Query 028490
Match_columns 208
No_of_seqs 29 out of 31
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 12:19:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028490.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028490hhsearch_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 93.0 4.7 0.0001 33.6 19.1 159 21-189 73-265 (273)
2 cd02861 E_set_proteins_like E 77.1 16 0.00034 26.2 6.8 67 21-116 13-80 (82)
3 cd07305 Porin3_Tom40 Transloca 75.4 56 0.0012 28.6 18.0 140 50-197 109-271 (279)
4 PF00593 TonB_dep_Rec: TonB de 69.0 1.8 3.9E-05 31.6 0.3 25 139-163 1-26 (277)
5 cd00342 gram_neg_porins Porins 61.9 98 0.0021 26.1 9.7 56 104-161 205-260 (329)
6 TIGR01981 sufD FeS assembly pr 60.3 63 0.0014 29.7 8.6 111 30-152 47-194 (366)
7 TIGR03503 conserved hypothetic 58.9 1E+02 0.0022 29.5 10.0 39 47-85 182-220 (374)
8 TIGR01782 TonB-Xanth-Caul TonB 55.5 98 0.0021 30.7 9.5 108 30-151 681-802 (845)
9 PF01459 Porin_3: Eukaryotic p 51.7 1.4E+02 0.0031 24.8 19.8 169 25-204 56-241 (273)
10 PF09087 Cyc-maltodext_N: Cycl 50.3 42 0.00091 25.9 4.9 62 5-66 18-81 (88)
11 PRK13285 flagellar assembly pr 44.3 52 0.0011 27.1 4.9 76 35-120 50-137 (148)
12 smart00159 PTX Pentraxin / C-r 43.8 1.4E+02 0.0031 24.9 7.6 66 40-111 61-127 (206)
13 TIGR01997 sufA_proteo FeS asse 43.6 30 0.00064 26.4 3.2 32 40-72 25-62 (107)
14 COG1629 CirA Outer membrane re 41.8 50 0.0011 29.6 4.7 67 133-208 500-566 (768)
15 PF00677 Lum_binding: Lumazine 41.6 54 0.0012 24.3 4.2 29 30-58 34-64 (85)
16 cd01347 ligand_gated_channel T 37.6 2.9E+02 0.0064 24.5 9.8 30 134-163 377-406 (635)
17 PF11854 DUF3374: Protein of u 37.6 4.5E+02 0.0097 26.6 11.1 118 42-160 204-362 (637)
18 PF07532 Big_4: Bacterial Ig-l 35.3 1E+02 0.0022 20.9 4.6 37 152-188 18-57 (59)
19 PF10162 G8: G8 domain; Inter 34.8 85 0.0018 24.6 4.6 28 89-116 34-63 (125)
20 PF06577 DUF1134: Protein of u 34.5 51 0.0011 28.5 3.5 49 14-65 51-104 (160)
21 TIGR02011 IscA iron-sulfur clu 34.2 55 0.0012 24.8 3.4 32 40-72 23-60 (105)
22 PF06727 DUF1207: Protein of u 33.8 4.2E+02 0.0092 25.2 11.0 111 33-170 137-258 (338)
23 PF13609 Porin_4: Gram-negativ 31.7 1.6E+02 0.0034 24.5 5.9 53 104-163 188-240 (311)
24 TIGR03341 YhgI_GntY IscR-regul 31.5 80 0.0017 27.0 4.3 32 40-72 23-62 (190)
25 PF14352 DUF4402: Domain of un 30.9 2.5E+02 0.0054 21.6 7.0 60 48-109 46-121 (130)
26 PF04357 DUF490: Family of unk 30.7 3.7E+02 0.008 23.5 8.4 32 140-171 344-377 (379)
27 KOG3126 Porin/voltage-dependen 30.6 4.4E+02 0.0095 24.4 12.2 106 74-189 111-226 (281)
28 PF01331 mRNA_cap_enzyme: mRNA 30.6 74 0.0016 26.0 3.8 15 88-102 68-82 (192)
29 PF01203 T2SN: Type II secreti 29.0 3.2E+02 0.0069 23.0 7.4 92 89-189 98-189 (221)
30 PF11383 DUF3187: Protein of u 27.3 5E+02 0.011 24.0 14.6 128 30-163 102-263 (319)
31 cd01347 ligand_gated_channel T 27.0 4.5E+02 0.0097 23.3 10.8 74 76-149 506-589 (635)
32 PRK11190 Fe/S biogenesis prote 26.5 1E+02 0.0022 26.6 4.0 33 40-73 24-64 (192)
33 KOG1047 Bifunctional leukotrie 25.0 2.3E+02 0.005 29.1 6.7 62 13-76 59-127 (613)
34 PF00167 FGF: Fibroblast growt 23.9 87 0.0019 24.0 2.9 49 95-146 54-102 (122)
35 PF07608 DUF1571: Protein of u 23.8 3.4E+02 0.0073 24.3 6.9 63 61-123 119-191 (213)
36 PF12100 DUF3576: Domain of un 23.8 1.2E+02 0.0027 24.4 3.8 26 20-45 40-66 (103)
37 PF07443 HARP: HepA-related pr 23.5 29 0.00063 25.0 0.2 14 132-145 22-35 (55)
38 TIGR01785 TonB-hemin TonB-depe 23.4 1.6E+02 0.0035 27.5 5.0 32 133-164 397-428 (665)
39 PF01803 LIM_bind: LIM-domain 22.6 1.8E+02 0.0038 25.0 4.8 90 57-146 33-137 (240)
40 PF07523 Big_3: Bacterial Ig-l 22.3 83 0.0018 21.7 2.3 40 20-59 15-58 (67)
41 TIGR03016 pepcterm_hypo_1 unch 22.3 5.9E+02 0.013 24.0 8.6 42 104-147 388-430 (431)
42 cd00342 gram_neg_porins Porins 22.2 2.4E+02 0.0052 23.8 5.4 54 104-159 241-294 (329)
43 TIGR03509 OMP_MtrB_PioB decahe 22.1 3.8E+02 0.0083 26.6 7.6 29 132-160 346-374 (649)
44 PF03100 CcmE: CcmE; InterPro 21.8 4.1E+02 0.0089 21.1 8.0 63 47-119 60-127 (131)
45 TIGR03067 Planc_TIGR03067 Plan 21.7 3.9E+02 0.0084 20.7 6.1 39 74-125 60-98 (107)
46 PF03168 LEA_2: Late embryogen 21.4 2.4E+02 0.0052 19.6 4.6 57 42-102 1-57 (101)
47 COG4771 FepA Outer membrane re 21.2 1.5E+02 0.0033 30.8 4.7 83 76-170 565-674 (699)
48 PRK09289 riboflavin synthase s 21.1 1.7E+02 0.0037 25.1 4.4 30 30-59 132-163 (194)
49 PF07705 CARDB: CARDB; InterP 20.9 2.9E+02 0.0063 19.0 7.9 71 21-105 18-90 (101)
50 PF07691 PA14: PA14 domain; I 20.8 3.6E+02 0.0078 20.0 10.7 24 151-174 111-137 (145)
51 PRK09504 sufA iron-sulfur clus 20.7 1.6E+02 0.0035 23.2 3.9 32 40-72 40-77 (122)
52 PF10082 DUF2320: Uncharacteri 20.5 6E+02 0.013 22.5 14.3 111 76-188 98-246 (381)
53 smart00758 PA14 domain in bact 20.4 3.8E+02 0.0082 20.1 11.3 71 27-100 4-82 (136)
54 TIGR00049 Iron-sulfur cluster 20.2 1.5E+02 0.0033 21.9 3.5 27 40-66 23-55 (105)
55 PF06009 Laminin_II: Laminin D 20.0 46 0.00099 26.6 0.7 22 98-120 103-124 (138)
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=92.97 E-value=4.7 Score=33.57 Aligned_cols=159 Identities=16% Similarity=0.203 Sum_probs=93.1
Q ss_pred cCceeEEEEEeeCCccCcCccEEEEe---cCc------eEEEeeeCCCCCeEEEEeeeeeecceeeeEEEeeecCCceeE
Q 028490 21 AGELKLRAYVIAGPALNASDLSFSVE---KPG------SFLVDFDVPQKNVRFQFMNTARILEKQLYMTYTHMTGENRTI 91 (208)
Q Consensus 21 aGdlklrAsf~~GpsL~~~GLsL~vE---KPG------sF~iDydv~~~d~rFQFmnt~~V~~K~lnlTYtH~~~~nrT~ 91 (208)
-+++++.+.+..- -.. ||.+.++ .|+ .+.+||.-+.-...+++.|.. ...+.++|..+.. .+-.
T Consensus 73 d~~~~~~~~~~~~-~~~--~l~~~~~~~~~~~~~~~~~~l~~~y~~~~~~~~~~~~~~~---~~~~~~s~~~~v~-~~~~ 145 (273)
T PF01459_consen 73 DNDGNLEASVRNK-LSP--GLKLKLSAQLSPGSGKKSAQLEADYKGDDFNATFKVDNDN---NPIFNASYVQSVT-PNLA 145 (273)
T ss_dssp TTEEEEEEEEESS-TTT--TEEEEEEEEE-TTTS-EEEEEEEEEEETTEEEEEEEEEST---S-EEEEEEEEEET--TEE
T ss_pred CCcccEEEEEecc-cCc--ceEEEEEEEEeecCCceeeEEEEEEecCCEEEEEEEcccC---CCcEEEEEEEecc-ccEE
Confidence 4455566655432 122 4444432 233 345666666655666666521 5568888888644 4678
Q ss_pred EeeEEEecCCCc-ee-----EEEEee-------------CCCeeEEEEEEeC---Ce-eeeeeecccCcc--eeeeEEEE
Q 028490 92 LDGTLLLDPTNK-IS-----ANYVLD-------------SRNLKLRYSYVHR---GM-ATFEPCYDFGKN--SWELAVSK 146 (208)
Q Consensus 92 lDgtl~~D~aNK-ls-----~~y~~~-------------s~n~klKYsYvH~---g~-tt~EP~yD~~~n--sWdfavs~ 146 (208)
|=+.+++|..++ +. ++|.-. .....+.=||.|. .+ .-.|=.++..++ ...+++.+
T Consensus 146 lG~e~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~~~~~~~l~~sy~~k~~~~~~~g~e~~~~~~~~~~~~~vG~~~ 225 (273)
T PF01459_consen 146 LGAEATYDLSSGKSSKYNAGLSYAARYTHPDYTASATLSNNFGTLTASYFQKVNDKLQLGAELTYNLSSRESTFTVGYQY 225 (273)
T ss_dssp EEEEEEEETTTTCEEEEEEEEEEEET----TEEEEEEE-ETTTEEEEEEEEESSTTEEEEEEEEEETTCCEEEEEEEEEE
T ss_pred EEEEEEEecccCCcCcceEEEEEeccccceeEEEEEEEcCCCCEEEEEEEEEeccceeeeeeeeecccCCCceEEEEEEE
Confidence 888899888863 43 444443 2345566778776 21 334445555554 55566677
Q ss_pred EecCCCeEEEEEecCceeEEEEEeeCCCCCCCCceEEEEEEec
Q 028490 147 TVFDGDVIRASYDKSRKVLDLGWLWKPSFNRDGKCKVSASFRL 189 (208)
Q Consensus 147 kv~~~d~vratY~~s~k~lgleWsr~s~~~~~G~fKv~a~~~L 189 (208)
++.+...+|+..++..+ +++-+...-.. +=.+-+++.++.
T Consensus 226 ~l~~~~~vk~kvds~g~-v~~~~~~~l~~--~~~l~ls~~~d~ 265 (273)
T PF01459_consen 226 KLDDSSTVKAKVDSNGR-VSASYEQKLNP--GVTLTLSAELDH 265 (273)
T ss_dssp EECTTEEEEEEEETTSE-EEEEEEEEECT--TEEEEEEEEECT
T ss_pred EcCcccEEEEEEcCCCE-EEEEEEEecCC--CcEEEEEEEEcc
Confidence 77777799999999887 44444443322 115777777666
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=77.14 E-value=16 Score=26.20 Aligned_cols=67 Identities=18% Similarity=0.343 Sum_probs=42.6
Q ss_pred cCceeEEEEEeeCCccCcCccEEEEecCceEEEeeeCCCCCeEEEEeeeeeecceeeeEEEeeecCCceeEEeeEEE-ec
Q 028490 21 AGELKLRAYVIAGPALNASDLSFSVEKPGSFLVDFDVPQKNVRFQFMNTARILEKQLYMTYTHMTGENRTILDGTLL-LD 99 (208)
Q Consensus 21 aGdlklrAsf~~GpsL~~~GLsL~vEKPGsF~iDydv~~~d~rFQFmnt~~V~~K~lnlTYtH~~~~nrT~lDgtl~-~D 99 (208)
|..|.|..+|-+ -+ ...|.-.+.|.|.+..+++....+|+| ++||... .|
T Consensus 13 a~~V~v~G~fn~---W~--~~~m~~~~~G~w~~~~~l~~G~y~Ykf------------------------~vdg~~~~~D 63 (82)
T cd02861 13 ADSVYLAGSFNN---WN--AIPMEREGDGLWVVTVELRPGRYEYKF------------------------VVDGEWVIVD 63 (82)
T ss_pred CCEEEEEeECCC---CC--cccCEECCCCcEEEEEeCCCCcEEEEE------------------------EECCEEeeCC
Confidence 456777766632 11 233333355899999999988888988 4455555 68
Q ss_pred CCCceeEEEEeeCCCee
Q 028490 100 PTNKISANYVLDSRNLK 116 (208)
Q Consensus 100 ~aNKls~~y~~~s~n~k 116 (208)
|.|.-...=.++..|+-
T Consensus 64 P~~~~~~~~~~g~~n~v 80 (82)
T cd02861 64 PNAAAYVDDGFGGKNAV 80 (82)
T ss_pred CCCCceecCCCCccceE
Confidence 87776655555555543
No 3
>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=75.42 E-value=56 Score=28.59 Aligned_cols=140 Identities=16% Similarity=0.136 Sum_probs=83.4
Q ss_pred eEEEeeeCCCCCeEEEEeeeeee-cceeeeEEEeeecCCceeEEeeEEEec--CCCcee-----EEEE---------eeC
Q 028490 50 SFLVDFDVPQKNVRFQFMNTARI-LEKQLYMTYTHMTGENRTILDGTLLLD--PTNKIS-----ANYV---------LDS 112 (208)
Q Consensus 50 sF~iDydv~~~d~rFQFmnt~~V-~~K~lnlTYtH~~~~nrT~lDgtl~~D--~aNKls-----~~y~---------~~s 112 (208)
-|.+||.-+....-+.-.|-.-+ ..-.+...|.|+-.+ +..|=+.+.++ |.++.+ ++|. ++
T Consensus 109 q~~~dy~g~d~t~~l~~~n~~~~~~sg~~~~~ylq~vt~-~l~lG~E~~~~~~~~~~~~~~~~~~rY~~~d~~~s~~l~- 186 (279)
T cd07305 109 QLELDYRGDDFTASLKLANPDILNETGIYVASYLQSVTP-KLALGGELVYQRVPGNGISVLSYAARYTAGNWIASGQLG- 186 (279)
T ss_pred EEEEEEcCCceEEEEEEeCCCcccccEEEEEEEEEEccC-cEEEEEEEEEEEcCCCCceeEEEEEEEccCCEEEEEEEc-
Confidence 46677765444444443333111 113567788886444 88888899988 777655 4444 12
Q ss_pred CCeeEEEEEEeC---Ce-eeeeeecccCcceeeeEE--EEEecCCCeEEEEEecCceeEEEEEeeCCCCCCCCceEEEEE
Q 028490 113 RNLKLRYSYVHR---GM-ATFEPCYDFGKNSWELAV--SKTVFDGDVIRASYDKSRKVLDLGWLWKPSFNRDGKCKVSAS 186 (208)
Q Consensus 113 ~n~klKYsYvH~---g~-tt~EP~yD~~~nsWdfav--s~kv~~~d~vratY~~s~k~lgleWsr~s~~~~~G~fKv~a~ 186 (208)
..+.++=||.|. .+ .-.|=.|++.++...+.+ .+.+. +-++|+..++..+ +++-|.+.-.. .=.+-+++.
T Consensus 187 ~~~~l~asY~~kvs~~l~lG~el~~~~~~~es~~tvg~~y~~~-~~~~k~~ids~g~-v~~~~e~~l~~--~~~l~ls~~ 262 (279)
T cd07305 187 AQGGLHLSYYRKLSDKLQLGVELELNLRTRESTATLGYQYDFR-QSRFRGSIDSNGK-VSAVLEKRLPL--PLSLLLSGE 262 (279)
T ss_pred CCCeEEEEEEEEcccceEeeeeeeecccCCceeEEEEEEEEcC-CCEEEEEEcCCCE-EEEEEEEecCC--CeEEEEEEE
Confidence 237788889887 11 334446666665555554 55544 7788999999887 78888766544 113445554
Q ss_pred EecCCCCCCCe
Q 028490 187 FRLGEGLYMPT 197 (208)
Q Consensus 187 ~~L~d~~K~pk 197 (208)
++. ..+.+|
T Consensus 263 ~d~--~~~~~k 271 (279)
T cd07305 263 LNH--VKNDYK 271 (279)
T ss_pred Ecc--cCCcce
Confidence 544 235555
No 4
>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=69.04 E-value=1.8 Score=31.61 Aligned_cols=25 Identities=32% Similarity=0.305 Sum_probs=13.2
Q ss_pred eeeeEE-EEEecCCCeEEEEEecCce
Q 028490 139 SWELAV-SKTVFDGDVIRASYDKSRK 163 (208)
Q Consensus 139 sWdfav-s~kv~~~d~vratY~~s~k 163 (208)
+|.+++ ++++.++-.+|++|-.+-+
T Consensus 1 sp~~~~~~y~~~~~~~l~~~~~~~~r 26 (277)
T PF00593_consen 1 SPRLGLTSYKPTDNLSLRASYGRGFR 26 (277)
T ss_dssp EEEEEEEEEEESTSEEEEEEEEEEEE
T ss_pred CceEEEEEEEECCCeEEEEEEEEeec
Confidence 355555 3555555555555554433
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=61.88 E-value=98 Score=26.13 Aligned_cols=56 Identities=20% Similarity=0.143 Sum_probs=35.4
Q ss_pred eeEEEEeeCCCeeEEEEEEeCCeeeeeeecccCcceeeeEEEEEecCCCeEEEEEecC
Q 028490 104 ISANYVLDSRNLKLRYSYVHRGMATFEPCYDFGKNSWELAVSKTVFDGDVIRASYDKS 161 (208)
Q Consensus 104 ls~~y~~~s~n~klKYsYvH~g~tt~EP~yD~~~nsWdfavs~kv~~~d~vratY~~s 161 (208)
+.+.|.++ ..+|.=.|.|..........+-..+.|.+++++++.+.=.+.+.|...
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 56677765 566666666543222111223345789999999998777788888653
No 6
>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=60.28 E-value=63 Score=29.66 Aligned_cols=111 Identities=21% Similarity=0.260 Sum_probs=64.2
Q ss_pred EeeCCccCcCccEEEEecCceEEEee----eCCCCCeEEEEeeeeee-------------cceeeeEEEeeecCCc-eeE
Q 028490 30 VIAGPALNASDLSFSVEKPGSFLVDF----DVPQKNVRFQFMNTARI-------------LEKQLYMTYTHMTGEN-RTI 91 (208)
Q Consensus 30 f~~GpsL~~~GLsL~vEKPGsF~iDy----dv~~~d~rFQFmnt~~V-------------~~K~lnlTYtH~~~~n-rT~ 91 (208)
|++|..+. -|+-.+++|....++| .++.++-+|..+|++.. .++|+.+.|+...+++ ...
T Consensus 47 ~~~G~~~~--~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~aln~a~~~~G~~i~v~~~~~~~~Pi~i~~~~~~~~~~~~~ 124 (366)
T TIGR01981 47 FVDGVIVP--DLSDALPLHPELLEDLLDALAVLSDEDRFLALNAALFNDGTVLYVPKGVEVEEPIEIKFIGVGGEKNFVH 124 (366)
T ss_pred EECCEEec--ChhhhhccCcceEEeehhcccCcCCccHHHHHHHHHhCCeEEEEECCCCCcCCCEEEEEEEcCCCcccee
Confidence 88888777 7776777887788887 44555566766665532 5689999998854332 111
Q ss_pred EeeEEEecCCCceeEEEEe-------------------eCCCeeEEEEEEeCCeeeeeeecccCcceeeeEEEEEecCCC
Q 028490 92 LDGTLLLDPTNKISANYVL-------------------DSRNLKLRYSYVHRGMATFEPCYDFGKNSWELAVSKTVFDGD 152 (208)
Q Consensus 92 lDgtl~~D~aNKls~~y~~-------------------~s~n~klKYsYvH~g~tt~EP~yD~~~nsWdfavs~kv~~~d 152 (208)
--=-+++...-++++...+ -..|.+|+|..++. .+.+++.|+-.+-.-+.|
T Consensus 125 ~~~~i~v~~~s~~~iie~~~~~~~~~~~~~~~~~~ei~~~~~A~l~~~~iq~----------~~~~~~~~~~~~~~~~~~ 194 (366)
T TIGR01981 125 PRLLIIVEKGSKITVIERFETISLNSGKAFTNSVVEITVGANASVIFVKVQF----------FSKNSTHFSNHRAFIGRD 194 (366)
T ss_pred eEEEEEECCCCEEEEEEEecCCCCCCcccEEEEEEEEEECCCCEEEEEEEEc----------CCCCcEEEEEeEEEEcCC
Confidence 1222334444444444444 22455555555443 356778887444333443
No 7
>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=58.91 E-value=1e+02 Score=29.52 Aligned_cols=39 Identities=8% Similarity=0.094 Sum_probs=36.2
Q ss_pred cCceEEEeeeCCCCCeEEEEeeeeeecceeeeEEEeeec
Q 028490 47 KPGSFLVDFDVPQKNVRFQFMNTARILEKQLYMTYTHMT 85 (208)
Q Consensus 47 KPGsF~iDydv~~~d~rFQFmnt~~V~~K~lnlTYtH~~ 85 (208)
.||-|.+.+-.-++-+.=||-..+.|-..|++.|++-+.
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 899999999999999998988899999999999999865
No 8
>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=55.52 E-value=98 Score=30.66 Aligned_cols=108 Identities=18% Similarity=0.148 Sum_probs=55.0
Q ss_pred EeeCCc-cCcCccEEEEecCceEEEeeeCCCCCeEEEEeeeeeecceeeeEEEeeecCCcee----EEeeEEEecCCCce
Q 028490 30 VIAGPA-LNASDLSFSVEKPGSFLVDFDVPQKNVRFQFMNTARILEKQLYMTYTHMTGENRT----ILDGTLLLDPTNKI 104 (208)
Q Consensus 30 f~~Gps-L~~~GLsL~vEKPGsF~iDydv~~~d~rFQFmnt~~V~~K~lnlTYtH~~~~nrT----~lDgtl~~D~aNKl 104 (208)
++|++. ..+.|+-|.+.++=.|+ |. +++...+ ..|+||+++..+.-. .-+-.|.-=|.+.+
T Consensus 681 ~~N~~~~~~~~G~El~~~~~~~~l-----p~------~~~~l~~---~~n~T~~~s~~~~~~~~~~~~~~~l~~~p~~~~ 746 (845)
T TIGR01782 681 PVNGGKAGKIRGVELGYQQTFDFL-----PG------PLSGFGV---QANYTYVDSEADPSVDGVQRRKLPLPGLSKNTA 746 (845)
T ss_pred eeeCCCCcEEEEEEEEEEEEcccC-----Cc------cccCcEE---EEEEEEEccccccccCCCCccccccCCCCcccE
Confidence 667763 55557777665442222 11 2344444 678888887543211 00112334456664
Q ss_pred eE--EEEeeCCCeeEEEEEEeCCeeee-------eeecccCcceeeeEEEEEecCC
Q 028490 105 SA--NYVLDSRNLKLRYSYVHRGMATF-------EPCYDFGKNSWELAVSKTVFDG 151 (208)
Q Consensus 105 s~--~y~~~s~n~klKYsYvH~g~tt~-------EP~yD~~~nsWdfavs~kv~~~ 151 (208)
.+ .|..+.=..+|.|.|+-.-...+ ++.+--+-..||+.+++++.++
T Consensus 747 n~~l~Y~~~~~~~~l~~~y~~~~~~~~~~~~~~~~~~~~~~y~~lDl~~sy~~~~~ 802 (845)
T TIGR01782 747 NATLYYEKGGFSARLSYNYRSDYLLDVGGSNINRLDRYVDPRGQLDLSASYQVSDH 802 (845)
T ss_pred EEEEEEECCCEEEEEEEEeechhhhhcccccccccccccccceEEEEEEEEecCCC
Confidence 44 45433233455555543322221 2233344567999999988644
No 9
>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=51.65 E-value=1.4e+02 Score=24.83 Aligned_cols=169 Identities=12% Similarity=0.087 Sum_probs=87.0
Q ss_pred eEEEEEeeCCccCcCccEEEEecCce--EEEeeeC-CCCCeEEEEeeeeeecc--eeeeEEEeeecCCceeEEeeEEEec
Q 028490 25 KLRAYVIAGPALNASDLSFSVEKPGS--FLVDFDV-PQKNVRFQFMNTARILE--KQLYMTYTHMTGENRTILDGTLLLD 99 (208)
Q Consensus 25 klrAsf~~GpsL~~~GLsL~vEKPGs--F~iDydv-~~~d~rFQFmnt~~V~~--K~lnlTYtH~~~~nrT~lDgtl~~D 99 (208)
+|.+.|. |+.+. +..+-++. ..+.+.- ..+..+..+.....-.. +..+|.-.+...+- .+.+.+..+
T Consensus 56 ~~~~~~~-~~~~~-----~~~~~d~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~y~~~~~--~~~~~~~~~ 127 (273)
T PF01459_consen 56 SFGAKYK-GPKLT-----VKGDTDNDGNLEASVRNKLSPGLKLKLSAQLSPGSGKKSAQLEADYKGDDF--NATFKVDND 127 (273)
T ss_dssp EEEEEEE-CEEEE-----EEEETTTEEEEEEEEESSTTTTEEEEEEEEE-TTTS-EEEEEEEEEEETTE--EEEEEEEES
T ss_pred EEEEEEe-Cceee-----EEEEeCCcccEEEEEecccCcceEEEEEEEEeecCCceeeEEEEEEecCCE--EEEEEEccc
Confidence 3344455 55444 33343443 3333333 23455555544433221 34444444422333 344555556
Q ss_pred CCCceeEEEEeeCC-CeeEEEEEEeC----CeeeeeeecccCcc----eeeeEEEEEecCCCeEEEEEecCc---eeEEE
Q 028490 100 PTNKISANYVLDSR-NLKLRYSYVHR----GMATFEPCYDFGKN----SWELAVSKTVFDGDVIRASYDKSR---KVLDL 167 (208)
Q Consensus 100 ~aNKls~~y~~~s~-n~klKYsYvH~----g~tt~EP~yD~~~n----sWdfavs~kv~~~d~vratY~~s~---k~lgl 167 (208)
....+.++|.+.-. +..|++...-+ ..+...-+.-+... .|.++++. -...+.++++|...- =.+|.
T Consensus 128 ~~~~~~~s~~~~v~~~~~lG~e~~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~~~~~-~~~~~~l~~sy~~k~~~~~~~g~ 206 (273)
T PF01459_consen 128 NNPIFNASYVQSVTPNLALGAEATYDLSSGKSSKYNAGLSYAARYTHPDYTASATL-SNNFGTLTASYFQKVNDKLQLGA 206 (273)
T ss_dssp TS-EEEEEEEEEET-TEEEEEEEEEETTTTCEEEEEEEEEEEET----TEEEEEEE--ETTTEEEEEEEEESSTTEEEEE
T ss_pred CCCcEEEEEEEeccccEEEEEEEEEecccCCcCcceEEEEEeccccceeEEEEEEE-cCCCCEEEEEEEEEeccceeeee
Confidence 68889999999877 78887776643 11211111222222 55555432 145888888886422 23777
Q ss_pred EEeeCCCCCCCCceEEEEEEecCCCCCCCeeEEEcee
Q 028490 168 GWLWKPSFNRDGKCKVSASFRLGEGLYMPTLTAESSW 204 (208)
Q Consensus 168 eWsr~s~~~~~G~fKv~a~~~L~d~~K~pkL~aEktW 204 (208)
|...+...+ .-.|-|.+...|.+.. .-|..+.+.|
T Consensus 207 e~~~~~~~~-~~~~~vG~~~~l~~~~-~vk~kvds~g 241 (273)
T PF01459_consen 207 ELTYNLSSR-ESTFTVGYQYKLDDSS-TVKAKVDSNG 241 (273)
T ss_dssp EEEEETTCC-EEEEEEEEEEEECTTE-EEEEEEETTS
T ss_pred eeeecccCC-CceEEEEEEEEcCccc-EEEEEEcCCC
Confidence 777776652 3468888888884443 4444444443
No 10
>PF09087 Cyc-maltodext_N: Cyclomaltodextrinase, N-terminal; InterPro: IPR015171 This domain is found at the N terminus of cyclomaltodextrinase. The domain assumes a beta-sandwich structure composed of the eight antiparallel beta-strands. A ten residue linker is also present at the C-terminal end, which connects the N-terminal domain to a distal domain in the protein. This domain participates in oligomerisation of the protein, wherein the N-terminal domain of one subunit contacts the active centre of the other subunit, and is also required for binding of cyclodextrin to substrate []. ; PDB: 3EDK_B 3EDD_A 3EDJ_B 3EDE_A 1H3G_B 3EDF_B.
Probab=50.28 E-value=42 Score=25.94 Aligned_cols=62 Identities=18% Similarity=0.324 Sum_probs=35.6
Q ss_pred eeeeeccceEEEEEEecCceeEEEE-EeeCCccCcCccEEEEecCceEEEeeeCC-CCCeEEEE
Q 028490 5 ISMRSRKGLTGTVAADAGELKLRAY-VIAGPALNASDLSFSVEKPGSFLVDFDVP-QKNVRFQF 66 (208)
Q Consensus 5 ~~~~~~~~~~atv~~~aGdlklrAs-f~~GpsL~~~GLsL~vEKPGsF~iDydv~-~~d~rFQF 66 (208)
+-+.|..-+.+.|+++--+|+|... -+.-|--=+=-|.++--|||.|.|.+.-+ ++..++.|
T Consensus 18 LmvyG~nI~~~~v~i~~~gV~i~~v~~~~npNYLFv~L~i~~akpg~~~i~~~~~~~~~~~~~Y 81 (88)
T PF09087_consen 18 LMVYGKNIASAEVSISYPGVTIKKVVKTDNPNYLFVYLDISDAKPGTFTINFKKGDKKKTTFDY 81 (88)
T ss_dssp EEEESTTGGGSEEEE-BTTEEEEEEEE-SSTTEEEEEEEE-T--SEEEEEEEEET-TEEEEEEE
T ss_pred EEEecCCcccCEEEEeCCCeEEEEEEecCCCCEEEEEEecCCCCCcEEEEEEEcCCCceEEEEe
Confidence 4456777777889999888998877 22222111002556622999999988866 44444443
No 11
>PRK13285 flagellar assembly protein FliW; Provisional
Probab=44.26 E-value=52 Score=27.13 Aligned_cols=76 Identities=18% Similarity=0.345 Sum_probs=53.6
Q ss_pred ccCcCccEEEEecCceEEEeeeCC-----------CCCeEEEEeeeeeecceeeeEEEeeecCCcee-EEeeEEEecCCC
Q 028490 35 ALNASDLSFSVEKPGSFLVDFDVP-----------QKNVRFQFMNTARILEKQLYMTYTHMTGENRT-ILDGTLLLDPTN 102 (208)
Q Consensus 35 sL~~~GLsL~vEKPGsF~iDydv~-----------~~d~rFQFmnt~~V~~K~lnlTYtH~~~~nrT-~lDgtl~~D~aN 102 (208)
|++=.+++|-|=.|..|.-||++. +..--...++.+.+-+. .+..| =|=|=++|++.|
T Consensus 50 S~dd~~~~F~vi~P~~~~~dY~~~l~~~~~~~L~i~~~~dv~v~~iVti~~~----------~~~~T~NL~APIViN~~~ 119 (148)
T PRK13285 50 SVEDPDLAFVVIDPFNFFPDYEFDLDEEELELLGIESEEDVLVLVIVTIPED----------PEKITANLQAPIIINKKK 119 (148)
T ss_pred ecCCCceEEEEeCHHHhCCCCccccCHHHHHhcCCCChhheEEEEEEEcCCC----------cccceEeecCCEEEECCC
Confidence 455447899999999999999965 22334456676666432 22222 256779999999
Q ss_pred ceeEEEEeeCCCeeEEEE
Q 028490 103 KISANYVLDSRNLKLRYS 120 (208)
Q Consensus 103 Kls~~y~~~s~n~klKYs 120 (208)
+...-..++..+..+||-
T Consensus 120 ~~g~QvIl~~~~y~~r~p 137 (148)
T PRK13285 120 RKGKQVILDNEKYSTKHP 137 (148)
T ss_pred CEEEEEEeCCCCCccccc
Confidence 999999998766666654
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=43.79 E-value=1.4e+02 Score=24.86 Aligned_cols=66 Identities=18% Similarity=0.265 Sum_probs=41.5
Q ss_pred ccEEEEecCceEEEeeeCCCCCeEEEEeeeeeecc-eeeeEEEeeecCCceeEEeeEEEecCCCceeEEEEee
Q 028490 40 DLSFSVEKPGSFLVDFDVPQKNVRFQFMNTARILE-KQLYMTYTHMTGENRTILDGTLLLDPTNKISANYVLD 111 (208)
Q Consensus 40 GLsL~vEKPGsF~iDydv~~~d~rFQFmnt~~V~~-K~lnlTYtH~~~~nrT~lDgtl~~D~aNKls~~y~~~ 111 (208)
.|-+..+++|.|.+-. +.+.+.+. ....-.+ .-|-+||.+..+.-+.++||.+. ...-++..|.+.
T Consensus 61 e~~~~~~~~~~~~l~i--~g~~~~~~--~~~~~g~W~hvc~tw~~~~g~~~lyvnG~~~--~~~~~~~g~~i~ 127 (206)
T smart00159 61 ELLLYKEKQGEYSLYI--GGKKVQFP--VPESDGKWHHICTTWESSSGIAELWVDGKPG--VRKGLAKGYTVK 127 (206)
T ss_pred eEEEEEcCCcEEEEEE--cCeEEEec--ccccCCceEEEEEEEECCCCcEEEEECCEEc--ccccccCCcEEC
Confidence 6666667888776654 33433332 1222111 45778999988999999999986 444455556665
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=43.55 E-value=30 Score=26.35 Aligned_cols=32 Identities=16% Similarity=0.435 Sum_probs=21.4
Q ss_pred ccEEEEecCc----eEEEe--eeCCCCCeEEEEeeeeee
Q 028490 40 DLSFSVEKPG----SFLVD--FDVPQKNVRFQFMNTARI 72 (208)
Q Consensus 40 GLsL~vEKPG----sF~iD--ydv~~~d~rFQFmnt~~V 72 (208)
||++.|+..| +|.++ -++...|..|++ +.++|
T Consensus 25 ~lRi~v~~~GC~G~~y~~~l~~~~~~~D~v~~~-~g~~v 62 (107)
T TIGR01997 25 GIRLGVKKTGCAGMEYVLDLVSEPKKDDDLIEH-DGAKV 62 (107)
T ss_pred EEEEEEECCCCCCcEEEeeecCCCCCCCEEEec-CCEEE
Confidence 7888888776 24444 356678888885 55554
No 14
>COG1629 CirA Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]
Probab=41.83 E-value=50 Score=29.56 Aligned_cols=67 Identities=19% Similarity=0.040 Sum_probs=45.5
Q ss_pred cccCcceeeeEEEEEecCCCeEEEEEecCceeEEEEEeeCCCCCCCCceEEEEEEecCCCCCCCeeEEEceecccC
Q 028490 133 YDFGKNSWELAVSKTVFDGDVIRASYDKSRKVLDLGWLWKPSFNRDGKCKVSASFRLGEGLYMPTLTAESSWDFEM 208 (208)
Q Consensus 133 yD~~~nsWdfavs~kv~~~d~vratY~~s~k~lgleWsr~s~~~~~G~fKv~a~~~L~d~~K~pkL~aEktWn~e~ 208 (208)
.....-+|.+.++++..++..++++|...-+.-++........ ..+... -....|.|-.|+.|++|+
T Consensus 500 ~~~~~~~p~~~~~~~~~~~~~~~~~~s~~~r~p~~~~~~~~~~-------~~~~~~--~~~gn~~Lkpe~s~~~e~ 566 (768)
T COG1629 500 RSDTAFSPSLGLVYDPTPDLSLYASYSRGFRPPSSDELYASFG-------TSADGG--ISLGNPNLKPETADQYEL 566 (768)
T ss_pred ccCceecceeEEEEecCCCceEEEEEeccccCCCccccccccc-------ccCCCc--cccCCCCCCCcccceeEE
Confidence 4456677999999999999999999988776555544333322 111100 245668888999999884
No 15
>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=41.60 E-value=54 Score=24.31 Aligned_cols=29 Identities=17% Similarity=0.261 Sum_probs=20.8
Q ss_pred EeeCCccCcCccEEEEe--cCceEEEeeeCC
Q 028490 30 VIAGPALNASDLSFSVE--KPGSFLVDFDVP 58 (208)
Q Consensus 30 f~~GpsL~~~GLsL~vE--KPGsF~iDydv~ 58 (208)
+.-|.|..++|.+|+|. ++..|.+|.-++
T Consensus 34 ~~~g~SIavnGvcLTV~~~~~~~f~~~l~~e 64 (85)
T PF00677_consen 34 LKIGGSIAVNGVCLTVTDINEDWFEVDLIPE 64 (85)
T ss_dssp G-TTSEEEETTEEEEEEEEETTEEEEEEEHH
T ss_pred CccCcEEEECCeeeEEEEecCCEEEEechHH
Confidence 44477887889999998 567777765544
No 16
>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=37.64 E-value=2.9e+02 Score=24.48 Aligned_cols=30 Identities=23% Similarity=0.278 Sum_probs=24.6
Q ss_pred ccCcceeeeEEEEEecCCCeEEEEEecCce
Q 028490 134 DFGKNSWELAVSKTVFDGDVIRASYDKSRK 163 (208)
Q Consensus 134 D~~~nsWdfavs~kv~~~d~vratY~~s~k 163 (208)
+...=++.+++++++.+..+++++|....+
T Consensus 377 ~~~~~~p~~~~~y~~~~~~~~~~~~~~~~~ 406 (635)
T cd01347 377 SYSHWSPSLGLVYKLTDGLSLYASYSQGFR 406 (635)
T ss_pred ccceeccceeEEEEcCCCEEEEEEeeeeec
Confidence 445557889999999999999999987655
No 17
>PF11854 DUF3374: Protein of unknown function (DUF3374); InterPro: IPR020016 Members of this protein family are integral proteins of the bacterial outer membrane, associated with multi-haem c-type cytochromes involved in electron transfer [, ]. The MtrB protein of Shewanella oneidensis MR-1 (SO1776) has been shown to form a complex with 1:1:1 stochiometry with the small, periplasmic decahaem cytochrome MtrA and large, surface-exposed decahaem cytochrome MtrC.
Probab=37.63 E-value=4.5e+02 Score=26.62 Aligned_cols=118 Identities=18% Similarity=0.272 Sum_probs=72.5
Q ss_pred EEEEecCceEE--------EeeeCCCCCeEEEEeeeeeecceeeeEEE--eeecCCc------------eeEEeeEEEe-
Q 028490 42 SFSVEKPGSFL--------VDFDVPQKNVRFQFMNTARILEKQLYMTY--THMTGEN------------RTILDGTLLL- 98 (208)
Q Consensus 42 sL~vEKPGsF~--------iDydv~~~d~rFQFmnt~~V~~K~lnlTY--tH~~~~n------------rT~lDgtl~~- 98 (208)
+|.++.|..=. +.+.|-|+.+++..+-..++..-+++.+. ..++-+. +.-+||.|..
T Consensus 204 ~l~~~n~~~~~~G~~~~~~~al~PDN~ahq~~~sg~y~l~~t~~~~~~~~g~mtQdd~f~~~t~~~~lp~~sldG~VdT~ 283 (637)
T PF11854_consen 204 SLTWQNPFNPTFGAATYGQMALAPDNQAHQVSLSGQYNLPRTRFSGRLSYGRMTQDDAFIPATIGPALPAQSLDGEVDTL 283 (637)
T ss_pred ceeecCCCCcccccccccccccCCCchheEEEEEEEEecCCcEEEEEEEEEEEecCccccccccccCCCccccCcEEEEe
Confidence 45566665544 37889999999999888888765555444 3333111 2335554422
Q ss_pred ----------cCCCceeEEEEeeC-CCeeEEEEE-------EeCCeeeeeeecccCcceeeeEEEEEecCCCeEEEEEec
Q 028490 99 ----------DPTNKISANYVLDS-RNLKLRYSY-------VHRGMATFEPCYDFGKNSWELAVSKTVFDGDVIRASYDK 160 (208)
Q Consensus 99 ----------D~aNKls~~y~~~s-~n~klKYsY-------vH~g~tt~EP~yD~~~nsWdfavs~kv~~~d~vratY~~ 160 (208)
-|.=+|+++|.+.- .|-.=-+.| ++ |.+..-+.||.-+..+++.+++|+..+-++.+.|+-
T Consensus 284 ~~~l~~tsr~~~~l~l~a~y~Y~DrDNkt~~~~~~~~~~d~~~-g~~~~N~~~d~tk~~~~~~a~YRl~~~~~l~~gy~~ 362 (637)
T PF11854_consen 284 DANLKLTSRPTPDLRLTASYRYSDRDNKTPVWEYPQYSIDSVT-GATARNTPYDYTKQNAKLDADYRLARGYRLEAGYEY 362 (637)
T ss_pred eeeEEEEeeEcCCcEEEEEEEEeeccCCCchhhccceeecccc-ccccccCcccccceeeeEEeEEEecCCcEEEEeeeE
Confidence 12223344444411 221111111 12 234466889999999999999999999999999974
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=35.28 E-value=1e+02 Score=20.93 Aligned_cols=37 Identities=14% Similarity=0.394 Sum_probs=26.3
Q ss_pred CeEEEEEecCce-eEEEEEeeCCC--CCCCCceEEEEEEe
Q 028490 152 DVIRASYDKSRK-VLDLGWLWKPS--FNRDGKCKVSASFR 188 (208)
Q Consensus 152 d~vratY~~s~k-~lgleWsr~s~--~~~~G~fKv~a~~~ 188 (208)
..|++.|...+. .+.++|...+. ...-|.|.|...+.
T Consensus 18 ~~V~v~~~dGs~~~~~V~W~~~~~~~~~~~G~y~v~G~v~ 57 (59)
T PF07532_consen 18 ETVTVTYSDGSTEEVPVTWDPIDPYDYNKPGTYTVTGTVE 57 (59)
T ss_pred CEEEEEECCCCEEEEEeEeCCCChhhccCCEEEEEEEEEe
Confidence 578888877665 89999985322 23358899988753
No 19
>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=34.77 E-value=85 Score=24.62 Aligned_cols=28 Identities=29% Similarity=0.482 Sum_probs=19.7
Q ss_pred eeEEeeEEEecC--CCceeEEEEeeCCCee
Q 028490 89 RTILDGTLLLDP--TNKISANYVLDSRNLK 116 (208)
Q Consensus 89 rT~lDgtl~~D~--aNKls~~y~~~s~n~k 116 (208)
..+++|+|.||+ ..+|.+.|.+=.++++
T Consensus 34 ~l~I~G~L~f~~~~~~~L~a~~I~V~~Gg~ 63 (125)
T PF10162_consen 34 SLIIGGTLIFDDDRDITLRAEYILVEGGGR 63 (125)
T ss_pred EEEEEEEEEEccCCCCEEEEEEEEECCCCe
Confidence 445699999998 5677888877544433
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=34.46 E-value=51 Score=28.46 Aligned_cols=49 Identities=16% Similarity=0.357 Sum_probs=37.2
Q ss_pred EEEEEEecCceeEEEE-----EeeCCccCcCccEEEEecCceEEEeeeCCCCCeEEE
Q 028490 14 TGTVAADAGELKLRAY-----VIAGPALNASDLSFSVEKPGSFLVDFDVPQKNVRFQ 65 (208)
Q Consensus 14 ~atv~~~aGdlklrAs-----f~~GpsL~~~GLsL~vEKPGsF~iDydv~~~d~rFQ 65 (208)
++-|+..-|.|-.|-- |-.|||| |+.++-.--=.|++.||+|.-+--||
T Consensus 51 ~~GlrYGeG~L~~k~~g~~~vyWqGPSi---G~D~G~~~~r~~~LVYnL~~~~~iy~ 104 (160)
T PF06577_consen 51 VVGLRYGEGTLYTKNAGQHKVYWQGPSI---GFDFGGNGSRVFMLVYNLPDPDDIYQ 104 (160)
T ss_pred EEEEEecccEEEEcCCCeeEEEEeCCce---eEeecCCceEEEEEEEcCCCHHHHhh
Confidence 4455666666666554 8899999 57787777778999999999887666
No 21
>TIGR02011 IscA iron-sulfur cluster assembly protein IscA. This clade is limited to the proteobacteria.
Probab=34.24 E-value=55 Score=24.80 Aligned_cols=32 Identities=19% Similarity=0.551 Sum_probs=21.3
Q ss_pred ccEEEEecCc----eEEEee--eCCCCCeEEEEeeeeee
Q 028490 40 DLSFSVEKPG----SFLVDF--DVPQKNVRFQFMNTARI 72 (208)
Q Consensus 40 GLsL~vEKPG----sF~iDy--dv~~~d~rFQFmnt~~V 72 (208)
+|+|.|+.+| +|.+.+ ++...|.-|++ +.++|
T Consensus 23 ~lRi~v~~~GCsG~~y~l~l~~~~~~~D~v~~~-~g~~v 60 (105)
T TIGR02011 23 GLRLGVKTSGCSGMAYVLEFVDEPTPDDIVFED-KGVKI 60 (105)
T ss_pred eEEEEEeCCCCCCEEEEeeecCCCCCCCEEEEc-CCEEE
Confidence 6788888765 455554 55667888885 55555
No 22
>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=33.85 E-value=4.2e+02 Score=25.19 Aligned_cols=111 Identities=14% Similarity=0.222 Sum_probs=73.7
Q ss_pred CCccCcCccEEEEecCceEEEeeeCCCCCeEEEEeeeeeecceeeeEEEeeecCCceeEEeeEEEecCCCceeEEEEeeC
Q 028490 33 GPALNASDLSFSVEKPGSFLVDFDVPQKNVRFQFMNTARILEKQLYMTYTHMTGENRTILDGTLLLDPTNKISANYVLDS 112 (208)
Q Consensus 33 GpsL~~~GLsL~vEKPGsF~iDydv~~~d~rFQFmnt~~V~~K~lnlTYtH~~~~nrT~lDgtl~~D~aNKls~~y~~~s 112 (208)
+.... |+.++||---...+|-+-+.+++ +|+-=+.+- ++||. .++.|++-++-|
T Consensus 137 ~~~~~--~~q~gl~~g~fs~F~l~~~~~~l----vnaDy~vgi--~~T~r------------------~~~fS~R~R~yH 190 (338)
T PF06727_consen 137 SRFAE--GWQFGLQGGVFSRFNLDAPSSDL----VNADYIVGI--PLTFR------------------RGEFSARFRLYH 190 (338)
T ss_pred CCccc--cEEEEeeceeecccCCCCccccc----cccceEEee--eeeee------------------ecCceEEEEEEE
Confidence 44566 99999998444444444444432 565444332 33443 357899999988
Q ss_pred CCeeEEEEEEeCCeeeeeeecccCcceeeeEEEEEecCCCeEEEEEe-----------cCceeEEEEEe
Q 028490 113 RNLKLRYSYVHRGMATFEPCYDFGKNSWELAVSKTVFDGDVIRASYD-----------KSRKVLDLGWL 170 (208)
Q Consensus 113 ~n~klKYsYvH~g~tt~EP~yD~~~nsWdfavs~kv~~~d~vratY~-----------~s~k~lgleWs 170 (208)
-..+|.+-|....++.|| .+++.-|.-++.+|+.+..+-+|=+-|+ ..+=..|+||.
T Consensus 191 iSSHlGDEfll~~~~~~~-r~n~S~E~l~l~~S~~~~P~lRvYgG~gyl~~~~p~~~~p~~~Q~GvE~r 258 (338)
T PF06727_consen 191 ISSHLGDEFLLRNLPNFE-RFNYSREFLDLFLSYDFTPNLRVYGGYGYLFHTDPSEIKPWSFQAGVEYR 258 (338)
T ss_pred eeccccchhhhccCCCCC-CcccChhhheeEEEeecCCCEEEEeeeeEEEEcCCCCCCCcEEEeeEEEc
Confidence 889999998877777886 5799999999999988754444433332 12335788887
No 23
>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=31.67 E-value=1.6e+02 Score=24.52 Aligned_cols=53 Identities=17% Similarity=0.302 Sum_probs=0.0
Q ss_pred eeEEEEeeCCCeeEEEEEEeCCeeeeeeecccCcceeeeEEEEEecCCCeEEEEEecCce
Q 028490 104 ISANYVLDSRNLKLRYSYVHRGMATFEPCYDFGKNSWELAVSKTVFDGDVIRASYDKSRK 163 (208)
Q Consensus 104 ls~~y~~~s~n~klKYsYvH~g~tt~EP~yD~~~nsWdfavs~kv~~~d~vratY~~s~k 163 (208)
+.+.|.++..+.++...|.+.....- ..+.|.+++++++ +.=.+.+.|+...+
T Consensus 188 ~~~~Y~~~~~~~~~~~~y~~~~~~~~------~~~~~~~ga~y~~-~~~~l~a~y~~~~~ 240 (311)
T PF13609_consen 188 AGASYSFGGFGLTVAAGYSSADDNGG------DNDAWGVGASYNF-GGFTLGAEYGQADN 240 (311)
T ss_dssp EEEEEEET-SSEEEEEEEEEEECCET------CEEEEEEEEEEEC-SSEEEEEEEEEEEE
T ss_pred EEEEEEcCCcceEEEeeeecccccch------heeeEEeeEEEEE-CcEEEEEEEEEEEe
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=31.53 E-value=80 Score=27.00 Aligned_cols=32 Identities=22% Similarity=0.490 Sum_probs=24.4
Q ss_pred ccEEEEecCc----eEEEee----eCCCCCeEEEEeeeeee
Q 028490 40 DLSFSVEKPG----SFLVDF----DVPQKNVRFQFMNTARI 72 (208)
Q Consensus 40 GLsL~vEKPG----sF~iDy----dv~~~d~rFQFmnt~~V 72 (208)
||+|+|++.| +|-++| ++...|..|++ +.++|
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 65665
No 25
>PF14352 DUF4402: Domain of unknown function (DUF4402)
Probab=30.94 E-value=2.5e+02 Score=21.65 Aligned_cols=60 Identities=23% Similarity=0.326 Sum_probs=36.5
Q ss_pred CceEEEeeeCCCCCeEEEEeeeeeecc----eeeeEEEee------------ecCCceeEEeeEEEecCCCceeEEEE
Q 028490 48 PGSFLVDFDVPQKNVRFQFMNTARILE----KQLYMTYTH------------MTGENRTILDGTLLLDPTNKISANYV 109 (208)
Q Consensus 48 PGsF~iDydv~~~d~rFQFmnt~~V~~----K~lnlTYtH------------~~~~nrT~lDgtl~~D~aNKls~~y~ 109 (208)
||.|.|.- -|++.+.+++..++.+.. ..+.++-.- ..+...--|-|+|.++ +|...+.|.
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 89999998 667888888875555532 233322221 1244445566777776 455566665
No 26
>PF04357 DUF490: Family of unknown function (DUF490); InterPro: IPR007452 This family contains several proteins of uncharacterised function.
Probab=30.73 E-value=3.7e+02 Score=23.54 Aligned_cols=32 Identities=19% Similarity=0.110 Sum_probs=19.2
Q ss_pred eeeEEEEEecCCCeEEEEEecC-ce-eEEEEEee
Q 028490 140 WELAVSKTVFDGDVIRASYDKS-RK-VLDLGWLW 171 (208)
Q Consensus 140 Wdfavs~kv~~~d~vratY~~s-~k-~lgleWsr 171 (208)
+++.+.|++...=++++.++.. .. -++|.|.+
T Consensus 344 ~~~~l~y~l~~~~~l~~~~~~~~~~~g~~l~y~~ 377 (379)
T PF04357_consen 344 GEFSLEYRLNPNLSLRGSSDSGNTSQGVDLIYRK 377 (379)
T ss_pred EEEEEEEEEcCCEEEEEEEEcCCCceEEEEEEEE
Confidence 5666667777666666666443 11 36666654
No 27
>KOG3126 consensus Porin/voltage-dependent anion-selective channel protein [Inorganic ion transport and metabolism]
Probab=30.61 E-value=4.4e+02 Score=24.40 Aligned_cols=106 Identities=12% Similarity=0.234 Sum_probs=58.7
Q ss_pred ceeeeEEEeeecCCceeEEeeEEEecCCCce-eEEEEeeCCCeeEEEEEEe----CCeeeeeeecccCcceeeeEEEEEe
Q 028490 74 EKQLYMTYTHMTGENRTILDGTLLLDPTNKI-SANYVLDSRNLKLRYSYVH----RGMATFEPCYDFGKNSWELAVSKTV 148 (208)
Q Consensus 74 ~K~lnlTYtH~~~~nrT~lDgtl~~D~aNKl-s~~y~~~s~n~klKYsYvH----~g~tt~EP~yD~~~nsWdfavs~kv 148 (208)
...+++.|.|.-.-=++ | .++-+|.+ -++-.+++.+--+.|-+.- +.++.. .+-++=..||+.+.-.+
T Consensus 111 s~Klk~~y~~~~~~~~~--~---~~~~~~P~i~~s~v~g~~g~l~G~~~~fDt~~~~~t~~--n~~lgy~~~d~~l~~~~ 183 (281)
T KOG3126|consen 111 SGKLKLSYARDHFNLGA--D---DFLTANPLILGSLVLGHEGWLLGYETTFDTASGKLTKY--NAALGYTTEDFTLHLNL 183 (281)
T ss_pred ceeeecccccccceeee--c---cccccCCeEEEEEEecccceEEEEeEEEeccCCcEeeE--EEEEEeecCCcEEEEEe
Confidence 45788888884322111 1 22222222 2233334444333333322 233333 33345567888888887
Q ss_pred c-CCCeEEEEEecCcee----EEEEEeeCCCCCCCCceEEEEEEec
Q 028490 149 F-DGDVIRASYDKSRKV----LDLGWLWKPSFNRDGKCKVSASFRL 189 (208)
Q Consensus 149 ~-~~d~vratY~~s~k~----lgleWsr~s~~~~~G~fKv~a~~~L 189 (208)
- +.+..+++||.-..- ..++|.+.++.. .|-|.+.-.|
T Consensus 184 nn~~~~~~s~yq~v~~~~~~~~~~~~~~~~~~~---~~~igt~Y~l 226 (281)
T KOG3126|consen 184 NNGTEFLASIYQRVNEKLETGANAEWIAGSSNT---RFTIGTKYAL 226 (281)
T ss_pred cccchhhhhhhhhhcchheeeeeEEEeecCCcc---EEEEEEEecc
Confidence 5 677888889876654 578999988642 5666665554
No 28
>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.
Probab=30.58 E-value=74 Score=26.02 Aligned_cols=15 Identities=47% Similarity=0.753 Sum_probs=12.6
Q ss_pred ceeEEeeEEEecCCC
Q 028490 88 NRTILDGTLLLDPTN 102 (208)
Q Consensus 88 nrT~lDgtl~~D~aN 102 (208)
.-|+|||.|++|-.+
T Consensus 68 ~~TLLDGElV~d~~~ 82 (192)
T PF01331_consen 68 QDTLLDGELVLDKDP 82 (192)
T ss_dssp CSEEEEEEEEEEECT
T ss_pred CCEEEEEEEEcccCC
Confidence 579999999999554
No 29
>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=29.04 E-value=3.2e+02 Score=23.00 Aligned_cols=92 Identities=16% Similarity=0.094 Sum_probs=59.6
Q ss_pred eeEEeeEEEecCCCceeEEEEeeCCCeeEEEEEEeCCeeeeeeecccCcceeeeEEEEEecCCCeEEEEEecCceeEEEE
Q 028490 89 RTILDGTLLLDPTNKISANYVLDSRNLKLRYSYVHRGMATFEPCYDFGKNSWELAVSKTVFDGDVIRASYDKSRKVLDLG 168 (208)
Q Consensus 89 rT~lDgtl~~D~aNKls~~y~~~s~n~klKYsYvH~g~tt~EP~yD~~~nsWdfavs~kv~~~d~vratY~~s~k~lgle 168 (208)
..-++|.+.++=..=....=.|.+-+++|.|.- ...++-.+.++++ +-...++- .++.+.+.-...+..+.++
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 445677776654432222223444556677763 4445666677777 44444443 3788999998888889988
Q ss_pred EeeCCCCCCCCceEEEEEEec
Q 028490 169 WLWKPSFNRDGKCKVSASFRL 189 (208)
Q Consensus 169 Wsr~s~~~~~G~fKv~a~~~L 189 (208)
..-.=.. .|.|++.+++..
T Consensus 171 g~~~l~~--~g~y~~~~~~~p 189 (221)
T PF01203_consen 171 GQASLSP--DGRYRLDGTVKP 189 (221)
T ss_pred EEEEEcC--CCeEEEEEEEec
Confidence 7765434 779999999885
No 30
>PF11383 DUF3187: Protein of unknown function (DUF3187); InterPro: IPR021523 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=27.32 E-value=5e+02 Score=23.99 Aligned_cols=128 Identities=19% Similarity=0.274 Sum_probs=77.5
Q ss_pred EeeCCccCcCccEE------EEec-------CceEEEeeeCCCCCeEEEEeeeeeecceeeeEEEee-ecCCceeEEeeE
Q 028490 30 VIAGPALNASDLSF------SVEK-------PGSFLVDFDVPQKNVRFQFMNTARILEKQLYMTYTH-MTGENRTILDGT 95 (208)
Q Consensus 30 f~~GpsL~~~GLsL------~vEK-------PGsF~iDydv~~~d~rFQFmnt~~V~~K~lnlTYtH-~~~~nrT~lDgt 95 (208)
+..|=-|+ |+.- |+.. ...|.|+| +...-.+++|-....+.+=++.+.|.= .....+..|=|+
T Consensus 102 ~~~~g~LD--g~i~~fHd~fGi~q~GR~~~~~~~f~~~~-~~~G~~~~~~~~~~~~gdv~~~~~yql~~~~~~~lslg~s 178 (319)
T PF11383_consen 102 YASGGHLD--GFIEDFHDFFGIPQNGRDEVPKDRFRYDY-PRYGIELFDFSGETLLGDVTLYLQYQLYQNDHHGLSLGGS 178 (319)
T ss_pred EecCCcch--hHHHHHHHhhCCCCCCcccccCCeEEEEe-cCCCcccccccCccchhheeEEEEEEEecCCCceEEEEEE
Confidence 55666777 7653 3332 35788888 456777888888877777788888864 334556677777
Q ss_pred EEecC--CCceeEEEEeeCCCeeEEEEEEeC----------------CeeeeeeecccCcceeeeE--EEEEecCCCeEE
Q 028490 96 LLLDP--TNKISANYVLDSRNLKLRYSYVHR----------------GMATFEPCYDFGKNSWELA--VSKTVFDGDVIR 155 (208)
Q Consensus 96 l~~D~--aNKls~~y~~~s~n~klKYsYvH~----------------g~tt~EP~yD~~~nsWdfa--vs~kv~~~d~vr 155 (208)
|-+.. ..++..+=+++ ....|.|+|.++ +.....|.|. ++.|.++ +-+++.+...+.
T Consensus 179 lk~~t~d~~~~~GSGs~d-~~l~ln~s~~~~~~~~~~~~~G~~~~~~~~~l~~~~~~--~~~~~~~~g~~y~~~~~~~l~ 255 (319)
T PF11383_consen 179 LKYPTGDSGRFTGSGSFD-QALQLNYSYRYGSKHSLYATLGYTFRGDSDVLEGIPYR--NNTWFGGLGYGYQLTENHSLL 255 (319)
T ss_pred EEecCCCcccccCCcccc-ceEEEEeeeccCCcceeeeeeeEEEecCcccccccccc--cceEEEEEEEEEEecCCEEEE
Confidence 77765 33333332222 334455555444 3222223444 5555554 456677899999
Q ss_pred EEEecCce
Q 028490 156 ASYDKSRK 163 (208)
Q Consensus 156 atY~~s~k 163 (208)
+-|+.++-
T Consensus 256 ~q~~~~qg 263 (319)
T PF11383_consen 256 AQYDYYQG 263 (319)
T ss_pred EEEEEeec
Confidence 98887754
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=27.03 E-value=4.5e+02 Score=23.35 Aligned_cols=74 Identities=16% Similarity=0.040 Sum_probs=37.8
Q ss_pred eeeEEEeeecCCc--eeEEeeEEEecCCCceeE--EEEee--CCCeeEEEEEEeCCeeeee----eecccCcceeeeEEE
Q 028490 76 QLYMTYTHMTGEN--RTILDGTLLLDPTNKISA--NYVLD--SRNLKLRYSYVHRGMATFE----PCYDFGKNSWELAVS 145 (208)
Q Consensus 76 ~lnlTYtH~~~~n--rT~lDgtl~~D~aNKls~--~y~~~--s~n~klKYsYvH~g~tt~E----P~yD~~~nsWdfavs 145 (208)
.++++|.+.+-+. ...-+..+...|...+++ +|.+. .=++.+.|.|+.+.-.+.. ...--+-..+|+.++
T Consensus 506 ~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~dl~~~ 585 (635)
T cd01347 506 TGSYTYTDTEVKRTDGATTGNRLPGIPKHTANLGLDYELPDEGLTAGGGVRYRGKQYADTANGNNTVKVPGYTLVDLSAS 585 (635)
T ss_pred EEEEEEEeeecccccccccCCcCCCCCCeeEEEEEEEecCCCCeEEEEEEEEEcceeccccCCccceecCCcEEEeeEEE
Confidence 5566777765321 122233456667777766 44444 2335555666544322211 001123346888888
Q ss_pred EEec
Q 028490 146 KTVF 149 (208)
Q Consensus 146 ~kv~ 149 (208)
+++.
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=26.48 E-value=1e+02 Score=26.57 Aligned_cols=33 Identities=18% Similarity=0.344 Sum_probs=24.3
Q ss_pred ccEEEEecCc----eEEEee----eCCCCCeEEEEeeeeeec
Q 028490 40 DLSFSVEKPG----SFLVDF----DVPQKNVRFQFMNTARIL 73 (208)
Q Consensus 40 GLsL~vEKPG----sF~iDy----dv~~~d~rFQFmnt~~V~ 73 (208)
||+|+|+++| ++-++| ++...|..|++ +.++|.
T Consensus 24 ~LRI~V~~gGCsG~~Y~~~~~~~~~~~~~D~v~e~-~gv~v~ 64 (192)
T PRK11190 24 QIRVFVINPGTPNAECGVSYCPPDAVEATDTELKF-DGFSAY 64 (192)
T ss_pred eEEEEEECCCcCCceeeeEEeecCCCCCCCEEEEe-CCEEEE
Confidence 8999999998 356666 34567888886 777763
No 33
>KOG1047 consensus Bifunctional leukotriene A4 hydrolase/aminopeptidase LTA4H [Lipid transport and metabolism; Posttranslational modification, protein turnover, chaperones; Defense mechanisms; Amino acid transport and metabolism]
Probab=25.00 E-value=2.3e+02 Score=29.13 Aligned_cols=62 Identities=16% Similarity=0.178 Sum_probs=43.6
Q ss_pred eEEEEEEecCceeEEEEEeeCCccCcCccEEEEecCce-------EEEeeeCCCCCeEEEEeeeeeeccee
Q 028490 13 LTGTVAADAGELKLRAYVIAGPALNASDLSFSVEKPGS-------FLVDFDVPQKNVRFQFMNTARILEKQ 76 (208)
Q Consensus 13 ~~atv~~~aGdlklrAsf~~GpsL~~~GLsL~vEKPGs-------F~iDydv~~~d~rFQFmnt~~V~~K~ 76 (208)
.+..|+++..+..++..+..+..= +|+.|.++-|-+ ..|.|.--....-+||+|.-.-.+|+
T Consensus 59 ~i~~v~i~~~~~~~~i~~~~~~~g--~~~~~~l~~~~~~a~~~~~l~i~y~Ts~~atalqwL~peQT~gk~ 127 (613)
T KOG1047|consen 59 SIRNVTINGEEPPFRIGFRQPFLG--SGQKLVLPAPSSKAGERLQLLIWYETSPSATALQWLNPEQTSGKK 127 (613)
T ss_pred eeEEeeccCCCCCCccCcccCCCC--CceEEEeccccccccCceEEEEEEeccCCcceeEEeccccccCCC
Confidence 344555666666666655333322 367777775555 78999988889999999999999987
No 34
>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=23.92 E-value=87 Score=24.00 Aligned_cols=49 Identities=16% Similarity=0.342 Sum_probs=42.5
Q ss_pred EEEecCCCceeEEEEeeCCCeeEEEEEEeCCeeeeeeecccCcceeeeEEEE
Q 028490 95 TLLLDPTNKISANYVLDSRNLKLRYSYVHRGMATFEPCYDFGKNSWELAVSK 146 (208)
Q Consensus 95 tl~~D~aNKls~~y~~~s~n~klKYsYvH~g~tt~EP~yD~~~nsWdfavs~ 146 (208)
=|.+|...+|.++-.+.. .|..+-.+..++-.++|-..+ .+.|-+|+.+
T Consensus 54 YLcmn~~G~ly~~~~~~~-~C~F~e~~~~n~y~~~~s~~~--~~~~yla~~~ 102 (122)
T PF00167_consen 54 YLCMNKCGRLYGSKNFNK-DCVFREELLENGYNTYESAKY--GRGWYLAFNR 102 (122)
T ss_dssp EEEEBTTSBEEEESSBTG-GGEEEEEEETTSEEEEEESTT--GTTEBCEBCT
T ss_pred EEEECCCCeEccccccCC-CceEEEEEccCCEEEEEeccC--CccEEEEECC
Confidence 378999999999877776 999999999999999998877 7788888776
No 35
>PF07608 DUF1571: Protein of unknown function (DUF1571); InterPro: IPR011465 This is a family of paralogous proteins found in Planctomycetacia and Betaproteobacteria.
Probab=23.79 E-value=3.4e+02 Score=24.26 Aligned_cols=63 Identities=14% Similarity=0.255 Sum_probs=48.7
Q ss_pred CeEEEEeeeeeecceee-eEEEeeecCCce-eEEeeEEEecCCCceeEEEEe--------eCCCeeEEEEEEe
Q 028490 61 NVRFQFMNTARILEKQL-YMTYTHMTGENR-TILDGTLLLDPTNKISANYVL--------DSRNLKLRYSYVH 123 (208)
Q Consensus 61 d~rFQFmnt~~V~~K~l-nlTYtH~~~~nr-T~lDgtl~~D~aNKls~~y~~--------~s~n~klKYsYvH 123 (208)
..+-.|.=...+.++|+ -|+++|++++.. ..==..+.||..++|=+.|.. +.+..-=+|+|.+
T Consensus 119 ~~~~~~~~~~~~~gr~~~~l~~~~p~~~~~~~f~~~~v~iD~e~~lpir~e~y~wp~~~~~~~~L~E~Y~y~~ 191 (213)
T PF07608_consen 119 ESEVTFVENATFDGRPVTALQYEHPTKRPQFDFHKAEVYIDDELGLPIRVEAYDWPESEDNDGELVEEYVYTD 191 (213)
T ss_pred ccceeeccccccCCceEEEEEEECCCCCCCcceeEEEEEEccccCCcEEEEeccCCCCCCCCCcEEEEEEEEe
Confidence 56777777888888775 689999887777 677777889999999998877 3445555788843
No 36
>PF12100 DUF3576: Domain of unknown function (DUF3576); InterPro: IPR021959 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 100 amino acids in length. This domain has a single completely conserved residue G that may be functionally important.
Probab=23.77 E-value=1.2e+02 Score=24.45 Aligned_cols=26 Identities=31% Similarity=0.308 Sum_probs=23.9
Q ss_pred ecCceeEEEE-EeeCCccCcCccEEEE
Q 028490 20 DAGELKLRAY-VIAGPALNASDLSFSV 45 (208)
Q Consensus 20 ~aGdlklrAs-f~~GpsL~~~GLsL~v 45 (208)
+.++-++|++ |+-+|.|++++|.++|
T Consensus 40 ~~~~er~k~tv~Ild~~Lradal~V~v 66 (103)
T PF12100_consen 40 PGPNERFKATVYILDRALRADALRVSV 66 (103)
T ss_pred CCCCeeEEEEEEEECccccCCceEEEE
Confidence 4788999999 9999999999999998
No 37
>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=23.46 E-value=29 Score=24.97 Aligned_cols=14 Identities=21% Similarity=0.631 Sum_probs=12.2
Q ss_pred ecccCcceeeeEEE
Q 028490 132 CYDFGKNSWELAVS 145 (208)
Q Consensus 132 ~yD~~~nsWdfavs 145 (208)
.||..+..|+|.++
T Consensus 22 ~YD~~Tr~W~F~L~ 35 (55)
T PF07443_consen 22 NYDPKTRKWNFSLE 35 (55)
T ss_pred ccCccceeeeeeHH
Confidence 69999999999853
No 38
>TIGR01785 TonB-hemin TonB-dependent heme/hemoglobin receptor family protein. This model represents the TonB-dependent outer membrane heme/hemoglobin receptor/transporter found in bacteria which live in contact with animals (which contain hemoglobin or other heme-bearing globins) or legumes (which contain leghemoglobin). Some species having hits to this model such as Nostoc, Caulobacter and Chlorobium do not have an obvious source of hemoglobin-like proteins in their biological niche and so the possibility exists that they act on some other substance.
Probab=23.40 E-value=1.6e+02 Score=27.52 Aligned_cols=32 Identities=22% Similarity=0.185 Sum_probs=25.0
Q ss_pred cccCcceeeeEEEEEecCCCeEEEEEecCcee
Q 028490 133 YDFGKNSWELAVSKTVFDGDVIRASYDKSRKV 164 (208)
Q Consensus 133 yD~~~nsWdfavs~kv~~~d~vratY~~s~k~ 164 (208)
.+...-++.+++++++.++-.++++|..+-+.
T Consensus 397 ~~~~~~~p~~~~~y~~~~~~~~~~~~~~~~r~ 428 (665)
T TIGR01785 397 RSYSRWSPSLGLSYKPVDWLTLYASYSQGFRA 428 (665)
T ss_pred ccccccCCcceEEEEecCCcEEEEeeeeeccC
Confidence 44556677889999999888999999877554
No 39
>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=22.59 E-value=1.8e+02 Score=24.97 Aligned_cols=90 Identities=16% Similarity=0.161 Sum_probs=48.9
Q ss_pred CCCCCeEEEEeeeeeecc-eeeeEEEee-ec----CCceeEEeeEEEecCCCce---eEEEEeeCCCeeEEEEEEeC---
Q 028490 57 VPQKNVRFQFMNTARILE-KQLYMTYTH-MT----GENRTILDGTLLLDPTNKI---SANYVLDSRNLKLRYSYVHR--- 124 (208)
Q Consensus 57 v~~~d~rFQFmnt~~V~~-K~lnlTYtH-~~----~~nrT~lDgtl~~D~aNKl---s~~y~~~s~n~klKYsYvH~--- 124 (208)
-|+.-.|+-+-+.-.-.. |+..|++.- +| --..-+.+-.+++|....- .+.+-++..+|.+.|.|.+|
T Consensus 33 ~~~a~lr~~~~~~~~~~~~k~FEi~~~~lPR~f~~~~~sGv~~~~~~l~~~~e~~l~ng~i~ie~~~~~~~~~y~~gs~v 112 (240)
T PF01803_consen 33 SPDAVLRISLWNEDGNGSPKQFEITRPLLPRYFRTLFESGVKRMQLVLDGPREQVLPNGSIFIECPRATFIYWYEDGSQV 112 (240)
T ss_pred CCCeeEEEEEEcCCCCCCCeeEEEchHHHHHHHHHHhcCCceEEEEEecCCceEEcCCCeEEEEECCEEEEEEECCceEE
Confidence 344455555554444333 555555432 11 1122344444555332221 23667777888888888776
Q ss_pred ---CeeeeeeecccCcceeeeEEEE
Q 028490 125 ---GMATFEPCYDFGKNSWELAVSK 146 (208)
Q Consensus 125 ---g~tt~EP~yD~~~nsWdfavs~ 146 (208)
|...+.=..++-=+.|||.+..
T Consensus 113 ~~~G~lr~~f~~~lKIe~~df~~~~ 137 (240)
T PF01803_consen 113 VHEGQLRAQFDPDLKIEWWDFCTRS 137 (240)
T ss_pred EEEeEEEEEECccccEEEEEEEeec
Confidence 3333444677888899988654
No 40
>PF07523 Big_3: Bacterial Ig-like domain (group 3); InterPro: IPR011080 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.; PDB: 2L7Y_A 2KPN_A.
Probab=22.34 E-value=83 Score=21.72 Aligned_cols=40 Identities=28% Similarity=0.360 Sum_probs=24.0
Q ss_pred ecCceeEEEEEeeCCccCcCccEEEE----ecCceEEEeeeCCC
Q 028490 20 DAGELKLRAYVIAGPALNASDLSFSV----EKPGSFLVDFDVPQ 59 (208)
Q Consensus 20 ~aGdlklrAsf~~GpsL~~~GLsL~v----EKPGsF~iDydv~~ 59 (208)
+.-++.++|..-+|-++..+++.+.. .|||.+.|-|....
T Consensus 15 d~~~~~v~at~~dG~~~~~~~~~vs~~~d~~~~G~y~Vt~~y~~ 58 (67)
T PF07523_consen 15 DPTGLFVTATYSDGTSLPLSDVTVSGTVDTSKAGTYTVTYTYKG 58 (67)
T ss_dssp -HHCHEEEEEETTS-ES-GCCSEEES---TTS-CCEEEEEEECT
T ss_pred CccCCEEEEEEcCCCEeceeeeEEEeeeecCCCceEEEEEEECC
Confidence 34457777777777777666666655 37777777666655
No 41
>TIGR03016 pepcterm_hypo_1 uncharacterized protein, PEP-CTERM system associated. Members of this protein family are found predominantly in exopolysaccharide biosynthesis operons marked by the presence of the EpsH-family putative exosortase and presence in the genome of the PEP-CTERM protein sorting signal. Members of this family may be distantly related to the EpsL family modeled in TIGR03014.
Probab=22.31 E-value=5.9e+02 Score=23.99 Aligned_cols=42 Identities=24% Similarity=0.301 Sum_probs=26.4
Q ss_pred eeEEEEeeC-CCeeEEEEEEeCCeeeeeeecccCcceeeeEEEEE
Q 028490 104 ISANYVLDS-RNLKLRYSYVHRGMATFEPCYDFGKNSWELAVSKT 147 (208)
Q Consensus 104 ls~~y~~~s-~n~klKYsYvH~g~tt~EP~yD~~~nsWdfavs~k 147 (208)
++++|.|.. -.+.|.|.|....- . -+..++..|.+-+.++.+
T Consensus 388 ~gl~Y~~~~~~~~~l~Y~y~~~dS-n-~~~~~Y~~N~i~l~l~~~ 430 (431)
T TIGR03016 388 AGLSYQLGENTTGSLTYRYQERDS-N-FEATDYTENRLMAEVTMT 430 (431)
T ss_pred EEEEEEecCCcEEEEEEEEEEecC-C-cccCchhheEEEEEEEEe
Confidence 567777742 44667777766542 2 256777777777776654
No 42
>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=22.17 E-value=2.4e+02 Score=23.79 Aligned_cols=54 Identities=20% Similarity=0.153 Sum_probs=31.8
Q ss_pred eeEEEEeeCCCeeEEEEEEeCCeeeeeeecccCcceeeeEEEEEecCCCeEEEEEe
Q 028490 104 ISANYVLDSRNLKLRYSYVHRGMATFEPCYDFGKNSWELAVSKTVFDGDVIRASYD 159 (208)
Q Consensus 104 ls~~y~~~s~n~klKYsYvH~g~tt~EP~yD~~~nsWdfavs~kv~~~d~vratY~ 159 (208)
+.+.|.|+. +.++...|.+.....-.. =+...+.|.+++.+.+...-.+-+.|.
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 567777763 566666665543211100 033456788888888877766766665
No 43
>TIGR03509 OMP_MtrB_PioB decaheme-associated outer membrane protein, MtrB/PioB family. Members of this protein family are integral proteins of the bacterial outer membrane, associated with multiheme c-type cytochromes involved in electron transfer. The MtrB protein of Shewanella oneidensis MR-1 (SO1776) has been shown to form a complex with 1:1:1 stochiometry with the small, periplasmic decaheme cytochrome MtrA and large, surface-exposed decaheme cytochrome MtrC.
Probab=22.09 E-value=3.8e+02 Score=26.63 Aligned_cols=29 Identities=31% Similarity=0.265 Sum_probs=19.6
Q ss_pred ecccCcceeeeEEEEEecCCCeEEEEEec
Q 028490 132 CYDFGKNSWELAVSKTVFDGDVIRASYDK 160 (208)
Q Consensus 132 ~yD~~~nsWdfavs~kv~~~d~vratY~~ 160 (208)
.||--+..+.+.+.+++.++.++.+.|+.
T Consensus 346 ~~d~~~~~~sl~~dy~l~~~~tLt~G~d~ 374 (649)
T TIGR03509 346 PYDKTKQKAELAADYRFTRSVKLTAGYDY 374 (649)
T ss_pred ccccceeeceEEEEEEecCCeEEEeeEEE
Confidence 36666667777777777666667766664
No 44
>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=21.83 E-value=4.1e+02 Score=21.09 Aligned_cols=63 Identities=21% Similarity=0.383 Sum_probs=40.9
Q ss_pred cCceEEEeeeCCCCCeEEEEeeeeeecceeeeEEEeeecCC-----ceeEEeeEEEecCCCceeEEEEeeCCCeeEEE
Q 028490 47 KPGSFLVDFDVPQKNVRFQFMNTARILEKQLYMTYTHMTGE-----NRTILDGTLLLDPTNKISANYVLDSRNLKLRY 119 (208)
Q Consensus 47 KPGsF~iDydv~~~d~rFQFmnt~~V~~K~lnlTYtH~~~~-----nrT~lDgtl~~D~aNKls~~y~~~s~n~klKY 119 (208)
+||| |.|++....++|+-... ++.+.+.|.-..++ ..-++.|.+ +..+.+.|.=.+- +|-=||
T Consensus 60 ~~gS--v~~~~~~~~~~F~i~D~----~~~i~V~Y~G~~Pd~F~eg~~VVv~G~~--~~~g~F~A~~lL~--KcpskY 127 (131)
T PF03100_consen 60 VEGS--VEYDPDGNTLTFTITDG----GKEIPVVYTGPLPDLFREGQGVVVEGRL--GEDGVFEATELLA--KCPSKY 127 (131)
T ss_dssp ECTT--EEE-TTSSEEEEEEE-S----S-EEEEEEES--CTT--TTSEEEEEEEE--CCTSEEEEEEEEE--TS----
T ss_pred ccCC--EEEcCCCCEEEEEEEEC----CcEEEEEECCCCCccccCCCeEEEEEEE--CCCCEEEEEEEEe--CCCCCC
Confidence 8898 88888888888887665 57799999986543 356889987 7777887776653 444444
No 45
>TIGR03067 Planc_TIGR03067 Planctomycetes uncharacterized domain TIGR03067. This domain occurs in several species, mostly from the Planctomycetes division of the bacteria. It is expanded into a paralogous family of at least twenty-five members in Gemmata obscuriglobus UQM 2246. This family appears related to TIGR03066, which also is expanded into a large paralogous family in Gemmata obscuriglobus.
Probab=21.66 E-value=3.9e+02 Score=20.68 Aligned_cols=39 Identities=21% Similarity=0.264 Sum_probs=24.7
Q ss_pred ceeeeEEEeeecCCceeEEeeEEEecCCCceeEEEEeeCCCeeEEEEEEeCC
Q 028490 74 EKQLYMTYTHMTGENRTILDGTLLLDPTNKISANYVLDSRNLKLRYSYVHRG 125 (208)
Q Consensus 74 ~K~lnlTYtH~~~~nrT~lDgtl~~D~aNKls~~y~~~s~n~klKYsYvH~g 125 (208)
.+|-.|+++...++. -..++.++|.|+. -+|+-||.-+|
T Consensus 60 ~~Pk~id~~~~~g~~-----------~g~~~~gIY~l~g--d~L~vC~~~~g 98 (107)
T TIGR03067 60 ANPKTIDLTSPDGPD-----------KGKTIKGIYKLDG--DTLTVCFSGGG 98 (107)
T ss_pred CCccEEEEEccCCCC-----------CCCEEEEEEEEcC--CEEEEEECCCC
Confidence 367777776533322 1246788999963 48888886554
No 46
>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=21.42 E-value=2.4e+02 Score=19.61 Aligned_cols=57 Identities=19% Similarity=0.257 Sum_probs=33.8
Q ss_pred EEEEecCceEEEeeeCCCCCeEEEEeeeeeecceeeeEEEeeecCCceeEEeeEEEecCCC
Q 028490 42 SFSVEKPGSFLVDFDVPQKNVRFQFMNTARILEKQLYMTYTHMTGENRTILDGTLLLDPTN 102 (208)
Q Consensus 42 sL~vEKPGsF~iDydv~~~d~rFQFmnt~~V~~K~lnlTYtH~~~~nrT~lDgtl~~D~aN 102 (208)
+|.|++|..|-|.|+--. ..+. ++...|......=.+.. .+.+.+.++..+.++..+
T Consensus 1 ~l~v~NPN~~~i~~~~~~--~~v~-~~g~~v~~~~~~~~~~i-~~~~~~~v~~~v~~~~~~ 57 (101)
T PF03168_consen 1 TLSVRNPNSFGIRYDSIE--YDVY-YNGQRVGTGGSLPPFTI-PARSSTTVPVPVSVDYSD 57 (101)
T ss_dssp EEEEEESSSS-EEEEEEE--EEEE-ESSSEEEEEEECE-EEE-SSSCEEEEEEEEEEEHHH
T ss_pred CEEEECCCceeEEEeCEE--EEEE-ECCEEEECccccCCeEE-CCCCcEEEEEEEEEcHHH
Confidence 478999999888885333 2222 26677763333333444 366667788887777653
No 47
>COG4771 FepA Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]
Probab=21.19 E-value=1.5e+02 Score=30.84 Aligned_cols=83 Identities=24% Similarity=0.272 Sum_probs=49.1
Q ss_pred eeeEEEeeecCCce------------eEEeeEEEecCCCceeEEEEeeCCCeeEEEEEEeCCeeeeeeecccCcc-----
Q 028490 76 QLYMTYTHMTGENR------------TILDGTLLLDPTNKISANYVLDSRNLKLRYSYVHRGMATFEPCYDFGKN----- 138 (208)
Q Consensus 76 ~lnlTYtH~~~~nr------------T~lDgtl~~D~aNKls~~y~~~s~n~klKYsYvH~g~tt~EP~yD~~~n----- 138 (208)
.+|+||+|+..++. -.++++|-.-+.++|++- ++++|.-. ..+|.++-..+
T Consensus 565 ~~nyTY~~seqk~~~~gg~pLs~~P~h~~N~~L~Wq~~~~ls~~---------~~~~~~Gk---q~~~~~~~s~~~~~~~ 632 (699)
T COG4771 565 SLNYTYTLSEQKDGDTGGKPLSDTPEHTLNSTLDWQPTEDLSLW---------LTWTYYGK---QPPPKHNYSGNPADGA 632 (699)
T ss_pred eeeeEEEeeccccccccCCccccCchhhhcccccceechhcccc---------ceeEEEec---ccCccccccCCccccc
Confidence 78999999652222 236777777777776653 33333211 11333322222
Q ss_pred ---------eeeeEEEEEecCCCeEEEE-EecCceeEEEEEe
Q 028490 139 ---------SWELAVSKTVFDGDVIRAS-YDKSRKVLDLGWL 170 (208)
Q Consensus 139 ---------sWdfavs~kv~~~d~vrat-Y~~s~k~lgleWs 170 (208)
-|+.++++++..+=+|+|. |---.|.|.=+|.
T Consensus 633 ~~~~~~~Yti~~~ga~y~~tkn~sL~agV~NLfDK~l~~~~~ 674 (699)
T COG4771 633 SGKYLGAYTIVDLGATYDVTKNVSLNAGVYNLFDKRLSRDGN 674 (699)
T ss_pred cccccCceEEEecceeeeeccceeeehhhhhhcchhhccccc
Confidence 4999999999999888864 4444555544433
No 48
>PRK09289 riboflavin synthase subunit alpha; Provisional
Probab=21.12 E-value=1.7e+02 Score=25.06 Aligned_cols=30 Identities=13% Similarity=0.271 Sum_probs=22.5
Q ss_pred EeeCCccCcCccEEEEe--cCceEEEeeeCCC
Q 028490 30 VIAGPALNASDLSFSVE--KPGSFLVDFDVPQ 59 (208)
Q Consensus 30 f~~GpsL~~~GLsL~vE--KPGsF~iDydv~~ 59 (208)
.+.|-|..+||.+|+|. ....|.+|.=|+.
T Consensus 132 l~~kgSIavdGvsLTV~~~~~~~f~v~lipeT 163 (194)
T PRK09289 132 IVEKGSIAVDGVSLTVNEVDGDRFSVNLIPHT 163 (194)
T ss_pred cccCCEEEEccEEEEEEEEcCCEEEEEEeHHH
Confidence 45688888889999998 5677777765554
No 49
>PF07705 CARDB: CARDB; InterPro: IPR011635 The APHP (acidic peptide-dependent hydrolases/peptidase) domain is found in a variety of different proteins.; PDB: 2KUT_A 2L0D_A 3IDU_A 2KL6_A.
Probab=20.91 E-value=2.9e+02 Score=19.01 Aligned_cols=71 Identities=17% Similarity=0.184 Sum_probs=33.3
Q ss_pred cCceeEEEEEee-CCccCcCccEEEEecCceEEEeeeCCCCCeEEEEeeeeeecc-eeeeEEEeeecCCceeEEeeEEEe
Q 028490 21 AGELKLRAYVIA-GPALNASDLSFSVEKPGSFLVDFDVPQKNVRFQFMNTARILE-KQLYMTYTHMTGENRTILDGTLLL 98 (208)
Q Consensus 21 aGdlklrAsf~~-GpsL~~~GLsL~vEKPGsF~iDydv~~~d~rFQFmnt~~V~~-K~lnlTYtH~~~~nrT~lDgtl~~ 98 (208)
...+++.+.+.| |..- +.++.+.+.-.|..+ .-+.+....-.+ +.+.++++.. ..-...-.+++
T Consensus 18 g~~~~i~~~V~N~G~~~-~~~~~v~~~~~~~~~----------~~~~i~~L~~g~~~~v~~~~~~~---~~G~~~i~~~i 83 (101)
T PF07705_consen 18 GEPVTITVTVKNNGTAD-AENVTVRLYLDGNSV----------STVTIPSLAPGESETVTFTWTPP---SPGSYTIRVVI 83 (101)
T ss_dssp TSEEEEEEEEEE-SSS--BEEEEEEEEETTEEE----------EEEEESEB-TTEEEEEEEEEE-S---S-CEEEEEEEE
T ss_pred CCEEEEEEEEEECCCCC-CCCEEEEEEECCcee----------ccEEECCcCCCcEEEEEEEEEeC---CCCeEEEEEEE
Confidence 455666666554 4432 224555544444333 222222222112 4455555543 33345578899
Q ss_pred cCCCcee
Q 028490 99 DPTNKIS 105 (208)
Q Consensus 99 D~aNKls 105 (208)
|+.|++.
T Consensus 84 D~~n~i~ 90 (101)
T PF07705_consen 84 DPDNDID 90 (101)
T ss_dssp STTTSS-
T ss_pred eeCCccc
Confidence 9999874
No 50
>PF07691 PA14: PA14 domain; InterPro: IPR011658 The PA14 domain forms an insert in bacterial beta-glucosidases, other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium pre-spore cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding [].; PDB: 2XVG_A 2XVK_A 2XVL_A 2XJU_A 2XJT_A 2XJQ_A 2XJS_A 2XJV_A 2XJP_A 2XJR_A ....
Probab=20.85 E-value=3.6e+02 Score=20.02 Aligned_cols=24 Identities=21% Similarity=0.217 Sum_probs=13.2
Q ss_pred CCeEEEEEecCcee---EEEEEeeCCC
Q 028490 151 GDVIRASYDKSRKV---LDLGWLWKPS 174 (208)
Q Consensus 151 ~d~vratY~~s~k~---lgleWsr~s~ 174 (208)
-..||..|...... +.|.|.+...
T Consensus 111 ~y~i~i~y~~~~~~~~~~~l~w~~p~~ 137 (145)
T PF07691_consen 111 KYPIRIEYFNRGGDASLIQLSWTPPGG 137 (145)
T ss_dssp EEEEEEEEEECSCSSCCEEEEEE-TTS
T ss_pred eEEEEEEEEECCCCCEEEEEEEECCCC
Confidence 45666666544332 4778876544
No 51
>PRK09504 sufA iron-sulfur cluster assembly scaffold protein; Provisional
Probab=20.71 E-value=1.6e+02 Score=23.20 Aligned_cols=32 Identities=13% Similarity=0.266 Sum_probs=21.2
Q ss_pred ccEEEEecCceEE------EeeeCCCCCeEEEEeeeeee
Q 028490 40 DLSFSVEKPGSFL------VDFDVPQKNVRFQFMNTARI 72 (208)
Q Consensus 40 GLsL~vEKPGsF~------iDydv~~~d~rFQFmnt~~V 72 (208)
||++.||.+|+-- ++.++...|..|++ +.++|
T Consensus 40 ~LRi~v~~gGCsG~~Y~~~l~~e~~~~D~v~e~-~g~~v 77 (122)
T PRK09504 40 GVRLGVKQTGCAGFGYVLDSVSEPDKDDLVFEH-DGAKL 77 (122)
T ss_pred eEEEEEECCCCCceEEEeeecCCCCCCCEEEEe-CCEEE
Confidence 8999999998432 23445567888875 44444
No 52
>PF10082 DUF2320: Uncharacterized protein conserved in bacteria (DUF2320); InterPro: IPR018759 This domain has no known function.
Probab=20.54 E-value=6e+02 Score=22.45 Aligned_cols=111 Identities=20% Similarity=0.198 Sum_probs=62.3
Q ss_pred eeeEEEeee---cCCceeEEeeEEEecC--CCceeEEEEeeC--CC--eeEEEEEEeCCeee---------eeeecccCc
Q 028490 76 QLYMTYTHM---TGENRTILDGTLLLDP--TNKISANYVLDS--RN--LKLRYSYVHRGMAT---------FEPCYDFGK 137 (208)
Q Consensus 76 ~lnlTYtH~---~~~nrT~lDgtl~~D~--aNKls~~y~~~s--~n--~klKYsYvH~g~tt---------~EP~yD~~~ 137 (208)
.++..|.+. ++.-.++....++-+| .|-+++.|.+.. +. ..+++.|.+-.-.. .-.-.|.-.
T Consensus 98 ~~~~~~~~~~e~~~~~~~~~~~~~~~~pv~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~Y~~~~~~~g~~~~~~~~d~~~ 177 (381)
T PF10082_consen 98 DLGGSYRRGHEPRGSGDTFGGSDVQDDPVERNTFSASYGYGARFGRGRLSLGAGYDRLRYDNARDSDGTTISTSDRDRDE 177 (381)
T ss_pred EEEEEEEEEeccCCCCccccccccccCceEEEEEEEEEEEEEEcCCEEEEEEEEEEEEEEecccccCCccccccccccce
Confidence 455566553 3444444433455555 688999999853 33 44555554431111 112235555
Q ss_pred ceeeeEEEEEecCCCeEE-------EEEe-------------cCceeEEEEEeeCCCCCCCCceEEEEEEe
Q 028490 138 NSWELAVSKTVFDGDVIR-------ASYD-------------KSRKVLDLGWLWKPSFNRDGKCKVSASFR 188 (208)
Q Consensus 138 nsWdfavs~kv~~~d~vr-------atY~-------------~s~k~lgleWsr~s~~~~~G~fKv~a~~~ 188 (208)
......+.+++...-.+- ..|+ ...-.+|++|.-..+. .|.++|.....
T Consensus 178 ~~~~~~~~Y~~~p~~~~~~~~~~~~~~Yd~~~~~~~~~rDs~~~~~~~G~~~~~t~~~--~g~~~~Gy~~~ 246 (381)
T PF10082_consen 178 YTAGARLGYRLSPGTSLFVEVRYTDRDYDNRADPNGSSRDSTGYEVLAGVSWDLTGKT--RGEAKVGYQRR 246 (381)
T ss_pred eEEEEEEEEecCCCcEEEEEEEEeEEEcccccCcccccccCCceEEEEEEEEcccCcE--EEEEEEEEEEe
Confidence 666666666555544442 2344 1233589999999999 88888875443
No 53
>smart00758 PA14 domain in bacterial beta-glucosidases other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins.
Probab=20.43 E-value=3.8e+02 Score=20.10 Aligned_cols=71 Identities=15% Similarity=0.240 Sum_probs=36.9
Q ss_pred EEEEeeCCccCcCccEEEEe--cCceEEEee-----eCCCCCeEEEEeeeeeeccee-eeEEEeeecCCceeEEeeEEEe
Q 028490 27 RAYVIAGPALNASDLSFSVE--KPGSFLVDF-----DVPQKNVRFQFMNTARILEKQ-LYMTYTHMTGENRTILDGTLLL 98 (208)
Q Consensus 27 rAsf~~GpsL~~~GLsL~vE--KPGsF~iDy-----dv~~~d~rFQFmnt~~V~~K~-lnlTYtH~~~~nrT~lDgtl~~ 98 (208)
++.|.+++.+. |+..... ....|.-.. .++..++-.+|-....+-+-= -.+. .-+.+.-|..|||.+++
T Consensus 4 ~~~y~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~g~i~~~~~G~y~f~-~~~~~~~~l~Idg~~vi 80 (136)
T smart00758 4 TGYYFENEKFS--GLPEIIDTDPLNTFYWDSDKFGEGEKADNFSVRWTGYLKPPEDGEYTFS-ITSDDGARLWIDGKLVI 80 (136)
T ss_pred EEEEeCCCCcC--CCccEEecCCcEEeeccCCCCCCCcCCCcEEEEEEEEEECCCCccEEEE-EEcCCcEEEEECCcEEE
Confidence 56666777776 6655322 333332222 233334455555555443211 1111 12457778889999999
Q ss_pred cC
Q 028490 99 DP 100 (208)
Q Consensus 99 D~ 100 (208)
|.
T Consensus 81 d~ 82 (136)
T smart00758 81 DN 82 (136)
T ss_pred cC
Confidence 85
No 54
>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=20.24 E-value=1.5e+02 Score=21.89 Aligned_cols=27 Identities=22% Similarity=0.418 Sum_probs=13.7
Q ss_pred ccEEEEecCce----EEEeee--CCCCCeEEEE
Q 028490 40 DLSFSVEKPGS----FLVDFD--VPQKNVRFQF 66 (208)
Q Consensus 40 GLsL~vEKPGs----F~iDyd--v~~~d~rFQF 66 (208)
+|+|.++.+|+ |.+.++ +...|.-++.
T Consensus 23 ~lRi~~~~~Gc~G~~~~l~l~~~~~~~D~~~~~ 55 (105)
T TIGR00049 23 GLRVGVKGGGCSGLQYGLEFDDEPNEDDEVFEQ 55 (105)
T ss_pred EEEEEEecCCCCCeEEEEeecCCCCCCCEEEEc
Confidence 56666666553 344443 3344666653
No 55
>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=20.00 E-value=46 Score=26.62 Aligned_cols=22 Identities=18% Similarity=0.288 Sum_probs=4.2
Q ss_pred ecCCCceeEEEEeeCCCeeEEEE
Q 028490 98 LDPTNKISANYVLDSRNLKLRYS 120 (208)
Q Consensus 98 ~D~aNKls~~y~~~s~n~klKYs 120 (208)
=|-|||+.+...|+ |+|.|-|-
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
Done!