Query 033248
Match_columns 123
No_of_seqs 91 out of 93
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 11:37:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033248.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033248hhsearch_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 5.9E-40 1.3E-44 246.4 8.5 119 1-123 1-127 (127)
2 PF06596 PsbX: Photosystem II 99.8 1.3E-20 2.7E-25 118.2 2.2 38 86-123 1-39 (39)
3 CHL00114 psbX photosystem II p 99.8 3.8E-20 8.2E-25 116.3 4.2 38 86-123 1-39 (39)
4 PF04956 TrbC: TrbC/VIRB2 fami 73.7 7.1 0.00015 26.2 4.0 21 66-86 15-35 (99)
5 PF14187 DUF4310: Domain of un 69.0 8.7 0.00019 31.7 4.3 41 75-117 94-134 (209)
6 PF07123 PsbW: Photosystem II 62.6 32 0.00069 26.9 6.1 56 61-118 66-127 (138)
7 TIGR03579 EF_0833 conserved hy 57.9 18 0.00039 29.9 4.2 32 85-116 100-131 (209)
8 PF12732 YtxH: YtxH-like prote 54.0 11 0.00023 24.8 2.0 16 93-108 1-16 (74)
9 PF09813 Coiled-coil_56: Coile 49.5 19 0.00042 26.8 2.8 30 89-118 48-77 (100)
10 PRK11273 glpT sn-glycerol-3-ph 42.5 86 0.0019 25.5 5.8 33 73-108 50-82 (452)
11 PHA02680 ORF090 IMV phosphoryl 39.6 23 0.0005 26.1 1.9 28 89-116 6-35 (91)
12 PF04835 Pox_A9: A9 protein co 39.3 43 0.00093 22.6 3.0 33 89-121 21-53 (54)
13 PF05767 Pox_A14: Poxvirus vir 37.5 19 0.0004 26.6 1.2 31 88-118 5-37 (92)
14 PF07423 DUF1510: Protein of u 32.0 50 0.0011 27.0 2.9 25 92-116 13-38 (217)
15 PHA03048 IMV membrane protein; 31.1 27 0.00059 25.8 1.2 29 89-117 6-36 (93)
16 PF13706 PepSY_TM_3: PepSY-ass 30.9 26 0.00057 20.8 0.9 26 95-122 11-37 (37)
17 PRK10927 essential cell divisi 30.8 49 0.0011 28.9 2.8 20 100-119 40-59 (319)
18 COG4062 MtrB Tetrahydromethano 29.2 48 0.001 25.1 2.2 17 89-105 76-92 (108)
19 COG2354 Uncharacterized protei 28.8 55 0.0012 28.5 2.8 21 86-106 274-294 (303)
20 TIGR03546 conserved hypothetic 28.3 65 0.0014 24.8 2.9 21 90-110 102-122 (154)
21 PHA02898 virion envelope prote 25.9 38 0.00082 25.0 1.2 30 89-118 6-37 (92)
22 TIGR02838 spore_V_AC stage V s 25.8 61 0.0013 25.2 2.3 21 86-106 13-33 (141)
23 PF05283 MGC-24: Multi-glycosy 24.6 30 0.00066 27.7 0.5 23 92-114 157-179 (186)
24 TIGR00712 glpT glycerol-3-phos 22.8 3E+02 0.0064 22.2 5.8 43 73-122 48-90 (438)
25 PF14575 EphA2_TM: Ephrin type 22.3 80 0.0017 21.4 2.1 22 94-115 3-24 (75)
26 TIGR03319 YmdA_YtgF conserved 21.8 32 0.00069 30.8 0.1 12 111-122 246-257 (514)
27 PF09835 DUF2062: Uncharacteri 21.5 88 0.0019 22.6 2.4 23 89-111 112-134 (154)
28 PHA00979 putative major coat p 21.1 2.2E+02 0.0047 20.5 4.2 42 71-114 21-67 (77)
29 PF11021 DUF2613: Protein of u 20.7 1.8E+02 0.0039 19.4 3.5 25 95-119 10-34 (56)
30 PRK00106 hypothetical protein; 20.2 36 0.00077 31.1 0.1 12 111-122 267-278 (535)
No 1
>PLN00088 predicted protein; Provisional
Probab=100.00 E-value=5.9e-40 Score=246.43 Aligned_cols=119 Identities=41% Similarity=0.558 Sum_probs=106.0
Q ss_pred Cccccc----cccchh-hhhhccc-CCCccccccCCC-CCccchhhhccCCCCccceeeehh-hhhHHHHhhHHHHHHhh
Q 033248 1 MASVSM----AMPLSS-ATQNRLI-QPSSESFLKPLP-VRPSKAARFLGKPKSRARLQVQAS-LKEKAVTGLTAAALTAS 72 (123)
Q Consensus 1 MAS~Sm----a~pl~~-at~~~~~-~pss~~~~~Plp-~r~~~~~~~~~~~~~~~r~~~~as-~k~k~~~gltaaa~~As 72 (123)
|||++| +.++++ ++|.|+. .++.|+|-.--| .|+++++.. .+|+|+|++++ +|||+++|+|++|++|+
T Consensus 1 ma~~~~~s~~~a~~~~~~t~~~~~k~~~~~g~~l~~p~~~~~~~~~~----~n~~r~~~~as~~~ekav~gltaaAl~As 76 (127)
T PLN00088 1 MACAAMASVSSAATAPLATLVWEAKLLSRQGLALAAPSGKKQVSVAI----SNRSRVVMSLPAKEDHNVASLTSLALLAA 76 (127)
T ss_pred CchHHHHHhhccccchhhHhhhhhhhhccccceecCCCCccchhhhh----cccceeEEecchHHHHHHHHHHHHHHHHH
Confidence 788775 357777 8899988 899998875445 677777755 34789999998 89999999999999999
Q ss_pred hcchHHHHhhcCCCChhHHHHHHHHHHhHHHHHHHhhheeeeeccCcccCC
Q 033248 73 MVIPEVAEAAGSGLSPSLKNFLLSIVAGGVVLAAIVGAVIGVANFDPVKRT 123 (123)
Q Consensus 73 ~~~P~vAeAa~~~mTPSL~NFL~SLvaGgvVv~~i~~Ali~VSq~D~V~R~ 123 (123)
|++|||||||++||||||+||||||+|||+|++.|+++||||||||||+|+
T Consensus 77 mv~pevAeAA~~gvTPSLsNFL~SLvaGgvVv~pI~~Ali~VSq~D~V~R~ 127 (127)
T PLN00088 77 AVVPEIAEAAQPGVSPSLKNLLLSVVAGGVVITVIGVAVAGVSTFDPVKRK 127 (127)
T ss_pred hhCHHHHHhccCCCChhHHHHHHHHHhhhhhhhhhheeeEEEeccCccccC
Confidence 999999999999999999999999999999999999999999999999996
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=99.80 E-value=1.3e-20 Score=118.24 Aligned_cols=38 Identities=58% Similarity=0.922 Sum_probs=29.4
Q ss_pred CChhHHHHHHHHHHhH-HHHHHHhhheeeeeccCcccCC
Q 033248 86 LSPSLKNFLLSIVAGG-VVLAAIVGAVIGVANFDPVKRT 123 (123)
Q Consensus 86 mTPSL~NFL~SLvaGg-vVv~~i~~Ali~VSq~D~V~R~ 123 (123)
|||||+|||+||+||| +|++.|+++|++|||+|+++|+
T Consensus 1 mTpSL~nfl~Sl~aG~~iVv~~i~~ali~VSq~D~v~R~ 39 (39)
T PF06596_consen 1 MTPSLSNFLLSLVAGAVIVVIPIAGALIFVSQFDRVKRS 39 (39)
T ss_dssp --HHHHHHHHHHHHHH-HHHHHHHHHHHHHHCCS-----
T ss_pred CCHhHHHHHHHHHhhhhhhhhhhhhheEEEeccCccccC
Confidence 8999999999999999 6666799999999999999996
No 3
>CHL00114 psbX photosystem II protein X; Reviewed
Probab=99.80 E-value=3.8e-20 Score=116.29 Aligned_cols=38 Identities=29% Similarity=0.511 Sum_probs=36.4
Q ss_pred CChhHHHHHHHHHHhHHHHH-HHhhheeeeeccCcccCC
Q 033248 86 LSPSLKNFLLSIVAGGVVLA-AIVGAVIGVANFDPVKRT 123 (123)
Q Consensus 86 mTPSL~NFL~SLvaGgvVv~-~i~~Ali~VSq~D~V~R~ 123 (123)
|||||+|||+||+||++|++ .|++||+||||+|+++|+
T Consensus 1 MTpSLsnF~~SL~~Ga~ivvipi~~aLifvSq~D~v~R~ 39 (39)
T CHL00114 1 MTPSLSAFINSLLLGAIIVVIPITLALLFVSQKDRTTRN 39 (39)
T ss_pred CChhHHHHHHHHHHHHHHhHHHhhhheEEEeccceeccC
Confidence 99999999999999999988 599999999999999996
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=73.69 E-value=7.1 Score=26.22 Aligned_cols=21 Identities=24% Similarity=0.164 Sum_probs=13.9
Q ss_pred HHHHHhhhcchHHHHhhcCCC
Q 033248 66 AAALTASMVIPEVAEAAGSGL 86 (123)
Q Consensus 66 aaa~~As~~~P~vAeAa~~~m 86 (123)
.+.+...+.+|+.|-|++.+.
T Consensus 15 ~~~~~~~~~~~~~A~A~~~~~ 35 (99)
T PF04956_consen 15 LLLALALLLLASPAFAQGGGG 35 (99)
T ss_pred HHHHHHHHHhCchhhhcCCCC
Confidence 344456777888888876554
No 5
>PF14187 DUF4310: Domain of unknown function (DUF4310)
Probab=69.02 E-value=8.7 Score=31.74 Aligned_cols=41 Identities=32% Similarity=0.526 Sum_probs=31.9
Q ss_pred chHHHHhhcCCCChhHHHHHHHHHHhHHHHHHHhhheeeeecc
Q 033248 75 IPEVAEAAGSGLSPSLKNFLLSIVAGGVVLAAIVGAVIGVANF 117 (123)
Q Consensus 75 ~P~vAeAa~~~mTPSL~NFL~SLvaGgvVv~~i~~Ali~VSq~ 117 (123)
+|.+--++ +.+-.++||-+||+-|+++=.+|...+|+|-+|
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 34444444 588899999999999999888888888887653
No 6
>PF07123 PsbW: Photosystem II reaction centre W protein (PsbW); InterPro: IPR009806 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 []. This family represents the low molecular weight transmembrane protein PsbW found in PSII, where it is a subunit of the oxygen-evolving complex. PsbW appears to have several roles, including guiding PSII biogenesis and assembly, stabilising dimeric PSII [], and facilitating PSII repair after photo-inhibition []. There appears to be two classes of PsbW, class 1 being found predominantly in algae and cyanobacteria, and class 2 being found predominantly in plants. This entry represents class 2 PsbW.; GO: 0015979 photosynthesis, 0009507 chloroplast, 0009523 photosystem II
Probab=62.60 E-value=32 Score=26.89 Aligned_cols=56 Identities=34% Similarity=0.282 Sum_probs=26.6
Q ss_pred HHhhHHHHHHhhhcchHHH---Hh---hcCCCChhHHHHHHHHHHhHHHHHHHhhheeeeeccC
Q 033248 61 VTGLTAAALTASMVIPEVA---EA---AGSGLSPSLKNFLLSIVAGGVVLAAIVGAVIGVANFD 118 (123)
Q Consensus 61 ~~gltaaa~~As~~~P~vA---eA---a~~~mTPSL~NFL~SLvaGgvVv~~i~~Ali~VSq~D 118 (123)
+..+.+++.++++..|-.| |. .|-|..=-|+|=++..+.=||.-.+ -+|.|+.+.|
T Consensus 66 a~~~aa~~a~~a~a~PA~ALVDeRlsteGTGL~lGlsn~~LgwIL~gVf~lI--WslY~~~~~~ 127 (138)
T PF07123_consen 66 AALLAAAAATAATASPALALVDERLSTEGTGLPLGLSNNLLGWILLGVFGLI--WSLYFVYTST 127 (138)
T ss_pred HHHHHHHHHHHhhcCcHHHHHHHHhcCCCccccccccCchhHHHHHHHHHHH--HHHHHhhccc
Confidence 3344444444566777443 21 2334445566666655544433332 2445555444
No 7
>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=57.87 E-value=18 Score=29.91 Aligned_cols=32 Identities=28% Similarity=0.427 Sum_probs=27.1
Q ss_pred CCChhHHHHHHHHHHhHHHHHHHhhheeeeec
Q 033248 85 GLSPSLKNFLLSIVAGGVVLAAIVGAVIGVAN 116 (123)
Q Consensus 85 ~mTPSL~NFL~SLvaGgvVv~~i~~Ali~VSq 116 (123)
+++-.++||-+||+-|+++=.+|...+|++-+
T Consensus 100 G~~~pv~nF~lsL~tG~~lG~~iG~iIi~~RK 131 (209)
T TIGR03579 100 GIVAPVENFGLSLLTGAVLGLAVGYVIILIRK 131 (209)
T ss_pred cccccHHHHHHHHHHHHHHHHHhheeEEEEEe
Confidence 68889999999999999887778777777654
No 8
>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=54.03 E-value=11 Score=24.80 Aligned_cols=16 Identities=44% Similarity=0.505 Sum_probs=11.4
Q ss_pred HHHHHHHhHHHHHHHh
Q 033248 93 FLLSIVAGGVVLAAIV 108 (123)
Q Consensus 93 FL~SLvaGgvVv~~i~ 108 (123)
||+++++|+++-++++
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 9
>PF09813 Coiled-coil_56: Coiled-coil domain-containing protein 56; InterPro: IPR018628 Members of this family of proteins have no known function.
Probab=49.53 E-value=19 Score=26.78 Aligned_cols=30 Identities=20% Similarity=0.294 Sum_probs=25.6
Q ss_pred hHHHHHHHHHHhHHHHHHHhhheeeeeccC
Q 033248 89 SLKNFLLSIVAGGVVLAAIVGAVIGVANFD 118 (123)
Q Consensus 89 SL~NFL~SLvaGgvVv~~i~~Ali~VSq~D 118 (123)
.-+|-+.++..|++|+++-+--+..|+|-|
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 358999999999999999887888888855
No 10
>PRK11273 glpT sn-glycerol-3-phosphate transporter; Provisional
Probab=42.47 E-value=86 Score=25.48 Aligned_cols=33 Identities=21% Similarity=0.308 Sum_probs=22.7
Q ss_pred hcchHHHHhhcCCCChhHHHHHHHHHHhHHHHHHHh
Q 033248 73 MVIPEVAEAAGSGLSPSLKNFLLSIVAGGVVLAAIV 108 (123)
Q Consensus 73 ~~~P~vAeAa~~~mTPSL~NFL~SLvaGgvVv~~i~ 108 (123)
...|.+.+. +++++-.+++.++..-+..++.+.
T Consensus 50 ~~~p~l~~~---g~s~~~~g~~~~~~~i~~~~~~~~ 82 (452)
T PRK11273 50 LAMPYLVEQ---GFSRGDLGFALSGISIAYGFSKFI 82 (452)
T ss_pred HhhHHHHHc---CCCHHHHHHHHHHHHHHHHHHHhh
Confidence 457887753 799988888877766665555433
No 11
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=39.63 E-value=23 Score=26.12 Aligned_cols=28 Identities=25% Similarity=0.419 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHhHHHHHH--Hhhheeeeec
Q 033248 89 SLKNFLLSIVAGGVVLAA--IVGAVIGVAN 116 (123)
Q Consensus 89 SL~NFL~SLvaGgvVv~~--i~~Ali~VSq 116 (123)
-++|+..+++.||++|.+ ...|.+=.|+
T Consensus 6 ~i~ny~s~vli~GIiLL~~ACIFAfidFSK 35 (91)
T PHA02680 6 TLKSYYSGVLICGVLLLTAACVFAFVDFSK 35 (91)
T ss_pred HHHHhccHHHHHHHHHHHHHHHHhhhhhhc
Confidence 489999999999999986 4446665565
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=39.28 E-value=43 Score=22.64 Aligned_cols=33 Identities=18% Similarity=0.108 Sum_probs=25.3
Q ss_pred hHHHHHHHHHHhHHHHHHHhhheeeeeccCccc
Q 033248 89 SLKNFLLSIVAGGVVLAAIVGAVIGVANFDPVK 121 (123)
Q Consensus 89 SL~NFL~SLvaGgvVv~~i~~Ali~VSq~D~V~ 121 (123)
|+.+-+.=++.+-++-.+++++|+.+|+.|..+
T Consensus 21 sF~fViik~vismimylilGi~L~yis~~~~~~ 53 (54)
T PF04835_consen 21 SFWFVIIKSVISMIMYLILGIALIYISSNDDKK 53 (54)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhhccCcccc
Confidence 455556666777777778999999999988654
No 13
>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=37.53 E-value=19 Score=26.58 Aligned_cols=31 Identities=23% Similarity=0.396 Sum_probs=22.9
Q ss_pred hhHHHHHHHHHHhHHHHHH--HhhheeeeeccC
Q 033248 88 PSLKNFLLSIVAGGVVLAA--IVGAVIGVANFD 118 (123)
Q Consensus 88 PSL~NFL~SLvaGgvVv~~--i~~Ali~VSq~D 118 (123)
--|+|+..+.+.||++|.+ +..|.+=.|+.-
T Consensus 5 ~~~~n~~S~vli~GiiLL~~aCIfAfidfsK~~ 37 (92)
T PF05767_consen 5 GFLSNYFSGVLIGGIILLIAACIFAFIDFSKNT 37 (92)
T ss_pred HHHHhccchHHHHHHHHHHHHHHHHhhhhccCC
Confidence 3589999999999999986 444555555443
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=32.01 E-value=50 Score=26.95 Aligned_cols=25 Identities=28% Similarity=0.224 Sum_probs=14.4
Q ss_pred HHHHHHHHhHHHHHHHhh-heeeeec
Q 033248 92 NFLLSIVAGGVVLAAIVG-AVIGVAN 116 (123)
Q Consensus 92 NFL~SLvaGgvVv~~i~~-Ali~VSq 116 (123)
|-+|=+..|-|+|++|++ .-+|+.+
T Consensus 13 N~iLNiaI~IV~lLIiiva~~lf~~~ 38 (217)
T PF07423_consen 13 NKILNIAIGIVSLLIIIVAYQLFFGG 38 (217)
T ss_pred hhhHHHHHHHHHHHHHHHhhhheecC
Confidence 556666667666666444 4455533
No 15
>PHA03048 IMV membrane protein; Provisional
Probab=31.13 E-value=27 Score=25.82 Aligned_cols=29 Identities=21% Similarity=0.438 Sum_probs=22.2
Q ss_pred hHHHHHHHHHHhHHHHHH--Hhhheeeeecc
Q 033248 89 SLKNFLLSIVAGGVVLAA--IVGAVIGVANF 117 (123)
Q Consensus 89 SL~NFL~SLvaGgvVv~~--i~~Ali~VSq~ 117 (123)
-++|+....+.||++|.+ ...|.|=.|+.
T Consensus 6 ~~~ny~S~vli~GIiLL~~aCIfAfidfsK~ 36 (93)
T PHA03048 6 MISNYFSTALIGGIILLAASCIFAFVDFSKN 36 (93)
T ss_pred HhhcccchHHHHHHHHHHHHHHHhhhhhhcC
Confidence 489999999999999986 44466555654
No 16
>PF13706 PepSY_TM_3: PepSY-associated TM helix
Probab=30.88 E-value=26 Score=20.78 Aligned_cols=26 Identities=27% Similarity=0.514 Sum_probs=15.2
Q ss_pred HHHHHhHHHHHH-HhhheeeeeccCcccC
Q 033248 95 LSIVAGGVVLAA-IVGAVIGVANFDPVKR 122 (123)
Q Consensus 95 ~SLvaGgvVv~~-i~~Ali~VSq~D~V~R 122 (123)
.+|+.|-+++++ ++|++... .|.++|
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 55555443 344444
No 17
>PRK10927 essential cell division protein FtsN; Provisional
Probab=30.77 E-value=49 Score=28.86 Aligned_cols=20 Identities=15% Similarity=0.351 Sum_probs=14.8
Q ss_pred hHHHHHHHhhheeeeeccCc
Q 033248 100 GGVVLAAIVGAVIGVANFDP 119 (123)
Q Consensus 100 GgvVv~~i~~Ali~VSq~D~ 119 (123)
...||++.+|+|.||++..+
T Consensus 40 Avavlv~fiGGLyFith~k~ 59 (319)
T PRK10927 40 AAAVLVTFIGGLYFITHHKK 59 (319)
T ss_pred HHHHHHHHhhheEEEecCCC
Confidence 34566677788999998765
No 18
>COG4062 MtrB Tetrahydromethanopterin S-methyltransferase, subunit B [Coenzyme metabolism]
Probab=29.22 E-value=48 Score=25.13 Aligned_cols=17 Identities=29% Similarity=0.333 Sum_probs=14.4
Q ss_pred hHHHHHHHHHHhHHHHH
Q 033248 89 SLKNFLLSIVAGGVVLA 105 (123)
Q Consensus 89 SL~NFL~SLvaGgvVv~ 105 (123)
-|+||+++++.|-.|.+
T Consensus 76 ~~tna~yGfviGl~i~a 92 (108)
T COG4062 76 YLTNAFYGFVIGLGIMA 92 (108)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 48999999999988844
No 19
>COG2354 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.77 E-value=55 Score=28.52 Aligned_cols=21 Identities=48% Similarity=0.699 Sum_probs=19.0
Q ss_pred CChhHHHHHHHHHHhHHHHHH
Q 033248 86 LSPSLKNFLLSIVAGGVVLAA 106 (123)
Q Consensus 86 mTPSL~NFL~SLvaGgvVv~~ 106 (123)
..|++-|+.+.+++|+++++.
T Consensus 274 ~~~t~~~~v~g~v~G~vvv~~ 294 (303)
T COG2354 274 LVPTLLNAVLGLVIGAVVVAL 294 (303)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999886
No 20
>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=28.27 E-value=65 Score=24.83 Aligned_cols=21 Identities=33% Similarity=0.420 Sum_probs=17.8
Q ss_pred HHHHHHHHHHhHHHHHHHhhh
Q 033248 90 LKNFLLSIVAGGVVLAAIVGA 110 (123)
Q Consensus 90 L~NFL~SLvaGgvVv~~i~~A 110 (123)
+..|..+++.|+++++.|.+.
T Consensus 102 l~~f~~tl~~Gg~l~Gli~~~ 122 (154)
T TIGR03546 102 LARFNNTIVMGSFVVGLILLP 122 (154)
T ss_pred HHHHHHHHHHhhHHHHHHHHH
Confidence 778889999999999986554
No 21
>PHA02898 virion envelope protein; Provisional
Probab=25.85 E-value=38 Score=25.03 Aligned_cols=30 Identities=27% Similarity=0.260 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHhHHHHHH--HhhheeeeeccC
Q 033248 89 SLKNFLLSIVAGGVVLAA--IVGAVIGVANFD 118 (123)
Q Consensus 89 SL~NFL~SLvaGgvVv~~--i~~Ali~VSq~D 118 (123)
-.+|+..+++.||++|.+ ...|.+=.|+.-
T Consensus 6 ~~~N~~s~vli~GIiLL~~ACIfAfidfSK~~ 37 (92)
T PHA02898 6 FFKNRPSYVVAFGIILLIVACICAYIELSKSE 37 (92)
T ss_pred hhhcCcchHHHHHHHHHHHHHHHheehhhcCC
Confidence 368999999999999986 444666566543
No 22
>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=25.79 E-value=61 Score=25.24 Aligned_cols=21 Identities=29% Similarity=0.594 Sum_probs=18.6
Q ss_pred CChhHHHHHHHHHHhHHHHHH
Q 033248 86 LSPSLKNFLLSIVAGGVVLAA 106 (123)
Q Consensus 86 mTPSL~NFL~SLvaGgvVv~~ 106 (123)
=.|.++|+++..+.||+|-++
T Consensus 13 k~~~~~n~l~AFlvGG~IC~i 33 (141)
T TIGR02838 13 KPPYLKNCVMAFLVGGLICLI 33 (141)
T ss_pred CCcHHHHHHHHHHhCcHHHHH
Confidence 468899999999999999875
No 23
>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=24.60 E-value=30 Score=27.71 Aligned_cols=23 Identities=35% Similarity=0.333 Sum_probs=15.2
Q ss_pred HHHHHHHHhHHHHHHHhhheeee
Q 033248 92 NFLLSIVAGGVVLAAIVGAVIGV 114 (123)
Q Consensus 92 NFL~SLvaGgvVv~~i~~Ali~V 114 (123)
-|=-.=+.||+||+.-..+++|+
T Consensus 157 ~FD~~SFiGGIVL~LGv~aI~ff 179 (186)
T PF05283_consen 157 TFDAASFIGGIVLTLGVLAIIFF 179 (186)
T ss_pred CCchhhhhhHHHHHHHHHHHHHH
Confidence 36666678999998755555443
No 24
>TIGR00712 glpT glycerol-3-phosphate transporter. This model describes a very hydrophobic protein, predicted to span the membrane at least 8 times. The two members confirmed experimentally as glycerol-3-phosphate transporters, from E. coli and B. subtilis, share more than 50 % amino acid identity. Proteins of the hexose phosphate and phosphoglycerate transport systems are also quite similar.
Probab=22.82 E-value=3e+02 Score=22.23 Aligned_cols=43 Identities=19% Similarity=0.272 Sum_probs=26.8
Q ss_pred hcchHHHHhhcCCCChhHHHHHHHHHHhHHHHHHHhhheeeeeccCcccC
Q 033248 73 MVIPEVAEAAGSGLSPSLKNFLLSIVAGGVVLAAIVGAVIGVANFDPVKR 122 (123)
Q Consensus 73 ~~~P~vAeAa~~~mTPSL~NFL~SLvaGgvVv~~i~~Ali~VSq~D~V~R 122 (123)
...|.+.| -+++++-.+++.++..-+..++.+..+.+ .|+..|
T Consensus 48 ~~~p~~~~---~g~s~~~~g~~~~~~~~~~~~~~~~~G~l----~dr~g~ 90 (438)
T TIGR00712 48 LAMPYLVE---QGFSKGELGFALSAISIAYGFSKFIMGSV----SDRSNP 90 (438)
T ss_pred hhhHHHHH---cCCCHhHhHHHHHHHHHHHHHhhhccchh----hhccCC
Confidence 35687776 27999988888777666555554333332 266554
No 25
>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=22.29 E-value=80 Score=21.41 Aligned_cols=22 Identities=32% Similarity=0.357 Sum_probs=12.5
Q ss_pred HHHHHHhHHHHHHHhhheeeee
Q 033248 94 LLSIVAGGVVLAAIVGAVIGVA 115 (123)
Q Consensus 94 L~SLvaGgvVv~~i~~Ali~VS 115 (123)
+++++.|.++++++.+.++++.
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 4566677666665544444443
No 26
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=21.82 E-value=32 Score=30.76 Aligned_cols=12 Identities=42% Similarity=0.891 Sum_probs=9.8
Q ss_pred eeeeeccCcccC
Q 033248 111 VIGVANFDPVKR 122 (123)
Q Consensus 111 li~VSq~D~V~R 122 (123)
.|.+|.||||+|
T Consensus 246 ~v~ls~fdp~rr 257 (514)
T TIGR03319 246 AVILSGFDPVRR 257 (514)
T ss_pred eEEecCCchHHH
Confidence 566899999987
No 27
>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=21.54 E-value=88 Score=22.62 Aligned_cols=23 Identities=30% Similarity=0.603 Sum_probs=18.8
Q ss_pred hHHHHHHHHHHhHHHHHHHhhhe
Q 033248 89 SLKNFLLSIVAGGVVLAAIVGAV 111 (123)
Q Consensus 89 SL~NFL~SLvaGgvVv~~i~~Al 111 (123)
.+.++++.++.|++|++++.+.+
T Consensus 112 ~~~~~~~~~~~G~~i~~~v~~~i 134 (154)
T PF09835_consen 112 SLWEFGLPFLLGSLILGIVLGII 134 (154)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 67889999999999999765543
No 28
>PHA00979 putative major coat protein
Probab=21.12 E-value=2.2e+02 Score=20.51 Aligned_cols=42 Identities=26% Similarity=0.374 Sum_probs=20.4
Q ss_pred hhhcchHHHHhhcCCCC-----hhHHHHHHHHHHhHHHHHHHhhheeee
Q 033248 71 ASMVIPEVAEAAGSGLS-----PSLKNFLLSIVAGGVVLAAIVGAVIGV 114 (123)
Q Consensus 71 As~~~P~vAeAa~~~mT-----PSL~NFL~SLvaGgvVv~~i~~Ali~V 114 (123)
|+|..|-.++. .+|. --|+..=-.+++=|++++.|.+++-.|
T Consensus 21 Aa~S~~a~a~~--~~~~d~~~a~dlsGvaa~V~a~Gv~iIGIa~Afk~I 67 (77)
T PHA00979 21 AVLSVPAMAAE--GGAADPFSAIDLSGVATKIGAAGLVIVGITMAYKSI 67 (77)
T ss_pred HHHhhhhhhcc--ccccchhhhhhhhhHHHHHHHhhhHhhhhhhhheec
Confidence 56777776532 2222 224444444555555555555554433
No 29
>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=20.67 E-value=1.8e+02 Score=19.45 Aligned_cols=25 Identities=36% Similarity=0.215 Sum_probs=13.2
Q ss_pred HHHHHhHHHHHHHhhheeeeeccCc
Q 033248 95 LSIVAGGVVLAAIVGAVIGVANFDP 119 (123)
Q Consensus 95 ~SLvaGgvVv~~i~~Ali~VSq~D~ 119 (123)
-|.|+|-++=++.++++-.+++.|.
T Consensus 10 aSaV~Gi~lG~~av~gvt~~~~~~s 34 (56)
T PF11021_consen 10 ASAVVGIVLGVAAVFGVTAAAQQDS 34 (56)
T ss_pred HHHHHHHHHHHHHHhhhheeeecCC
Confidence 4556655544444455555555554
No 30
>PRK00106 hypothetical protein; Provisional
Probab=20.17 E-value=36 Score=31.07 Aligned_cols=12 Identities=42% Similarity=1.007 Sum_probs=9.5
Q ss_pred eeeeeccCcccC
Q 033248 111 VIGVANFDPVKR 122 (123)
Q Consensus 111 li~VSq~D~V~R 122 (123)
.|.+|.||||+|
T Consensus 267 ~v~lS~fdpvRR 278 (535)
T PRK00106 267 VVVLSGFDPIRR 278 (535)
T ss_pred eEEEeCCChHHH
Confidence 456888998887
Done!