Query 028082
Match_columns 214
No_of_seqs 29 out of 31
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 05:58:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028082.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028082hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01459 Porin_3: Eukaryotic p 89.6 11 0.00025 31.5 21.7 133 58-195 108-265 (273)
2 cd02861 E_set_proteins_like E 82.4 8.6 0.00019 27.7 6.9 50 51-124 30-80 (82)
3 PF00593 TonB_dep_Rec: TonB de 71.3 1.7 3.8E-05 32.0 0.6 22 148-169 2-24 (277)
4 cd07306 Porin3_VDAC Voltage-de 69.1 80 0.0017 27.7 22.1 82 122-204 181-269 (276)
5 cd00342 gram_neg_porins Porins 68.5 74 0.0016 27.1 11.5 56 112-169 205-260 (329)
6 PF13609 Porin_4: Gram-negativ 65.7 80 0.0017 26.4 10.2 28 143-171 247-274 (311)
7 TIGR01981 sufD FeS assembly pr 61.8 54 0.0012 30.2 8.5 82 37-118 44-143 (366)
8 TIGR03503 conserved hypothetic 55.1 1.2E+02 0.0026 29.2 9.8 39 55-93 182-220 (374)
9 TIGR01782 TonB-Xanth-Caul TonB 52.4 81 0.0018 31.4 8.5 107 39-159 680-802 (845)
10 PF10082 DUF2320: Uncharacteri 51.1 1.8E+02 0.0039 25.9 10.1 110 84-193 98-245 (381)
11 cd07305 Porin3_Tom40 Transloca 44.6 2.2E+02 0.0048 25.0 22.5 141 58-203 109-271 (279)
12 smart00159 PTX Pentraxin / C-r 42.1 1.7E+02 0.0038 24.5 7.8 72 43-120 56-128 (206)
13 TIGR01997 sufA_proteo FeS asse 41.3 43 0.00093 25.6 3.8 33 47-80 24-62 (107)
14 PF06727 DUF1207: Protein of u 40.4 1.8E+02 0.004 27.7 8.5 111 43-178 137-258 (338)
15 PF13715 DUF4480: Domain of un 40.2 1.3E+02 0.0028 21.2 5.9 35 18-74 16-50 (88)
16 KOG3126 Porin/voltage-dependen 39.4 3.2E+02 0.0069 25.4 12.0 55 140-195 167-226 (281)
17 COG1629 CirA Outer membrane re 38.7 23 0.0005 31.9 2.2 67 141-214 500-566 (768)
18 PF07532 Big_4: Bacterial Ig-l 38.6 70 0.0015 21.9 4.2 36 159-194 17-57 (59)
19 PF13609 Porin_4: Gram-negativ 36.9 2.5E+02 0.0054 23.5 14.0 89 72-170 218-307 (311)
20 PF06577 DUF1134: Protein of u 36.2 44 0.00096 29.0 3.4 55 18-73 50-104 (160)
21 cd01347 ligand_gated_channel T 34.2 3.4E+02 0.0074 24.3 10.2 31 142-172 377-407 (635)
22 PF14352 DUF4402: Domain of un 33.8 2.3E+02 0.0049 22.0 8.2 60 56-117 46-121 (130)
23 PRK13285 flagellar assembly pr 33.5 91 0.002 25.9 4.8 71 48-128 55-137 (148)
24 TIGR03341 YhgI_GntY IscR-regul 32.9 80 0.0017 27.1 4.5 32 48-80 23-62 (190)
25 PF00677 Lum_binding: Lumazine 32.8 1.3E+02 0.0027 22.4 5.0 48 19-66 10-64 (85)
26 KOG1719 Dual specificity phosp 32.5 4.6 0.0001 35.4 -3.1 55 27-105 75-132 (183)
27 PF10162 G8: G8 domain; Inter 31.7 89 0.0019 24.6 4.3 29 97-125 34-64 (125)
28 PRK15216 putative fimbrial bio 31.7 3.4E+02 0.0073 26.2 8.7 73 85-183 23-95 (340)
29 PF00167 FGF: Fibroblast growt 30.9 80 0.0017 24.3 3.8 50 103-155 54-103 (122)
30 PF03168 LEA_2: Late embryogen 29.2 1.4E+02 0.003 21.0 4.6 57 50-110 1-57 (101)
31 cd01347 ligand_gated_channel T 28.4 4.3E+02 0.0094 23.6 8.7 74 84-157 506-589 (635)
32 PRK11190 Fe/S biogenesis prote 27.9 95 0.0021 26.8 4.1 42 47-89 23-72 (192)
33 PF03100 CcmE: CcmE; InterPro 26.6 3.3E+02 0.0073 21.7 7.7 65 53-127 58-127 (131)
34 PF07443 HARP: HepA-related pr 26.2 22 0.00047 25.7 -0.1 14 140-153 22-35 (55)
35 smart00089 PKD Repeats in poly 25.5 2.3E+02 0.0049 19.4 5.4 26 42-67 38-65 (79)
36 PRK09840 catecholate sideropho 25.5 1.2E+02 0.0027 29.5 4.9 31 142-172 510-540 (761)
37 PF06009 Laminin_II: Laminin D 25.1 33 0.00071 27.6 0.8 22 106-128 103-124 (138)
38 PF01203 T2SN: Type II secreti 24.4 4E+02 0.0087 22.5 7.2 92 97-195 98-189 (221)
39 COG5400 Uncharacterized protei 23.1 64 0.0014 28.8 2.2 55 18-73 95-149 (205)
40 TIGR00049 Iron-sulfur cluster 22.6 1.3E+02 0.0028 22.4 3.5 10 48-57 23-32 (105)
41 cd00342 gram_neg_porins Porins 22.4 2E+02 0.0044 24.4 5.1 54 112-167 241-294 (329)
42 PF13116 DUF3971: Protein of u 22.3 3.2E+02 0.0069 23.2 6.2 71 27-105 53-127 (288)
43 PRK13282 flagellar assembly pr 22.1 3.7E+02 0.0081 22.0 6.4 62 48-120 37-110 (128)
44 PF00856 SET: SET domain; Int 21.8 1.8E+02 0.0039 21.1 4.1 40 114-166 122-161 (162)
45 PRK09504 sufA iron-sulfur clus 20.6 1.9E+02 0.0042 22.9 4.3 47 33-80 18-77 (122)
46 PF01803 LIM_bind: LIM-domain 20.4 1.8E+02 0.0039 25.1 4.4 41 114-154 91-137 (240)
47 PF11383 DUF3187: Protein of u 20.2 7.1E+02 0.015 23.1 13.5 129 40-172 102-264 (319)
No 1
>PF01459 Porin_3: Eukaryotic porin; InterPro: IPR001925 The major protein of the outer mitochondrial membrane of eukaryotes is a porin that forms a voltage-dependent anion-selective channel (VDAC) that behaves as a general diffusion pore for small hydrophilic molecules [, , , ]. The channel adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. This protein contains about 280 amino acids and its sequence is composed of between 12 to 16 beta-strands that span the mitochondrial outer membrane. Yeast contains two members of this family (genes POR1 and POR2); vertebrates have at least three members (genes VDAC1, VDAC2 and VDAC3) [].; GO: 0008308 voltage-gated anion channel activity, 0006820 anion transport, 0044070 regulation of anion transport, 0055085 transmembrane transport, 0005741 mitochondrial outer membrane; PDB: 3EMN_X 2K4T_A 2JK4_A.
Probab=89.58 E-value=11 Score=31.53 Aligned_cols=133 Identities=15% Similarity=0.209 Sum_probs=82.3
Q ss_pred eEEEEeeCCCCCeeEEEeeeeeecceeeeEEEeecCCCceeEEeeEEEEeCCC-ceE-----EEEEec------------
Q 028082 58 FFIVDYNVPKKDFRFQFMNSVRVADKPLNLTYIHGRGDNRTILEGTLVFDSAN-KVS-----ANHVLG------------ 119 (214)
Q Consensus 58 sF~iDy~~~~~d~rFQFmnt~~V~~k~lnlTY~H~~~~nrT~ldgtl~~D~aN-K~s-----~~y~~~------------ 119 (214)
.+.+||.-+.-...+++.|. ....+.+.|..+.. .+-.|=+.+++|..+ ++. ++|.-.
T Consensus 108 ~l~~~y~~~~~~~~~~~~~~---~~~~~~~s~~~~v~-~~~~lG~e~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~ 183 (273)
T PF01459_consen 108 QLEADYKGDDFNATFKVDND---NNPIFNASYVQSVT-PNLALGAEATYDLSSGKSSKYNAGLSYAARYTHPDYTASATL 183 (273)
T ss_dssp EEEEEEEETTEEEEEEEEES---TS-EEEEEEEEEET--TEEEEEEEEEETTTTCEEEEEEEEEEEET----TEEEEEEE
T ss_pred EEEEEEecCCEEEEEEEccc---CCCcEEEEEEEecc-ccEEEEEEEEEecccCCcCcceEEEEEeccccceeEEEEEEE
Confidence 34566665555555555551 25568888888744 467888999998886 444 455555
Q ss_pred -CCCeeEEEEEEeC---Ce-eeEEeecccccc--ceeeEEEEeecCCCeEEEEEecCcceEEEEEeeCCCCCcceEEEEe
Q 028082 120 -SGNCKLKYTYVHG---GL-TTFEQWYDLAKN--SWDFAVSRKVYGDDMFRASYQTSSKALALEWSRNSKINGDFKIQAA 192 (214)
Q Consensus 120 -s~~c~lKY~YvH~---g~-tt~EP~yd~~~n--sWdfavs~k~~g~d~vratY~~~~k~lgleWsr~sk~~G~fKv~a~ 192 (214)
.....+.-+|.|. .+ .-.|=.++..++ ...+++.+++.+...+|+..++.. .+++-+...-..+=.|-+++.
T Consensus 184 ~~~~~~l~~sy~~k~~~~~~~g~e~~~~~~~~~~~~~vG~~~~l~~~~~vk~kvds~g-~v~~~~~~~l~~~~~l~ls~~ 262 (273)
T PF01459_consen 184 SNNFGTLTASYFQKVNDKLQLGAELTYNLSSRESTFTVGYQYKLDDSSTVKAKVDSNG-RVSASYEQKLNPGVTLTLSAE 262 (273)
T ss_dssp -ETTTEEEEEEEEESSTTEEEEEEEEEETTCCEEEEEEEEEEEECTTEEEEEEEETTS-EEEEEEEEEECTTEEEEEEEE
T ss_pred cCCCCEEEEEEEEEeccceeeeeeeeecccCCCceEEEEEEEEcCcccEEEEEEcCCC-EEEEEEEEecCCCcEEEEEEE
Confidence 1345556677776 22 334445555544 455666777777779999999887 455555544333334666776
Q ss_pred eec
Q 028082 193 LNL 195 (214)
Q Consensus 193 ~~L 195 (214)
+|.
T Consensus 263 ~d~ 265 (273)
T PF01459_consen 263 LDH 265 (273)
T ss_dssp ECT
T ss_pred Ecc
Confidence 666
No 2
>cd02861 E_set_proteins_like E or "early" set-like proteins. These alpha amylase-like sugar utilizing enzymes which may be related to the immunoglobulin and/or fibronectin type III superfamilies are associated with different types of catalytic domains at either the N-terminal or C-terminal end. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase.
Probab=82.38 E-value=8.6 Score=27.74 Aligned_cols=50 Identities=18% Similarity=0.456 Sum_probs=34.5
Q ss_pred EEeecCceEEEEeeCCCCCeeEEEeeeeeecceeeeEEEeecCCCceeEEeeEEE-EeCCCceEEEEEecCCCee
Q 028082 51 LAVEKPGFFIVDYNVPKKDFRFQFMNSVRVADKPLNLTYIHGRGDNRTILEGTLV-FDSANKVSANHVLGSGNCK 124 (214)
Q Consensus 51 L~vEKPGsF~iDy~~~~~d~rFQFmnt~~V~~k~lnlTY~H~~~~nrT~ldgtl~-~D~aNK~s~~y~~~s~~c~ 124 (214)
|.-.+.|.|.+...++....+|+| ++||... .||.|.-...=.|+..||-
T Consensus 30 m~~~~~G~w~~~~~l~~G~y~Ykf------------------------~vdg~~~~~DP~~~~~~~~~~g~~n~v 80 (82)
T cd02861 30 MEREGDGLWVVTVELRPGRYEYKF------------------------VVDGEWVIVDPNAAAYVDDGFGGKNAV 80 (82)
T ss_pred CEECCCCcEEEEEeCCCCcEEEEE------------------------EECCEEeeCCCCCCceecCCCCccceE
Confidence 333355899999999998889998 3455555 6887776666666655553
No 3
>PF00593 TonB_dep_Rec: TonB dependent receptor; InterPro: IPR000531 In Escherichia coli the TonB protein interacts with outer membrane receptor proteins that carry out high-affinity binding and energy-dependent uptake of specific substrates into the periplasmic space []. These substrates are either poorly permeable through the porin channels or are encountered at very low concentrations. In the absence of TonB, these receptors bind their substrates but do not carry out active transport. TonB-dependent regulatory systems consist of six components: a specialised outer membrane-localised TonB-dependent receptor (TonB-dependent transducer) that interacts with its energising TonB-ExbBD protein complex, a cytoplasmic membrane-localised anti-sigma factor and an extracytoplasmic function (ECF)-subfamily sigma factor []. The TonB complex senses signals from outside the bacterial cell and transmits them via two membranes into the cytoplasm, leading to transcriptional activation of target genes. The proteins that are currently known or presumed to interact with TonB include BtuB [], CirA, FatA, FcuT, FecA [], FhuA [], FhuE, FepA [], FptA, HemR, IrgA, IutA, PfeA, PupA and Tbp1. The TonB protein also interacts with some colicins. Most of these proteins contain a short conserved region at their N terminus []. This entry covers the conserved part of the beta-barrel structure at the C-terminal.; GO: 0004872 receptor activity, 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2YSU_A 1NQG_A 3M8D_A 2GSK_A 3RGN_A 1NQE_A 3M8B_A 1NQH_A 3RGM_A 1NQF_A ....
Probab=71.30 E-value=1.7 Score=31.96 Aligned_cols=22 Identities=27% Similarity=0.215 Sum_probs=10.6
Q ss_pred eeeEE-EEeecCCCeEEEEEecC
Q 028082 148 WDFAV-SRKVYGDDMFRASYQTS 169 (214)
Q Consensus 148 Wdfav-s~k~~g~d~vratY~~~ 169 (214)
|.+++ ++++.++-.+|++|-.+
T Consensus 2 p~~~~~~y~~~~~~~l~~~~~~~ 24 (277)
T PF00593_consen 2 PRLGLTSYKPTDNLSLRASYGRG 24 (277)
T ss_dssp EEEEEEEEEESTSEEEEEEEEEE
T ss_pred ceEEEEEEEECCCeEEEEEEEEe
Confidence 44455 35555555555554443
No 4
>cd07306 Porin3_VDAC Voltage-dependent anion channel of the outer mitochondrial membrane. The voltage-dependent anion channel (VDAC) regulates the flux of mostly anionic metabolites through the outer mitochondrial membrane, which is highly permeable to small molecules. VDAC is the most abundant protein in the outer membrane, and membrane potentials can toggle VDAC between open or high-conducting and closed or low-conducting forms. VDAC binds to and is regulated in part by hexokinase, an interaction that renders mitochondria less susceptible to pro-apoptotic signals, most likely by intefering with VDAC's capability to respond to Bcl-2 family proteins. While VDAC appears to play a key role in mitochondrially induced cell death, a proposed involvement in forming the mitochondrial permeability transition pore, which is characteristic for damaged mitochondria and apoptosis, has been challenged by more recent studies.
Probab=69.10 E-value=80 Score=27.69 Aligned_cols=82 Identities=12% Similarity=0.176 Sum_probs=50.5
Q ss_pred CeeEEEEEEeC---Ce-eeEEeecc--ccccceeeEEEEeecCCCeEEEEEecCcceEEEEEeeCCCCCcceEEEEeeec
Q 028082 122 NCKLKYTYVHG---GL-TTFEQWYD--LAKNSWDFAVSRKVYGDDMFRASYQTSSKALALEWSRNSKINGDFKIQAALNL 195 (214)
Q Consensus 122 ~c~lKY~YvH~---g~-tt~EP~yd--~~~nsWdfavs~k~~g~d~vratY~~~~k~lgleWsr~sk~~G~fKv~a~~~L 195 (214)
...++=+|.|. .+ .-.|=.++ -...++.++..|++..+-.+||-.+... .+++-+.+.=..+=.+-+++.++.
T Consensus 181 ~~~l~~S~~~kv~~~l~~g~e~~~~~~~~~~~~~vg~~y~l~~~~~vkakv~~~g-~v~~~y~~kl~~~v~~tls~~~d~ 259 (276)
T cd07306 181 GKTLRGSYFHKVSPRLAVGAKVTWYSGTNETTFAVGGQYALDPDALVKAKVNNDG-QLGLSYQHKLRPGVTLTLSAGFDA 259 (276)
T ss_pred CCEEEEEEEEEcCCCeEEEEEEEEecCCCCcEEEEEEEEEcCCCCEEEEEECCCc-eEEEEEEEEcCCCcEEEEEEEeec
Confidence 46677778876 11 23443444 3446899999999999899999998666 556666553333323445555555
Q ss_pred ch-hcCCCee
Q 028082 196 AE-ELRVPKL 204 (214)
Q Consensus 196 ~d-~~K~pkl 204 (214)
.. ..+.+|+
T Consensus 260 ~~~~~~~~K~ 269 (276)
T cd07306 260 KNLNQGGHKF 269 (276)
T ss_pred cCcCCCCCeE
Confidence 22 2356663
No 5
>cd00342 gram_neg_porins Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers are stabilized by hytrophillic clamping of Loop L2. Loop 3 bends into the pore, creating an elliptical constriction of about 7 x 11A, large enough to allow passage of a glucose molecule without steric hindrance. Removal of the C-terminal residue (usuallly F) destabilizes the trimer and removal of the 16th beta-sheet abolishes trimerization. Unlike typical membrane proteins, porins lack long hydrophobic stretches. Short turns are found at the smooth, periplasmic end, longer irregular loops are found at the rough, extracellular end. C-terminal residue forms salt bridge with N-terminus.
Probab=68.47 E-value=74 Score=27.05 Aligned_cols=56 Identities=14% Similarity=0.069 Sum_probs=35.1
Q ss_pred eEEEEEecCCCeeEEEEEEeCCeeeEEeeccccccceeeEEEEeecCCCeEEEEEecC
Q 028082 112 VSANHVLGSGNCKLKYTYVHGGLTTFEQWYDLAKNSWDFAVSRKVYGDDMFRASYQTS 169 (214)
Q Consensus 112 ~s~~y~~~s~~c~lKY~YvH~g~tt~EP~yd~~~nsWdfavs~k~~g~d~vratY~~~ 169 (214)
+.+.|.++ .-.|.=.|.|..........+-..+.|.+++++++.+.=.+.+.|...
T Consensus 205 ~ga~Y~~~--~~~v~a~y~~~~~~~~~~~~~~~~~~~~lga~Y~~~~~~~~~~~y~~~ 260 (329)
T cd00342 205 AGASYDFG--GLKLGAGYTNTRNDNGGGGGSAKFNGYELGATYQLTPALRLGAAYYYT 260 (329)
T ss_pred EEEEEEEc--cEEEEEEEEEEEccCCCCCCceEEEEEEEeEEEEcCCceEEEEEEEEE
Confidence 56777776 455655565543221111223445789999999998777788888654
No 6
>PF13609 Porin_4: Gram-negative porin; PDB: 2FGR_A 2FGQ_X 1E54_A 2POR_A 3POR_A 1PRN_A 6PRN_A 8PRN_A 1H6S_1 3PRN_A ....
Probab=65.69 E-value=80 Score=26.44 Aligned_cols=28 Identities=14% Similarity=0.191 Sum_probs=19.4
Q ss_pred ccccceeeEEEEeecCCCeEEEEEecCcc
Q 028082 143 LAKNSWDFAVSRKVYGDDMFRASYQTSSK 171 (214)
Q Consensus 143 ~~~nsWdfavs~k~~g~d~vratY~~~~k 171 (214)
...+.|.+++++++ +.-.+.+.|.....
T Consensus 247 ~~~~~~~~~~~Y~~-~~~~~~~~y~~~~~ 274 (311)
T PF13609_consen 247 SDQDAYYVGAAYTF-GKWTLYAGYGYSDS 274 (311)
T ss_dssp EEEEEEEEEEEEEE-TTEEEEEEEEEEEE
T ss_pred ccceEEEEEEEEEe-CCEEEEEEEEEEEc
Confidence 55667777777777 66777777765543
No 7
>TIGR01981 sufD FeS assembly protein SufD, group 1. This protein, SufD, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. SufB and SufD are homologous. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component.
Probab=61.85 E-value=54 Score=30.24 Aligned_cols=82 Identities=16% Similarity=0.243 Sum_probs=52.1
Q ss_pred eeeeecCCcccceEEEeecCceEEEEe----eCCCCCeeEEEeeeeee-------------cceeeeEEEeecCCCc-ee
Q 028082 37 DATVVNGPSLNGLALAVEKPGFFIVDY----NVPKKDFRFQFMNSVRV-------------ADKPLNLTYIHGRGDN-RT 98 (214)
Q Consensus 37 Datf~~GpsL~GL~L~vEKPGsF~iDy----~~~~~d~rFQFmnt~~V-------------~~k~lnlTY~H~~~~n-rT 98 (214)
...|++|..+..|+-.+++|.-..++| .++.++-+|..+|++.. .++|+.+.|+...+++ ..
T Consensus 44 ~lv~~~G~~~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~aln~a~~~~G~~i~v~~~~~~~~Pi~i~~~~~~~~~~~~ 123 (366)
T TIGR01981 44 RLVFVDGVIVPDLSDALPLHPELLEDLLDALAVLSDEDRFLALNAALFNDGTVLYVPKGVEVEEPIEIKFIGVGGEKNFV 123 (366)
T ss_pred eEEEECCEEecChhhhhccCcceEEeehhcccCcCCccHHHHHHHHHhCCeEEEEECCCCCcCCCEEEEEEEcCCCccce
Confidence 467889988888888888888888887 44545566766665422 5689999999864332 12
Q ss_pred EEeeEEEEeCCCceEEEEEe
Q 028082 99 ILEGTLVFDSANKVSANHVL 118 (214)
Q Consensus 99 ~ldgtl~~D~aNK~s~~y~~ 118 (214)
..-=-+++...-++++...+
T Consensus 124 ~~~~~i~v~~~s~~~iie~~ 143 (366)
T TIGR01981 124 HPRLLIIVEKGSKITVIERF 143 (366)
T ss_pred eeEEEEEECCCCEEEEEEEe
Confidence 22222344444555555444
No 8
>TIGR03503 conserved hypothetical protein TIGR03503. This set of conserved hypothetical protein has a phylogenetic range that closely matches that of TIGR03501, a putative C-terminal protein targeting signal.
Probab=55.13 E-value=1.2e+02 Score=29.20 Aligned_cols=39 Identities=23% Similarity=0.296 Sum_probs=36.7
Q ss_pred cCceEEEEeeCCCCCeeEEEeeeeeecceeeeEEEeecC
Q 028082 55 KPGFFIVDYNVPKKDFRFQFMNSVRVADKPLNLTYIHGR 93 (214)
Q Consensus 55 KPGsF~iDy~~~~~d~rFQFmnt~~V~~k~lnlTY~H~~ 93 (214)
.||-|.+.+-..++-+.=||-..+.|-..|++.+++-++
T Consensus 182 ~~G~Y~~~v~~~n~vF~R~~~q~v~V~p~Pi~~~~~~~~ 220 (374)
T TIGR03503 182 APGEYRPTYQSRNPVFLREVEQPVLVYPLPVSYTVIQSE 220 (374)
T ss_pred CCceEEEEEEEcCceEEEEEEEeEEEECCCeeEEEEccC
Confidence 899999999999999999999999999999999999875
No 9
>TIGR01782 TonB-Xanth-Caul TonB-dependent receptor. This model represents a family of TonB-dependent outer-membrane receptors which are found mainly in Xanthomonas and Caulobacter. These appear to represent the expansion of a paralogous family in that the 22 X. axonopodis (21 in X. campestris) and 18 C. crescentus sequences are more closely related to each other than any of the many TonB-dependent receptors found in other species. In fact, the Crescentus and Xanthomonas sequences are inseparable on a phylogenetic tree using a PAM-weighted neighbor-joining method, indicating that one of the two genuses may have acquired this set of receptors from the other. The mechanism by which this family is shared between Xanthomonas, a gamma proteobacterial plant pathogen and Caulobacter, an alpha proteobacterial aquatic organism is unclear.
Probab=52.40 E-value=81 Score=31.45 Aligned_cols=107 Identities=22% Similarity=0.242 Sum_probs=56.1
Q ss_pred eeecCC---cccceEEEeecCceEEEEeeCCCCCeeEEEeeeeeecceeeeEEEeecCCCcee----EEeeEEEEeCCCc
Q 028082 39 TVVNGP---SLNGLALAVEKPGFFIVDYNVPKKDFRFQFMNSVRVADKPLNLTYIHGRGDNRT----ILEGTLVFDSANK 111 (214)
Q Consensus 39 tf~~Gp---sL~GL~L~vEKPGsF~iDy~~~~~d~rFQFmnt~~V~~k~lnlTY~H~~~~nrT----~ldgtl~~D~aNK 111 (214)
+++|++ .+.|+-|.+.++=.|+ |. +++...+ ..|+||+|++.+.-. .-+-.|.-=|.+.
T Consensus 680 ~~~N~~~~~~~~G~El~~~~~~~~l-----p~------~~~~l~~---~~n~T~~~s~~~~~~~~~~~~~~~l~~~p~~~ 745 (845)
T TIGR01782 680 RPVNGGKAGKIRGVELGYQQTFDFL-----PG------PLSGFGV---QANYTYVDSEADPSVDGVQRRKLPLPGLSKNT 745 (845)
T ss_pred EeeeCCCCcEEEEEEEEEEEEcccC-----Cc------cccCcEE---EEEEEEEccccccccCCCCccccccCCCCccc
Confidence 455665 2677777665432222 11 2344445 778899998644211 0011233345555
Q ss_pred eE--EEEEecCCCeeEEEEEEeCCeeeE-------EeeccccccceeeEEEEeecCC
Q 028082 112 VS--ANHVLGSGNCKLKYTYVHGGLTTF-------EQWYDLAKNSWDFAVSRKVYGD 159 (214)
Q Consensus 112 ~s--~~y~~~s~~c~lKY~YvH~g~tt~-------EP~yd~~~nsWdfavs~k~~g~ 159 (214)
+. +.|..+.=..+|.|.|+-.-+..+ ++.+--+-..||+.+++++.++
T Consensus 746 ~n~~l~Y~~~~~~~~l~~~y~~~~~~~~~~~~~~~~~~~~~~y~~lDl~~sy~~~~~ 802 (845)
T TIGR01782 746 ANATLYYEKGGFSARLSYNYRSDYLLDVGGSNINRLDRYVDPRGQLDLSASYQVSDH 802 (845)
T ss_pred EEEEEEEECCCEEEEEEEEeechhhhhcccccccccccccccceEEEEEEEEecCCC
Confidence 43 445544344666777765432221 2333444567999999998644
No 10
>PF10082 DUF2320: Uncharacterized protein conserved in bacteria (DUF2320); InterPro: IPR018759 This domain has no known function.
Probab=51.10 E-value=1.8e+02 Score=25.88 Aligned_cols=110 Identities=19% Similarity=0.179 Sum_probs=62.0
Q ss_pred eeeEEEeec---CCCceeEEeeEEEEeC--CCceEEEEEecC--CC--eeEEEEEEeCCe--------e-eEEeeccccc
Q 028082 84 PLNLTYIHG---RGDNRTILEGTLVFDS--ANKVSANHVLGS--GN--CKLKYTYVHGGL--------T-TFEQWYDLAK 145 (214)
Q Consensus 84 ~lnlTY~H~---~~~nrT~ldgtl~~D~--aNK~s~~y~~~s--~~--c~lKY~YvH~g~--------t-t~EP~yd~~~ 145 (214)
.++..|.+. ++.-.++....++-+| .|-+++.|.++. +. -.+++.|.+-.- + ..-.-.|.-.
T Consensus 98 ~~~~~~~~~~e~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~Y~~~~~~~g~~~~~~~~d~~~ 177 (381)
T PF10082_consen 98 DLGGSYRRGHEPRGSGDTFGGSDVQDDPVERNTFSASYGYGARFGRGRLSLGAGYDRLRYDNARDSDGTTISTSDRDRDE 177 (381)
T ss_pred EEEEEEEEEeccCCCCccccccccccCceEEEEEEEEEEEEEEcCCEEEEEEEEEEEEEEecccccCCccccccccccce
Confidence 455566554 3444444433445555 688888888853 22 445555544211 1 1112235555
Q ss_pred cceeeEEEEeecCCCeEEE-------EEe-------------cCcceEEEEEeeCCCCCcceEEEEee
Q 028082 146 NSWDFAVSRKVYGDDMFRA-------SYQ-------------TSSKALALEWSRNSKINGDFKIQAAL 193 (214)
Q Consensus 146 nsWdfavs~k~~g~d~vra-------tY~-------------~~~k~lgleWsr~sk~~G~fKv~a~~ 193 (214)
......+.+++.+.-.+-+ .|+ ...-.+|++|.-..|..|.++|....
T Consensus 178 ~~~~~~~~Y~~~p~~~~~~~~~~~~~~Yd~~~~~~~~~rDs~~~~~~~G~~~~~t~~~~g~~~~Gy~~ 245 (381)
T PF10082_consen 178 YTAGARLGYRLSPGTSLFVEVRYTDRDYDNRADPNGSSRDSTGYEVLAGVSWDLTGKTRGEAKVGYQR 245 (381)
T ss_pred eEEEEEEEEecCCCcEEEEEEEEeEEEcccccCcccccccCCceEEEEEEEEcccCcEEEEEEEEEEE
Confidence 5666666666555444422 344 12335899999999999999987643
No 11
>cd07305 Porin3_Tom40 Translocase of outer mitochondrial membrane 40 (Tom40). Tom40 forms a channel in the mitochondrial outer membrane with a pore about 1.5 to 2.5 nanometers wide. It functions as a transport channel for unfolded protein chains and forms a complex with Tom5, Tom6, Tom7, and Tom22. The primary receptors Tom20 and Tom70 recruit the unfolded precursor protein from the mitochondrial-import stimulating factor (MSF) or cytosolic Hsc70. The precursor passes through the Tom40 channel and through another channel in the inner membrane, formed by Tim23, to be finally translocated into the mitochondrial matrix. The process depends on a proton motive force across the inner membrane and requires a contact site where the outer and inner membranes come close. Tom40 is also involved in inserting outer membrane proteins into the membrane, most likely not via a lateral opening in the pore, but by transfering precursor proteins to an outer membrane sorting and assembly machinery.
Probab=44.56 E-value=2.2e+02 Score=25.04 Aligned_cols=141 Identities=17% Similarity=0.198 Sum_probs=84.2
Q ss_pred eEEEEeeCCCCCeeEEEeeeeee-cceeeeEEEeecCCCceeEEeeEEEEe--CCCceE-----EEEEecC-------CC
Q 028082 58 FFIVDYNVPKKDFRFQFMNSVRV-ADKPLNLTYIHGRGDNRTILEGTLVFD--SANKVS-----ANHVLGS-------GN 122 (214)
Q Consensus 58 sF~iDy~~~~~d~rFQFmnt~~V-~~k~lnlTY~H~~~~nrT~ldgtl~~D--~aNK~s-----~~y~~~s-------~~ 122 (214)
-|.+||.-+....-+.-.|-.-+ ..-.+...|.|+-.+ +..|=+.+.++ |.++.+ ++|.-+. ++
T Consensus 109 q~~~dy~g~d~t~~l~~~n~~~~~~sg~~~~~ylq~vt~-~l~lG~E~~~~~~~~~~~~~~~~~~rY~~~d~~~s~~l~~ 187 (279)
T cd07305 109 QLELDYRGDDFTASLKLANPDILNETGIYVASYLQSVTP-KLALGGELVYQRVPGNGISVLSYAARYTAGNWIASGQLGA 187 (279)
T ss_pred EEEEEEcCCceEEEEEEeCCCcccccEEEEEEEEEEccC-cEEEEEEEEEEEcCCCCceeEEEEEEEccCCEEEEEEEcC
Confidence 35566655444333333332100 113567889997544 88889999999 777655 4454111 23
Q ss_pred -eeEEEEEEeC---Ce-eeEEeeccccccceeeEE--EEeecCCCeEEEEEecCcceEEEEEeeCCCCCcceEEEEeeec
Q 028082 123 -CKLKYTYVHG---GL-TTFEQWYDLAKNSWDFAV--SRKVYGDDMFRASYQTSSKALALEWSRNSKINGDFKIQAALNL 195 (214)
Q Consensus 123 -c~lKY~YvH~---g~-tt~EP~yd~~~nsWdfav--s~k~~g~d~vratY~~~~k~lgleWsr~sk~~G~fKv~a~~~L 195 (214)
+.++=||.|. .+ .-.|=.|++.++...+.+ .+.+. +-++|+..++.. .+++-|.+.-...=.+-+++.+|.
T Consensus 188 ~~~l~asY~~kvs~~l~lG~el~~~~~~~es~~tvg~~y~~~-~~~~k~~ids~g-~v~~~~e~~l~~~~~l~ls~~~d~ 265 (279)
T cd07305 188 QGGLHLSYYRKLSDKLQLGVELELNLRTRESTATLGYQYDFR-QSRFRGSIDSNG-KVSAVLEKRLPLPLSLLLSGELNH 265 (279)
T ss_pred CCeEEEEEEEEcccceEeeeeeeecccCCceeEEEEEEEEcC-CCEEEEEEcCCC-EEEEEEEEecCCCeEEEEEEEEcc
Confidence 7888899887 11 334556666666555555 45444 778899999877 678888766544433445555554
Q ss_pred chhcCCCe
Q 028082 196 AEELRVPK 203 (214)
Q Consensus 196 ~d~~K~pk 203 (214)
. .+.+|
T Consensus 266 ~--~~~~k 271 (279)
T cd07305 266 V--KNDYK 271 (279)
T ss_pred c--CCcce
Confidence 2 35565
No 12
>smart00159 PTX Pentraxin / C-reactive protein / pentaxin family. This family form a doscoid pentameric structure. Human serum amyloid P demonstrates calcium-mediated ligand-binding.
Probab=42.15 E-value=1.7e+02 Score=24.53 Aligned_cols=72 Identities=15% Similarity=0.105 Sum_probs=45.0
Q ss_pred CCcccceEEEeecCceEEEEeeCCCCCeeEEEeeeeeecc-eeeeEEEeecCCCceeEEeeEEEEeCCCceEEEEEecC
Q 028082 43 GPSLNGLALAVEKPGFFIVDYNVPKKDFRFQFMNSVRVAD-KPLNLTYIHGRGDNRTILEGTLVFDSANKVSANHVLGS 120 (214)
Q Consensus 43 GpsL~GL~L~vEKPGsF~iDy~~~~~d~rFQFmnt~~V~~-k~lnlTY~H~~~~nrT~ldgtl~~D~aNK~s~~y~~~s 120 (214)
+..-+.|-+-.+++|.|.+-. +.+.+.+. ....-.+ .-|-+||.+..+.-+.++||.+. ...-++..|.+.+
T Consensus 56 ~~~~ne~~~~~~~~~~~~l~i--~g~~~~~~--~~~~~g~W~hvc~tw~~~~g~~~lyvnG~~~--~~~~~~~g~~i~~ 128 (206)
T smart00159 56 KGQDNELLLYKEKQGEYSLYI--GGKKVQFP--VPESDGKWHHICTTWESSSGIAELWVDGKPG--VRKGLAKGYTVKP 128 (206)
T ss_pred CCCCCeEEEEEcCCcEEEEEE--cCeEEEec--ccccCCceEEEEEEEECCCCcEEEEECCEEc--ccccccCCcEECC
Confidence 333456666677888777654 34433332 1222111 45788999988999999999986 4444566666664
No 13
>TIGR01997 sufA_proteo FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria.
Probab=41.31 E-value=43 Score=25.61 Aligned_cols=33 Identities=27% Similarity=0.467 Sum_probs=22.6
Q ss_pred cceEEEeecCc----eEEEE--eeCCCCCeeEEEeeeeee
Q 028082 47 NGLALAVEKPG----FFIVD--YNVPKKDFRFQFMNSVRV 80 (214)
Q Consensus 47 ~GL~L~vEKPG----sF~iD--y~~~~~d~rFQFmnt~~V 80 (214)
.||++.|+..| +|.++ -++...|..|++ +.++|
T Consensus 24 ~~lRi~v~~~GC~G~~y~~~l~~~~~~~D~v~~~-~g~~v 62 (107)
T TIGR01997 24 VGIRLGVKKTGCAGMEYVLDLVSEPKKDDDLIEH-DGAKV 62 (107)
T ss_pred cEEEEEEECCCCCCcEEEeeecCCCCCCCEEEec-CCEEE
Confidence 38999999876 34454 356678888885 55554
No 14
>PF06727 DUF1207: Protein of unknown function (DUF1207); InterPro: IPR009599 This family consists of a number of hypothetical bacterial proteins of around 410 residues in length, which seem to be specific to Chlamydia species. The function of this family is unknown.
Probab=40.37 E-value=1.8e+02 Score=27.68 Aligned_cols=111 Identities=18% Similarity=0.225 Sum_probs=67.2
Q ss_pred CCcccceEEEeecCceEEEEeeCCCCCeeEEEeeeeeecceeeeEEEeecCCCceeEEeeEEEEeCCCceEEEEEecCCC
Q 028082 43 GPSLNGLALAVEKPGFFIVDYNVPKKDFRFQFMNSVRVADKPLNLTYIHGRGDNRTILEGTLVFDSANKVSANHVLGSGN 122 (214)
Q Consensus 43 GpsL~GL~L~vEKPGsF~iDy~~~~~d~rFQFmnt~~V~~k~lnlTY~H~~~~nrT~ldgtl~~D~aNK~s~~y~~~s~~ 122 (214)
+....|+-+|||---...+|-+-+..|+ +|+-=+.+- ++||- .++.|++-++---.
T Consensus 137 ~~~~~~~q~gl~~g~fs~F~l~~~~~~l----vnaDy~vgi--~~T~r------------------~~~fS~R~R~yHiS 192 (338)
T PF06727_consen 137 SRFAEGWQFGLQGGVFSRFNLDAPSSDL----VNADYIVGI--PLTFR------------------RGEFSARFRLYHIS 192 (338)
T ss_pred CCccccEEEEeeceeecccCCCCccccc----cccceEEee--eeeee------------------ecCceEEEEEEEee
Confidence 4567899999998444444444444432 555333332 22332 34566666665556
Q ss_pred eeEEEEEEeCCeeeEEeeccccccceeeEEEEeecCCCeEEEEEe----c-------CcceEEEEEe
Q 028082 123 CKLKYTYVHGGLTTFEQWYDLAKNSWDFAVSRKVYGDDMFRASYQ----T-------SSKALALEWS 178 (214)
Q Consensus 123 c~lKY~YvH~g~tt~EP~yd~~~nsWdfavs~k~~g~d~vratY~----~-------~~k~lgleWs 178 (214)
.+|.+-|....++.|| .+++.-|.-++.+|+.+..+-+|=+-|+ + .+=+.|+||.
T Consensus 193 SHlGDEfll~~~~~~~-r~n~S~E~l~l~~S~~~~P~lRvYgG~gyl~~~~p~~~~p~~~Q~GvE~r 258 (338)
T PF06727_consen 193 SHLGDEFLLRNLPNFE-RFNYSREFLDLFLSYDFTPNLRVYGGYGYLFHTDPSEIKPWSFQAGVEYR 258 (338)
T ss_pred ccccchhhhccCCCCC-CcccChhhheeEEEeecCCCEEEEeeeeEEEEcCCCCCCCcEEEeeEEEc
Confidence 6777777766667776 5789999999998887755544444333 1 2235677777
No 15
>PF13715 DUF4480: Domain of unknown function (DUF4480)
Probab=40.21 E-value=1.3e+02 Score=21.15 Aligned_cols=35 Identities=26% Similarity=0.547 Sum_probs=22.5
Q ss_pred eEEEEEEecCceEEEeEeeeeeeecCCcccceEEEeecCceEEEEeeCCCCCeeEEE
Q 028082 18 AAATVAFNAGDVKLRASLTDATVVNGPSLNGLALAVEKPGFFIVDYNVPKKDFRFQF 74 (214)
Q Consensus 18 a~atv~~~aGD~klrAs~TDatf~~GpsL~GL~L~vEKPGsF~iDy~~~~~d~rFQF 74 (214)
.-|+|.+.-++ ..+.||+ -|.|.|+ +|.++..++|
T Consensus 16 ~~a~V~~~~~~---~~~~Td~-----------------~G~F~i~--~~~g~~~l~i 50 (88)
T PF13715_consen 16 PGATVYLKNTK---KGTVTDE-----------------NGRFSIK--LPEGDYTLKI 50 (88)
T ss_pred cCeEEEEeCCc---ceEEECC-----------------CeEEEEE--EcCCCeEEEE
Confidence 35666666555 5566665 6889998 5566655555
No 16
>KOG3126 consensus Porin/voltage-dependent anion-selective channel protein [Inorganic ion transport and metabolism]
Probab=39.38 E-value=3.2e+02 Score=25.40 Aligned_cols=55 Identities=24% Similarity=0.373 Sum_probs=39.2
Q ss_pred eccccccceeeEEEEeec-CCCeEEEEEecCcce----EEEEEeeCCCCCcceEEEEeeec
Q 028082 140 WYDLAKNSWDFAVSRKVY-GDDMFRASYQTSSKA----LALEWSRNSKINGDFKIQAALNL 195 (214)
Q Consensus 140 ~yd~~~nsWdfavs~k~~-g~d~vratY~~~~k~----lgleWsr~sk~~G~fKv~a~~~L 195 (214)
.+-++=..||+.+.-.+- +.+..+++||.-..- ..++|++-++ .-.|-|.+.-.|
T Consensus 167 n~~lgy~~~d~~l~~~~nn~~~~~~s~yq~v~~~~~~~~~~~~~~~~~-~~~~~igt~Y~l 226 (281)
T KOG3126|consen 167 NAALGYTTEDFTLHLNLNNGTEFLASIYQRVNEKLETGANAEWIAGSS-NTRFTIGTKYAL 226 (281)
T ss_pred EEEEEeecCCcEEEEEecccchhhhhhhhhhcchheeeeeEEEeecCC-ccEEEEEEEecc
Confidence 334455778888888885 677888899876654 6799999987 445666655544
No 17
>COG1629 CirA Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]
Probab=38.73 E-value=23 Score=31.87 Aligned_cols=67 Identities=18% Similarity=0.035 Sum_probs=44.9
Q ss_pred ccccccceeeEEEEeecCCCeEEEEEecCcceEEEEEeeCCCCCcceEEEEeeecchhcCCCeeEEeeeccccC
Q 028082 141 YDLAKNSWDFAVSRKVYGDDMFRASYQTSSKALALEWSRNSKINGDFKIQAALNLAEELRVPKLTAESTWNFEM 214 (214)
Q Consensus 141 yd~~~nsWdfavs~k~~g~d~vratY~~~~k~lgleWsr~sk~~G~fKv~a~~~L~d~~K~pkl~aEktWn~e~ 214 (214)
.....-+|.+.++++..++..++++|...-+.-++......... .+... -..-.|.|-.|+.|++|+
T Consensus 500 ~~~~~~~p~~~~~~~~~~~~~~~~~~s~~~r~p~~~~~~~~~~~-----~~~~~--~~~gn~~Lkpe~s~~~e~ 566 (768)
T COG1629 500 RSDTAFSPSLGLVYDPTPDLSLYASYSRGFRPPSSDELYASFGT-----SADGG--ISLGNPNLKPETADQYEL 566 (768)
T ss_pred ccCceecceeEEEEecCCCceEEEEEeccccCCCcccccccccc-----cCCCc--cccCCCCCCCcccceeEE
Confidence 34456679999999999999999999887765554433322211 11100 244568888999999884
No 18
>PF07532 Big_4: Bacterial Ig-like domain (group 4); InterPro: IPR011081 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.
Probab=38.65 E-value=70 Score=21.87 Aligned_cols=36 Identities=11% Similarity=0.421 Sum_probs=26.3
Q ss_pred CCeEEEEEecCcc-eEEEEEeeCCCC----CcceEEEEeee
Q 028082 159 DDMFRASYQTSSK-ALALEWSRNSKI----NGDFKIQAALN 194 (214)
Q Consensus 159 ~d~vratY~~~~k-~lgleWsr~sk~----~G~fKv~a~~~ 194 (214)
-..|++.|...+. .+.++|...+.. -|.|.|...+.
T Consensus 17 P~~V~v~~~dGs~~~~~V~W~~~~~~~~~~~G~y~v~G~v~ 57 (59)
T PF07532_consen 17 PETVTVTYSDGSTEEVPVTWDPIDPYDYNKPGTYTVTGTVE 57 (59)
T ss_pred CCEEEEEECCCCEEEEEeEeCCCChhhccCCEEEEEEEEEe
Confidence 3578888887766 899999953222 48999988753
No 19
>PF13609 Porin_4: Gram-negative porin; PDB: 2FGR_A 2FGQ_X 1E54_A 2POR_A 3POR_A 1PRN_A 6PRN_A 8PRN_A 1H6S_1 3PRN_A ....
Probab=36.88 E-value=2.5e+02 Score=23.48 Aligned_cols=89 Identities=16% Similarity=0.099 Sum_probs=53.5
Q ss_pred EEEeeeeeecceeeeEEEeecCCCcee-EEeeEEEEeCCCceEEEEEecCCCeeEEEEEEeCCeeeEEeeccccccceee
Q 028082 72 FQFMNSVRVADKPLNLTYIHGRGDNRT-ILEGTLVFDSANKVSANHVLGSGNCKLKYTYVHGGLTTFEQWYDLAKNSWDF 150 (214)
Q Consensus 72 FQFmnt~~V~~k~lnlTY~H~~~~nrT-~ldgtl~~D~aNK~s~~y~~~s~~c~lKY~YvH~g~tt~EP~yd~~~nsWdf 150 (214)
+.+--...+.+=.|...|.|...++.. ..|.... .+.+.|.++ +-++.-.|.|... ....+...+.|.+
T Consensus 218 ~~~ga~y~~~~~~l~a~y~~~~~~~~~~~~~~~~~-----~~~~~Y~~~--~~~~~~~y~~~~~---~~~~~~~~~~~~~ 287 (311)
T PF13609_consen 218 WGVGASYNFGGFTLGAEYGQADNDGSGGDSDQDAY-----YVGAAYTFG--KWTLYAGYGYSDS---ADGSDDDATSYAV 287 (311)
T ss_dssp EEEEEEEECSSEEEEEEEEEEEEECCCCCEEEEEE-----EEEEEEEET--TEEEEEEEEEEEE----GCCTEEEEEEEE
T ss_pred EEeeEEEEECcEEEEEEEEEEEecCccccccceEE-----EEEEEEEeC--CEEEEEEEEEEEc---cCCCCCCeEEEEE
Confidence 344444444444566667764332221 1222222 278888884 4445445543321 3366777889999
Q ss_pred EEEEeecCCCeEEEEEecCc
Q 028082 151 AVSRKVYGDDMFRASYQTSS 170 (214)
Q Consensus 151 avs~k~~g~d~vratY~~~~ 170 (214)
++.|+|..+=++.+.|+...
T Consensus 288 g~~Y~~~~~~~~~a~y~~~~ 307 (311)
T PF13609_consen 288 GVDYDFSKNTSLYAEYAYTD 307 (311)
T ss_dssp EEEEEEETTEEEEEEEEEEE
T ss_pred EEEEEcCCCEEEEEEEEEEE
Confidence 99999999999999998643
No 20
>PF06577 DUF1134: Protein of unknown function (DUF1134); InterPro: IPR008325 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=36.17 E-value=44 Score=28.96 Aligned_cols=55 Identities=20% Similarity=0.398 Sum_probs=44.4
Q ss_pred eEEEEEEecCceEEEeEeeeeeeecCCcccceEEEeecCceEEEEeeCCCCCeeEE
Q 028082 18 AAATVAFNAGDVKLRASLTDATVVNGPSLNGLALAVEKPGFFIVDYNVPKKDFRFQ 73 (214)
Q Consensus 18 a~atv~~~aGD~klrAs~TDatf~~GpsL~GL~L~vEKPGsF~iDy~~~~~d~rFQ 73 (214)
-++=|+..-|.|-.|-.-.=--|-.|||| |+.+|-.--=.|++.||+|.-+--||
T Consensus 50 ~~~GlrYGeG~L~~k~~g~~~vyWqGPSi-G~D~G~~~~r~~~LVYnL~~~~~iy~ 104 (160)
T PF06577_consen 50 FVVGLRYGEGTLYTKNAGQHKVYWQGPSI-GFDFGGNGSRVFMLVYNLPDPDDIYQ 104 (160)
T ss_pred EEEEEEecccEEEEcCCCeeEEEEeCCce-eEeecCCceEEEEEEEcCCCHHHHhh
Confidence 37778888888888876554478899998 78888887778999999999887766
No 21
>cd01347 ligand_gated_channel TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel. Energy (proton-motive force) and TonB-dependent conformational alteration of channel (parts of plug, and loops 7 and 8) allow passage of ligand. FepA residues 12-18 form the TonB box, which mediates the interaction with the TonB-containing inner membrane complex. TonB preferentially interacts with ligand-bound receptors. Transport thru the channel may resemble passage thru an air lock. In this model, ligand binding leads to closure of the extracellular end of pore, then a TonB-mediated signal facillitates opening of the interior side of pore, deforming the N-terminal plug and allowing passage of the ligand to the periplasm. Such a mechanism would prevent the free diffusion of small molecules thru the pore.
Probab=34.20 E-value=3.4e+02 Score=24.25 Aligned_cols=31 Identities=19% Similarity=0.123 Sum_probs=24.9
Q ss_pred cccccceeeEEEEeecCCCeEEEEEecCcce
Q 028082 142 DLAKNSWDFAVSRKVYGDDMFRASYQTSSKA 172 (214)
Q Consensus 142 d~~~nsWdfavs~k~~g~d~vratY~~~~k~ 172 (214)
+...=++.+++++++.+..+++++|....+.
T Consensus 377 ~~~~~~p~~~~~y~~~~~~~~~~~~~~~~~~ 407 (635)
T cd01347 377 SYSHWSPSLGLVYKLTDGLSLYASYSQGFRA 407 (635)
T ss_pred ccceeccceeEEEEcCCCEEEEEEeeeeecC
Confidence 4455578899999999999999999876543
No 22
>PF14352 DUF4402: Domain of unknown function (DUF4402)
Probab=33.84 E-value=2.3e+02 Score=22.02 Aligned_cols=60 Identities=18% Similarity=0.285 Sum_probs=36.1
Q ss_pred CceEEEEeeCCCCCeeEEEeeeeeec----ceeeeEEEee------------cCCCceeEEeeEEEEeCCCceEEEEE
Q 028082 56 PGFFIVDYNVPKKDFRFQFMNSVRVA----DKPLNLTYIH------------GRGDNRTILEGTLVFDSANKVSANHV 117 (214)
Q Consensus 56 PGsF~iDy~~~~~d~rFQFmnt~~V~----~k~lnlTY~H------------~~~~nrT~ldgtl~~D~aNK~s~~y~ 117 (214)
||.|.|.- -|++.+.+++..++.+. +..+.++-.- ..+...--|-|+|.++ +|...+.|.
T Consensus 46 ~a~f~V~G-~~~~~v~it~p~~~~l~~~~g~~~~~v~~~~~~~~~~~~~~~~~~g~~~~~VGGtL~v~-~~~~~G~Ys 121 (130)
T PF14352_consen 46 PAEFTVSG-EPGSNVSITLPSTITLTNSNGGNTMTVTNFTGNSSGSSTTTLDTGGSATFNVGGTLNVP-ANQAAGTYS 121 (130)
T ss_pred CEEEEEEc-CCCCEEEEEecCCEEEecCCCCceEEEEeeecccccccceEecCCCcEEEEEEEEEEcC-CCCCCeEEE
Confidence 99999999 66788888887555552 2333333222 1134444566777666 455566665
No 23
>PRK13285 flagellar assembly protein FliW; Provisional
Probab=33.51 E-value=91 Score=25.86 Aligned_cols=71 Identities=17% Similarity=0.271 Sum_probs=50.7
Q ss_pred ceEEEeecCceEEEEeeCC-----------CCCeeEEEeeeeeecceeeeEEEeecCCCcee-EEeeEEEEeCCCceEEE
Q 028082 48 GLALAVEKPGFFIVDYNVP-----------KKDFRFQFMNSVRVADKPLNLTYIHGRGDNRT-ILEGTLVFDSANKVSAN 115 (214)
Q Consensus 48 GL~L~vEKPGsF~iDy~~~-----------~~d~rFQFmnt~~V~~k~lnlTY~H~~~~nrT-~ldgtl~~D~aNK~s~~ 115 (214)
+|+|-|=.|..|.-||++. +..--...++.+.+.+. .+..| =|=|=++|++.|+...-
T Consensus 55 ~~~F~vi~P~~~~~dY~~~l~~~~~~~L~i~~~~dv~v~~iVti~~~----------~~~~T~NL~APIViN~~~~~g~Q 124 (148)
T PRK13285 55 DLAFVVIDPFNFFPDYEFDLDEEELELLGIESEEDVLVLVIVTIPED----------PEKITANLQAPIIINKKKRKGKQ 124 (148)
T ss_pred ceEEEEeCHHHhCCCCccccCHHHHHhcCCCChhheEEEEEEEcCCC----------cccceEeecCCEEEECCCCEEEE
Confidence 5899999999999999965 22334456777766432 22323 25677999999999999
Q ss_pred EEecCCCeeEEEE
Q 028082 116 HVLGSGNCKLKYT 128 (214)
Q Consensus 116 y~~~s~~c~lKY~ 128 (214)
..+......++|-
T Consensus 125 vIl~~~~y~~r~p 137 (148)
T PRK13285 125 VILDNEKYSTKHP 137 (148)
T ss_pred EEeCCCCCccccc
Confidence 9998766555553
No 24
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=32.94 E-value=80 Score=27.15 Aligned_cols=32 Identities=31% Similarity=0.597 Sum_probs=24.8
Q ss_pred ceEEEeecCc----eEEEEe----eCCCCCeeEEEeeeeee
Q 028082 48 GLALAVEKPG----FFIVDY----NVPKKDFRFQFMNSVRV 80 (214)
Q Consensus 48 GL~L~vEKPG----sF~iDy----~~~~~d~rFQFmnt~~V 80 (214)
||+++|++.| +|-++| ++...|..|++ +.++|
T Consensus 23 ~LRv~V~~gGCsG~~Y~l~~~~~~~~~~~D~v~e~-~g~~v 62 (190)
T TIGR03341 23 GIRVFVVNPGTPYAECCVSYCPPDEVEPSDIKLEF-NGFSA 62 (190)
T ss_pred eEEEEEECCccCCceeeeEEcccCCCCCCCEEEEe-CCEEE
Confidence 7999999999 456666 45678899986 66666
No 25
>PF00677 Lum_binding: Lumazine binding domain; InterPro: IPR001783 The following proteins have been shown [, ] to be structurally and evolutionary related: Riboflavin synthase alpha chain (2.5.1.9 from EC) (RS-alpha) (gene ribC in Escherichia coli, ribB in Bacillus subtilis and Photobacterium leiognathi, RIB5 in yeast. This enzyme synthesises riboflavin from two moles of 6,7- dimethyl-8-(1'-D-ribityl)lumazine (Lum), a pteridine-derivative. Photobacterium phosphoreum lumazine protein (LumP) (gene luxL). LumP is a protein that modulates the colour of the bioluminescence emission of bacterial luciferase. In the presence of LumP, light emission is shifted to higher energy values (shorter wavelength). LumP binds non-covalently to 6,7-dimethyl-8-(1'-D-ribityl)lumazine. Vibrio fischeri yellow fluorescent protein (YFP) (gene luxY). Like LumP, YFP modulates light emission but towards a longer wavelength. YFP binds non-covalently to FMN. These proteins seem to have evolved from the duplication of a domain of about 100 residues. In its C-terminal section, this domain contains a conserved motif [KR]-V-N-[LI]-E which has been proposed to be the binding site for lumazine (Lum) and some of its derivatives. RS-alpha which binds two molecules of Lum has two perfect copies of this motif, while LumP which binds one molecule of Lum, has a Glu instead of Lys/Arg in the first position of the second copy of the motif. Similarly, YFP, which binds to one molecule of FMN, also seems to have a potentially dysfunctional binding site by substitution of Gly for Glu in the last position of the first copy of the motif.; GO: 0004746 riboflavin synthase activity, 0009231 riboflavin biosynthetic process; PDB: 3DDY_A 1KZL_A 3A3G_B 3A35_B 3A3B_B 1I8D_C 1PKV_B 1HZE_B 1I18_B.
Probab=32.76 E-value=1.3e+02 Score=22.45 Aligned_cols=48 Identities=25% Similarity=0.406 Sum_probs=31.6
Q ss_pred EEEEEEecCceEEEeEeeeeeee---cCC--cccceEEEee--cCceEEEEeeCC
Q 028082 19 AATVAFNAGDVKLRASLTDATVV---NGP--SLNGLALAVE--KPGFFIVDYNVP 66 (214)
Q Consensus 19 ~atv~~~aGD~klrAs~TDatf~---~Gp--sL~GL~L~vE--KPGsF~iDy~~~ 66 (214)
+..+.-.....+++..+.+.-|. -|. ++||++|.|. .+..|.+|.-++
T Consensus 10 I~~i~~~~~~~~~~i~~~~~~~~~~~~g~SIavnGvcLTV~~~~~~~f~~~l~~e 64 (85)
T PF00677_consen 10 IISIEKNGDSQRLRIEIPDKILSDLKIGGSIAVNGVCLTVTDINEDWFEVDLIPE 64 (85)
T ss_dssp EEEEEEESSEEEEEEEESTGGGGTG-TTSEEEETTEEEEEEEEETTEEEEEEEHH
T ss_pred EEEEEECCCCEEEEEEcCHHHHhhCccCcEEEECCeeeEEEEecCCEEEEechHH
Confidence 45555556777777777644332 233 4999999998 567777776544
No 26
>KOG1719 consensus Dual specificity phosphatase [Defense mechanisms]
Probab=32.46 E-value=4.6 Score=35.41 Aligned_cols=55 Identities=33% Similarity=0.419 Sum_probs=42.5
Q ss_pred CceEEEeEeeeeeeecCCcccceEEEeecCceEEEEeeCCCCCeeEEEeeeeeecceeeeEEEee---cCCCceeEEeeE
Q 028082 27 GDVKLRASLTDATVVNGPSLNGLALAVEKPGFFIVDYNVPKKDFRFQFMNSVRVADKPLNLTYIH---GRGDNRTILEGT 103 (214)
Q Consensus 27 GD~klrAs~TDatf~~GpsL~GL~L~vEKPGsF~iDy~~~~~d~rFQFmnt~~V~~k~lnlTY~H---~~~~nrT~ldgt 103 (214)
|==.|..+.+|-|| -|+++.|..||| |++...-+|| -+|.| +|++.+|++-|-
T Consensus 75 giE~L~i~T~D~~~--~Ps~~~i~~aVe-------------------Fi~k~asLGk---tvYVHCKAGRtRSaTvV~cY 130 (183)
T KOG1719|consen 75 GIEFLVIPTRDYTG--APSLENIQKAVE-------------------FIHKNASLGK---TVYVHCKAGRTRSATVVACY 130 (183)
T ss_pred cceeEEeccccccC--CCCHHHHHHHHH-------------------HHHhccccCC---eEEEEecCCCccchhhhhhh
Confidence 44467888999988 799999999886 6666666676 56999 568888988776
Q ss_pred EE
Q 028082 104 LV 105 (214)
Q Consensus 104 l~ 105 (214)
|+
T Consensus 131 Lm 132 (183)
T KOG1719|consen 131 LM 132 (183)
T ss_pred hh
Confidence 64
No 27
>PF10162 G8: G8 domain; InterPro: IPR019316 This entry represents a domain found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix [].
Probab=31.74 E-value=89 Score=24.63 Aligned_cols=29 Identities=34% Similarity=0.556 Sum_probs=20.3
Q ss_pred eeEEeeEEEEeC--CCceEEEEEecCCCeeE
Q 028082 97 RTILEGTLVFDS--ANKVSANHVLGSGNCKL 125 (214)
Q Consensus 97 rT~ldgtl~~D~--aNK~s~~y~~~s~~c~l 125 (214)
..+++|+|.||+ ..+|.+.|.+=.++++|
T Consensus 34 ~l~I~G~L~f~~~~~~~L~a~~I~V~~Gg~l 64 (125)
T PF10162_consen 34 SLIIGGTLIFDDDRDITLRAEYILVEGGGRL 64 (125)
T ss_pred EEEEEEEEEEccCCCCEEEEEEEEECCCCeE
Confidence 445699999998 56777777766554443
No 28
>PRK15216 putative fimbrial biosynthesis regulatory protein; Provisional
Probab=31.67 E-value=3.4e+02 Score=26.24 Aligned_cols=73 Identities=22% Similarity=0.313 Sum_probs=51.8
Q ss_pred eeEEEeecCCCceeEEeeEEEEeCCCceEEEEEecCCCeeEEEEEEeCCeeeEEeeccccccceeeEEEEeecCCCeEEE
Q 028082 85 LNLTYIHGRGDNRTILEGTLVFDSANKVSANHVLGSGNCKLKYTYVHGGLTTFEQWYDLAKNSWDFAVSRKVYGDDMFRA 164 (214)
Q Consensus 85 lnlTY~H~~~~nrT~ldgtl~~D~aNK~s~~y~~~s~~c~lKY~YvH~g~tt~EP~yd~~~nsWdfavs~k~~g~d~vra 164 (214)
=+|||+|. .++=.-++++.|.--....|.|+--.|.=-++- |-+||+ |.-| -|.-+|+||.
T Consensus 23 ~~it~~~~----~~i~~d~~~l~~~q~~~~~~~f~d~~c~~t~~v-----t~~~~s--------d~iv--g~~~~d~vkl 83 (340)
T PRK15216 23 ATLTNTKD----YTIQSDSLMLGGEESAIITNGFTDANCSNSDVV-----TKLETS--------DHII--GMGPNDSVKL 83 (340)
T ss_pred eEEeeccc----eEEecceEEeccceeeEeeccccccccccCcee-----eccCcc--------ceEE--eeCCCCeEEE
Confidence 36788875 444445599999999999999998889765543 778886 2221 2445777776
Q ss_pred EEecCcceEEEEEeeCCCC
Q 028082 165 SYQTSSKALALEWSRNSKI 183 (214)
Q Consensus 165 tY~~~~k~lgleWsr~sk~ 183 (214)
.|-+||..+.-+
T Consensus 84 -------kl~~~w~~~~~i 95 (340)
T PRK15216 84 -------KLKVEWQSSSAI 95 (340)
T ss_pred -------EEEEEEecCCce
Confidence 588999877654
No 29
>PF00167 FGF: Fibroblast growth factor; InterPro: IPR002348 The interleukin-1 (IL1) and heparin-binding growth factor (HBGF) families share low sequence similarity (about 25% []) but have very similar structures. Coupled with the Kunitz-type soybean trypsin inhibitors (STI), they form a structural superfamily. Despite their structural correspondence, however, they show no sequence similarity to the STI family. The crystal structures of interleukin-1 beta and HBGF1 have been solved, showing both families to have the same 12-stranded beta-sheet structure []; the beta-sheets are arranged in 3 similar lobes around a central axis, 6 strands forming an anti-parallel beta-barrel [, ]. The beta-sheets are generally well preserved and the crystal structures superimpose in these areas. The intervening loops are less well conserved - the loop between beta-strands 6 and 7 is slightly longer in interleukin-1 beta.; GO: 0008083 growth factor activity; PDB: 1AFC_F 1BAR_A 2P39_A 1EV2_D 2BFH_A 4FGF_A 1BAS_A 1BFG_A 1FQ9_B 1CVS_A ....
Probab=30.88 E-value=80 Score=24.34 Aligned_cols=50 Identities=16% Similarity=0.415 Sum_probs=43.5
Q ss_pred EEEEeCCCceEEEEEecCCCeeEEEEEEeCCeeeEEeeccccccceeeEEEEe
Q 028082 103 TLVFDSANKVSANHVLGSGNCKLKYTYVHGGLTTFEQWYDLAKNSWDFAVSRK 155 (214)
Q Consensus 103 tl~~D~aNK~s~~y~~~s~~c~lKY~YvH~g~tt~EP~yd~~~nsWdfavs~k 155 (214)
=|.+|...+|.++-.++. .|.++-.+..++-.++|-..+ .+.|-.|+.++
T Consensus 54 YLcmn~~G~ly~~~~~~~-~C~F~e~~~~n~y~~~~s~~~--~~~~yla~~~~ 103 (122)
T PF00167_consen 54 YLCMNKCGRLYGSKNFNK-DCVFREELLENGYNTYESAKY--GRGWYLAFNRR 103 (122)
T ss_dssp EEEEBTTSBEEEESSBTG-GGEEEEEEETTSEEEEEESTT--GTTEBCEBCTT
T ss_pred EEEECCCCeEccccccCC-CceEEEEEccCCEEEEEeccC--CccEEEEECCC
Confidence 378999999999988886 999999999999999998877 77888887663
No 30
>PF03168 LEA_2: Late embryogenesis abundant protein; InterPro: IPR004864 Different types of LEA proteins are expressed at different stages of late embryogenesis in higher plant seed embryos and under conditions of dehydration stress [, ]. The function of these proteins is unknown. ; PDB: 3BUT_A 1XO8_A 1YYC_A.
Probab=29.25 E-value=1.4e+02 Score=20.99 Aligned_cols=57 Identities=18% Similarity=0.243 Sum_probs=33.9
Q ss_pred EEEeecCceEEEEeeCCCCCeeEEEeeeeeecceeeeEEEeecCCCceeEEeeEEEEeCCC
Q 028082 50 ALAVEKPGFFIVDYNVPKKDFRFQFMNSVRVADKPLNLTYIHGRGDNRTILEGTLVFDSAN 110 (214)
Q Consensus 50 ~L~vEKPGsF~iDy~~~~~d~rFQFmnt~~V~~k~lnlTY~H~~~~nrT~ldgtl~~D~aN 110 (214)
+|.|++|..|-|.|+--. ..+. ++...|+.....=.+..+ +.+.+.++..+.++..+
T Consensus 1 ~l~v~NPN~~~i~~~~~~--~~v~-~~g~~v~~~~~~~~~~i~-~~~~~~v~~~v~~~~~~ 57 (101)
T PF03168_consen 1 TLSVRNPNSFGIRYDSIE--YDVY-YNGQRVGTGGSLPPFTIP-ARSSTTVPVPVSVDYSD 57 (101)
T ss_dssp EEEEEESSSS-EEEEEEE--EEEE-ESSSEEEEEEECE-EEES-SSCEEEEEEEEEEEHHH
T ss_pred CEEEECCCceeEEEeCEE--EEEE-ECCEEEECccccCCeEEC-CCCcEEEEEEEEEcHHH
Confidence 478899999888885333 2222 266777633333334444 56667788888887753
No 31
>cd01347 ligand_gated_channel TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel. Energy (proton-motive force) and TonB-dependent conformational alteration of channel (parts of plug, and loops 7 and 8) allow passage of ligand. FepA residues 12-18 form the TonB box, which mediates the interaction with the TonB-containing inner membrane complex. TonB preferentially interacts with ligand-bound receptors. Transport thru the channel may resemble passage thru an air lock. In this model, ligand binding leads to closure of the extracellular end of pore, then a TonB-mediated signal facillitates opening of the interior side of pore, deforming the N-terminal plug and allowing passage of the ligand to the periplasm. Such a mechanism would prevent the free diffusion of small molecules thru the pore.
Probab=28.43 E-value=4.3e+02 Score=23.62 Aligned_cols=74 Identities=9% Similarity=-0.098 Sum_probs=39.0
Q ss_pred eeeEEEeecCCCc--eeEEeeEEEEeCCCceEE--EEEec--CCCeeEEEEEEeCCeeeEE----eeccccccceeeEEE
Q 028082 84 PLNLTYIHGRGDN--RTILEGTLVFDSANKVSA--NHVLG--SGNCKLKYTYVHGGLTTFE----QWYDLAKNSWDFAVS 153 (214)
Q Consensus 84 ~lnlTY~H~~~~n--rT~ldgtl~~D~aNK~s~--~y~~~--s~~c~lKY~YvH~g~tt~E----P~yd~~~nsWdfavs 153 (214)
.++++|.|++-+. ...-+..+...|...+++ +|.+. .=++.+.|.|+.+...+.. ...--+-..+|+.++
T Consensus 506 ~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~dl~~~ 585 (635)
T cd01347 506 TGSYTYTDTEVKRTDGATTGNRLPGIPKHTANLGLDYELPDEGLTAGGGVRYRGKQYADTANGNNTVKVPGYTLVDLSAS 585 (635)
T ss_pred EEEEEEEeeecccccccccCCcCCCCCCeeEEEEEEEecCCCCeEEEEEEEEEcceeccccCCccceecCCcEEEeeEEE
Confidence 5667777775431 122233455667776666 45554 3345566666655322211 001123346888888
Q ss_pred Eeec
Q 028082 154 RKVY 157 (214)
Q Consensus 154 ~k~~ 157 (214)
+++.
T Consensus 586 y~~~ 589 (635)
T cd01347 586 YQFT 589 (635)
T ss_pred EEeC
Confidence 8886
No 32
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=27.93 E-value=95 Score=26.85 Aligned_cols=42 Identities=21% Similarity=0.331 Sum_probs=28.3
Q ss_pred cceEEEeecCc----eEEEEe----eCCCCCeeEEEeeeeeecceeeeEEE
Q 028082 47 NGLALAVEKPG----FFIVDY----NVPKKDFRFQFMNSVRVADKPLNLTY 89 (214)
Q Consensus 47 ~GL~L~vEKPG----sF~iDy----~~~~~d~rFQFmnt~~V~~k~lnlTY 89 (214)
.||+++|+++| ++-++| ++...|..|++ +.++|.=-+..+-|
T Consensus 23 ~~LRI~V~~gGCsG~~Y~~~~~~~~~~~~~D~v~e~-~gv~v~Vd~~S~~~ 72 (192)
T PRK11190 23 TQIRVFVINPGTPNAECGVSYCPPDAVEATDTELKF-DGFSAYVDELSAPF 72 (192)
T ss_pred ceEEEEEECCCcCCceeeeEEeecCCCCCCCEEEEe-CCEEEEECcchHhH
Confidence 48999999998 346666 34567888886 77777433433333
No 33
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=26.57 E-value=3.3e+02 Score=21.72 Aligned_cols=65 Identities=23% Similarity=0.442 Sum_probs=41.4
Q ss_pred eecCceEEEEeeCCCCCeeEEEeeeeeecceeeeEEEeecCCC-----ceeEEeeEEEEeCCCceEEEEEecCCCeeEEE
Q 028082 53 VEKPGFFIVDYNVPKKDFRFQFMNSVRVADKPLNLTYIHGRGD-----NRTILEGTLVFDSANKVSANHVLGSGNCKLKY 127 (214)
Q Consensus 53 vEKPGsF~iDy~~~~~d~rFQFmnt~~V~~k~lnlTY~H~~~~-----nrT~ldgtl~~D~aNK~s~~y~~~s~~c~lKY 127 (214)
+=+||| |.|++....++|+-... ++.+.+.|.=..++ ..-++.|.+ +..+.+.+.=.+- +|-=||
T Consensus 58 ~V~~gS--v~~~~~~~~~~F~i~D~----~~~i~V~Y~G~~Pd~F~eg~~VVv~G~~--~~~g~F~A~~lL~--KcpskY 127 (131)
T PF03100_consen 58 LVVEGS--VEYDPDGNTLTFTITDG----GKEIPVVYTGPLPDLFREGQGVVVEGRL--GEDGVFEATELLA--KCPSKY 127 (131)
T ss_dssp EEECTT--EEE-TTSSEEEEEEE-S----S-EEEEEEES--CTT--TTSEEEEEEEE--CCTSEEEEEEEEE--TS----
T ss_pred EEccCC--EEEcCCCCEEEEEEEEC----CcEEEEEECCCCCccccCCCeEEEEEEE--CCCCEEEEEEEEe--CCCCCC
Confidence 338998 88888888888887665 57799999886543 356889987 7777777765554 454444
No 34
>PF07443 HARP: HepA-related protein (HARP); InterPro: IPR010003 This entry represents a conserved region approximately 60 residues long within eukaryotic HepA-related protein (HARP). This exhibits single-stranded DNA-dependent ATPase activity, and is ubiquitously expressed in human and mouse tissues []. Family members may contain more than one copy of this region.; GO: 0004386 helicase activity, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0016568 chromatin modification, 0005634 nucleus
Probab=26.18 E-value=22 Score=25.72 Aligned_cols=14 Identities=29% Similarity=0.790 Sum_probs=12.2
Q ss_pred eccccccceeeEEE
Q 028082 140 WYDLAKNSWDFAVS 153 (214)
Q Consensus 140 ~yd~~~nsWdfavs 153 (214)
.||..+..|+|.++
T Consensus 22 ~YD~~Tr~W~F~L~ 35 (55)
T PF07443_consen 22 NYDPKTRKWNFSLE 35 (55)
T ss_pred ccCccceeeeeeHH
Confidence 69999999999853
No 35
>smart00089 PKD Repeats in polycystic kidney disease 1 (PKD1) and other proteins. Polycystic kidney disease 1 protein contains 14 repeats, present elsewhere such as in microbial collagenases.
Probab=25.51 E-value=2.3e+02 Score=19.41 Aligned_cols=26 Identities=31% Similarity=0.511 Sum_probs=15.0
Q ss_pred cCCcccce--EEEeecCceEEEEeeCCC
Q 028082 42 NGPSLNGL--ALAVEKPGFFIVDYNVPK 67 (214)
Q Consensus 42 ~GpsL~GL--~L~vEKPGsF~iDy~~~~ 67 (214)
+|..+.+- +...++||.|.|-..+-+
T Consensus 38 dg~~~~~~~~~~~y~~~G~y~v~l~v~n 65 (79)
T smart00089 38 DGTSSTGPTVTHTYTKPGTYTVTLTVTN 65 (79)
T ss_pred CCCccCCCCEEEEeCCCcEEEEEEEEEc
Confidence 44444443 444468998876655543
No 36
>PRK09840 catecholate siderophore receptor Fiu; Provisional
Probab=25.46 E-value=1.2e+02 Score=29.54 Aligned_cols=31 Identities=13% Similarity=0.154 Sum_probs=25.7
Q ss_pred cccccceeeEEEEeecCCCeEEEEEecCcce
Q 028082 142 DLAKNSWDFAVSRKVYGDDMFRASYQTSSKA 172 (214)
Q Consensus 142 d~~~nsWdfavs~k~~g~d~vratY~~~~k~ 172 (214)
++..-+|.+++.+++.++.++.++|-.+-+.
T Consensus 510 ~~~~~sp~~gl~y~~~~~~~~yasys~gfr~ 540 (761)
T PRK09840 510 SGNLVNWKAGALYKLTENGNVYINYAVSQQP 540 (761)
T ss_pred CCCeecceEEEEEEeCCCceEEEEeecccCC
Confidence 4455688999999999999999999776643
No 37
>PF06009 Laminin_II: Laminin Domain II; InterPro: IPR010307 It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure [].; GO: 0007155 cell adhesion, 0005604 basement membrane; PDB: 2WJS_A.
Probab=25.14 E-value=33 Score=27.59 Aligned_cols=22 Identities=23% Similarity=0.415 Sum_probs=4.2
Q ss_pred EeCCCceEEEEEecCCCeeEEEE
Q 028082 106 FDSANKVSANHVLGSGNCKLKYT 128 (214)
Q Consensus 106 ~D~aNK~s~~y~~~s~~c~lKY~ 128 (214)
=|-|||+.+...|+ |+|.|-|-
T Consensus 103 R~~An~IkV~m~F~-g~s~velr 124 (138)
T PF06009_consen 103 RDAANRIKVSMKFN-GNSGVELR 124 (138)
T ss_dssp ---------B--------EEEE-
T ss_pred HHHHhheeeeeEEC-CCceeeeC
Confidence 36799999999998 99988773
No 38
>PF01203 T2SN: Type II secretion system (T2SS), protein N; InterPro: IPR022792 The secretion pathway (GSP) for the export of proteins (also called the type II pathway) [] requires a number of protein components. One of them is known as the 'N' protein and has been sequenced in a variety of bacteria such as Aeromonas hydrophila (gene exeN); Erwinia carotovora (gene outN); Klebsiella pneumoniae (gene pulN); or Vibrio cholerae (gene epsN). The size of the 'N' protein is around 250 amino acids. It apparently contains a single transmembrane domain located in the N-terminal section. The short N-terminal domain is predicted to be cytoplasmic and the large C-terminal domain periplasmic.
Probab=24.38 E-value=4e+02 Score=22.55 Aligned_cols=92 Identities=15% Similarity=0.195 Sum_probs=58.8
Q ss_pred eeEEeeEEEEeCCCceEEEEEecCCCeeEEEEEEeCCeeeEEeeccccccceeeEEEEeecCCCeEEEEEecCcceEEEE
Q 028082 97 RTILEGTLVFDSANKVSANHVLGSGNCKLKYTYVHGGLTTFEQWYDLAKNSWDFAVSRKVYGDDMFRASYQTSSKALALE 176 (214)
Q Consensus 97 rT~ldgtl~~D~aNK~s~~y~~~s~~c~lKY~YvH~g~tt~EP~yd~~~nsWdfavs~k~~g~d~vratY~~~~k~lgle 176 (214)
..-++|.+.++=.+=....-.|..-.++|.|.- ....+-.+.++++ +-...++- .++.+.+.-...+..+.++
T Consensus 98 p~~~~G~~~l~~~~~~~~~~~c~~a~G~l~w~~--a~v~~~~~~~~lg--~~~~~l~c---~~g~l~~~l~~~~g~l~l~ 170 (221)
T PF01203_consen 98 PVPLSGQLELDIDELRFGDGRCQQAEGQLVWQN--AAVASPLGWLPLG--SLSGDLSC---QDGQLVLTLSDQSGPLQLD 170 (221)
T ss_pred ccccceEEEEEeeeeEecCCCeEeeEEEEEEec--ccccccCCCCccc--CEEEEEEe---cCCEEEEEEeCCCCceEEE
Confidence 345566666654432222222333445566663 3445566667777 44444443 3789999998899999998
Q ss_pred EeeCCCCCcceEEEEeeec
Q 028082 177 WSRNSKINGDFKIQAALNL 195 (214)
Q Consensus 177 Wsr~sk~~G~fKv~a~~~L 195 (214)
..=.=...|.|++.+++..
T Consensus 171 g~~~l~~~g~y~~~~~~~p 189 (221)
T PF01203_consen 171 GQASLSPDGRYRLDGTVKP 189 (221)
T ss_pred EEEEEcCCCeEEEEEEEec
Confidence 8776556788999998885
No 39
>COG5400 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.13 E-value=64 Score=28.83 Aligned_cols=55 Identities=18% Similarity=0.318 Sum_probs=46.2
Q ss_pred eEEEEEEecCceEEEeEeeeeeeecCCcccceEEEeecCceEEEEeeCCCCCeeEE
Q 028082 18 AAATVAFNAGDVKLRASLTDATVVNGPSLNGLALAVEKPGFFIVDYNVPKKDFRFQ 73 (214)
Q Consensus 18 a~atv~~~aGD~klrAs~TDatf~~GpsL~GL~L~vEKPGsF~iDy~~~~~d~rFQ 73 (214)
-+|-|+..-|-|--|-.-+--.|--|||| |+.+|=+---.||+.||++.-|..|+
T Consensus 95 fIaGltYGeG~LytKn~g~h~vFWQGPsl-GwD~GGqgsRvmmLvYnL~~v~aly~ 149 (205)
T COG5400 95 FIAGLTYGEGTLYTKNAGDHKVFWQGPSL-GWDWGGQGSRVMMLVYNLDDVDALYR 149 (205)
T ss_pred eEeeeeeccceEEecCCCCcceEeeCCcc-ccccCCCceEEEEEEecCCCHHHHHh
Confidence 38888888777777777777789999998 78888887788999999999888775
No 40
>TIGR00049 Iron-sulfur cluster assembly accessory protein. Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry.
Probab=22.64 E-value=1.3e+02 Score=22.39 Aligned_cols=10 Identities=40% Similarity=0.694 Sum_probs=5.2
Q ss_pred ceEEEeecCc
Q 028082 48 GLALAVEKPG 57 (214)
Q Consensus 48 GL~L~vEKPG 57 (214)
+|+|.++.+|
T Consensus 23 ~lRi~~~~~G 32 (105)
T TIGR00049 23 GLRVGVKGGG 32 (105)
T ss_pred EEEEEEecCC
Confidence 4555555544
No 41
>cd00342 gram_neg_porins Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers are stabilized by hytrophillic clamping of Loop L2. Loop 3 bends into the pore, creating an elliptical constriction of about 7 x 11A, large enough to allow passage of a glucose molecule without steric hindrance. Removal of the C-terminal residue (usuallly F) destabilizes the trimer and removal of the 16th beta-sheet abolishes trimerization. Unlike typical membrane proteins, porins lack long hydrophobic stretches. Short turns are found at the smooth, periplasmic end, longer irregular loops are found at the rough, extracellular end. C-terminal residue forms salt bridge with N-terminus.
Probab=22.44 E-value=2e+02 Score=24.39 Aligned_cols=54 Identities=15% Similarity=0.014 Sum_probs=30.0
Q ss_pred eEEEEEecCCCeeEEEEEEeCCeeeEEeeccccccceeeEEEEeecCCCeEEEEEe
Q 028082 112 VSANHVLGSGNCKLKYTYVHGGLTTFEQWYDLAKNSWDFAVSRKVYGDDMFRASYQ 167 (214)
Q Consensus 112 ~s~~y~~~s~~c~lKY~YvH~g~tt~EP~yd~~~nsWdfavs~k~~g~d~vratY~ 167 (214)
+.+.|.|+. +-++...|.+.....-.. =+...+.|.+++.|.+...-.|-+.|.
T Consensus 241 lga~Y~~~~-~~~~~~~y~~~~~~~~~~-~~~~~~~~~~G~~Y~~~~~~~l~~~y~ 294 (329)
T cd00342 241 LGATYQLTP-ALRLGAAYYYTKDRNDGG-GDGKANQVALGADYALSKRTDLYAEYG 294 (329)
T ss_pred EeEEEEcCC-ceEEEEEEEEEeccCCCC-CCCCeEEEEEEEeEeeccchhheeeee
Confidence 456777764 555655555432111100 023445677777777777666666665
No 42
>PF13116 DUF3971: Protein of unknown function
Probab=22.26 E-value=3.2e+02 Score=23.23 Aligned_cols=71 Identities=17% Similarity=0.291 Sum_probs=46.0
Q ss_pred CceEEEeEeeeeeeec---CCcccceEEEee-cCceEEEEeeCCCCCeeEEEeeeeeecceeeeEEEeecCCCceeEEee
Q 028082 27 GDVKLRASLTDATVVN---GPSLNGLALAVE-KPGFFIVDYNVPKKDFRFQFMNSVRVADKPLNLTYIHGRGDNRTILEG 102 (214)
Q Consensus 27 GD~klrAs~TDatf~~---GpsL~GL~L~vE-KPGsF~iDy~~~~~d~rFQFmnt~~V~~k~lnlTY~H~~~~nrT~ldg 102 (214)
|.+++.+.++|+++.= =|.|+++.-.++ +.+.+.|+-+=+ + +..+.+.+=.+.+...+.+... ..|+|
T Consensus 53 ~~~~~~~~v~~~~l~~~~~wP~l~~~~g~l~~~~~~l~i~~~~g----~---~~~~~l~~~~v~I~~l~~~~~~-l~i~~ 124 (288)
T PF13116_consen 53 GSFQADADVSDATLRFDPDWPPLTDVDGRLRFDNNRLRITADSG----R---LGGVDLSDGSVRIPDLFGKDPV-LTIDG 124 (288)
T ss_pred CEEEEEEEEeeeEEEeCCCCCccccceEEEEEECCEEEEEECce----E---EcceEeeEEEEEEccccCCCcE-EEEEE
Confidence 7788899999999884 366888887777 667777765433 2 2345555555666555553333 66666
Q ss_pred EEE
Q 028082 103 TLV 105 (214)
Q Consensus 103 tl~ 105 (214)
.+.
T Consensus 125 ~~~ 127 (288)
T PF13116_consen 125 KAS 127 (288)
T ss_pred Eee
Confidence 655
No 43
>PRK13282 flagellar assembly protein FliW; Provisional
Probab=22.12 E-value=3.7e+02 Score=21.95 Aligned_cols=62 Identities=16% Similarity=0.235 Sum_probs=45.9
Q ss_pred ceEEEeecCceEEEEeeCC-----------CCCeeEEEeeeeeecceeeeEEEeecCCCcee-EEeeEEEEeCCCceEEE
Q 028082 48 GLALAVEKPGFFIVDYNVP-----------KKDFRFQFMNSVRVADKPLNLTYIHGRGDNRT-ILEGTLVFDSANKVSAN 115 (214)
Q Consensus 48 GL~L~vEKPGsF~iDy~~~-----------~~d~rFQFmnt~~V~~k~lnlTY~H~~~~nrT-~ldgtl~~D~aNK~s~~ 115 (214)
+|+|-|=.|..|. ||++. +..--...++.+.+.+. .+..| =|=|=++|++.|+...-
T Consensus 37 ~laFvvi~P~~~~-dY~~~l~~~~~~~L~i~~~~dv~v~~iVti~~~----------~~~~T~NL~APIVIN~~~~~g~Q 105 (128)
T PRK13282 37 SFSFTLINPFALR-EYEFEIPTYYKELLELEEASNLLIANIMVIQTP----------IEESTVNFLAPVVFNLDNNTMGQ 105 (128)
T ss_pred ceEEEEeCcccee-cceeeCCHHHHHhcCCCChhheEEEEEEEcCCC----------cccccchhcCcEEEECCCCEEEE
Confidence 4899999999999 99987 33344567777777431 22223 36688999999999999
Q ss_pred EEecC
Q 028082 116 HVLGS 120 (214)
Q Consensus 116 y~~~s 120 (214)
..+..
T Consensus 106 vIL~~ 110 (128)
T PRK13282 106 VVLDS 110 (128)
T ss_pred EeeCC
Confidence 88874
No 44
>PF00856 SET: SET domain; InterPro: IPR001214 The SET domain appears generally as one part of a larger multidomain protein, and recently there were described three structures of very different proteins with distinct domain compositions: Neurospora crassa DIM-5, a member of the Su(var) family of HKMTs which methylate histone H3 on lysine 9,human SET7 (also called SET9), which methylates H3 on lysine 4 and garden pea Rubisco LSMT, an enzyme that does not modify histones, but instead methylates lysine 14 in the flexible tail of the large subunit of the enzyme Rubisco. The SET domain itself turned out to be an uncommon structure. Although in all three studies, electron density maps revealed the location of the AdoMet or AdoHcy cofactor, the SET domain bears no similarity at all to the canonical/AdoMet-dependent methyltransferase fold. Strictly conserved in the C-terminal motif of the SET domain tyrosine could be involved in abstracting a proton from the protonated amino group of the substrate lysine, promoting its nucleophilic attack on the sulphonium methyl group of the AdoMet cofactor. In contrast to the AdoMet-dependent protein methyltranferases of the classical type, which tend to bind their polypeptide substrates on top of the cofactor, it is noted from the Rubisco LSMT structure that the AdoMet seems to bind in a separate cleft, suggesting how a polypeptide substrate could be subjected to multiple rounds of methylation without having to be released from the enzyme. In contrast, SET7/9 is able to add only a single methyl group to its substrate. It has been demonstrated that association of SET domain and myotubularin-related proteins modulates growth control []. The SET domain-containing Drosophila melanogaster (Fruit fly) protein, enhancer of zeste, has a function in segment determination and the mammalian homologue may be involved in the regulation of gene transcription and chromatin structure. Histone lysine methylation is part of the histone code that regulated chromatin function and epigenetic control of gene function. Histone lysine methyltransferases (HMTase) differ both in their substrate specificity for the various acceptor lysines as well as in their product specificity for the number of methyl groups (one, two, or three) they transfer. With just one exception [], the HMTases belong to SET family that can be classified according to the sequences surrounding the SET domain [, ]. Structural studies on the human SET7/9, a mono-methylase, have revealed the molecular basis for the specificity of the enzyme for the histone-target and the roles of the invariant residues in the SET domain in determining the methylation specificities []. The pre-SET domain, as found in the SUV39 SET family, contains nine invariant cysteine residues that are grouped into two segments separated by a region of variable length. These 9 cysteines coordinate 3 zinc ions to form to form a triangular cluster, where each of the zinc ions is coordinated by 4 four cysteines to give a tetrahedral configuration. The function of this domain is structural, holding together 2 long segments of random coils. The C-terminal region including the post-SET domain is disordered when not interacting with a histone tail and in the absence of zinc. The three conserved cysteines in the post-SET domain form a zinc-binding site when coupled to a fourth conserved cysteine in the knot-like structure close to the SET domain active site []. The structured post-SET region brings in the C-terminal residues that participate in S-adenosylmethine-binding and histone tail interactions. The three conserved cysteine residues are essential for HMTase activity, as replacement with serine abolishes HMTase activity [], []. ; GO: 0005515 protein binding; PDB: 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3H6L_A 3SMT_A 3K5K_A ....
Probab=21.81 E-value=1.8e+02 Score=21.07 Aligned_cols=40 Identities=18% Similarity=0.297 Sum_probs=26.1
Q ss_pred EEEEecCCCeeEEEEEEeCCeeeEEeeccccccceeeEEEEeecCCCeEEEEE
Q 028082 114 ANHVLGSGNCKLKYTYVHGGLTTFEQWYDLAKNSWDFAVSRKVYGDDMFRASY 166 (214)
Q Consensus 114 ~~y~~~s~~c~lKY~YvH~g~tt~EP~yd~~~nsWdfavs~k~~g~d~vratY 166 (214)
.||++. .||.+.+.+. -......|-+.+.+..++-|-.+|
T Consensus 122 ~NHsc~-pn~~~~~~~~------------~~~~~~~~~a~r~I~~GeEi~isY 161 (162)
T PF00856_consen 122 LNHSCD-PNCEVSFDFD------------GDGGCLVVRATRDIKKGEEIFISY 161 (162)
T ss_dssp SEEESS-TSEEEEEEEE------------TTTTEEEEEESS-B-TTSBEEEES
T ss_pred eccccc-cccceeeEee------------cccceEEEEECCccCCCCEEEEEE
Confidence 578885 4888877775 334455666777777777777766
No 45
>PRK09504 sufA iron-sulfur cluster assembly scaffold protein; Provisional
Probab=20.64 E-value=1.9e+02 Score=22.88 Aligned_cols=47 Identities=23% Similarity=0.399 Sum_probs=29.6
Q ss_pred eEeeeeeee-------cCCcccceEEEeecCceEEE------EeeCCCCCeeEEEeeeeee
Q 028082 33 ASLTDATVV-------NGPSLNGLALAVEKPGFFIV------DYNVPKKDFRFQFMNSVRV 80 (214)
Q Consensus 33 As~TDatf~-------~GpsL~GL~L~vEKPGsF~i------Dy~~~~~d~rFQFmnt~~V 80 (214)
.++||++.. .-|.-.||++.||.+|+--. +.++...|..|++ +.+.|
T Consensus 18 I~iT~~A~~~i~~l~~~~~~~~~LRi~v~~gGCsG~~Y~~~l~~e~~~~D~v~e~-~g~~v 77 (122)
T PRK09504 18 LTLTPAAAAHIRELMAKQPGMKGVRLGVKQTGCAGFGYVLDSVSEPDKDDLVFEH-DGAKL 77 (122)
T ss_pred EEECHHHHHHHHHHHhcCCCCceEEEEEECCCCCceEEEeeecCCCCCCCEEEEe-CCEEE
Confidence 567777653 12333489999999995322 3445567888885 54444
No 46
>PF01803 LIM_bind: LIM-domain binding protein; InterPro: IPR002691 The LIM-domain binding protein, binds to the LIM domain IPR001781 from INTERPRO of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) P70662 from SWISSPROT is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons []. It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development []. The Drosophila melanogaster protein Chip O18353 from SWISSPROT is required for segmentation and activity of a remote wing margin enhancer []. Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development []. It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions [].; GO: 0003712 transcription cofactor activity, 0005634 nucleus
Probab=20.42 E-value=1.8e+02 Score=25.08 Aligned_cols=41 Identities=22% Similarity=0.323 Sum_probs=28.2
Q ss_pred EEEEecCCCeeEEEEEEeC------CeeeEEeeccccccceeeEEEE
Q 028082 114 ANHVLGSGNCKLKYTYVHG------GLTTFEQWYDLAKNSWDFAVSR 154 (214)
Q Consensus 114 ~~y~~~s~~c~lKY~YvH~------g~tt~EP~yd~~~nsWdfavs~ 154 (214)
+.+-+...+|.+.|.|.+| |...+.=..++-=+.|||.+..
T Consensus 91 g~i~ie~~~~~~~~~y~~gs~v~~~G~lr~~f~~~lKIe~~df~~~~ 137 (240)
T PF01803_consen 91 GSIFIECPRATFIYWYEDGSQVVHEGQLRAQFDPDLKIEWWDFCTRS 137 (240)
T ss_pred CeEEEEECCEEEEEEECCceEEEEEeEEEEEECccccEEEEEEEeec
Confidence 3566667788888888776 3334444667888899988654
No 47
>PF11383 DUF3187: Protein of unknown function (DUF3187); InterPro: IPR021523 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=20.15 E-value=7.1e+02 Score=23.14 Aligned_cols=129 Identities=19% Similarity=0.263 Sum_probs=78.5
Q ss_pred eecCCcccceE------EEeecC-------ceEEEEeeCCCCCeeEEEeeeeeecceeeeEEEee-cCCCceeEEeeEEE
Q 028082 40 VVNGPSLNGLA------LAVEKP-------GFFIVDYNVPKKDFRFQFMNSVRVADKPLNLTYIH-GRGDNRTILEGTLV 105 (214)
Q Consensus 40 f~~GpsL~GL~------L~vEKP-------GsF~iDy~~~~~d~rFQFmnt~~V~~k~lnlTY~H-~~~~nrT~ldgtl~ 105 (214)
+.+|=-|||+. ||+... ..|.|+| +..+-.+++|-....+.+-++.+.|.= .....+..|=|+|-
T Consensus 102 ~~~~g~LDg~i~~fHd~fGi~q~GR~~~~~~~f~~~~-~~~G~~~~~~~~~~~~gdv~~~~~yql~~~~~~~lslg~slk 180 (319)
T PF11383_consen 102 YASGGHLDGFIEDFHDFFGIPQNGRDEVPKDRFRYDY-PRYGIELFDFSGETLLGDVTLYLQYQLYQNDHHGLSLGGSLK 180 (319)
T ss_pred EecCCcchhHHHHHHHhhCCCCCCcccccCCeEEEEe-cCCCcccccccCccchhheeEEEEEEEecCCCceEEEEEEEE
Confidence 44566788886 444433 5788888 467778889988877777788888754 33455667777777
Q ss_pred EeC--CCceEEEEEecCCCeeEEEEEEeC----------------CeeeEEeeccccccceeeE--EEEeecCCCeEEEE
Q 028082 106 FDS--ANKVSANHVLGSGNCKLKYTYVHG----------------GLTTFEQWYDLAKNSWDFA--VSRKVYGDDMFRAS 165 (214)
Q Consensus 106 ~D~--aNK~s~~y~~~s~~c~lKY~YvH~----------------g~tt~EP~yd~~~nsWdfa--vs~k~~g~d~vrat 165 (214)
+.. +.++..+=+++ ..-.|.|+|.++ +.....|.+. ++.|.++ +-+++.+...+.+-
T Consensus 181 ~~t~d~~~~~GSGs~d-~~l~ln~s~~~~~~~~~~~~~G~~~~~~~~~l~~~~~~--~~~~~~~~g~~y~~~~~~~l~~q 257 (319)
T PF11383_consen 181 YPTGDSGRFTGSGSFD-QALQLNYSYRYGSKHSLYATLGYTFRGDSDVLEGIPYR--NNTWFGGLGYGYQLTENHSLLAQ 257 (319)
T ss_pred ecCCCcccccCCcccc-ceEEEEeeeccCCcceeeeeeeEEEecCcccccccccc--cceEEEEEEEEEEecCCEEEEEE
Confidence 765 33333332222 233444444444 3222223444 5555554 55667799999999
Q ss_pred EecCcce
Q 028082 166 YQTSSKA 172 (214)
Q Consensus 166 Y~~~~k~ 172 (214)
|+.++-.
T Consensus 258 ~~~~qg~ 264 (319)
T PF11383_consen 258 YDYYQGF 264 (319)
T ss_pred EEEeecc
Confidence 8877643
Done!