sum_probs=23.9
Q ss_pred eeeecCCCceEEecCCCCcccccc----CccEEee
Q 031764 82 QRYTDSNEGFTLLRPSSWIKVDKA----GATVLFE 112 (153)
Q Consensus 82 ~~y~D~~dGYsflyP~gW~~v~~~----G~dv~F~ 112 (153)
-++-|...||+|+.|.||.+.+-. |..+.=+
T Consensus 110 grvdn~~gGFS~vvP~GW~~Sda~~L~yG~alls~ 144 (297)
T PF07174_consen 110 GRVDNAAGGFSYVVPAGWVESDASHLDYGSALLSK 144 (297)
T ss_pred ccccccccceEEeccCCccccccceeecceeeecc
Confidence 466778999999999999988843 5555544
No 13
>PF05984 Cytomega_UL20A: Cytomegalovirus UL20A protein; InterPro: IPR009245 This family consists of several Cytomegalovirus UL20A proteins. UL20A is thought to be a glycoprotein [].
Probab=46.11 E-value=18 Score=26.92 Aligned_cols=20 Identities=20% Similarity=0.242 Sum_probs=17.0
Q ss_pred chhHHHHHHHHHHHHhhhcC
Q 031764 49 LSKRELCLSSFVLILNGLYP 68 (153)
Q Consensus 49 ~~RR~~ll~i~~~~~t~~l~ 68 (153)
+.||-++|++++..++++|.
T Consensus 1 MaRRlwiLslLAVtLtVALA 20 (100)
T PF05984_consen 1 MARRLWILSLLAVTLTVALA 20 (100)
T ss_pred CchhhHHHHHHHHHHHHHhh
Confidence 46899999999999888865
No 14
>PRK10943 cold shock-like protein CspC; Provisional
Probab=33.26 E-value=51 Score=22.39 Aligned_cols=27 Identities=15% Similarity=0.469 Sum_probs=19.9
Q ss_pred CceeeecCCCceEEecCCCCccccccCccEEee
Q 031764 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (153)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (153)
|--..-|...||-|+-|.+ .|.||+||
T Consensus 6 G~Vk~f~~~kGfGFI~~~~------g~~dvFvH 32 (69)
T PRK10943 6 GQVKWFNESKGFGFITPAD------GSKDVFVH 32 (69)
T ss_pred eEEEEEeCCCCcEEEecCC------CCeeEEEE
Confidence 5555667889999999864 45677765
No 15
>COG4709 Predicted membrane protein [Function unknown]
Probab=31.00 E-value=30 Score=28.92 Aligned_cols=19 Identities=16% Similarity=0.433 Sum_probs=14.4
Q ss_pred CCcccCCCHHHHHHHHHHH
Q 031764 131 ASLGEFGTPQFVADKLIQA 149 (153)
Q Consensus 131 ~sL~dfGsPeeVg~~L~~a 149 (153)
+=+.|||+|+|+|..+..+
T Consensus 45 EI~~~LG~P~eiA~ei~s~ 63 (195)
T COG4709 45 EIAKDLGDPKEIAAEILSE 63 (195)
T ss_pred HHHHHhCCHHHHHHHHHHH
Confidence 3478999999988766543
No 16
>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=28.27 E-value=76 Score=20.50 Aligned_cols=25 Identities=24% Similarity=0.639 Sum_probs=18.3
Q ss_pred eeecCCCceEEecCCCCccccccCccEEeec
Q 031764 83 RYTDSNEGFTLLRPSSWIKVDKAGATVLFEE 113 (153)
Q Consensus 83 ~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D 113 (153)
..-|...||-|+-|.+ .|.|++|+-
T Consensus 6 k~~~~~kGfGFI~~~~------~g~diffh~ 30 (65)
T cd04458 6 KWFDDEKGFGFITPDD------GGEDVFVHI 30 (65)
T ss_pred EEEECCCCeEEEecCC------CCcCEEEEh
Confidence 3456779999998876 567777763
No 17
>PRK09890 cold shock protein CspG; Provisional
Probab=28.14 E-value=67 Score=21.87 Aligned_cols=28 Identities=18% Similarity=0.530 Sum_probs=21.2
Q ss_pred cCceeeecCCCceEEecCCCCccccccCccEEee
Q 031764 79 MELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (153)
Q Consensus 79 ~gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (153)
.|-..+-|...||-|+-|.+ .|.||+|+
T Consensus 6 ~G~Vk~f~~~kGfGFI~~~~------g~~dvFvH 33 (70)
T PRK09890 6 TGLVKWFNADKGFGFITPDD------GSKDVFVH 33 (70)
T ss_pred eEEEEEEECCCCcEEEecCC------CCceEEEE
Confidence 36666677899999999973 45678777
No 18
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=28.08 E-value=34 Score=27.52 Aligned_cols=17 Identities=41% Similarity=0.688 Sum_probs=14.9
Q ss_pred CCCHHHHHHHHHHHHhc
Q 031764 136 FGTPQFVADKLIQAEKR 152 (153)
Q Consensus 136 fGsPeeVg~~L~~ae~~ 152 (153)
||+|+|-|+.+++++.+
T Consensus 52 fG~P~~~a~eli~~~~k 68 (206)
T PF06570_consen 52 FGDPKEYADELIKPLPK 68 (206)
T ss_pred cCCHHHHHHHHhccccC
Confidence 89999999999988654
No 19
>PF12559 Inhibitor_I10: Serine endopeptidase inhibitors; InterPro: IPR022217 This family includes both microviridins and marinostatins. It seems likely that in both cases it is the C terminus which becomes the active inhibitor after post-translational modifications of the full length, pre-peptide. it is the ester linkages within the key, 12-residue. region that circularise the molecule giving it its inhibitory conformation. ; PDB: 1IXU_A.
Probab=27.54 E-value=25 Score=23.82 Aligned_cols=12 Identities=42% Similarity=0.515 Sum_probs=4.0
Q ss_pred ceEEecCCCCcc
Q 031764 90 GFTLLRPSSWIK 101 (153)
Q Consensus 90 GYsflyP~gW~~ 101 (153)
..++.||++|.+
T Consensus 44 ~~TlKyPSD~ee 55 (56)
T PF12559_consen 44 IQTLKYPSDWEE 55 (56)
T ss_dssp -----SS-SS--
T ss_pred CcceeCCCcccc
Confidence 489999999975
No 20
>cd03130 GATase1_CobB Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase. Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase. CobB plays a role in cobalamin biosythesis catalyzing the conversion of cobyrinic acid to cobyrinic acid a,c-diamide. CobB belongs to the triad family of amidotransferases. Two of the three residues of the catalytic triad that are involved in glutamine binding, hydrolysis and transfer of the resulting ammonia to the acceptor substrate in other triad aminodotransferases are conserved in CobB.
Probab=27.12 E-value=25 Score=28.02 Aligned_cols=42 Identities=14% Similarity=0.112 Sum_probs=32.3
Q ss_pred CCceEEecCCCCccccccCccEEeecCC--CCCceeEEEEeeCC
Q 031764 88 NEGFTLLRPSSWIKVDKAGATVLFEEAN--KGTNNLGVVVNPVR 129 (153)
Q Consensus 88 ~dGYsflyP~gW~~v~~~G~dv~F~D~~--~~~eNVsV~VsPv~ 129 (153)
+.-|.|+||......+..|.++.+-++. +...+...+|.|=.
T Consensus 6 d~aF~f~y~e~~~~l~~~G~~v~~~s~~~~~~l~~~D~lilPGG 49 (198)
T cd03130 6 DEAFNFYYPENLELLEAAGAELVPFSPLKDEELPDADGLYLGGG 49 (198)
T ss_pred cCccccccHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEECCC
Confidence 5789999999999999999999887764 33334666776654
No 21
>PRK15464 cold shock-like protein CspH; Provisional
Probab=25.90 E-value=70 Score=22.01 Aligned_cols=27 Identities=19% Similarity=0.258 Sum_probs=19.3
Q ss_pred CceeeecCCCceEEecCCCCccccccCccEEee
Q 031764 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (153)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (153)
|-..+-|...||-|+-|.+ .|.||++|
T Consensus 7 G~Vk~fn~~KGfGFI~~~~------g~~DvFvH 33 (70)
T PRK15464 7 GIVKTFDRKSGKGFIIPSD------GRKEVQVH 33 (70)
T ss_pred EEEEEEECCCCeEEEccCC------CCccEEEE
Confidence 5455567899999998874 35677655
No 22
>PF12318 FAD-SLDH: Membrane bound FAD containing D-sorbitol dehydrogenase ; InterPro: IPR024651 There are two types of membrane-bound D-sorbitol dehydrogenase: PQQ-SLDH (pyrroloquinoline quinone sorbitol dehydrogenase) and FAD-SLDH (FAD-containing sorbitol dehydrogenase). FAD-SLDH is involved in oxidation of D-sorbitol to L-sorbose and consists of a large, small and cytochrome c subunits []. This entry represents the small subunit of the FAD-containing D-sorbitol dehydrogenase. This family of proteins is found in bacteria and contains a conserved ALM sequence motif. The role of the small subunit is unknown. Gluconate dehydrogenases and fructose dehydrogenases are also included in this entry.
Probab=25.21 E-value=66 Score=25.60 Aligned_cols=8 Identities=50% Similarity=0.646 Sum_probs=6.7
Q ss_pred cchhHHHH
Q 031764 48 RLSKRELC 55 (153)
Q Consensus 48 ~~~RR~~l 55 (153)
+++||++|
T Consensus 1 g~sRR~~L 8 (168)
T PF12318_consen 1 GLSRRRLL 8 (168)
T ss_pred CCcHHHHH
Confidence 46899999
No 23
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=24.05 E-value=96 Score=21.53 Aligned_cols=43 Identities=14% Similarity=0.291 Sum_probs=26.8
Q ss_pred CceeeecCCCceEEecCCCCccccccCccEEeecC---------CCCCceeEEEEeeC
Q 031764 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFEEA---------NKGTNNLGVVVNPV 128 (153)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D~---------~~~~eNVsV~VsPv 128 (153)
|-..+-|...||-|+-|.+ .|.||++|=. ....+.|...+..-
T Consensus 4 G~Vkwfn~~KGfGFI~~~~------gg~dVFvH~s~i~~~g~~~l~~G~~V~f~~~~~ 55 (74)
T PRK09937 4 GTVKWFNNAKGFGFICPEG------GGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQG 55 (74)
T ss_pred eEEEEEeCCCCeEEEeeCC------CCccEEEEEeeccccCCCCCCCCCEEEEEEEEC
Confidence 4445567789999998863 4577776611 23445566555544
No 24
>TIGR02381 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam model pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication.
Probab=24.05 E-value=99 Score=20.81 Aligned_cols=27 Identities=11% Similarity=0.449 Sum_probs=19.5
Q ss_pred CceeeecCCCceEEecCCCCccccccCccEEee
Q 031764 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (153)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (153)
|-..+-|...||-|+-|.+ .|.|++|+
T Consensus 4 G~Vk~f~~~kGfGFI~~~~------g~~dvfvH 30 (68)
T TIGR02381 4 GIVKWFNNAKGFGFICPEG------VDGDIFAH 30 (68)
T ss_pred eEEEEEeCCCCeEEEecCC------CCccEEEE
Confidence 5455667889999998874 35677765
No 25
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=23.28 E-value=70 Score=27.00 Aligned_cols=23 Identities=30% Similarity=0.648 Sum_probs=18.7
Q ss_pred CCcccCCCHHHHHHHHHHHHhcC
Q 031764 131 ASLGEFGTPQFVADKLIQAEKRK 153 (153)
Q Consensus 131 ~sL~dfGsPeeVg~~L~~ae~~k 153 (153)
+.--||=+|+||++||++-.|+|
T Consensus 68 ~rag~f~~P~eVaeRL~ei~K~~ 90 (228)
T COG5014 68 KRAGDFLSPEEVAERLLEISKKR 90 (228)
T ss_pred cccccccCHHHHHHHHHHHHHhc
Confidence 45568999999999998876654
No 26
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=22.85 E-value=1e+02 Score=20.92 Aligned_cols=27 Identities=15% Similarity=0.441 Sum_probs=19.9
Q ss_pred CceeeecCCCceEEecCCCCccccccCccEEee
Q 031764 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (153)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (153)
|--.+-|...||-|+-|.+ .|.|++|+
T Consensus 6 G~Vk~f~~~kGyGFI~~~~------g~~dvfvH 32 (69)
T PRK09507 6 GNVKWFNESKGFGFITPED------GSKDVFVH 32 (69)
T ss_pred eEEEEEeCCCCcEEEecCC------CCeeEEEE
Confidence 5455567789999998874 45788876
No 27
>PRK15463 cold shock-like protein CspF; Provisional
Probab=22.62 E-value=1e+02 Score=21.02 Aligned_cols=27 Identities=22% Similarity=0.319 Sum_probs=20.1
Q ss_pred CceeeecCCCceEEecCCCCccccccCccEEee
Q 031764 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (153)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (153)
|-..+-|...||-|+-|.+ .|.||++|
T Consensus 7 G~Vk~fn~~kGfGFI~~~~------g~~DvFvH 33 (70)
T PRK15463 7 GIVKTFDGKSGKGLITPSD------GRKDVQVH 33 (70)
T ss_pred EEEEEEeCCCceEEEecCC------CCccEEEE
Confidence 5555667889999999864 45677766
No 28
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=22.56 E-value=2.5e+02 Score=19.13 Aligned_cols=34 Identities=26% Similarity=0.337 Sum_probs=24.9
Q ss_pred ceeeecCCCceEEecCCCCccccc--cCccEEeecC
Q 031764 81 LQRYTDSNEGFTLLRPSSWIKVDK--AGATVLFEEA 114 (153)
Q Consensus 81 f~~y~D~~dGYsflyP~gW~~v~~--~G~dv~F~D~ 114 (153)
+--+.|+++..+.+||+.|+..+. +|....|.|.
T Consensus 22 ~l~~~~~~G~v~~L~Pn~~~~~~~v~ag~~~~iP~~ 57 (83)
T PF14326_consen 22 YLFYIDADGKVTLLFPNRYQPDNFVKAGQTYTIPDP 57 (83)
T ss_pred EEEEECCCCCEEEEecCccccCceEcCCceEEcCCC
Confidence 345678888899999999888763 3666666643
No 29
>PRK14998 cold shock-like protein CspD; Provisional
Probab=22.01 E-value=1.1e+02 Score=21.04 Aligned_cols=27 Identities=15% Similarity=0.477 Sum_probs=19.5
Q ss_pred CceeeecCCCceEEecCCCCccccccCccEEee
Q 031764 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (153)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (153)
|-...-|...||-|+-|.+ .|.||++|
T Consensus 4 G~Vkwfn~~kGfGFI~~~~------g~~dVFvH 30 (73)
T PRK14998 4 GTVKWFNNAKGFGFICPEG------GGEDIFAH 30 (73)
T ss_pred eEEEEEeCCCceEEEecCC------CCccEEEE
Confidence 4445557789999999875 45677766
No 30
>TIGR03741 PRTRC_E PRTRC system protein E. A novel genetic system characterized by six or seven major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family averages about 150 amino acids in length, but the last third contains low-complexity sequence that complicates sequence comparisons. This model does not include the low-complexity region.
Probab=21.66 E-value=1.9e+02 Score=21.63 Aligned_cols=30 Identities=27% Similarity=0.445 Sum_probs=20.3
Q ss_pred ceeEEEEeeCCCCCc--ccC-------CCHHHHHHHHHH
Q 031764 119 NNLGVVVNPVRVASL--GEF-------GTPQFVADKLIQ 148 (153)
Q Consensus 119 eNVsV~VsPv~~~sL--~df-------GsPeeVg~~L~~ 148 (153)
+++.|+|.|..+... ..+ |+|+|.-+.+..
T Consensus 24 d~l~V~v~P~~~~~~~d~~l~~Pl~L~gTp~ELD~gF~~ 62 (104)
T TIGR03741 24 DKLTVTVTPTPKSGAKDGALTKPLVLTGTPAELDAGFAG 62 (104)
T ss_pred CEEEEEEeeccccccccccccCCeeeccCHHHHHHHHHH
Confidence 389999999843222 344 899996665553
No 31
>PF08338 DUF1731: Domain of unknown function (DUF1731); InterPro: IPR013549 This domain of unknown function appears towards the C terminus of proteins of the NAD dependent epimerase/dehydratase family (IPR001509 from INTERPRO) in bacteria, eukaryotes and archaea. Many of the proteins in which it is found are involved in cell-division inhibition. ; PDB: 3OH8_A.
Probab=20.72 E-value=37 Score=21.79 Aligned_cols=10 Identities=30% Similarity=0.720 Sum_probs=4.6
Q ss_pred CCceEEecCC
Q 031764 88 NEGFTLLRPS 97 (153)
Q Consensus 88 ~dGYsflyP~ 97 (153)
+.||+|.||.
T Consensus 30 ~~GF~F~~p~ 39 (48)
T PF08338_consen 30 EAGFQFRYPT 39 (48)
T ss_dssp HTT---S-SS
T ss_pred HCCCcccCCC
Confidence 5799999985
No 32
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=20.53 E-value=41 Score=26.12 Aligned_cols=18 Identities=22% Similarity=0.340 Sum_probs=16.0
Q ss_pred CCCceEEec-CCCCccccc
Q 031764 87 SNEGFTLLR-PSSWIKVDK 104 (153)
Q Consensus 87 ~~dGYsfly-P~gW~~v~~ 104 (153)
.+.||.|+| |-.|.+.+.
T Consensus 80 ~~Ggy~yiY~~i~~ee~k~ 98 (126)
T COG3355 80 KGGGYYYLYKPIDPEEIKK 98 (126)
T ss_pred CCCceeEEEecCCHHHHHH
Confidence 689999999 999998773
No 33
>PRK10354 RNA chaperone/anti-terminator; Provisional
Probab=20.11 E-value=1.2e+02 Score=20.56 Aligned_cols=27 Identities=15% Similarity=0.543 Sum_probs=19.6
Q ss_pred CceeeecCCCceEEecCCCCccccccCccEEee
Q 031764 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (153)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (153)
|-...-|...||-|+-|.+ .|.|++|+
T Consensus 7 G~Vk~f~~~kGfGFI~~~~------g~~dvfvH 33 (70)
T PRK10354 7 GIVKWFNADKGFGFITPDD------GSKDVFVH 33 (70)
T ss_pred EEEEEEeCCCCcEEEecCC------CCccEEEE
Confidence 5555667889999998873 34677765
No 34
>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=20.09 E-value=1.2e+02 Score=19.57 Aligned_cols=25 Identities=16% Similarity=0.622 Sum_probs=17.3
Q ss_pred eeeecCCCceEEecCCCCccccccCccEEee
Q 031764 82 QRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (153)
Q Consensus 82 ~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (153)
-..-|..+||-|+.+.+ .+.|++|+
T Consensus 5 V~~~~~~kgyGFI~~~~------~~~diFfh 29 (66)
T PF00313_consen 5 VKWFDDEKGYGFITSDD------GGEDIFFH 29 (66)
T ss_dssp EEEEETTTTEEEEEETT------SSSEEEEE
T ss_pred EEEEECCCCceEEEEcc------cceeEEec
Confidence 34456788999988764 34477776
Done!