Query 030275
Match_columns 180
No_of_seqs 146 out of 204
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 11:16:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030275.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030275hhsearch_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 3.4E-32 7.5E-37 235.1 11.6 117 60-179 75-203 (286)
2 PLN00042 photosystem II oxygen 100.0 2.1E-31 4.5E-36 229.5 11.2 120 58-179 46-192 (260)
3 PF01789 PsbP: PsbP; InterPro 99.9 3E-25 6.6E-30 179.5 8.7 97 83-179 11-110 (175)
4 PLN00066 PsbP domain-containin 99.9 2.5E-22 5.5E-27 173.9 13.1 121 59-179 42-202 (262)
5 PLN00067 PsbP domain-containin 99.9 2.7E-21 5.8E-26 167.0 12.2 120 57-179 38-200 (263)
6 PLN03152 hypothetical protein; 99.0 1.1E-09 2.3E-14 93.7 5.8 98 61-161 30-166 (241)
7 PF12712 DUF3805: Domain of un 92.0 0.25 5.5E-06 40.2 4.3 46 96-141 2-47 (153)
8 PF10518 TAT_signal: TAT (twin 71.2 5.6 0.00012 23.1 2.7 15 61-75 1-15 (26)
9 PF07174 FAP: Fibronectin-atta 57.9 21 0.00046 32.1 5.0 81 97-178 111-214 (297)
10 PF08006 DUF1700: Protein of u 55.7 7.1 0.00015 31.5 1.6 21 145-165 45-65 (181)
11 TIGR02811 formate_TAT formate 55.1 18 0.0004 25.4 3.4 11 59-69 6-16 (66)
12 PLN00058 photosystem II reacti 44.1 25 0.00054 27.0 2.8 21 59-79 46-66 (103)
13 PF12559 Inhibitor_I10: Serine 36.8 13 0.00029 25.7 0.3 12 104-115 44-55 (56)
14 PF10399 UCR_Fe-S_N: Ubiquitin 34.9 33 0.00072 22.1 1.9 15 57-71 4-18 (41)
15 PRK10882 hydrogenase 2 protein 33.7 62 0.0013 29.3 4.2 12 62-73 1-12 (328)
16 PRK10943 cold shock-like prote 33.5 58 0.0012 22.7 3.2 28 93-126 5-32 (69)
17 cd04458 CSP_CDS Cold-Shock Pro 29.6 83 0.0018 20.8 3.4 28 94-127 3-30 (65)
18 TIGR03741 PRTRC_E PRTRC system 29.1 1E+02 0.0022 23.6 4.1 33 133-165 24-65 (104)
19 PRK11615 hypothetical protein; 28.4 2.5E+02 0.0054 23.8 6.6 62 97-165 42-108 (185)
20 PF08786 DUF1795: Domain of un 26.9 60 0.0013 24.4 2.5 52 106-164 3-54 (130)
21 PRK09890 cold shock protein Cs 26.0 87 0.0019 21.8 3.0 28 93-126 6-33 (70)
22 TIGR02381 cspD cold shock doma 25.0 1.1E+02 0.0023 21.1 3.3 20 93-112 3-22 (68)
23 PRK09937 stationary phase/star 24.7 1.1E+02 0.0024 21.7 3.4 28 93-126 3-30 (74)
24 PF12712 DUF3805: Domain of un 24.4 54 0.0012 26.9 1.9 26 90-115 14-39 (153)
25 PF05757 PsbQ: Oxygen evolving 24.0 27 0.00059 29.7 0.1 16 58-73 25-40 (202)
26 COG4784 Putative Zn-dependent 23.9 57 0.0012 30.7 2.2 33 85-117 274-309 (479)
27 PRK09507 cspE cold shock prote 23.2 1.1E+02 0.0024 21.2 3.1 28 93-126 5-32 (69)
28 PRK14998 cold shock-like prote 22.6 1.3E+02 0.0028 21.2 3.4 20 93-112 3-22 (73)
29 COG4709 Predicted membrane pro 22.5 43 0.00093 28.6 1.0 18 145-162 45-62 (195)
30 PRK15464 cold shock-like prote 22.1 1.2E+02 0.0026 21.3 3.1 20 93-112 6-25 (70)
31 PRK15463 cold shock-like prote 21.9 1.2E+02 0.0026 21.2 3.1 28 93-126 6-33 (70)
32 KOG1466 Translation initiation 21.8 38 0.00083 30.6 0.6 62 104-165 243-313 (313)
33 PF00313 CSD: 'Cold-shock' DNA 21.6 1.4E+02 0.003 19.8 3.2 27 94-126 3-29 (66)
34 PLN00054 photosystem I reactio 21.6 1.1E+02 0.0024 24.7 3.1 27 60-86 26-54 (139)
35 PF12553 DUF3742: Protein of u 21.0 1.2E+02 0.0026 20.6 2.8 19 96-114 34-52 (54)
36 PF10633 NPCBM_assoc: NPCBM-as 20.2 1.3E+02 0.0029 20.6 3.0 38 104-143 25-62 (78)
No 1
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=99.97 E-value=3.4e-32 Score=235.09 Aligned_cols=117 Identities=31% Similarity=0.544 Sum_probs=101.3
Q ss_pred cccchHHHHHHHHH-Hh-HhhhcCCCCcccccccccCceeeeeCCCCeEEeccCCCeeeeecCceeeeeCCCCCCcceEE
Q 030275 60 DKCGRRQMIAVGVI-AP-WVSLVNQTPPSFAAESNKGFLSVTDKKDGYSFVYPFGWQEVIIEGQDKVFKDVIEPLESVSV 137 (180)
Q Consensus 60 ~~~~RR~aL~~~~~-aa-~~s~~~~a~~A~Ae~~~~gf~~y~D~~dGYsf~yP~~W~~v~~~G~dv~F~D~~~~~eNVsV 137 (180)
..++||++|+.++. +. +.+.++ ...|+|+ +.||++|+|+.|||+|+||.||++|.+.|+|++|||+++.+|||||
T Consensus 75 ~~~~rr~~~~~~l~~~~~~~s~~~-~~~a~a~--~~~l~~y~D~~DGY~FlYP~GWi~V~~~G~DVvFrD~Ie~~ENVSV 151 (286)
T PLN00059 75 CAVGRRKSMMMGLLMSGLIVSEAN-LPTAFAS--IPVFREYIDTFDGYSFKYPQNWIQVRGAGADIFFRDPVVLDENLSV 151 (286)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhc-CchhhcC--CcccceeEcCCCCeEEeCCCCCeEeccCCCceEEeccCccccceEE
Confidence 57789999865553 33 344443 3477876 4589999999999999999999999999999999999999999999
Q ss_pred EEecCC---CCCcccCCCHHHHHHHHHHHhcCCC-------CCceeeeecee
Q 030275 138 NLIPTG---KQDIRDFGPPQEVAETLIKKFLAPP-------TQKTKIIAASE 179 (180)
Q Consensus 138 ~Vsp~~---k~sI~dlG~PeeVa~~L~~~~~~~p-------~~~a~Li~a~e 179 (180)
+|+|++ +++|+|||+|+||||+|+++++++| +++++||+|++
T Consensus 152 ~ISs~sss~~~sLeDLGsP~eVgerLlkqvLa~f~str~GsgReaeLVsA~~ 203 (286)
T PLN00059 152 EFSSPSSSKYTSLEDLGSPEEVGKRVLRQYLTEFMSTRLGVKREANILSTSS 203 (286)
T ss_pred EEecCCcccCCChHHcCCHHHHHHHHHHHHhcccccccCCCCcceEEEEeee
Confidence 999876 5999999999999999999999974 58999999985
No 2
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=99.97 E-value=2.1e-31 Score=229.53 Aligned_cols=120 Identities=26% Similarity=0.405 Sum_probs=105.8
Q ss_pred cccccchHHHHHHHHHH-hHhhhcCCCCccccc--------ccccCceeeeeCCCCeEEeccCCCee---eeecCceeee
Q 030275 58 SLDKCGRRQMIAVGVIA-PWVSLVNQTPPSFAA--------ESNKGFLSVTDKKDGYSFVYPFGWQE---VIIEGQDKVF 125 (180)
Q Consensus 58 ~~~~~~RR~aL~~~~~a-a~~s~~~~a~~A~Ae--------~~~~gf~~y~D~~dGYsf~yP~~W~~---v~~~G~dv~F 125 (180)
+...++||.+|+++++| +..+.++|+++||+| +..+||.+|. +|||+|+||++|++ ++++|+|++|
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 34668899999888885 567899999999987 3469999994 69999999999995 4577999999
Q ss_pred eCCCCCCcceEEEEecCCCCCcccCCCHHH----HHHHHHHHhcCCC-----CC------ceeeeecee
Q 030275 126 KDVIEPLESVSVNLIPTGKQDIRDFGPPQE----VAETLIKKFLAPP-----TQ------KTKIIAASE 179 (180)
Q Consensus 126 ~D~~~~~eNVsV~Vsp~~k~sI~dlG~Pee----Va~~L~~~~~~~p-----~~------~a~Li~a~e 179 (180)
||+++++|||||+|+|+++++|+|||+||| |+++|++|++.++ |+ +++||++++
T Consensus 124 ~D~~~~~eNVSV~Ispt~k~sI~dlGsPee~l~~vgylL~kq~~a~~t~s~~Gf~p~~vata~Lleas~ 192 (260)
T PLN00042 124 EDNFDATSNLSVMVTPTDKKSITDYGSPEEFLSKVSYLLGKQAYSGETASEGGFDANAVATAAVLESST 192 (260)
T ss_pred eccccccccEEEEEecCCcCCHhhcCCHHHHHHHHHHHHHhhhccCccccccCcCcccccceeEEEeee
Confidence 999999999999999999999999999999 9999999999876 22 689999875
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=99.92 E-value=3e-25 Score=179.48 Aligned_cols=97 Identities=46% Similarity=0.774 Sum_probs=83.5
Q ss_pred CCcccccccccCceeeeeCCCCeEEeccCCCeeeeecCceeeeeCCCCCCcceEEEEecCCCC-CcccCCCHHHHHHHHH
Q 030275 83 TPPSFAAESNKGFLSVTDKKDGYSFVYPFGWQEVIIEGQDKVFKDVIEPLESVSVNLIPTGKQ-DIRDFGPPQEVAETLI 161 (180)
Q Consensus 83 a~~A~Ae~~~~gf~~y~D~~dGYsf~yP~~W~~v~~~G~dv~F~D~~~~~eNVsV~Vsp~~k~-sI~dlG~PeeVa~~L~ 161 (180)
+..+.+++..+||++|.|+++||+|+||++|+++++.|+|++|+|+++.++||+|+|+|+.+. +|+|||+|++|+++|+
T Consensus 11 ~~~~~~~~~~~~~~~y~d~~~~y~f~~P~gW~~~~~~G~~v~f~d~~~~~~nvsV~v~p~~~~~sl~~lGs~~~va~~l~ 90 (175)
T PF01789_consen 11 ANVACAAEASTGFQPYTDSDDGYSFLYPSGWEEVDVSGADVVFRDPIDADENVSVVVSPVPKDFSLEDLGSPEEVAERLL 90 (175)
T ss_dssp -----STT--SSEEEEEECTTTEEEEEETTEEEEESTTEEEEEEETTETTSEEEEEEEE-STS-SGGGG-SHHHHHHHHH
T ss_pred chhhhcccCCCCceEEEcCCCCEEEECCCCCeecCCCCeEEEEECcccccceEEEEEEecCCcCchhhcCCHHHHHHHHh
Confidence 333444567899999999999999999999999999999999999999999999999999985 9999999999999999
Q ss_pred HHhcCCCC--Cceeeeecee
Q 030275 162 KKFLAPPT--QKTKIIAASE 179 (180)
Q Consensus 162 ~~~~~~p~--~~a~Li~a~e 179 (180)
++.+++++ +.++||++.+
T Consensus 91 ~~~~~~~~~~~~a~li~a~~ 110 (175)
T PF01789_consen 91 NGELASPGSGREAELISASE 110 (175)
T ss_dssp HHCCCHCTSSEEEEEEEEEE
T ss_pred hhhcccccCCcceEEEEeee
Confidence 99998886 8999999875
No 4
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=99.88 E-value=2.5e-22 Score=173.86 Aligned_cols=121 Identities=21% Similarity=0.406 Sum_probs=97.1
Q ss_pred ccccchHHHHHHHHHHhHhhhcCCCCcccc--------------cccccCceeeeeCCC-------------CeEEeccC
Q 030275 59 LDKCGRRQMIAVGVIAPWVSLVNQTPPSFA--------------AESNKGFLSVTDKKD-------------GYSFVYPF 111 (180)
Q Consensus 59 ~~~~~RR~aL~~~~~aa~~s~~~~a~~A~A--------------e~~~~gf~~y~D~~d-------------GYsf~yP~ 111 (180)
...++||.+|+.++++++...++.+..++| +....||++|..+.. .|+|+||+
T Consensus 42 ~~~~~rr~~~~s~~~~~~~~~~~~~~~~~a~~~g~~ag~~~~~s~~~~~g~~~~~rp~~~~Gg~G~~~~~i~~Y~F~yP~ 121 (262)
T PLN00066 42 ATAVSRRSALASGAAAASSAVLAFPGEGLAVKQGLLAGRVPGLSEPDENGWRTYRRPEGKSGGHGVGWSEITPYSFKVPQ 121 (262)
T ss_pred cchhhHHHHHHHHHHHHhhhhhcCCcchhhhhhcccccCCCCCCCccccceEEEecCccccCcCCCCccccCCeEEECCC
Confidence 466799999986666543333333333332 344589999998876 39999999
Q ss_pred CCeeeeec-----CceeeeeCCCCCCcceEEEEecC--------CCCCcccCCCHHHHHHHHHHHhcCCCCCceeeeece
Q 030275 112 GWQEVIIE-----GQDKVFKDVIEPLESVSVNLIPT--------GKQDIRDFGPPQEVAETLIKKFLAPPTQKTKIIAAS 178 (180)
Q Consensus 112 ~W~~v~~~-----G~dv~F~D~~~~~eNVsV~Vsp~--------~k~sI~dlG~PeeVa~~L~~~~~~~p~~~a~Li~a~ 178 (180)
||.++.++ |+++.||+..+.++||+|+|+|+ ++++|+|||+||+|++.|++++++.+.++++||+++
T Consensus 122 GW~ev~VS~~d~gg~~vd~Rf~~~~~~nvsVvVspv~rla~~~~~~~sI~dLGspeeVi~~l~~~v~g~~~~e~eLl~a~ 201 (262)
T PLN00066 122 GWEEVPVSIADLGGTEIDLRFASDKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEKVISGFGPELIGEPVEEGKVLSME 201 (262)
T ss_pred CCeEeecccccCCCCceEEEeccCCCccEEEEEeccccccccccCCCChHHcCCHHHHHHHHHHHhcCCCccccceeEee
Confidence 99999987 66666666668899999999997 569999999999999999999999999999999987
Q ss_pred e
Q 030275 179 E 179 (180)
Q Consensus 179 e 179 (180)
+
T Consensus 202 ~ 202 (262)
T PLN00066 202 V 202 (262)
T ss_pred e
Confidence 5
No 5
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=99.86 E-value=2.7e-21 Score=166.99 Aligned_cols=120 Identities=20% Similarity=0.352 Sum_probs=91.1
Q ss_pred CcccccchHHHHHHHHHHhHhhhcCCCCcccc-c----------ccccCceeeeeC-----------CCCeEEeccCCCe
Q 030275 57 NSLDKCGRRQMIAVGVIAPWVSLVNQTPPSFA-A----------ESNKGFLSVTDK-----------KDGYSFVYPFGWQ 114 (180)
Q Consensus 57 ~~~~~~~RR~aL~~~~~aa~~s~~~~a~~A~A-e----------~~~~gf~~y~D~-----------~dGYsf~yP~~W~ 114 (180)
.....+.||+.|..++.+.+.+.... .++.| | ....||.-|.-. -.||+|+||.||+
T Consensus 38 ~~~~~~~rr~~~~~~~~~~~~~~~~~-~~~~~~~~~v~~~lp~~~~~~~~~~f~~~~~~tpalra~~i~gY~FlyP~gW~ 116 (263)
T PLN00067 38 RAAVVIHRRELLLGLALAPLILIAPE-PPAEAREVEVGSYLPPSPSDPSFVLFKASPKDTPALRAGNVQPYQFILPPTWK 116 (263)
T ss_pred cccchhHHHHHHhhhhhhhhhhccCC-chhhhheehhhcccCCCCCCCceEEEecCCCCCcccccCCcccceEeCCCCCc
Confidence 44556789999864444433333322 22222 1 334578777532 2389999999999
Q ss_pred eeeec----C-----------ceeeeeCCCCCCcceEEEEecC------CCCCcccCCCHHHHHHHHHHHhcCCCCCcee
Q 030275 115 EVIIE----G-----------QDKVFKDVIEPLESVSVNLIPT------GKQDIRDFGPPQEVAETLIKKFLAPPTQKTK 173 (180)
Q Consensus 115 ~v~~~----G-----------~dv~F~D~~~~~eNVsV~Vsp~------~k~sI~dlG~PeeVa~~L~~~~~~~p~~~a~ 173 (180)
++++. | +|++|+|++ ++||+|+|+|+ ++++|+|||+|++|+++|++.++++++++++
T Consensus 117 ~v~Vs~~~sGnycqp~c~~p~~dv~F~D~~--dgnVSVIVSPV~r~t~k~~~sIeDlGsPeeVl~~Lg~~v~g~~~~~~e 194 (263)
T PLN00067 117 QTRVANILSGNYCQPKCAEPWVEVKFEDEK--QGKVQVVASPLIRLTNKPNATIEEIGSPEKLIASLGPFVTGNSYDPDE 194 (263)
T ss_pred CccccccccCccccccccCCCceEEEeCCC--CCCEEEEEecccccccCCCCChHHccCHHHHHHHhhHHhhcCCCCCcc
Confidence 98886 4 899999955 68999999997 4589999999999999999999999999999
Q ss_pred eeecee
Q 030275 174 IIAASE 179 (180)
Q Consensus 174 Li~a~e 179 (180)
||++++
T Consensus 195 LLeAs~ 200 (263)
T PLN00067 195 LLETSV 200 (263)
T ss_pred eEEeee
Confidence 999975
No 6
>PLN03152 hypothetical protein; Provisional
Probab=98.95 E-value=1.1e-09 Score=93.71 Aligned_cols=98 Identities=28% Similarity=0.446 Sum_probs=67.2
Q ss_pred ccchHHHHHHHHHHhHhhhc--CCCCccccc------------ccccCceeeeeCCCCeEEeccCCCeeee----ec---
Q 030275 61 KCGRRQMIAVGVIAPWVSLV--NQTPPSFAA------------ESNKGFLSVTDKKDGYSFVYPFGWQEVI----IE--- 119 (180)
Q Consensus 61 ~~~RR~aL~~~~~aa~~s~~--~~a~~A~Ae------------~~~~gf~~y~D~~dGYsf~yP~~W~~v~----~~--- 119 (180)
...||+.+.-.++++..++. .+...++|+ -+...|-.| -++||++-||-+++.+- +.
T Consensus 30 ~~~~r~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~nt~~w~~~--~g~gf~~~~pp~f~di~e~~~~~~g~ 107 (241)
T PLN03152 30 GASRRDFILHTASLCASSLAAQNPLPPSLADPSKPSKPLLSGIANTKSWFQF--YGDGFSIRVPPSFEDIMEPEDYNAGL 107 (241)
T ss_pred cccccceeeehhHHHHhhhhcCCCCCccccCCCCCCCchheeeecchhhhhh--hCCceEEeCCCChhhhcChhhccccc
Confidence 44588877544443333332 234445554 123446666 59999999999998532 11
Q ss_pred ---C-------ceeeeeCCCCCCcceEEEEecCC--------CCCcccCCCHHHHHHHHH
Q 030275 120 ---G-------QDKVFKDVIEPLESVSVNLIPTG--------KQDIRDFGPPQEVAETLI 161 (180)
Q Consensus 120 ---G-------~dv~F~D~~~~~eNVsV~Vsp~~--------k~sI~dlG~PeeVa~~L~ 161 (180)
| -.++|..+ |.+|||||+|+|++ .++|+|||+|+|||+.|+
T Consensus 108 ~~yg~~akp~~~~aRf~s~-D~sEnVSVVIspv~~LK~tfle~kDLtDLGsp~EVgkv~v 166 (241)
T PLN03152 108 SLYGDKAKPRTFAARFASP-DGSEVLSVVIRPSNQLKITFLEAKDITDLGSLKEAAKIFV 166 (241)
T ss_pred ceecCCCCCcceeeeecCC-CCCceEEEEEecCccccccccccCChhHcCCHHHHHHhhC
Confidence 2 24677775 78999999999974 599999999999997766
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=92.01 E-value=0.25 Score=40.16 Aligned_cols=46 Identities=13% Similarity=0.140 Sum_probs=27.6
Q ss_pred eeeeeCCCCeEEeccCCCeeeeecCceeeeeCCCCCCcceEEEEec
Q 030275 96 LSVTDKKDGYSFVYPFGWQEVIIEGQDKVFKDVIEPLESVSVNLIP 141 (180)
Q Consensus 96 ~~y~D~~dGYsf~yP~~W~~v~~~G~dv~F~D~~~~~eNVsV~Vsp 141 (180)
+.|..++.=|+..||.+|.|.+-......|-|+..=+.|..+..-.
T Consensus 2 kKfiSpg~WFS~~YP~~W~EfED~E~sflFYnp~~WTGNfRISayk 47 (153)
T PF12712_consen 2 KKFISPGAWFSMEYPADWNEFEDGEGSFLFYNPDQWTGNFRISAYK 47 (153)
T ss_dssp EEEE-GGG-EEEEE-TT-EEE---TTEEEEE-SSS---EEEEEEEE
T ss_pred CcccCCCceEEEecCCCcchhccCCcceEEEChHHhcCceEEEEEe
Confidence 5688888889999999999988433455688888889999876654
No 8
>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=71.18 E-value=5.6 Score=23.09 Aligned_cols=15 Identities=33% Similarity=0.470 Sum_probs=10.1
Q ss_pred ccchHHHHHHHHHHh
Q 030275 61 KCGRRQMIAVGVIAP 75 (180)
Q Consensus 61 ~~~RR~aL~~~~~aa 75 (180)
.++||+.|..+++++
T Consensus 1 ~~sRR~fLk~~~a~~ 15 (26)
T PF10518_consen 1 NLSRRQFLKGGAAAA 15 (26)
T ss_pred CCcHHHHHHHHHHHH
Confidence 367999996555433
No 9
>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=57.87 E-value=21 Score=32.08 Aligned_cols=81 Identities=27% Similarity=0.380 Sum_probs=45.4
Q ss_pred eeeeCCCCeEEeccCCCeeeeec----CceeeeeCCC--------CCCcc-eEEEEecCCCCCccc--CCCHHHHHHHHH
Q 030275 97 SVTDKKDGYSFVYPFGWQEVIIE----GQDKVFKDVI--------EPLES-VSVNLIPTGKQDIRD--FGPPQEVAETLI 161 (180)
Q Consensus 97 ~y~D~~dGYsf~yP~~W~~v~~~----G~dv~F~D~~--------~~~eN-VsV~Vsp~~k~sI~d--lG~PeeVa~~L~ 161 (180)
++.|...||+|++|.||.+-+-. |+.+.-+-.. .+..| -+|++-..+. +|=+ --+-.+.+.+|.
T Consensus 111 rvdn~~gGFS~vvP~GW~~Sda~~L~yG~alls~~~~~~~~~~~~~p~andt~v~lgrld~-kl~a~ae~dn~kaa~rl~ 189 (297)
T PF07174_consen 111 RVDNAAGGFSYVVPAGWVESDASHLDYGSALLSKQTGEPPMPGQPPPVANDTSVVLGRLDL-KLFASAEPDNTKAAVRLA 189 (297)
T ss_pred cccccccceEEeccCCccccccceeecceeeeccCCCCCCCCCCCCCcCCCceEEeccccc-cccccccCChHHHHHHHh
Confidence 56667789999999999975532 5555443221 11233 3444444542 1111 123445888888
Q ss_pred HH---hcCC-C----CCceeeeece
Q 030275 162 KK---FLAP-P----TQKTKIIAAS 178 (180)
Q Consensus 162 ~~---~~~~-p----~~~a~Li~a~ 178 (180)
.. +|-+ | +|+...+++.
T Consensus 190 sdmgeffmp~pg~rinq~~~~l~~~ 214 (297)
T PF07174_consen 190 SDMGEFFMPYPGTRINQETTPLDAN 214 (297)
T ss_pred ccccceeccCCCccccccccccccC
Confidence 75 4444 2 5666666653
No 10
>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=55.70 E-value=7.1 Score=31.49 Aligned_cols=21 Identities=24% Similarity=0.650 Sum_probs=17.5
Q ss_pred CCcccCCCHHHHHHHHHHHhc
Q 030275 145 QDIRDFGPPQEVAETLIKKFL 165 (180)
Q Consensus 145 ~sI~dlG~PeeVa~~L~~~~~ 165 (180)
.=+++||+|+|+|..+..++.
T Consensus 45 eii~~LG~P~~iA~~i~~~~~ 65 (181)
T PF08006_consen 45 EIIAELGSPKEIAREILAEYS 65 (181)
T ss_pred HHHHHcCCHHHHHHHHHHhhh
Confidence 558999999999999987643
No 11
>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=55.08 E-value=18 Score=25.43 Aligned_cols=11 Identities=18% Similarity=0.332 Sum_probs=8.3
Q ss_pred ccccchHHHHH
Q 030275 59 LDKCGRRQMIA 69 (180)
Q Consensus 59 ~~~~~RR~aL~ 69 (180)
...++||..|.
T Consensus 6 ~~~~sRR~Flk 16 (66)
T TIGR02811 6 KADPSRRDLLK 16 (66)
T ss_pred cCCccHHHHHH
Confidence 45668999984
No 12
>PLN00058 photosystem II reaction center subunit T; Provisional
Probab=44.11 E-value=25 Score=27.00 Aligned_cols=21 Identities=24% Similarity=0.230 Sum_probs=14.0
Q ss_pred ccccchHHHHHHHHHHhHhhh
Q 030275 59 LDKCGRRQMIAVGVIAPWVSL 79 (180)
Q Consensus 59 ~~~~~RR~aL~~~~~aa~~s~ 79 (180)
+...+||.+|...++++..+.
T Consensus 46 e~~~gRR~~mfaaaAaav~s~ 66 (103)
T PLN00058 46 QSTTMRRDLMFTAAAAAVCSL 66 (103)
T ss_pred cchhhHHHHHHHHHHHHHHhh
Confidence 466789999976665554444
No 13
>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=36.76 E-value=13 Score=25.69 Aligned_cols=12 Identities=33% Similarity=0.772 Sum_probs=4.0
Q ss_pred CeEEeccCCCee
Q 030275 104 GYSFVYPFGWQE 115 (180)
Q Consensus 104 GYsf~yP~~W~~ 115 (180)
.++..||++|.+
T Consensus 44 ~~TlKyPSD~ee 55 (56)
T PF12559_consen 44 IQTLKYPSDWEE 55 (56)
T ss_dssp -----SS-SS--
T ss_pred CcceeCCCcccc
Confidence 389999999985
No 14
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=34.94 E-value=33 Score=22.09 Aligned_cols=15 Identities=20% Similarity=0.313 Sum_probs=6.5
Q ss_pred CcccccchHHHHHHH
Q 030275 57 NSLDKCGRRQMIAVG 71 (180)
Q Consensus 57 ~~~~~~~RR~aL~~~ 71 (180)
.+....+||..|.++
T Consensus 4 ~~~~~~~RRdFL~~a 18 (41)
T PF10399_consen 4 NEPVDPTRRDFLTIA 18 (41)
T ss_dssp ------HHHHHHHHH
T ss_pred CCCCCchHHHHHHHH
Confidence 345667799988533
No 15
>PRK10882 hydrogenase 2 protein HybA; Provisional
Probab=33.66 E-value=62 Score=29.31 Aligned_cols=12 Identities=17% Similarity=0.346 Sum_probs=8.1
Q ss_pred cchHHHHHHHHH
Q 030275 62 CGRRQMIAVGVI 73 (180)
Q Consensus 62 ~~RR~aL~~~~~ 73 (180)
++||..|..+++
T Consensus 1 ~~RR~fl~~~~~ 12 (328)
T PRK10882 1 MNRRNFLKAASA 12 (328)
T ss_pred CCHHHHHHHHHH
Confidence 469999964433
No 16
>PRK10943 cold shock-like protein CspC; Provisional
Probab=33.53 E-value=58 Score=22.65 Aligned_cols=28 Identities=21% Similarity=0.464 Sum_probs=20.5
Q ss_pred cCceeeeeCCCCeEEeccCCCeeeeecCceeeee
Q 030275 93 KGFLSVTDKKDGYSFVYPFGWQEVIIEGQDKVFK 126 (180)
Q Consensus 93 ~gf~~y~D~~dGYsf~yP~~W~~v~~~G~dv~F~ 126 (180)
.|...+-|...||-|+-|.+ .|.|++|+
T Consensus 5 ~G~Vk~f~~~kGfGFI~~~~------g~~dvFvH 32 (69)
T PRK10943 5 KGQVKWFNESKGFGFITPAD------GSKDVFVH 32 (69)
T ss_pred ceEEEEEeCCCCcEEEecCC------CCeeEEEE
Confidence 56667778899999999975 23566654
No 17
>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=29.64 E-value=83 Score=20.84 Aligned_cols=28 Identities=25% Similarity=0.470 Sum_probs=19.3
Q ss_pred CceeeeeCCCCeEEeccCCCeeeeecCceeeeeC
Q 030275 94 GFLSVTDKKDGYSFVYPFGWQEVIIEGQDKVFKD 127 (180)
Q Consensus 94 gf~~y~D~~dGYsf~yP~~W~~v~~~G~dv~F~D 127 (180)
|-....|...||-|+-|.+ .|.|++|+-
T Consensus 3 G~Vk~~~~~kGfGFI~~~~------~g~diffh~ 30 (65)
T cd04458 3 GTVKWFDDEKGFGFITPDD------GGEDVFVHI 30 (65)
T ss_pred EEEEEEECCCCeEEEecCC------CCcCEEEEh
Confidence 3444567889999998887 456666653
No 18
>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=29.10 E-value=1e+02 Score=23.61 Aligned_cols=33 Identities=21% Similarity=0.390 Sum_probs=23.5
Q ss_pred cceEEEEecCCCCCc--ccC-------CCHHHHHHHHHHHhc
Q 030275 133 ESVSVNLIPTGKQDI--RDF-------GPPQEVAETLIKKFL 165 (180)
Q Consensus 133 eNVsV~Vsp~~k~sI--~dl-------G~PeeVa~~L~~~~~ 165 (180)
+++.|.|.|..+... ..+ |+|+|..+.|...+-
T Consensus 24 d~l~V~v~P~~~~~~~d~~l~~Pl~L~gTp~ELD~gF~~ai~ 65 (104)
T TIGR03741 24 DKLTVTVTPTPKSGAKDGALTKPLVLTGTPAELDAGFAGALG 65 (104)
T ss_pred CEEEEEEeeccccccccccccCCeeeccCHHHHHHHHHHHHH
Confidence 389999999754222 333 999998888886543
No 19
>PRK11615 hypothetical protein; Provisional
Probab=28.35 E-value=2.5e+02 Score=23.84 Aligned_cols=62 Identities=19% Similarity=0.158 Sum_probs=36.4
Q ss_pred eeeeCCCCeEEeccCCCeeeeec-C----ceeeeeCCCCCCcceEEEEecCCCCCcccCCCHHHHHHHHHHHhc
Q 030275 97 SVTDKKDGYSFVYPFGWQEVIIE-G----QDKVFKDVIEPLESVSVNLIPTGKQDIRDFGPPQEVAETLIKKFL 165 (180)
Q Consensus 97 ~y~D~~dGYsf~yP~~W~~v~~~-G----~dv~F~D~~~~~eNVsV~Vsp~~k~sI~dlG~PeeVa~~L~~~~~ 165 (180)
...=-+.+.+|..|.|+....++ | .--+|-|. .+.=.|+|+.-+. +=++ -+..+.+|..|-.
T Consensus 42 ~VSLLdGKl~FtLPag~sdqsgk~Gtq~nn~~vYad~---tg~kavIVi~gD~-~~~~---Ld~la~rl~~qQr 108 (185)
T PRK11615 42 PVSLLDGKLSFTLPADMSDQSGKLGTQANNMHVYADA---TGQKAVIVILGDD-TNED---LAVLAKRLEDQQR 108 (185)
T ss_pred eeEEeccEEEEEcCCccccccccccccccceEEEEcC---CCCEEEEEEeCCC-Chhh---HHHHHHHHHHHHH
Confidence 33335678999999999976554 3 33567773 3344444444331 1122 3567888887643
No 20
>PF08786 DUF1795: Domain of unknown function (DUF1795); InterPro: IPR014894 This is a bacterial protein of unknown function. It forms an antiparallel beta sheet structure and contains some alpha helical regions. ; PDB: 1TU1_A 3LYD_A.
Probab=26.89 E-value=60 Score=24.39 Aligned_cols=52 Identities=19% Similarity=0.245 Sum_probs=25.6
Q ss_pred EEeccCCCeeeeecCceeeeeCCCCCCcceEEEEecCCCCCcccCCCHHHHHHHHHHHh
Q 030275 106 SFVYPFGWQEVIIEGQDKVFKDVIEPLESVSVNLIPTGKQDIRDFGPPQEVAETLIKKF 164 (180)
Q Consensus 106 sf~yP~~W~~v~~~G~dv~F~D~~~~~eNVsV~Vsp~~k~sI~dlG~PeeVa~~L~~~~ 164 (180)
+|..|.+|+...+ .-.++.|.....-|+.|.-.+.. +=.+.++..++.+++.
T Consensus 3 ~~~lP~~~~D~t~--nv~~~~~~~~~~~slvIsR~~l~-----~g~tl~~~~~~q~~~l 54 (130)
T PF08786_consen 3 SLTLPDGWQDRTM--NVLVLPDSGGSGPSLVISRDPLP-----DGETLEDYLQRQLAQL 54 (130)
T ss_dssp EEEEETTSEE--B--EEEEE--BTTB-EEEEEEEE--------TTS-HHHHHHHHHHHH
T ss_pred eEeCCCcceeceE--EEEEccCCCCCcceEEEEeccCC-----CCCCHHHHHHHHHHHH
Confidence 5778999997655 44556665433334444333333 2235667777777665
No 21
>PRK09890 cold shock protein CspG; Provisional
Probab=26.02 E-value=87 Score=21.81 Aligned_cols=28 Identities=18% Similarity=0.442 Sum_probs=21.0
Q ss_pred cCceeeeeCCCCeEEeccCCCeeeeecCceeeee
Q 030275 93 KGFLSVTDKKDGYSFVYPFGWQEVIIEGQDKVFK 126 (180)
Q Consensus 93 ~gf~~y~D~~dGYsf~yP~~W~~v~~~G~dv~F~ 126 (180)
.|-..+-|...||-|+-|.+ .|.|++|+
T Consensus 6 ~G~Vk~f~~~kGfGFI~~~~------g~~dvFvH 33 (70)
T PRK09890 6 TGLVKWFNADKGFGFITPDD------GSKDVFVH 33 (70)
T ss_pred eEEEEEEECCCCcEEEecCC------CCceEEEE
Confidence 56777778999999999974 23566655
No 22
>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=25.00 E-value=1.1e+02 Score=21.12 Aligned_cols=20 Identities=25% Similarity=0.629 Sum_probs=16.0
Q ss_pred cCceeeeeCCCCeEEeccCC
Q 030275 93 KGFLSVTDKKDGYSFVYPFG 112 (180)
Q Consensus 93 ~gf~~y~D~~dGYsf~yP~~ 112 (180)
+|-..+-|...||-|+-|.+
T Consensus 3 ~G~Vk~f~~~kGfGFI~~~~ 22 (68)
T TIGR02381 3 IGIVKWFNNAKGFGFICPEG 22 (68)
T ss_pred CeEEEEEeCCCCeEEEecCC
Confidence 35666778899999999875
No 23
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=24.66 E-value=1.1e+02 Score=21.72 Aligned_cols=28 Identities=29% Similarity=0.576 Sum_probs=19.5
Q ss_pred cCceeeeeCCCCeEEeccCCCeeeeecCceeeee
Q 030275 93 KGFLSVTDKKDGYSFVYPFGWQEVIIEGQDKVFK 126 (180)
Q Consensus 93 ~gf~~y~D~~dGYsf~yP~~W~~v~~~G~dv~F~ 126 (180)
.|-..+-|...||-|+-|.+ .|.|++|+
T Consensus 3 ~G~Vkwfn~~KGfGFI~~~~------gg~dVFvH 30 (74)
T PRK09937 3 KGTVKWFNNAKGFGFICPEG------GGEDIFAH 30 (74)
T ss_pred CeEEEEEeCCCCeEEEeeCC------CCccEEEE
Confidence 35556678889999999874 23555554
No 24
>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=24.37 E-value=54 Score=26.87 Aligned_cols=26 Identities=19% Similarity=0.381 Sum_probs=15.4
Q ss_pred ccccCceeeeeCCCCeEEeccCCCee
Q 030275 90 ESNKGFLSVTDKKDGYSFVYPFGWQE 115 (180)
Q Consensus 90 ~~~~gf~~y~D~~dGYsf~yP~~W~~ 115 (180)
.-|.+|..|.|.+|-|.|+=|..|+.
T Consensus 14 ~YP~~W~EfED~E~sflFYnp~~WTG 39 (153)
T PF12712_consen 14 EYPADWNEFEDGEGSFLFYNPDQWTG 39 (153)
T ss_dssp EE-TT-EEE---TTEEEEE-SSS---
T ss_pred ecCCCcchhccCCcceEEEChHHhcC
Confidence 34688999999999999999999995
No 25
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 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 PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=24.04 E-value=27 Score=29.74 Aligned_cols=16 Identities=13% Similarity=0.241 Sum_probs=0.0
Q ss_pred cccccchHHHHHHHHH
Q 030275 58 SLDKCGRRQMIAVGVI 73 (180)
Q Consensus 58 ~~~~~~RR~aL~~~~~ 73 (180)
.....+||.+|+.+++
T Consensus 25 ~~~~~~RRa~l~~l~a 40 (202)
T PF05757_consen 25 AQQQTSRRAVLGSLLA 40 (202)
T ss_dssp ----------------
T ss_pred ccccccHHHHHHHHHH
Confidence 4556679999874443
No 26
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=23.93 E-value=57 Score=30.74 Aligned_cols=33 Identities=15% Similarity=0.311 Sum_probs=25.3
Q ss_pred cccccccccCce---eeeeCCCCeEEeccCCCeeee
Q 030275 85 PSFAAESNKGFL---SVTDKKDGYSFVYPFGWQEVI 117 (180)
Q Consensus 85 ~A~Ae~~~~gf~---~y~D~~dGYsf~yP~~W~~v~ 117 (180)
.-|+..+.+||. .|.-++=|++|.||.||.-..
T Consensus 274 ~lyGDSp~eGyvRgq~FlH~~Lg~tf~~P~Gf~IdN 309 (479)
T COG4784 274 LLYGDSPQEGYVRGQTFLHPELGVTFDVPDGFKIDN 309 (479)
T ss_pred cccCCCcccceecccceeccccceEEecCCceEecC
Confidence 446666677875 577788899999999999644
No 27
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=23.20 E-value=1.1e+02 Score=21.19 Aligned_cols=28 Identities=21% Similarity=0.439 Sum_probs=20.5
Q ss_pred cCceeeeeCCCCeEEeccCCCeeeeecCceeeee
Q 030275 93 KGFLSVTDKKDGYSFVYPFGWQEVIIEGQDKVFK 126 (180)
Q Consensus 93 ~gf~~y~D~~dGYsf~yP~~W~~v~~~G~dv~F~ 126 (180)
.|-..+-|...||-|+-|.+ .|.|++|+
T Consensus 5 ~G~Vk~f~~~kGyGFI~~~~------g~~dvfvH 32 (69)
T PRK09507 5 KGNVKWFNESKGFGFITPED------GSKDVFVH 32 (69)
T ss_pred ceEEEEEeCCCCcEEEecCC------CCeeEEEE
Confidence 46666778899999999875 23566664
No 28
>PRK14998 cold shock-like protein CspD; Provisional
Probab=22.55 E-value=1.3e+02 Score=21.25 Aligned_cols=20 Identities=25% Similarity=0.612 Sum_probs=15.7
Q ss_pred cCceeeeeCCCCeEEeccCC
Q 030275 93 KGFLSVTDKKDGYSFVYPFG 112 (180)
Q Consensus 93 ~gf~~y~D~~dGYsf~yP~~ 112 (180)
.|-..+-|...||-|+-|.+
T Consensus 3 ~G~Vkwfn~~kGfGFI~~~~ 22 (73)
T PRK14998 3 TGTVKWFNNAKGFGFICPEG 22 (73)
T ss_pred CeEEEEEeCCCceEEEecCC
Confidence 35556678889999999985
No 29
>COG4709 Predicted membrane protein [Function unknown]
Probab=22.46 E-value=43 Score=28.58 Aligned_cols=18 Identities=28% Similarity=0.671 Sum_probs=13.4
Q ss_pred CCcccCCCHHHHHHHHHH
Q 030275 145 QDIRDFGPPQEVAETLIK 162 (180)
Q Consensus 145 ~sI~dlG~PeeVa~~L~~ 162 (180)
.=+.|||+|+|+|..+..
T Consensus 45 EI~~~LG~P~eiA~ei~s 62 (195)
T COG4709 45 EIAKDLGDPKEIAAEILS 62 (195)
T ss_pred HHHHHhCCHHHHHHHHHH
Confidence 447899999997655544
No 30
>PRK15464 cold shock-like protein CspH; Provisional
Probab=22.09 E-value=1.2e+02 Score=21.34 Aligned_cols=20 Identities=30% Similarity=0.629 Sum_probs=16.1
Q ss_pred cCceeeeeCCCCeEEeccCC
Q 030275 93 KGFLSVTDKKDGYSFVYPFG 112 (180)
Q Consensus 93 ~gf~~y~D~~dGYsf~yP~~ 112 (180)
.|-..+-|.+.||-|+-|.+
T Consensus 6 ~G~Vk~fn~~KGfGFI~~~~ 25 (70)
T PRK15464 6 TGIVKTFDRKSGKGFIIPSD 25 (70)
T ss_pred eEEEEEEECCCCeEEEccCC
Confidence 45566778899999999985
No 31
>PRK15463 cold shock-like protein CspF; Provisional
Probab=21.86 E-value=1.2e+02 Score=21.21 Aligned_cols=28 Identities=21% Similarity=0.354 Sum_probs=20.4
Q ss_pred cCceeeeeCCCCeEEeccCCCeeeeecCceeeee
Q 030275 93 KGFLSVTDKKDGYSFVYPFGWQEVIIEGQDKVFK 126 (180)
Q Consensus 93 ~gf~~y~D~~dGYsf~yP~~W~~v~~~G~dv~F~ 126 (180)
.|-..+-|.+.||-|+-|.+ .|.|++++
T Consensus 6 ~G~Vk~fn~~kGfGFI~~~~------g~~DvFvH 33 (70)
T PRK15463 6 TGIVKTFDGKSGKGLITPSD------GRKDVQVH 33 (70)
T ss_pred eEEEEEEeCCCceEEEecCC------CCccEEEE
Confidence 46667778899999999975 23566654
No 32
>KOG1466 consensus Translation initiation factor 2B, alpha subunit (eIF-2Balpha/GCN3) [Translation, ribosomal structure and biogenesis]
Probab=21.82 E-value=38 Score=30.60 Aligned_cols=62 Identities=21% Similarity=0.334 Sum_probs=45.2
Q ss_pred CeEEeccCCCeeeeecCceeeeeCCCCCCcceEEE-----EecCCC--CCcccCC--CHHHHHHHHHHHhc
Q 030275 104 GYSFVYPFGWQEVIIEGQDKVFKDVIEPLESVSVN-----LIPTGK--QDIRDFG--PPQEVAETLIKKFL 165 (180)
Q Consensus 104 GYsf~yP~~W~~v~~~G~dv~F~D~~~~~eNVsV~-----Vsp~~k--~sI~dlG--~PeeVa~~L~~~~~ 165 (180)
+|.=+||-+=...+..++-.-|.++....|++.+. .+|+.. --++||| +|..|.+.|+|=|+
T Consensus 243 KFvRlfPLnQ~Dlp~~~~p~~f~~~~~~~~~~~~e~p~vDYTpPeyiTlL~TDLGvltPSaVsdELIKlYl 313 (313)
T KOG1466|consen 243 KFVRLFPLNQKDLPPALPPFKFSRPVPEREDVEREHPTVDYTPPEYLTLLFTDLGVLTPSAVSDELIKLYL 313 (313)
T ss_pred ceeeeccCcccccccccCCcccCCCCCcHHhhhhcCCCcccChHHHHHHHHhhccccChhhhhHHHHHhhC
Confidence 45557888777777778888899988776666655 455444 4567888 68889999998664
No 33
>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=21.63 E-value=1.4e+02 Score=19.83 Aligned_cols=27 Identities=30% Similarity=0.519 Sum_probs=18.4
Q ss_pred CceeeeeCCCCeEEeccCCCeeeeecCceeeee
Q 030275 94 GFLSVTDKKDGYSFVYPFGWQEVIIEGQDKVFK 126 (180)
Q Consensus 94 gf~~y~D~~dGYsf~yP~~W~~v~~~G~dv~F~ 126 (180)
|.....|...||-|+.+.+= +.|++|+
T Consensus 3 G~V~~~~~~kgyGFI~~~~~------~~diFfh 29 (66)
T PF00313_consen 3 GTVKWFDDEKGYGFITSDDG------GEDIFFH 29 (66)
T ss_dssp EEEEEEETTTTEEEEEETTS------SSEEEEE
T ss_pred EEEEEEECCCCceEEEEccc------ceeEEec
Confidence 44456678899999988752 2366665
No 34
>PLN00054 photosystem I reaction center subunit N; Provisional
Probab=21.57 E-value=1.1e+02 Score=24.72 Aligned_cols=27 Identities=11% Similarity=0.053 Sum_probs=13.5
Q ss_pred cccchHHHHHHHHHH--hHhhhcCCCCcc
Q 030275 60 DKCGRRQMIAVGVIA--PWVSLVNQTPPS 86 (180)
Q Consensus 60 ~~~~RR~aL~~~~~a--a~~s~~~~a~~A 86 (180)
..-+||.+|..++++ .++..++++.+.
T Consensus 26 ~~~grraa~~~Laa~l~~~aa~~~~AnAg 54 (139)
T PLN00054 26 ASDGRRAALVGLAATLFSTAAAAASANAG 54 (139)
T ss_pred cccchHHHHHHHHHHHHHHHhcccccchh
Confidence 344588888644433 223334344444
No 35
>PF12553 DUF3742: Protein of unknown function (DUF3742); InterPro: IPR022213 This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important.
Probab=20.95 E-value=1.2e+02 Score=20.62 Aligned_cols=19 Identities=5% Similarity=0.085 Sum_probs=14.1
Q ss_pred eeeeeCCCCeEEeccCCCe
Q 030275 96 LSVTDKKDGYSFVYPFGWQ 114 (180)
Q Consensus 96 ~~y~D~~dGYsf~yP~~W~ 114 (180)
..+.+.-+||-++-|..|+
T Consensus 34 ~E~R~G~~GfGlY~~~~~r 52 (54)
T PF12553_consen 34 PEWREGPAGFGLYDGDEYR 52 (54)
T ss_pred HhheecCCCcccccCCccc
Confidence 3456678889888888775
No 36
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=20.19 E-value=1.3e+02 Score=20.58 Aligned_cols=38 Identities=16% Similarity=0.165 Sum_probs=16.9
Q ss_pred CeEEeccCCCeeeeecCceeeeeCCCCCCcceEEEEecCC
Q 030275 104 GYSFVYPFGWQEVIIEGQDKVFKDVIEPLESVSVNLIPTG 143 (180)
Q Consensus 104 GYsf~yP~~W~~v~~~G~dv~F~D~~~~~eNVsV~Vsp~~ 143 (180)
..++..|.||. +...+..+..=.+ .....+.+.|.+..
T Consensus 25 ~~~l~~P~GW~-~~~~~~~~~~l~p-G~s~~~~~~V~vp~ 62 (78)
T PF10633_consen 25 SLSLSLPEGWT-VSASPASVPSLPP-GESVTVTFTVTVPA 62 (78)
T ss_dssp EEEEE--TTSE----EEEEE--B-T-TSEEEEEEEEEE-T
T ss_pred EEEEeCCCCcc-ccCCccccccCCC-CCEEEEEEEEECCC
Confidence 46778899999 4444333331111 23455666666654
Done!