Query 030424
Match_columns 177
No_of_seqs 123 out of 177
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 13:31:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030424.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030424hhsearch_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 1.9E-30 4E-35 225.3 11.6 109 43-152 71-183 (286)
2 PLN00042 photosystem II oxygen 100.0 1.5E-28 3.4E-33 212.3 10.2 119 45-165 46-195 (260)
3 PF01789 PsbP: PsbP; InterPro 99.9 9.6E-23 2.1E-27 164.1 5.9 77 79-155 21-98 (175)
4 PLN00067 PsbP domain-containin 99.8 1.5E-18 3.3E-23 150.5 9.2 115 46-164 40-202 (263)
5 PLN00066 PsbP domain-containin 99.7 1.1E-16 2.5E-21 139.0 10.4 116 48-164 44-204 (262)
6 PLN03152 hypothetical protein; 99.0 6.6E-10 1.4E-14 95.5 7.9 70 77-149 74-168 (241)
7 PF12712 DUF3805: Domain of un 88.1 0.6 1.3E-05 38.3 3.5 63 82-153 2-64 (153)
8 TIGR02811 formate_TAT formate 61.7 6.8 0.00015 27.8 2.1 15 47-61 7-21 (66)
9 PF08006 DUF1700: Protein of u 60.9 5 0.00011 32.3 1.5 21 131-151 45-65 (181)
10 PF10518 TAT_signal: TAT (twin 59.2 14 0.0003 21.7 2.8 21 48-68 1-21 (26)
11 PF07174 FAP: Fibronectin-atta 44.6 32 0.00069 31.2 4.0 65 82-148 110-190 (297)
12 COG4709 Predicted membrane pro 35.6 17 0.00038 31.1 0.9 29 132-160 46-79 (195)
13 PF05984 Cytomega_UL20A: Cytom 32.0 40 0.00086 25.8 2.2 19 50-68 2-20 (100)
14 TIGR03741 PRTRC_E PRTRC system 28.3 76 0.0016 24.5 3.3 34 119-152 24-66 (104)
15 PRK10943 cold shock-like prote 27.5 71 0.0015 22.3 2.8 28 79-112 5-32 (69)
16 COG1797 CobB Cobyrinic acid a, 27.0 28 0.0006 33.3 0.8 66 80-152 245-312 (451)
17 PF12559 Inhibitor_I10: Serine 23.1 34 0.00074 23.9 0.4 12 90-101 44-55 (56)
18 cd04458 CSP_CDS Cold-Shock Pro 23.0 1.1E+02 0.0023 20.3 2.9 25 83-113 6-30 (65)
19 PRK09890 cold shock protein Cs 22.8 95 0.002 21.7 2.7 28 79-112 6-33 (70)
20 PF12318 FAD-SLDH: Membrane bo 22.7 77 0.0017 25.9 2.5 8 48-55 1-8 (168)
21 PRK15464 cold shock-like prote 21.2 98 0.0021 21.9 2.5 27 80-112 7-33 (70)
No 1
>PLN00059 PsbP domain-containing protein 1; Provisional
Probab=99.97 E-value=1.9e-30 Score=225.30 Aligned_cols=109 Identities=19% Similarity=0.331 Sum_probs=93.0
Q ss_pred HhhhccchhHHHHH-HHHHHHHhhhcCCCCCCCCccccCceeeecCCCceEEecCCCCccccccCCcEEeecCCCCCcee
Q 030424 43 ELSSLRLSKRELCL-SSFVLILNGLYPKLSKASLPEEMELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFEEANKGTNNL 121 (177)
Q Consensus 43 ~~~~~~~~RR~lll-~il~~~~t~~ll~~s~~a~A~e~gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D~~~~~eNV 121 (177)
....|.+.||.+++ ++++.++..+..+ .+.++|+..||++|+|+.|||+|+||.||++|++.|+||+|||+++.+|||
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 44568899999855 4433444434333 335778888999999999999999999999999999999999999999999
Q ss_pred EEEEeeCC---CCCcccCCCHHHHHHHHHHHHhh
Q 030424 122 GVVVNPVR---VASLGEFGTPQFVADKLIQAEKR 152 (177)
Q Consensus 122 sV~VsPv~---~~SI~dfGsPeeVg~~L~k~e~~ 152 (177)
||+|+|++ +++|+|||+|+||||+|++++++
T Consensus 150 SV~ISs~sss~~~sLeDLGsP~eVgerLlkqvLa 183 (286)
T PLN00059 150 SVEFSSPSSSKYTSLEDLGSPEEVGKRVLRQYLT 183 (286)
T ss_pred EEEEecCCcccCCChHHcCCHHHHHHHHHHHHhc
Confidence 99999885 89999999999999999998877
No 2
>PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional
Probab=99.95 E-value=1.5e-28 Score=212.28 Aligned_cols=119 Identities=24% Similarity=0.319 Sum_probs=91.0
Q ss_pred hhccchhHHHHHHHHHHHHhhhcCCCCCCCCccc----------cCceeeecCCCceEEecCCCCcccc---ccCCcEEe
Q 030424 45 SSLRLSKRELCLSSFVLILNGLYPKLSKASLPEE----------MELQRYTDSNEGFTLLRPSSWIKVD---KAGATVLF 111 (177)
Q Consensus 45 ~~~~~~RR~lll~il~~~~t~~ll~~s~~a~A~e----------~gf~~y~D~~dGYsflyP~gW~~v~---~~G~dv~F 111 (177)
.....+||++|+.++..++.++-++.+.++++++ .||.+|. +|||+|+||++|++++ .+|+|++|
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 3466789988765432222223233233344443 6999995 5999999999999776 56999999
Q ss_pred ecCCCCCceeEEEEeeCCCCCcccCCCHHH----HHHHHHHHHhhcC--------------CCcccchhhhh
Q 030424 112 EEANKGTNNLGVVVNPVRVASLGEFGTPQF----VADKLIQAEKRKN--------------VHDIDLDETMV 165 (177)
Q Consensus 112 ~D~~~~~eNVsV~VsPv~~~SI~dfGsPee----Vg~~L~k~e~~k~--------------st~~d~~e~~~ 165 (177)
||+++++|||+|+|+|+++++|+|||+||| |+++|.|+....+ ..++|++++.+
T Consensus 124 ~D~~~~~eNVSV~Ispt~k~sI~dlGsPee~l~~vgylL~kq~~a~~t~s~~Gf~p~~vata~Lleas~re~ 195 (260)
T PLN00042 124 EDNFDATSNLSVMVTPTDKKSITDYGSPEEFLSKVSYLLGKQAYSGETASEGGFDANAVATAAVLESSTQEV 195 (260)
T ss_pred eccccccccEEEEEecCCcCCHhhcCCHHHHHHHHHHHHHhhhccCccccccCcCcccccceeEEEeeeEEe
Confidence 999999999999999999999999999999 9999999887743 23577766654
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=99.87 E-value=9.6e-23 Score=164.08 Aligned_cols=77 Identities=39% Similarity=0.696 Sum_probs=70.7
Q ss_pred cCceeeecCCCceEEecCCCCccccccCCcEEeecCCCCCceeEEEEeeCCCC-CcccCCCHHHHHHHHHHHHhhcCC
Q 030424 79 MELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFEEANKGTNNLGVVVNPVRVA-SLGEFGTPQFVADKLIQAEKRKNV 155 (177)
Q Consensus 79 ~gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D~~~~~eNVsV~VsPv~~~-SI~dfGsPeeVg~~L~k~e~~k~s 155 (177)
.||++|.|+.+||+|.||.||+++++.|+|++|+|+++.++||+|+|+|+... +|+|||+|+|||++|++++.+++.
T Consensus 21 ~~~~~y~d~~~~y~f~~P~gW~~~~~~G~~v~f~d~~~~~~nvsV~v~p~~~~~sl~~lGs~~~va~~l~~~~~~~~~ 98 (175)
T PF01789_consen 21 TGFQPYTDSDDGYSFLYPSGWEEVDVSGADVVFRDPIDADENVSVVVSPVPKDFSLEDLGSPEEVAERLLNGELASPG 98 (175)
T ss_dssp SSEEEEEECTTTEEEEEETTEEEEESTTEEEEEEETTETTSEEEEEEEE-STS-SGGGG-SHHHHHHHHHHHCCCHCT
T ss_pred CCceEEEcCCCCEEEECCCCCeecCCCCeEEEEECcccccceEEEEEEecCCcCchhhcCCHHHHHHHHhhhhccccc
Confidence 79999999999999999999999999999999999999999999999999855 999999999999999998876544
No 4
>PLN00067 PsbP domain-containing protein 6; Provisional
Probab=99.76 E-value=1.5e-18 Score=150.46 Aligned_cols=115 Identities=19% Similarity=0.299 Sum_probs=83.5
Q ss_pred hccchhHHHHHHHHHHHHhhhcCCCCCCCCccc-------------cCceeeec-----------CCCceEEecCCCCcc
Q 030424 46 SLRLSKRELCLSSFVLILNGLYPKLSKASLPEE-------------MELQRYTD-----------SNEGFTLLRPSSWIK 101 (177)
Q Consensus 46 ~~~~~RR~lll~il~~~~t~~ll~~s~~a~A~e-------------~gf~~y~D-----------~~dGYsflyP~gW~~ 101 (177)
.....||++|+|+.+.++. +++... .+.|.| .||--|.- ...||+|+||.||++
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 3456899999988754332 223222 233444 36666642 357999999999999
Q ss_pred cccc----C-----------CcEEeecCCCCCceeEEEEeeC------CCCCcccCCCHHHHHHHHHHHHhh---cCCCc
Q 030424 102 VDKA----G-----------ATVLFEEANKGTNNLGVVVNPV------RVASLGEFGTPQFVADKLIQAEKR---KNVHD 157 (177)
Q Consensus 102 v~~~----G-----------~dv~F~D~~~~~eNVsV~VsPv------~~~SI~dfGsPeeVg~~L~k~e~~---k~st~ 157 (177)
++++ | +|++|+|+. ++||+|+|+|+ ++++|+|||+|++|+++|.+.... ++..+
T Consensus 118 v~Vs~~~sGnycqp~c~~p~~dv~F~D~~--dgnVSVIVSPV~r~t~k~~~sIeDlGsPeeVl~~Lg~~v~g~~~~~~eL 195 (263)
T PLN00067 118 TRVANILSGNYCQPKCAEPWVEVKFEDEK--QGKVQVVASPLIRLTNKPNATIEEIGSPEKLIASLGPFVTGNSYDPDEL 195 (263)
T ss_pred ccccccccCccccccccCCCceEEEeCCC--CCCEEEEEecccccccCCCCChHHccCHHHHHHHhhHHhhcCCCCCcce
Confidence 9986 4 899999955 77999999998 468999999999999999887766 22344
Q ss_pred ccchhhh
Q 030424 158 IDLDETM 164 (177)
Q Consensus 158 ~d~~e~~ 164 (177)
+|.+++.
T Consensus 196 LeAs~re 202 (263)
T PLN00067 196 LETSVEK 202 (263)
T ss_pred EEeeeEe
Confidence 5555543
No 5
>PLN00066 PsbP domain-containing protein 4; Provisional
Probab=99.69 E-value=1.1e-16 Score=138.97 Aligned_cols=116 Identities=19% Similarity=0.261 Sum_probs=86.3
Q ss_pred cchhHHHHHHHHHHHHhhhcCCCCCCCCc----------------cccCceeeecC-------------CCceEEecCCC
Q 030424 48 RLSKRELCLSSFVLILNGLYPKLSKASLP----------------EEMELQRYTDS-------------NEGFTLLRPSS 98 (177)
Q Consensus 48 ~~~RR~lll~il~~~~t~~ll~~s~~a~A----------------~e~gf~~y~D~-------------~dGYsflyP~g 98 (177)
.++||.+|.++++++ ....++.+..++| .+.||+.|..+ ...|+|+||.|
T Consensus 44 ~~~rr~~~~s~~~~~-~~~~~~~~~~~~a~~~g~~ag~~~~~s~~~~~g~~~~~rp~~~~Gg~G~~~~~i~~Y~F~yP~G 122 (262)
T PLN00066 44 AVSRRSALASGAAAA-SSAVLAFPGEGLAVKQGLLAGRVPGLSEPDENGWRTYRRPEGKSGGHGVGWSEITPYSFKVPQG 122 (262)
T ss_pred hhhHHHHHHHHHHHH-hhhhhcCCcchhhhhhcccccCCCCCCCccccceEEEecCccccCcCCCCccccCCeEEECCCC
Confidence 369999998766542 2222333333332 22588998765 26799999999
Q ss_pred Ccccccc-----CCcEEeecCCCCCceeEEEEeeC--------CCCCcccCCCHHHHHHHHHHHHhh---cCCCcccchh
Q 030424 99 WIKVDKA-----GATVLFEEANKGTNNLGVVVNPV--------RVASLGEFGTPQFVADKLIQAEKR---KNVHDIDLDE 162 (177)
Q Consensus 99 W~~v~~~-----G~dv~F~D~~~~~eNVsV~VsPv--------~~~SI~dfGsPeeVg~~L~k~e~~---k~st~~d~~e 162 (177)
|.++.++ |+++.|++.++.++||+|+|+|+ ++++|+|||+||+|++.|++.... ++..++++++
T Consensus 123 W~ev~VS~~d~gg~~vd~Rf~~~~~~nvsVvVspv~rla~~~~~~~sI~dLGspeeVi~~l~~~v~g~~~~e~eLl~a~~ 202 (262)
T PLN00066 123 WEEVPVSIADLGGTEIDLRFASDKEGRLKVVVAPVLRFADNLGDNATIEEIGPPEKVISGFGPELIGEPVEEGKVLSMEV 202 (262)
T ss_pred CeEeecccccCCCCceEEEeccCCCccEEEEEeccccccccccCCCChHHcCCHHHHHHHHHHHhcCCCccccceeEeee
Confidence 9999986 77888888889999999999998 589999999999999999986543 3455666665
Q ss_pred hh
Q 030424 163 TM 164 (177)
Q Consensus 163 ~~ 164 (177)
+.
T Consensus 203 re 204 (262)
T PLN00066 203 AE 204 (262)
T ss_pred ee
Confidence 43
No 6
>PLN03152 hypothetical protein; Provisional
Probab=99.04 E-value=6.6e-10 Score=95.45 Aligned_cols=70 Identities=17% Similarity=0.377 Sum_probs=53.8
Q ss_pred cccCceeeecCCCceEEecCCCCcccccc-----------------CCcEEeecCCCCCceeEEEEeeC--------CCC
Q 030424 77 EEMELQRYTDSNEGFTLLRPSSWIKVDKA-----------------GATVLFEEANKGTNNLGVVVNPV--------RVA 131 (177)
Q Consensus 77 ~e~gf~~y~D~~dGYsflyP~gW~~v~~~-----------------G~dv~F~D~~~~~eNVsV~VsPv--------~~~ 131 (177)
++..+-.| .++||+.-||..+..+-++ --.++|..+ |++|||||+|+|+ +.+
T Consensus 74 nt~~w~~~--~g~gf~~~~pp~f~di~e~~~~~~g~~~yg~~akp~~~~aRf~s~-D~sEnVSVVIspv~~LK~tfle~k 150 (241)
T PLN03152 74 NTKSWFQF--YGDGFSIRVPPSFEDIMEPEDYNAGLSLYGDKAKPRTFAARFASP-DGSEVLSVVIRPSNQLKITFLEAK 150 (241)
T ss_pred cchhhhhh--hCCceEEeCCCChhhhcChhhcccccceecCCCCCcceeeeecCC-CCCceEEEEEecCccccccccccC
Confidence 33344444 4899999999999876532 234555544 5899999999997 589
Q ss_pred CcccCCCHHHHHHHHHHH
Q 030424 132 SLGEFGTPQFVADKLIQA 149 (177)
Q Consensus 132 SI~dfGsPeeVg~~L~k~ 149 (177)
+|+|||+|+|||+.|+-.
T Consensus 151 DLtDLGsp~EVgkv~vP~ 168 (241)
T PLN03152 151 DITDLGSLKEAAKIFVPG 168 (241)
T ss_pred ChhHcCCHHHHHHhhCCC
Confidence 999999999999888754
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=88.15 E-value=0.6 Score=38.31 Aligned_cols=63 Identities=16% Similarity=0.358 Sum_probs=36.2
Q ss_pred eeeecCCCceEEecCCCCccccccCCcEEeecCCCCCceeEEEEeeCCCCCcccCCCHHHHHHHHHHHHhhc
Q 030424 82 QRYTDSNEGFTLLRPSSWIKVDKAGATVLFEEANKGTNNLGVVVNPVRVASLGEFGTPQFVADKLIQAEKRK 153 (177)
Q Consensus 82 ~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D~~~~~eNVsV~VsPv~~~SI~dfGsPeeVg~~L~k~e~~k 153 (177)
.-|..++.=|++.||.+|.++.......+|=||..=+-|..+. +-+..+ ..-|...+++|++.
T Consensus 2 kKfiSpg~WFS~~YP~~W~EfED~E~sflFYnp~~WTGNfRIS--ayk~~~-------~~ygk~~i~~EL~e 64 (153)
T PF12712_consen 2 KKFISPGAWFSMEYPADWNEFEDGEGSFLFYNPDQWTGNFRIS--AYKGGS-------AQYGKECIRQELKE 64 (153)
T ss_dssp EEEE-GGG-EEEEE-TT-EEE---TTEEEEE-SSS---EEEEE--EEE--S-------TTHHHHHHHHHHHH
T ss_pred CcccCCCceEEEecCCCcchhccCCcceEEEChHHhcCceEEE--EEeccc-------ccchHHHHHHHHHh
Confidence 4578888889999999999999777888899999999999554 443111 22455566666663
No 8
>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=61.66 E-value=6.8 Score=27.80 Aligned_cols=15 Identities=27% Similarity=0.025 Sum_probs=11.4
Q ss_pred ccchhHHHHHHHHHH
Q 030424 47 LRLSKRELCLSSFVL 61 (177)
Q Consensus 47 ~~~~RR~lll~il~~ 61 (177)
...+||++|.++++.
T Consensus 7 ~~~sRR~Flk~lg~~ 21 (66)
T TIGR02811 7 ADPSRRDLLKGLGVG 21 (66)
T ss_pred CCccHHHHHHHHHHH
Confidence 467999999877643
No 9
>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=60.89 E-value=5 Score=32.32 Aligned_cols=21 Identities=19% Similarity=0.471 Sum_probs=17.3
Q ss_pred CCcccCCCHHHHHHHHHHHHh
Q 030424 131 ASLGEFGTPQFVADKLIQAEK 151 (177)
Q Consensus 131 ~SI~dfGsPeeVg~~L~k~e~ 151 (177)
.=+++||+|+|+|..++.+..
T Consensus 45 eii~~LG~P~~iA~~i~~~~~ 65 (181)
T PF08006_consen 45 EIIAELGSPKEIAREILAEYS 65 (181)
T ss_pred HHHHHcCCHHHHHHHHHHhhh
Confidence 347899999999999987553
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=59.20 E-value=14 Score=21.66 Aligned_cols=21 Identities=14% Similarity=0.110 Sum_probs=14.4
Q ss_pred cchhHHHHHHHHHHHHhhhcC
Q 030424 48 RLSKRELCLSSFVLILNGLYP 68 (177)
Q Consensus 48 ~~~RR~lll~il~~~~t~~ll 68 (177)
+.+||++|-+.+..++...+.
T Consensus 1 ~~sRR~fLk~~~a~~a~~~~~ 21 (26)
T PF10518_consen 1 NLSRRQFLKGGAAAAAAAALG 21 (26)
T ss_pred CCcHHHHHHHHHHHHHHHHhc
Confidence 368999998777665555433
No 11
>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=44.58 E-value=32 Score=31.19 Aligned_cols=65 Identities=23% Similarity=0.434 Sum_probs=39.6
Q ss_pred eeeecCCCceEEecCCCCcccccc----CCcEEeecCCCC---------CceeEEEEeeCC---CCCcccCCCHHHHHHH
Q 030424 82 QRYTDSNEGFTLLRPSSWIKVDKA----GATVLFEEANKG---------TNNLGVVVNPVR---VASLGEFGTPQFVADK 145 (177)
Q Consensus 82 ~~y~D~~dGYsflyP~gW~~v~~~----G~dv~F~D~~~~---------~eNVsV~VsPv~---~~SI~dfGsPeeVg~~ 145 (177)
-++.|...||+|+.|.||.+.+-. |..+.=+-..++ .+.-+|++-..+ +.+.+ -+-...+.|
T Consensus 110 grvdn~~gGFS~vvP~GW~~Sda~~L~yG~alls~~~~~~~~~~~~~p~andt~v~lgrld~kl~a~ae--~dn~kaa~r 187 (297)
T PF07174_consen 110 GRVDNAAGGFSYVVPAGWVESDASHLDYGSALLSKQTGEPPMPGQPPPVANDTSVVLGRLDLKLFASAE--PDNTKAAVR 187 (297)
T ss_pred ccccccccceEEeccCCccccccceeecceeeeccCCCCCCCCCCCCCcCCCceEEecccccccccccc--CChHHHHHH
Confidence 467778999999999999988843 666665433222 134445555544 12211 234457777
Q ss_pred HHH
Q 030424 146 LIQ 148 (177)
Q Consensus 146 L~k 148 (177)
|..
T Consensus 188 l~s 190 (297)
T PF07174_consen 188 LAS 190 (297)
T ss_pred Hhc
Confidence 765
No 12
>COG4709 Predicted membrane protein [Function unknown]
Probab=35.58 E-value=17 Score=31.11 Aligned_cols=29 Identities=17% Similarity=0.282 Sum_probs=18.7
Q ss_pred CcccCCCHHHHHHHHH-----HHHhhcCCCcccc
Q 030424 132 SLGEFGTPQFVADKLI-----QAEKRKNVHDIDL 160 (177)
Q Consensus 132 SI~dfGsPeeVg~~L~-----k~e~~k~st~~d~ 160 (177)
=+.|||+|+|+|..+. |++.-|+++.+.+
T Consensus 46 I~~~LG~P~eiA~ei~s~~~~k~~~~~~~~~n~~ 79 (195)
T COG4709 46 IAKDLGDPKEIAAEILSERGIKKEEVKPTQKNVR 79 (195)
T ss_pred HHHHhCCHHHHHHHHHHHccchHHhccCcccchH
Confidence 3789999999876554 4444455554443
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=31.96 E-value=40 Score=25.83 Aligned_cols=19 Identities=21% Similarity=0.205 Sum_probs=16.1
Q ss_pred hhHHHHHHHHHHHHhhhcC
Q 030424 50 SKRELCLSSFVLILNGLYP 68 (177)
Q Consensus 50 ~RR~lll~il~~~~t~~ll 68 (177)
.||-++|++|+..++++|.
T Consensus 2 aRRlwiLslLAVtLtVALA 20 (100)
T PF05984_consen 2 ARRLWILSLLAVTLTVALA 20 (100)
T ss_pred chhhHHHHHHHHHHHHHhh
Confidence 5888899999988888865
No 14
>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=28.27 E-value=76 Score=24.49 Aligned_cols=34 Identities=26% Similarity=0.393 Sum_probs=24.2
Q ss_pred ceeEEEEeeCCCCCc--ccC-------CCHHHHHHHHHHHHhh
Q 030424 119 NNLGVVVNPVRVASL--GEF-------GTPQFVADKLIQAEKR 152 (177)
Q Consensus 119 eNVsV~VsPv~~~SI--~df-------GsPeeVg~~L~k~e~~ 152 (177)
+++.|+|.|..+... ..+ |+|+|.-+.+..+...
T Consensus 24 d~l~V~v~P~~~~~~~d~~l~~Pl~L~gTp~ELD~gF~~ai~~ 66 (104)
T TIGR03741 24 DKLTVTVTPTPKSGAKDGALTKPLVLTGTPAELDAGFAGALGQ 66 (104)
T ss_pred CEEEEEEeeccccccccccccCCeeeccCHHHHHHHHHHHHHh
Confidence 389999999843222 344 9999988888766554
No 15
>PRK10943 cold shock-like protein CspC; Provisional
Probab=27.54 E-value=71 Score=22.29 Aligned_cols=28 Identities=14% Similarity=0.436 Sum_probs=20.1
Q ss_pred cCceeeecCCCceEEecCCCCccccccCCcEEee
Q 030424 79 MELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (177)
Q Consensus 79 ~gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (177)
.|--..-|...||-|+-|.+ .|.||+||
T Consensus 5 ~G~Vk~f~~~kGfGFI~~~~------g~~dvFvH 32 (69)
T PRK10943 5 KGQVKWFNESKGFGFITPAD------GSKDVFVH 32 (69)
T ss_pred ceEEEEEeCCCCcEEEecCC------CCeeEEEE
Confidence 35555667889999999864 45677765
No 16
>COG1797 CobB Cobyrinic acid a,c-diamide synthase [Coenzyme metabolism]
Probab=26.95 E-value=28 Score=33.33 Aligned_cols=66 Identities=20% Similarity=0.300 Sum_probs=43.5
Q ss_pred CceeeecCCCceEEecCCCCccccccCCcEEeecCCCCCceeEEEEeeCCCCCcccC--CCHHHHHHHHHHHHhh
Q 030424 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFEEANKGTNNLGVVVNPVRVASLGEF--GTPQFVADKLIQAEKR 152 (177)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D~~~~~eNVsV~VsPv~~~SI~df--GsPeeVg~~L~k~e~~ 152 (177)
|.+-=+-.+.-|.|+||.....-+..|+.++|=+|..-.+ | | +.-+.==+ |=||-.++.|-+++..
T Consensus 245 ~~rIAVA~D~AF~FyY~~nl~~Lr~~GAelv~FSPL~D~~-l-----P-~~~D~vYlgGGYPElfA~~L~~n~~~ 312 (451)
T COG1797 245 GVRIAVARDAAFNFYYPENLELLREAGAELVFFSPLADEE-L-----P-PDVDAVYLGGGYPELFAEELSANESM 312 (451)
T ss_pred CceEEEEecchhccccHHHHHHHHHCCCEEEEeCCcCCCC-C-----C-CCCCEEEeCCCChHHHHHHHhhCHHH
Confidence 3444444578899999999999999999998866653211 1 0 01111113 4499999999998743
No 17
>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=23.08 E-value=34 Score=23.89 Aligned_cols=12 Identities=42% Similarity=0.515 Sum_probs=4.0
Q ss_pred ceEEecCCCCcc
Q 030424 90 GFTLLRPSSWIK 101 (177)
Q Consensus 90 GYsflyP~gW~~ 101 (177)
..++.||++|.+
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 18
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=23.00 E-value=1.1e+02 Score=20.33 Aligned_cols=25 Identities=24% Similarity=0.639 Sum_probs=18.1
Q ss_pred eeecCCCceEEecCCCCccccccCCcEEeec
Q 030424 83 RYTDSNEGFTLLRPSSWIKVDKAGATVLFEE 113 (177)
Q Consensus 83 ~y~D~~dGYsflyP~gW~~v~~~G~dv~F~D 113 (177)
..-|...||-|+-|.+ .|.|++||-
T Consensus 6 k~~~~~kGfGFI~~~~------~g~diffh~ 30 (65)
T cd04458 6 KWFDDEKGFGFITPDD------GGEDVFVHI 30 (65)
T ss_pred EEEECCCCeEEEecCC------CCcCEEEEh
Confidence 3456778999998876 567777763
No 19
>PRK09890 cold shock protein CspG; Provisional
Probab=22.80 E-value=95 Score=21.72 Aligned_cols=28 Identities=18% Similarity=0.530 Sum_probs=21.0
Q ss_pred cCceeeecCCCceEEecCCCCccccccCCcEEee
Q 030424 79 MELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (177)
Q Consensus 79 ~gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (177)
.|-..+-|...||-|+-|.+ .|.||+||
T Consensus 6 ~G~Vk~f~~~kGfGFI~~~~------g~~dvFvH 33 (70)
T PRK09890 6 TGLVKWFNADKGFGFITPDD------GSKDVFVH 33 (70)
T ss_pred eEEEEEEECCCCcEEEecCC------CCceEEEE
Confidence 36566667889999999973 45677776
No 20
>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=22.73 E-value=77 Score=25.93 Aligned_cols=8 Identities=50% Similarity=0.646 Sum_probs=6.7
Q ss_pred cchhHHHH
Q 030424 48 RLSKRELC 55 (177)
Q Consensus 48 ~~~RR~ll 55 (177)
+.+||++|
T Consensus 1 g~sRR~~L 8 (168)
T PF12318_consen 1 GLSRRRLL 8 (168)
T ss_pred CCcHHHHH
Confidence 46899999
No 21
>PRK15464 cold shock-like protein CspH; Provisional
Probab=21.18 E-value=98 Score=21.91 Aligned_cols=27 Identities=19% Similarity=0.258 Sum_probs=19.0
Q ss_pred CceeeecCCCceEEecCCCCccccccCCcEEee
Q 030424 80 ELQRYTDSNEGFTLLRPSSWIKVDKAGATVLFE 112 (177)
Q Consensus 80 gf~~y~D~~dGYsflyP~gW~~v~~~G~dv~F~ 112 (177)
|--.+-|...||-|+-|.+ .|.||++|
T Consensus 7 G~Vk~fn~~KGfGFI~~~~------g~~DvFvH 33 (70)
T PRK15464 7 GIVKTFDRKSGKGFIIPSD------GRKEVQVH 33 (70)
T ss_pred EEEEEEECCCCeEEEccCC------CCccEEEE
Confidence 4445567889999998874 35666654
Done!