Query 033308
Match_columns 122
No_of_seqs 91 out of 93
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 12:19:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033308.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033308hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00088 predicted protein; Pr 100.0 2.7E-39 5.8E-44 242.6 8.1 119 1-121 1-126 (127)
2 PF06596 PsbX: Photosystem II 99.8 4.5E-20 9.8E-25 115.6 2.7 37 85-121 1-38 (39)
3 CHL00114 psbX photosystem II p 99.8 1.3E-19 2.8E-24 113.8 3.8 37 85-121 1-38 (39)
4 PF04956 TrbC: TrbC/VIRB2 fami 70.4 11 0.00023 25.3 4.3 52 66-118 16-75 (99)
5 PF14187 DUF4310: Domain of un 67.4 9.1 0.0002 31.6 4.1 41 74-116 94-134 (209)
6 TIGR03579 EF_0833 conserved hy 55.5 19 0.00041 29.8 3.9 40 74-115 92-131 (209)
7 PF12732 YtxH: YtxH-like prote 51.4 13 0.00028 24.4 2.0 16 92-107 1-16 (74)
8 PF09813 Coiled-coil_56: Coile 48.3 19 0.00041 26.8 2.6 30 88-117 48-77 (100)
9 PF13706 PepSY_TM_3: PepSY-ass 40.2 18 0.00039 21.5 1.2 26 94-121 11-37 (37)
10 PHA02680 ORF090 IMV phosphoryl 38.9 28 0.0006 25.7 2.2 29 87-115 5-35 (91)
11 PF05767 Pox_A14: Poxvirus vir 37.3 22 0.00048 26.1 1.6 31 87-117 5-37 (92)
12 PF04835 Pox_A9: A9 protein co 33.3 72 0.0016 21.5 3.4 33 88-120 21-53 (54)
13 PHA03048 IMV membrane protein; 30.7 32 0.0007 25.4 1.5 29 88-116 6-36 (93)
14 PF07423 DUF1510: Protein of u 29.9 63 0.0014 26.3 3.2 25 91-115 13-38 (217)
15 COG4062 MtrB Tetrahydromethano 29.7 55 0.0012 24.8 2.6 18 87-104 75-92 (108)
16 PRK10927 essential cell divisi 28.7 54 0.0012 28.6 2.7 22 97-118 38-59 (319)
17 TIGR03546 conserved hypothetic 28.4 56 0.0012 25.2 2.5 21 89-109 102-122 (154)
18 COG2354 Uncharacterized protei 25.9 66 0.0014 28.0 2.8 21 85-105 274-294 (303)
19 PF05283 MGC-24: Multi-glycosy 25.1 35 0.00077 27.3 1.0 23 91-113 157-179 (186)
20 PHA02898 virion envelope prote 25.0 46 0.00099 24.6 1.5 30 88-117 6-37 (92)
21 TIGR02838 spore_V_AC stage V s 23.5 70 0.0015 24.9 2.3 21 85-105 13-33 (141)
22 PF14575 EphA2_TM: Ephrin type 22.4 97 0.0021 21.0 2.6 22 93-114 3-24 (75)
23 PF09835 DUF2062: Uncharacteri 21.8 1E+02 0.0022 22.3 2.7 24 88-111 112-135 (154)
24 PF11021 DUF2613: Protein of u 20.6 1.9E+02 0.0042 19.3 3.6 25 94-118 10-34 (56)
25 TIGR02761 TraE_TIGR type IV co 20.0 92 0.002 23.8 2.3 25 90-114 17-41 (181)
No 1
>PLN00088 predicted protein; Provisional
Probab=100.00 E-value=2.7e-39 Score=242.62 Aligned_cols=119 Identities=36% Similarity=0.503 Sum_probs=103.4
Q ss_pred CCcccccc-ccccccc-ccccc---cccccccc-ccCCCCchhhhhhhcCCCCceEEeecchhHHHHHHHH-HHHHhhhc
Q 033308 1 MTSSSAIS-MAIPLTH-ASQKM---VVNSEAFF-KPLPVKPSKVLAAASKSSGRFEVEASSLKEKAVTALM-AALAASMV 73 (122)
Q Consensus 1 MAS~Sa~s-ma~pla~-as~~~---~pss~~ff-~Plp~rps~~~~~~~~~~~r~~v~As~~k~k~~~glt-aa~~Asm~ 73 (122)
|||++..+ .+.++++ +++.| .++.|+|- .+-+.||+++...+| |+|+|++++.+|||+++|+| +|++|+|+
T Consensus 1 ma~~~~~s~~~a~~~~~~t~~~~~k~~~~~g~~l~~p~~~~~~~~~~~n--~~r~~~~as~~~ekav~gltaaAl~Asmv 78 (127)
T PLN00088 1 MACAAMASVSSAATAPLATLVWEAKLLSRQGLALAAPSGKKQVSVAISN--RSRVVMSLPAKEDHNVASLTSLALLAAAV 78 (127)
T ss_pred CchHHHHHhhccccchhhHhhhhhhhhccccceecCCCCccchhhhhcc--cceeEEecchHHHHHHHHHHHHHHHHHhh
Confidence 77776555 4667777 77774 59999993 331378888887755 69999999669999999999 89999999
Q ss_pred chHHHHhcCCCCChhHHHHHHHHHHHHHHHHHHHhhheeeecCCCccc
Q 033308 74 IPEVAEAAGPGVSSSLTNFLLSIAAGGVVLAALIGAVIGVSNFDPIKR 121 (122)
Q Consensus 74 ~P~vAeAa~~~mTPSL~NFL~SlvaGgvVv~~i~~ali~VSq~D~V~R 121 (122)
+||||||||+||||||+||||||+|||+|++.|+++||||||||||+|
T Consensus 79 ~pevAeAA~~gvTPSLsNFL~SLvaGgvVv~pI~~Ali~VSq~D~V~R 126 (127)
T PLN00088 79 VPEIAEAAQPGVSPSLKNLLLSVVAGGVVITVIGVAVAGVSTFDPVKR 126 (127)
T ss_pred CHHHHHhccCCCChhHHHHHHHHHhhhhhhhhhheeeEEEeccCcccc
Confidence 999999999999999999999999999999999999999999999999
No 2
>PF06596 PsbX: Photosystem II reaction centre X protein (PsbX); InterPro: IPR009518 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. The low molecular weight transmembrane protein PsbX found in PSII is associated with the oxygen-evolving complex. Its expression is light-regulated. PsbX appears to be involved in the regulation of the amount of PSII [], and may be involved in the binding or turnover of quinone molecules at the Qb (PsbA) site [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0016020 membrane; PDB: 3ARC_x 3A0H_X 3A0B_X 3PRR_X 1S5L_x 4FBY_j 3PRQ_X 3KZI_X 3BZ2_X 3BZ1_X.
Probab=99.79 E-value=4.5e-20 Score=115.59 Aligned_cols=37 Identities=51% Similarity=0.829 Sum_probs=29.4
Q ss_pred CChhHHHHHHHHHHHH-HHHHHHHhhheeeecCCCccc
Q 033308 85 VSSSLTNFLLSIAAGG-VVLAALIGAVIGVSNFDPIKR 121 (122)
Q Consensus 85 mTPSL~NFL~SlvaGg-vVv~~i~~ali~VSq~D~V~R 121 (122)
|||||+|||+||+||| +|++.|+++|++|||+|+|+|
T Consensus 1 mTpSL~nfl~Sl~aG~~iVv~~i~~ali~VSq~D~v~R 38 (39)
T PF06596_consen 1 MTPSLSNFLLSLVAGAVIVVIPIAGALIFVSQFDRVKR 38 (39)
T ss_dssp --HHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCS----
T ss_pred CCHhHHHHHHHHHhhhhhhhhhhhhheEEEeccCcccc
Confidence 8999999999999999 666679999999999999999
No 3
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=99.78 E-value=1.3e-19 Score=113.76 Aligned_cols=37 Identities=27% Similarity=0.419 Sum_probs=35.7
Q ss_pred CChhHHHHHHHHHHHHHHHH-HHHhhheeeecCCCccc
Q 033308 85 VSSSLTNFLLSIAAGGVVLA-ALIGAVIGVSNFDPIKR 121 (122)
Q Consensus 85 mTPSL~NFL~SlvaGgvVv~-~i~~ali~VSq~D~V~R 121 (122)
|||||+|||+||+||++|++ .|+++|+||||+|+++|
T Consensus 1 MTpSLsnF~~SL~~Ga~ivvipi~~aLifvSq~D~v~R 38 (39)
T CHL00114 1 MTPSLSAFINSLLLGAIIVVIPITLALLFVSQKDRTTR 38 (39)
T ss_pred CChhHHHHHHHHHHHHHHhHHHhhhheEEEeccceecc
Confidence 89999999999999999988 59999999999999999
No 4
>PF04956 TrbC: TrbC/VIRB2 family; InterPro: IPR007039 Conjugal transfer protein, TrbC has been identified as a subunit of the pilus precursor in bacteria. The protein undergoes three processing steps before gaining its mature cyclic structure[]. This family also contains several VirB2 type IV secretion proteins. The virB2 gene encodes a putative type IV secretion system and is known to be a pathogenicity factor in Bartonella species [].
Probab=70.38 E-value=11 Score=25.34 Aligned_cols=52 Identities=15% Similarity=0.214 Sum_probs=26.8
Q ss_pred HHHHhhhcchHHHHhcCCCCChhH-------HHHHHH-HHHHHHHHHHHHhhheeeecCCC
Q 033308 66 AALAASMVIPEVAEAAGPGVSSSL-------TNFLLS-IAAGGVVLAALIGAVIGVSNFDP 118 (122)
Q Consensus 66 aa~~Asm~~P~vAeAa~~~mTPSL-------~NFL~S-lvaGgvVv~~i~~ali~VSq~D~ 118 (122)
..+...+.+|+.|-|++.+. ... .++|.+ +.-.-.+++++..++....+.+.
T Consensus 16 ~~~~~~~~~~~~A~A~~~~~-~~~~~~l~~i~~~l~gp~~~~i~~i~ii~~g~~~~~g~~~ 75 (99)
T PF04956_consen 16 LLALALLLLASPAFAQGGGG-DPWTSFLCKIIDWLTGPIGKAIAIIAIIVAGIMMMFGRQS 75 (99)
T ss_pred HHHHHHHHhCchhhhcCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcC
Confidence 55556777888888876654 333 334444 22222233345555555554443
No 5
>PF14187 DUF4310: Domain of unknown function (DUF4310)
Probab=67.41 E-value=9.1 Score=31.58 Aligned_cols=41 Identities=29% Similarity=0.484 Sum_probs=32.0
Q ss_pred chHHHHhcCCCCChhHHHHHHHHHHHHHHHHHHHhhheeeecC
Q 033308 74 IPEVAEAAGPGVSSSLTNFLLSIAAGGVVLAALIGAVIGVSNF 116 (122)
Q Consensus 74 ~P~vAeAa~~~mTPSL~NFL~SlvaGgvVv~~i~~ali~VSq~ 116 (122)
+|.+--++ |.+-.++||-+||+-|+++=.+|...+|++-+|
T Consensus 94 ipAllL~~--Gi~~p~~~F~laLl~G~~iG~~iG~iIi~iRK~ 134 (209)
T PF14187_consen 94 IPALLLSA--GITAPLENFPLALLTGAVIGLIIGYIIILIRKF 134 (209)
T ss_pred hHHHHHhc--cccchHHHhHHHHHHHHHHHHHHhheeEEEEee
Confidence 34444454 688899999999999999888888888877653
No 6
>TIGR03579 EF_0833 conserved hypothetical protein EF_0833/AHA_3914. Members of this family of relatively rare proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown.
Probab=55.50 E-value=19 Score=29.77 Aligned_cols=40 Identities=28% Similarity=0.404 Sum_probs=30.2
Q ss_pred chHHHHhcCCCCChhHHHHHHHHHHHHHHHHHHHhhheeeec
Q 033308 74 IPEVAEAAGPGVSSSLTNFLLSIAAGGVVLAALIGAVIGVSN 115 (122)
Q Consensus 74 ~P~vAeAa~~~mTPSL~NFL~SlvaGgvVv~~i~~ali~VSq 115 (122)
+|.+--.+ |++-.++||-+||+-|+++=.+|...+|++-+
T Consensus 92 vpAllL~~--G~~~pv~nF~lsL~tG~~lG~~iG~iIi~~RK 131 (209)
T TIGR03579 92 VPAILLGA--GIVAPVENFGLSLLTGAVLGLAVGYVIILIRK 131 (209)
T ss_pred hHHHHHhc--cccccHHHHHHHHHHHHHHHHHhheeEEEEEe
Confidence 34444444 68999999999999999887777777776544
No 7
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=51.38 E-value=13 Score=24.39 Aligned_cols=16 Identities=44% Similarity=0.409 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHH
Q 033308 92 FLLSIAAGGVVLAALI 107 (122)
Q Consensus 92 FL~SlvaGgvVv~~i~ 107 (122)
|++++++|+++-++++
T Consensus 1 F~~g~l~Ga~~Ga~~g 16 (74)
T PF12732_consen 1 FLLGFLAGAAAGAAAG 16 (74)
T ss_pred CHHHHHHHHHHHHHHH
Confidence 7888888887655443
No 8
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=48.28 E-value=19 Score=26.78 Aligned_cols=30 Identities=23% Similarity=0.290 Sum_probs=25.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhheeeecCC
Q 033308 88 SLTNFLLSIAAGGVVLAALIGAVIGVSNFD 117 (122)
Q Consensus 88 SL~NFL~SlvaGgvVv~~i~~ali~VSq~D 117 (122)
.-+|-+.++..|++|+++-+--+..|+|-|
T Consensus 48 R~rN~~Tgl~L~~~v~gIY~YTi~sV~Qe~ 77 (100)
T PF09813_consen 48 RRRNLLTGLALGAFVVGIYAYTIYSVKQED 77 (100)
T ss_pred hhhhHHHHHHHHHHHHHHHhheeeeechhh
Confidence 358999999999999999877888888865
No 9
>PF13706 PepSY_TM_3: PepSY-associated TM helix
Probab=40.20 E-value=18 Score=21.46 Aligned_cols=26 Identities=35% Similarity=0.483 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHH-HHhhheeeecCCCccc
Q 033308 94 LSIAAGGVVLAA-LIGAVIGVSNFDPIKR 121 (122)
Q Consensus 94 ~SlvaGgvVv~~-i~~ali~VSq~D~V~R 121 (122)
++|+.|-+.+++ ++|++... .|.++|
T Consensus 11 ~Gl~~g~~l~~~~~tG~~~~f--~~ei~r 37 (37)
T PF13706_consen 11 LGLILGLLLFVIFLTGAVMVF--RDEIDR 37 (37)
T ss_pred HHHHHHHHHHHHHHHhHHHHH--HHhhcC
Confidence 567777777775 66655444 455554
No 10
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=38.92 E-value=28 Score=25.66 Aligned_cols=29 Identities=21% Similarity=0.342 Sum_probs=22.3
Q ss_pred hhHHHHHHHHHHHHHHHHH--HHhhheeeec
Q 033308 87 SSLTNFLLSIAAGGVVLAA--LIGAVIGVSN 115 (122)
Q Consensus 87 PSL~NFL~SlvaGgvVv~~--i~~ali~VSq 115 (122)
--++|+..+++.||++|.+ ...|.+=.|+
T Consensus 5 ~~i~ny~s~vli~GIiLL~~ACIFAfidFSK 35 (91)
T PHA02680 5 ETLKSYYSGVLICGVLLLTAACVFAFVDFSK 35 (91)
T ss_pred HHHHHhccHHHHHHHHHHHHHHHHhhhhhhc
Confidence 3589999999999999986 4446665565
No 11
>PF05767 Pox_A14: Poxvirus virion envelope protein A14; InterPro: IPR008785 This family consists of several Poxvirus virion envelope protein A14-like sequences. A14 is a component of the virion membrane and has been found to be an H1 phosphatase substrate in vivo and in vitro. A14 is hyperphosphorylated on serine residues in the absence of H1 expression [].; GO: 0019031 viral envelope
Probab=37.28 E-value=22 Score=26.13 Aligned_cols=31 Identities=29% Similarity=0.417 Sum_probs=22.9
Q ss_pred hhHHHHHHHHHHHHHHHHH--HHhhheeeecCC
Q 033308 87 SSLTNFLLSIAAGGVVLAA--LIGAVIGVSNFD 117 (122)
Q Consensus 87 PSL~NFL~SlvaGgvVv~~--i~~ali~VSq~D 117 (122)
--|+|+..+.+.||++|.+ ...|.+=.|+.-
T Consensus 5 ~~~~n~~S~vli~GiiLL~~aCIfAfidfsK~~ 37 (92)
T PF05767_consen 5 GFLSNYFSGVLIGGIILLIAACIFAFIDFSKNT 37 (92)
T ss_pred HHHHhccchHHHHHHHHHHHHHHHHhhhhccCC
Confidence 4589999999999999986 444555555443
No 12
>PF04835 Pox_A9: A9 protein conserved region; InterPro: IPR006920 This entry represents a family of Chordopoxvirus A9 proteins. Chordopoxvirus belongs to the family Poxviridae and is the cause of vertebrate infections [].
Probab=33.29 E-value=72 Score=21.54 Aligned_cols=33 Identities=21% Similarity=0.082 Sum_probs=24.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhheeeecCCCcc
Q 033308 88 SLTNFLLSIAAGGVVLAALIGAVIGVSNFDPIK 120 (122)
Q Consensus 88 SL~NFL~SlvaGgvVv~~i~~ali~VSq~D~V~ 120 (122)
|+.+-+.=++.+-++-.+++++|+.+|+.|.-+
T Consensus 21 sF~fViik~vismimylilGi~L~yis~~~~~~ 53 (54)
T PF04835_consen 21 SFWFVIIKSVISMIMYLILGIALIYISSNDDKK 53 (54)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhccCcccc
Confidence 455556666777777778999999999988643
No 13
>PHA03048 IMV membrane protein; Provisional
Probab=30.68 E-value=32 Score=25.40 Aligned_cols=29 Identities=28% Similarity=0.438 Sum_probs=21.9
Q ss_pred hHHHHHHHHHHHHHHHHH--HHhhheeeecC
Q 033308 88 SLTNFLLSIAAGGVVLAA--LIGAVIGVSNF 116 (122)
Q Consensus 88 SL~NFL~SlvaGgvVv~~--i~~ali~VSq~ 116 (122)
-++|+....+.||++|.+ ...|.+=.|+.
T Consensus 6 ~~~ny~S~vli~GIiLL~~aCIfAfidfsK~ 36 (93)
T PHA03048 6 MISNYFSTALIGGIILLAASCIFAFVDFSKN 36 (93)
T ss_pred HhhcccchHHHHHHHHHHHHHHHhhhhhhcC
Confidence 489999999999999986 34455555554
No 14
>PF07423 DUF1510: Protein of unknown function (DUF1510); InterPro: IPR009988 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=29.90 E-value=63 Score=26.33 Aligned_cols=25 Identities=32% Similarity=0.250 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHh-hheeeec
Q 033308 91 NFLLSIAAGGVVLAALIG-AVIGVSN 115 (122)
Q Consensus 91 NFL~SlvaGgvVv~~i~~-ali~VSq 115 (122)
|-+|=++.|-|+|.+|++ .-+|+.+
T Consensus 13 N~iLNiaI~IV~lLIiiva~~lf~~~ 38 (217)
T PF07423_consen 13 NKILNIAIGIVSLLIIIVAYQLFFGG 38 (217)
T ss_pred hhhHHHHHHHHHHHHHHHhhhheecC
Confidence 556666677666666444 4455533
No 15
>COG4062 MtrB Tetrahydromethanopterin S-methyltransferase, subunit B [Coenzyme metabolism]
Probab=29.66 E-value=55 Score=24.76 Aligned_cols=18 Identities=28% Similarity=0.305 Sum_probs=14.8
Q ss_pred hhHHHHHHHHHHHHHHHH
Q 033308 87 SSLTNFLLSIAAGGVVLA 104 (122)
Q Consensus 87 PSL~NFL~SlvaGgvVv~ 104 (122)
--|+||+++++.|-.|.+
T Consensus 75 G~~tna~yGfviGl~i~a 92 (108)
T COG4062 75 GYLTNAFYGFVIGLGIMA 92 (108)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 358999999999988844
No 16
>PRK10927 essential cell division protein FtsN; Provisional
Probab=28.74 E-value=54 Score=28.61 Aligned_cols=22 Identities=23% Similarity=0.386 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHhhheeeecCCC
Q 033308 97 AAGGVVLAALIGAVIGVSNFDP 118 (122)
Q Consensus 97 vaGgvVv~~i~~ali~VSq~D~ 118 (122)
+....||++.+|+|.||+++.+
T Consensus 38 alAvavlv~fiGGLyFith~k~ 59 (319)
T PRK10927 38 AIAAAVLVTFIGGLYFITHHKK 59 (319)
T ss_pred HHHHHHHHHHhhheEEEecCCC
Confidence 3445567777888999998664
No 17
>TIGR03546 conserved hypothetical protein TIGR03546. Members of this family are uncharacterized proteins, usually encoded by a gene adjacent to a member of family TIGR03545, which is also uncharacterized.
Probab=28.45 E-value=56 Score=25.17 Aligned_cols=21 Identities=24% Similarity=0.381 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 033308 89 LTNFLLSIAAGGVVLAALIGA 109 (122)
Q Consensus 89 L~NFL~SlvaGgvVv~~i~~a 109 (122)
+..|..+++.|+++++.|.+.
T Consensus 102 l~~f~~tl~~Gg~l~Gli~~~ 122 (154)
T TIGR03546 102 LARFNNTIVMGSFVVGLILLP 122 (154)
T ss_pred HHHHHHHHHHhhHHHHHHHHH
Confidence 778889999999999986654
No 18
>COG2354 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.85 E-value=66 Score=28.01 Aligned_cols=21 Identities=33% Similarity=0.510 Sum_probs=18.9
Q ss_pred CChhHHHHHHHHHHHHHHHHH
Q 033308 85 VSSSLTNFLLSIAAGGVVLAA 105 (122)
Q Consensus 85 mTPSL~NFL~SlvaGgvVv~~ 105 (122)
..|++-|+.+.+++|+++++.
T Consensus 274 ~~~t~~~~v~g~v~G~vvv~~ 294 (303)
T COG2354 274 LVPTLLNAVLGLVIGAVVVAL 294 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999876
No 19
>PF05283 MGC-24: Multi-glycosylated core protein 24 (MGC-24); InterPro: IPR007947 CD164 is a mucin-like receptor, or sialomucin, with specificity in receptor/ ligand interactions that depends on the structural characteristics of the mucin-like receptor. Its functions include mediating, or regulating, haematopoietic progenitor cell adhesion and the negative regulation of their growth and/or-differentiation. It exists in the native state as a disulphide- linked homodimer of two 80-85kDa subunits. It is usually expressed by CD34+ and CD341o/- haematopoietic stem cells and associated microenvironmental cells. It contains, in its extracellular region, two mucin domains (I and II) linked by a non-mucin domain, which has been predicted to contain intra- disulphide bridges. This receptor may play a key role in haematopoiesis by facilitating the adhesion of human CD34+ cells to bone marrow stroma and by negatively regulating CD34+ CD341o/- haematopoietic progenitor cell proliferation. These effects involve the CD164 class I and/or II epitopes recognised by the monoclonal antibodies (mAbs) 105A5 and 103B2/9E10. These epitopes are carbohydrate-dependent and are located on the N-terminal mucin domain I [, ]. It has been found that murine MGC-24v and rat endolyn share significant sequence similarities with human CD164. However, CD164 lacks the consensus glycosaminoglycan (GAG)-attachment site found in MGC-24; it is possible that GAG-association is responsible for the high molecular weight of the epithelial-derived MGC-24 glycoprotein []. Genomic structure studies have placed CD164 within the mucin-subgroup that comprises multiple exons, and demonstrate the diverse chromosomal distribution of this family of molecules. Molecules with such multiple exons may have sophisticated regulatory mechanisms that involve not only post-translational modifications of the oligosaccharide side chains, but also differential exon usage. Although differences in the intron and exon sizes are seen between the mouse and human genes, the predicted proteins are similar in size and structure, maintaining functionally important motifs that regulate cell proliferation or subcellular distribution []. CD164 is a gene whose expression depends on differential usage of poly- adenylation sites within the 3'-UTR. The conserved distribution of the 3.2- and 1.2-kb CD164 transcripts between mouse and human suggests that (i) a mechanism may exist to regulate tissue-specific polyadenylation, and (ii) differences in polyadenylation are important for the expression and function of CD164 in different tissues. Two other aspects of the structure of CD164 are of particular interest. First, it shares one of several conserved features of a cytokine-binding pocket - in this respect, it is notable that evidence exists for a class of cell-surface sialomucin modulators that directly interact with growth factor receptors to regulate their response to physiological ligands. Second, its cytoplasmic tail contains a C-terminal YHTL motif found in many endocytic membrane proteins or receptors. These Tyr-based motifs bind to adaptor proteins, which mediate the sorting of membrane proteins into transport vesicles from the plasma membrane to the endosomes, and between intracellular compartments.
Probab=25.15 E-value=35 Score=27.30 Aligned_cols=23 Identities=30% Similarity=0.296 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHhhheee
Q 033308 91 NFLLSIAAGGVVLAALIGAVIGV 113 (122)
Q Consensus 91 NFL~SlvaGgvVv~~i~~ali~V 113 (122)
-|=-.=+.||+||+.-..+++|+
T Consensus 157 ~FD~~SFiGGIVL~LGv~aI~ff 179 (186)
T PF05283_consen 157 TFDAASFIGGIVLTLGVLAIIFF 179 (186)
T ss_pred CCchhhhhhHHHHHHHHHHHHHH
Confidence 46666678999998755555543
No 20
>PHA02898 virion envelope protein; Provisional
Probab=25.05 E-value=46 Score=24.57 Aligned_cols=30 Identities=27% Similarity=0.207 Sum_probs=22.2
Q ss_pred hHHHHHHHHHHHHHHHHH--HHhhheeeecCC
Q 033308 88 SLTNFLLSIAAGGVVLAA--LIGAVIGVSNFD 117 (122)
Q Consensus 88 SL~NFL~SlvaGgvVv~~--i~~ali~VSq~D 117 (122)
-.+|+..+++.||++|.+ ...|.+=.|+..
T Consensus 6 ~~~N~~s~vli~GIiLL~~ACIfAfidfSK~~ 37 (92)
T PHA02898 6 FFKNRPSYVVAFGIILLIVACICAYIELSKSE 37 (92)
T ss_pred hhhcCcchHHHHHHHHHHHHHHHheehhhcCC
Confidence 368999999999999986 444555555543
No 21
>TIGR02838 spore_V_AC stage V sporulation protein AC. This model describes stage V sporulation protein AC, a paralog of stage V sporulation protein AE. Both are proteins found to present in a species if and only if that species is one of the Firmicutes capable of endospore formation, as of the time of the publication of the genome of Carboxydothermus hydrogenoformans. Mutants in spoVAC have a stage V sproulation defect.
Probab=23.45 E-value=70 Score=24.87 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=18.7
Q ss_pred CChhHHHHHHHHHHHHHHHHH
Q 033308 85 VSSSLTNFLLSIAAGGVVLAA 105 (122)
Q Consensus 85 mTPSL~NFL~SlvaGgvVv~~ 105 (122)
=.|.++|+++..+.||+|-++
T Consensus 13 k~~~~~n~l~AFlvGG~IC~i 33 (141)
T TIGR02838 13 KPPYLKNCVMAFLVGGLICLI 33 (141)
T ss_pred CCcHHHHHHHHHHhCcHHHHH
Confidence 468899999999999999875
No 22
>PF14575 EphA2_TM: Ephrin type-A receptor 2 transmembrane domain; PDB: 3KUL_A 2XVD_A 2VX1_A 2VWV_A 2VX0_A 2VWY_A 2VWZ_A 2VWW_A 2VWU_A 2VWX_A ....
Probab=22.39 E-value=97 Score=20.96 Aligned_cols=22 Identities=32% Similarity=0.304 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHhhheeee
Q 033308 93 LLSIAAGGVVLAALIGAVIGVS 114 (122)
Q Consensus 93 L~SlvaGgvVv~~i~~ali~VS 114 (122)
.++++.|.++++++.+.++++.
T Consensus 3 i~~~~~g~~~ll~~v~~~~~~~ 24 (75)
T PF14575_consen 3 IASIIVGVLLLLVLVIIVIVCF 24 (75)
T ss_dssp HHHHHHHHHHHHHHHHHHHCCC
T ss_pred EehHHHHHHHHHHhheeEEEEE
Confidence 4566667666665554455443
No 23
>PF09835 DUF2062: Uncharacterized protein conserved in bacteria (DUF2062); InterPro: IPR018639 This domain, found in various prokaryotic proteins, has no known function. It is found at the C-terminal of family 2 glycosyltransferase proteins, in addition to proteins of unknown function.
Probab=21.76 E-value=1e+02 Score=22.25 Aligned_cols=24 Identities=29% Similarity=0.508 Sum_probs=19.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhe
Q 033308 88 SLTNFLLSIAAGGVVLAALIGAVI 111 (122)
Q Consensus 88 SL~NFL~SlvaGgvVv~~i~~ali 111 (122)
.+.++++.++.|++|++++.+.+.
T Consensus 112 ~~~~~~~~~~~G~~i~~~v~~~i~ 135 (154)
T PF09835_consen 112 SLWEFGLPFLLGSLILGIVLGIIS 135 (154)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678899999999999998665443
No 24
>PF11021 DUF2613: Protein of unknown function (DUF2613); InterPro: IPR022566 This is a family of putative small secreted proteins expressed by Actinobacteria. The function is not known.
Probab=20.60 E-value=1.9e+02 Score=19.29 Aligned_cols=25 Identities=24% Similarity=0.145 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHhhheeeecCCC
Q 033308 94 LSIAAGGVVLAALIGAVIGVSNFDP 118 (122)
Q Consensus 94 ~SlvaGgvVv~~i~~ali~VSq~D~ 118 (122)
-|.++|-++=++.++++-..++.|.
T Consensus 10 aSaV~Gi~lG~~av~gvt~~~~~~s 34 (56)
T PF11021_consen 10 ASAVVGIVLGVAAVFGVTAAAQQDS 34 (56)
T ss_pred HHHHHHHHHHHHHHhhhheeeecCC
Confidence 4556655544445555555666664
No 25
>TIGR02761 TraE_TIGR type IV conjugative transfer system protein TraE. TraE is a component of type IV secretion systems involved in conjugative transfer of plasmid DNA. The function of the TraE protein is unknown.
Probab=20.02 E-value=92 Score=23.81 Aligned_cols=25 Identities=24% Similarity=0.454 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhheeee
Q 033308 90 TNFLLSIAAGGVVLAALIGAVIGVS 114 (122)
Q Consensus 90 ~NFL~SlvaGgvVv~~i~~ali~VS 114 (122)
-|+++.++.|++++..+.+......
T Consensus 17 ~n~l~~l~~~~l~~~~ll~~~~~~~ 41 (181)
T TIGR02761 17 RNLLFVLVSGVLAVNVLLSIVLIVA 41 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5888888888887776555444443
Done!