Query 027666
Match_columns 220
No_of_seqs 158 out of 1959
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 13:21:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027666.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027666hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR03008 pepcterm_CAAX CAAX p 99.9 1.6E-19 3.5E-24 145.5 20.9 140 74-217 66-213 (222)
2 PF02517 Abi: CAAX protease se 99.8 2.4E-19 5.2E-24 125.7 11.4 87 126-212 4-91 (91)
3 COG1266 Predicted metal-depend 99.8 1.5E-16 3.4E-21 128.4 21.3 88 124-211 121-212 (226)
4 KOG4130 Prenyl protein proteas 99.0 2.3E-08 5E-13 80.1 16.0 85 129-213 131-236 (291)
5 COG4449 Predicted protease of 97.0 0.00046 9.9E-09 61.1 2.8 81 129-209 712-809 (827)
6 PF10086 DUF2324: Putative mem 96.0 0.4 8.8E-06 39.0 13.6 30 125-155 60-89 (223)
7 COG2339 prsW Membrane proteina 94.4 2.6 5.6E-05 35.4 17.0 16 128-143 106-121 (274)
8 PF13367 PrsW-protease: Protea 90.9 6.6 0.00014 30.8 14.3 34 182-215 132-174 (191)
9 COG4377 Predicted membrane pro 76.4 38 0.00083 27.2 12.3 46 126-176 77-122 (258)
10 PHA02758 hypothetical protein; 56.8 28 0.00061 28.2 5.0 49 165-213 221-288 (321)
11 PF07185 DUF1404: Protein of u 39.8 1.8E+02 0.0039 22.6 9.3 68 129-197 5-100 (169)
12 PF01102 Glycophorin_A: Glycop 31.9 76 0.0017 23.3 3.6 24 36-59 71-94 (122)
13 PF11190 DUF2976: Protein of u 27.1 2.1E+02 0.0046 19.6 5.6 22 74-95 59-80 (87)
14 PF05437 AzlD: Branched-chain 23.7 2.5E+02 0.0053 19.2 5.6 25 183-207 68-92 (99)
15 TIGR01478 STEVOR variant surfa 22.9 1.3E+02 0.0028 25.5 3.8 12 51-62 280-291 (295)
16 PRK03356 L-carnitine/gamma-but 21.9 1.6E+02 0.0035 27.1 4.7 68 130-197 92-165 (504)
17 TIGR02359 thiW thiW protein. L 21.8 3.8E+02 0.0081 20.6 6.0 27 181-207 74-100 (160)
18 PRK09400 secE preprotein trans 21.2 2.3E+02 0.005 18.0 4.5 18 81-98 38-55 (61)
19 PTZ00370 STEVOR; Provisional 20.4 1.4E+02 0.003 25.4 3.6 12 51-62 276-287 (296)
No 1
>TIGR03008 pepcterm_CAAX CAAX prenyl protease-related protein. The CAAX prenyl protease, in eukaryotes, catalyzes three covalent modifications, including cleavage and acylation, at the C-terminus of certain proteins in a process connected to protein sorting. This family describes a bacterial protein family homologous to one domain of the CAAX-processing enzyme. Members of this protein family are found in genomes that carry a predicted protein sorting system, PEP-CTERM/exosortase, usually in the vicinity of the EpsH homolog that is the hallmark of the system. The function of this protein is unknown, but it may relate to protein motification.
Probab=99.86 E-value=1.6e-19 Score=145.51 Aligned_cols=140 Identities=17% Similarity=0.239 Sum_probs=93.1
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcCCCcHHHHHHhhcCChHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 027666 74 AERNWLLASALGFAVLTSLVFLASLVADRLFGAKAANNPLVREILLSSDISATAIVLVNCIIAPLLEEAVYRGFLLTSLA 153 (220)
Q Consensus 74 ~~~~~~~~~~~g~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~pi~EEl~fRg~l~~~l~ 153 (220)
+.++...+...|.+...+.. ..+.......+.++.++....+...+........++..++++|+.||++|||++++.+.
T Consensus 66 ~~~~~l~gi~~Gv~~f~lwi-~~~~~~~~~~~~~~~~~~~i~~~~~~~~~l~~~~l~~~~l~vpi~EElfFRG~l~~~l~ 144 (222)
T TIGR03008 66 RPRHLLFSAAVGVAVFVLWV-NLDWLLPFQGEPAGFDPSQIGNAGLTRWVLIAFRLAGATLVVPVMEELFWRSFLLRYLQ 144 (222)
T ss_pred cHHHHHHHHHHHHHHHHHHH-HHHHHHhhcCCccccchhhhhcccchhhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 34677777777776554432 22222222212222222212111110111111234567889999999999999999997
Q ss_pred hh-c-------ChhHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHhhCCchHHHHHHHHHhHHHHHHH
Q 027666 154 ST-M-------SWRNAVVISSAIFSVAHFSIDNFLQLFIIGCVLGSSYCWSGNLISSIAIHSLYNASILMII 217 (220)
Q Consensus 154 ~~-~-------~~~~ail~ss~iF~~~H~~~~~~~~~~~~gl~~~~~y~~t~~l~~~i~~H~~~N~~~~i~~ 217 (220)
++ + ..+.+.++||++||+.|. +....++.|+++|++|.||||++.|+.+|+.+|...-...
T Consensus 145 ~~~f~~~~~~~~~~~a~lisSllFal~H~---~~~~~~l~Gli~~~l~~~tgsL~~~I~~H~~~N~ll~~~v 213 (222)
T TIGR03008 145 QSDFESVPGGRFHWPSFLAVTLLFGLEHH---LIVAGLIAGLAYNLLLLRTGSIMACILAHAVTNGLLGLWV 213 (222)
T ss_pred HhcccccccccccHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhCChHHHHHHHHHHHHHHHHHH
Confidence 63 1 136799999999999997 3555678899999999999999999999999999866544
No 2
>PF02517 Abi: CAAX protease self-immunity; InterPro: IPR003675 Members of this family are probably proteases (after a isoprenyl group is attached to the Cys residue in the C-terminal CAAX motif of a protein to attach it to the membrane, the AAX tripeptide is removed by one of the CAAX prenyl proteases). The family contains the Q03530 from SWISSPROT CAAX prenyl protease []. The proteins contain a highly conserved Glu-Glu motif at the amino end of the alignment. The alignment also contains two histidine residues that may be involved in zinc binding []. While these proteins are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes where they are probably involved in self-immunity. Investigation of the bacteriocin-like loci in the Gram positive bacteria locus from Lactobacillus sakei 23K confirmed that the bacteriocin-like genes (sak23Kalphabeta) exhibited antimicrobial activity when expressed in a heterologous host and that the associated Abi gene (sak23Ki) conferred immunity against the cognate bacteriocin. Interestingly, the immunity genes from three similar systems conferred a high degree of cross-immunity against each other's bacteriocins, suggesting the recognition of a common receptor. Site-directed mutagenesis demonstrated that the conserved motifs constituting the putative proteolytic active site of the Abi proteins are essential for the immunity function of Sak23Ki - thus a new concept in self-immunity []. This family also includes lysostaphin resistance protein A [].; GO: 0016020 membrane
Probab=99.82 E-value=2.4e-19 Score=125.68 Aligned_cols=87 Identities=33% Similarity=0.571 Sum_probs=79.4
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHhhcChhHHHHHHHHHHHHhhhch-HHHHHHHHHHHHHHHHHHhhCCchHHHH
Q 027666 126 TAIVLVNCIIAPLLEEAVYRGFLLTSLASTMSWRNAVVISSAIFSVAHFSI-DNFLQLFIIGCVLGSSYCWSGNLISSIA 204 (220)
Q Consensus 126 ~~~~~~~~i~~pi~EEl~fRg~l~~~l~~~~~~~~ail~ss~iF~~~H~~~-~~~~~~~~~gl~~~~~y~~t~~l~~~i~ 204 (220)
+...+...+.+|+.||++|||++++.++++.+...++++|+++|++.|.+. .+....++.|+.+++.|.||||+|+++.
T Consensus 4 ~~~~~~~~~~~~~~EEl~fRg~l~~~l~~~~~~~~a~~is~~~f~~~H~~~~~~~~~~~~~g~~~~~~~~~t~sl~~~i~ 83 (91)
T PF02517_consen 4 LIFFLVMILIAPIAEELFFRGFLFNRLRRRFNPWFAILISSLLFALWHLPNGPQFIYAFLFGLLFGYLYLRTGSLWAAII 83 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHcCChHHHHH
Confidence 345678899999999999999999999999777999999999999999975 4578889999999999999999999999
Q ss_pred HHHHHhHH
Q 027666 205 IHSLYNAS 212 (220)
Q Consensus 205 ~H~~~N~~ 212 (220)
+|..+|.+
T Consensus 84 ~H~~~n~~ 91 (91)
T PF02517_consen 84 AHALWNLV 91 (91)
T ss_pred HHHHHHcC
Confidence 99999963
No 3
>COG1266 Predicted metal-dependent membrane protease [General function prediction only]
Probab=99.77 E-value=1.5e-16 Score=128.44 Aligned_cols=88 Identities=39% Similarity=0.558 Sum_probs=81.1
Q ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHhhcChhHHHHHHHHHHHHhhhch----HHHHHHHHHHHHHHHHHHhhCCc
Q 027666 124 SATAIVLVNCIIAPLLEEAVYRGFLLTSLASTMSWRNAVVISSAIFSVAHFSI----DNFLQLFIIGCVLGSSYCWSGNL 199 (220)
Q Consensus 124 ~~~~~~~~~~i~~pi~EEl~fRg~l~~~l~~~~~~~~ail~ss~iF~~~H~~~----~~~~~~~~~gl~~~~~y~~t~~l 199 (220)
......+...+.+|+.||++|||++++++.++++.+.++++||++||+.|.+. ......+..|+++++.|.||||+
T Consensus 121 ~~~~~~~~~~i~~~l~EEl~fRg~l~~~l~~~~~~~~a~iissllFal~H~~~~~~~~~~~~~~~~gli~~~~~~~t~~l 200 (226)
T COG1266 121 WLLLFFLVLLILAPLAEELLFRGYLLGALARRFGPLLAIIISSLLFALLHLPNGLLLLYFLLYFIAGLILGLLYLRTGSL 200 (226)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHhcCcHHHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHhCCc
Confidence 34556788999999999999999999999999999999999999999999964 56778889999999999999999
Q ss_pred hHHHHHHHHHhH
Q 027666 200 ISSIAIHSLYNA 211 (220)
Q Consensus 200 ~~~i~~H~~~N~ 211 (220)
+.++..|..+|.
T Consensus 201 ~~~i~~H~~~N~ 212 (226)
T COG1266 201 WVPILLHALINL 212 (226)
T ss_pred HHHHHHHHHHHH
Confidence 999999999995
No 4
>KOG4130 consensus Prenyl protein protease [Posttranslational modification, protein turnover, chaperones]
Probab=99.04 E-value=2.3e-08 Score=80.10 Aligned_cols=85 Identities=29% Similarity=0.342 Sum_probs=72.8
Q ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHhh-cChhHHHHHHHHHHHHhhhch--------------------HHHHHHHHHHH
Q 027666 129 VLVNCIIAPLLEEAVYRGFLLTSLAST-MSWRNAVVISSAIFSVAHFSI--------------------DNFLQLFIIGC 187 (220)
Q Consensus 129 ~~~~~i~~pi~EEl~fRg~l~~~l~~~-~~~~~ail~ss~iF~~~H~~~--------------------~~~~~~~~~gl 187 (220)
.+-.-+++|+.||++||.-+.....+- ++...++..+.+.||..|.+. .|+.++.+.|-
T Consensus 131 ~~RN~iiaPLtEElvfracmlp~~l~~~~s~l~avF~~PLfFGvAH~HHiyEqL~~g~~~~~~ilL~t~fQfsYTtlFG~ 210 (291)
T KOG4130|consen 131 WFRNFIIAPLTEELVFRACMLPTYLNLIQSSLQAVFWQPLFFGVAHAHHIYEQLQEGSMTTVSILLTTCFQFSYTTLFGG 210 (291)
T ss_pred HHHhhhhccchHHHHHHHHHHHHHHHhhhcchhhHHHhhHHHhHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHH
Confidence 356899999999999999999998876 788889999999999999852 23556667777
Q ss_pred HHHHHHHhhCCchHHHHHHHHHhHHH
Q 027666 188 VLGSSYCWSGNLISSIAIHSLYNASI 213 (220)
Q Consensus 188 ~~~~~y~~t~~l~~~i~~H~~~N~~~ 213 (220)
.=+.++.|||++|.|+.+|+.+|...
T Consensus 211 yTaflF~rTghl~~~iLvHAfCN~MG 236 (291)
T KOG4130|consen 211 YTAFLFVRTGHLWCPILVHAFCNIMG 236 (291)
T ss_pred HHHHHhhhcCCchHHHHHHHHHhhcC
Confidence 77778899999999999999999754
No 5
>COG4449 Predicted protease of the Abi (CAAX) family [General function prediction only]
Probab=97.02 E-value=0.00046 Score=61.07 Aligned_cols=81 Identities=21% Similarity=0.178 Sum_probs=59.4
Q ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHhhcChhHHHHHHH--HHHHHhhhch---------------HHHHHHHHHHHHHHH
Q 027666 129 VLVNCIIAPLLEEAVYRGFLLTSLASTMSWRNAVVISS--AIFSVAHFSI---------------DNFLQLFIIGCVLGS 191 (220)
Q Consensus 129 ~~~~~i~~pi~EEl~fRg~l~~~l~~~~~~~~ail~ss--~iF~~~H~~~---------------~~~~~~~~~gl~~~~ 191 (220)
++...++..+.||+.||..+...=.+...+|..+-... ++|.++|.-. .......+.|+....
T Consensus 712 iL~vIl~PAl~EElvFRvvLlP~P~E~r~~W~tl~a~~~l~LfvLyHplnA~T~y~rg~PvFf~PiFL~ltglLGL~Ctv 791 (827)
T COG4449 712 ILTVILIPALGEELVFRVVLLPGPGEGRRPWVTLGAATGLVLFVLYHPLNALTFYPRGAPVFFRPIFLLLTGLLGLGCTV 791 (827)
T ss_pred hhhheehhhccccceeEEEecCCCCccccchHhHHHHHHHHHHHHhhhhhhhhccccCCcceeccHHHHHHHHHhhhhhh
Confidence 45566777789999999999876555434444333333 4899999732 123455688999999
Q ss_pred HHHhhCCchHHHHHHHHH
Q 027666 192 SYCWSGNLISSIAIHSLY 209 (220)
Q Consensus 192 ~y~~t~~l~~~i~~H~~~ 209 (220)
.|.-|+|+|+.+..|-..
T Consensus 792 ty~vT~SlW~iV~lHW~v 809 (827)
T COG4449 792 TYRVTGSLWPIVLLHWAV 809 (827)
T ss_pred hHHhccchHHHHHHHHHH
Confidence 999999999999999754
No 6
>PF10086 DUF2324: Putative membrane peptidase family (DUF2324); InterPro: IPR011397 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are predicted to be integral membrane proteins (with several transmembrane segments).
Probab=95.96 E-value=0.4 Score=39.00 Aligned_cols=30 Identities=20% Similarity=0.162 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHHHhh
Q 027666 125 ATAIVLVNCIIAPLLEEAVYRGFLLTSLAST 155 (220)
Q Consensus 125 ~~~~~~~~~i~~pi~EEl~fRg~l~~~l~~~ 155 (220)
.....+..++.+++.||. -|-.-++.+.+|
T Consensus 60 ~~l~~ly~~l~AGiFEE~-gR~i~~k~l~kk 89 (223)
T PF10086_consen 60 PILYALYGGLMAGIFEET-GRYIGFKYLLKK 89 (223)
T ss_pred HHHHHHHHHHHHHHHHHH-HHHHHHHHHHHc
Confidence 344678899999999994 344444444443
No 7
>COG2339 prsW Membrane proteinase, regulator of anti-sigma factor [Posttranslational modification, protein turnover, chaperones]
Probab=94.44 E-value=2.6 Score=35.36 Aligned_cols=16 Identities=31% Similarity=0.553 Sum_probs=13.3
Q ss_pred HHHHHHHHhhHHHHHH
Q 027666 128 IVLVNCIIAPLLEEAV 143 (220)
Q Consensus 128 ~~~~~~i~~pi~EEl~ 143 (220)
..+...+.+|+.||..
T Consensus 106 ~~l~~al~~G~vEE~~ 121 (274)
T COG2339 106 LFLGSALLAGLVEEPL 121 (274)
T ss_pred HHHHHHHhhhhhHHHH
Confidence 4577889999999986
No 8
>PF13367 PrsW-protease: Protease prsW family
Probab=90.85 E-value=6.6 Score=30.78 Aligned_cols=34 Identities=21% Similarity=0.316 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHhh---------CCchHHHHHHHHHhHHHHH
Q 027666 182 LFIIGCVLGSSYCWS---------GNLISSIAIHSLYNASILM 215 (220)
Q Consensus 182 ~~~~gl~~~~~y~~t---------~~l~~~i~~H~~~N~~~~i 215 (220)
..+.|..++....++ ..+..++..|.++|.....
T Consensus 132 t~i~g~~l~~~~~~~~~~~~~~~~~~~~~a~~lH~~~N~~~~~ 174 (191)
T PF13367_consen 132 TAIFGYGLGLAKRRRKRGFRLALLLGFLLAVLLHGLWNFPLSL 174 (191)
T ss_pred HHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 345565566555322 2366789999999998765
No 9
>COG4377 Predicted membrane protein [Function unknown]
Probab=76.35 E-value=38 Score=27.19 Aligned_cols=46 Identities=13% Similarity=0.206 Sum_probs=34.0
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHhhcChhHHHHHHHHHHHHhhhch
Q 027666 126 TAIVLVNCIIAPLLEEAVYRGFLLTSLASTMSWRNAVVISSAIFSVAHFSI 176 (220)
Q Consensus 126 ~~~~~~~~i~~pi~EEl~fRg~l~~~l~~~~~~~~ail~ss~iF~~~H~~~ 176 (220)
.+..+..+..+++.||-- |-..++.+.||...+ -.++.||+.|...
T Consensus 77 l~y~IYG~lMAg~FEE~g-R~l~~rfl~kR~~~~----Ad~lAyglGHgGl 122 (258)
T COG4377 77 LIYIIYGLLMAGFFEETG-RLLFFRFLEKRSLEK----ADALAYGLGHGGL 122 (258)
T ss_pred cHHHHHHHHHHHHHHHHh-HHHHHHHHHhCcccc----hhHHHHhcccccH
Confidence 346788999999999964 666666777665433 3678899999864
No 10
>PHA02758 hypothetical protein; Provisional
Probab=56.83 E-value=28 Score=28.24 Aligned_cols=49 Identities=33% Similarity=0.554 Sum_probs=30.6
Q ss_pred HHHHHHHhhhchHHH-------HHHHHHHHHHHH------------HHHhhCCchHHHHHHHHHhHHH
Q 027666 165 SSAIFSVAHFSIDNF-------LQLFIIGCVLGS------------SYCWSGNLISSIAIHSLYNASI 213 (220)
Q Consensus 165 ss~iF~~~H~~~~~~-------~~~~~~gl~~~~------------~y~~t~~l~~~i~~H~~~N~~~ 213 (220)
....|+.+|.+.... ...+..|+.++. -.+|.+++..+++-|..+|.-.
T Consensus 221 anamfailhlpsrl~agykmtgsdlfaigiaf~ill~inf~arwlw~iyke~giiasiighafynagv 288 (321)
T PHA02758 221 ANAMFAILHLPSRLAAGYKMTGSDLFAIGIAFGILLLINFGARWLWEIYKEGGIIASIIGHAFYNAGV 288 (321)
T ss_pred HHHHHHHHhChHHHhhccccccchhhhHHHHHHHhheeecchhhHHHHHhcCCchhhhhhHHHHHhHH
Confidence 456789999874221 112333333332 2246789999999999999754
No 11
>PF07185 DUF1404: Protein of unknown function (DUF1404); InterPro: IPR009844 This family consists of several archaeal proteins of around 180 residues in length. Members of this family seem to be found exclusively in Sulfolobus tokodaii and Sulfolobus solfataricus. The function of this family is unknown.
Probab=39.84 E-value=1.8e+02 Score=22.64 Aligned_cols=68 Identities=22% Similarity=0.220 Sum_probs=42.6
Q ss_pred HHHHHHHhhHHHHHHHH---------------HHHHHHHHhhcChhHHHHHHHHHHHHhhhchH-------------HHH
Q 027666 129 VLVNCIIAPLLEEAVYR---------------GFLLTSLASTMSWRNAVVISSAIFSVAHFSID-------------NFL 180 (220)
Q Consensus 129 ~~~~~i~~pi~EEl~fR---------------g~l~~~l~~~~~~~~ail~ss~iF~~~H~~~~-------------~~~ 180 (220)
.+....++|..||+-++ |.+.+....|.+. ...++.+..=..+|.+.. +-+
T Consensus 5 ~l~i~~vNP~te~l~~~~~~~~M~sHY~L~~~g~llgy~~~k~~~-~~~i~g~~~~v~WhlP~~F~l~a~~~~~Rii~el 83 (169)
T PF07185_consen 5 FLIIASVNPFTESLEFYNPIAYMLSHYALFWGGFLLGYKLFKGKI-IFLILGIIPAVFWHLPYFFDLSASSLWYRIIDEL 83 (169)
T ss_pred HHHHHHhhhhHHHHhccChHHHHHHHHHHHHHHHHHHHHHhcccc-hhhhhhhHHHHHHhccHHHHHHHHHHHHHHHHHH
Confidence 35566777777776644 5555544434333 347788888899999731 234
Q ss_pred HHHHHHHHHHHHHHhhC
Q 027666 181 QLFIIGCVLGSSYCWSG 197 (220)
Q Consensus 181 ~~~~~gl~~~~~y~~t~ 197 (220)
..++.|++.|..-.+-+
T Consensus 84 Sl~lgGiL~Gss~~~m~ 100 (169)
T PF07185_consen 84 SLFLGGILIGSSIPSMS 100 (169)
T ss_pred HHHHHHHHhcchHHHHH
Confidence 45678888887665433
No 12
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=31.87 E-value=76 Score=23.25 Aligned_cols=24 Identities=8% Similarity=0.023 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhcC
Q 027666 36 LSLLLFQVLELSAALFLLSRTIKP 59 (220)
Q Consensus 36 ~~~l~~~~~~~~~~l~~~~~~~~~ 59 (220)
+..++.++..+++..+++||++|+
T Consensus 71 ~gv~aGvIg~Illi~y~irR~~Kk 94 (122)
T PF01102_consen 71 FGVMAGVIGIILLISYCIRRLRKK 94 (122)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHS--
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc
Confidence 344444444333344455554444
No 13
>PF11190 DUF2976: Protein of unknown function (DUF2976); InterPro: IPR021356 Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition.
Probab=27.15 E-value=2.1e+02 Score=19.61 Aligned_cols=22 Identities=14% Similarity=0.294 Sum_probs=14.5
Q ss_pred cchhHHHHHHHHHHHHHHHHHH
Q 027666 74 AERNWLLASALGFAVLTSLVFL 95 (220)
Q Consensus 74 ~~~~~~~~~~~g~~~~~~~~~~ 95 (220)
.|.++.....+|..++...+.+
T Consensus 59 ~W~~fg~~~vVGvvLlv~viwL 80 (87)
T PF11190_consen 59 TWGDFGATVVVGVVLLVFVIWL 80 (87)
T ss_pred cHHHhhhHHHHHHHHHHHHHHH
Confidence 7788887777777665544433
No 14
>PF05437 AzlD: Branched-chain amino acid transport protein (AzlD); InterPro: IPR008407 This family consists of a number of bacterial and archaeal branched-chain amino acid transport proteins. AzlD, a member of this group, has been shown by mutational analysis to be involved in branched-chain amino acid transport, and to be involved in conferring resistance to 4-azaleucine []. However, its exact role in these processes is not yet clear []. Based on its hydropathy profile, it has been suggested to be a membrane protein [].
Probab=23.70 E-value=2.5e+02 Score=19.18 Aligned_cols=25 Identities=20% Similarity=0.114 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHhhCCchHHHHHHH
Q 027666 183 FIIGCVLGSSYCWSGNLISSIAIHS 207 (220)
Q Consensus 183 ~~~gl~~~~~y~~t~~l~~~i~~H~ 207 (220)
......-..++.|+||+..++..=.
T Consensus 68 l~a~~~~~~~~~~~~~~~~~v~~G~ 92 (99)
T PF05437_consen 68 LIAALVAALVALRTRNLLLSVLAGV 92 (99)
T ss_pred HHHHHHHHHHHHHHcchHHHHHHHH
Confidence 3344444445667778877776543
No 15
>TIGR01478 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits.
Probab=22.93 E-value=1.3e+02 Score=25.51 Aligned_cols=12 Identities=25% Similarity=0.332 Sum_probs=5.7
Q ss_pred HHHHHhhcCCCc
Q 027666 51 FLLSRTIKPEYD 62 (220)
Q Consensus 51 ~~~~~~~~~~~~ 62 (220)
++++||||+.++
T Consensus 280 iWlyrrRK~swk 291 (295)
T TIGR01478 280 IWLYRRRKKSWK 291 (295)
T ss_pred HHHHHhhccccc
Confidence 344455555444
No 16
>PRK03356 L-carnitine/gamma-butyrobetaine antiporter; Provisional
Probab=21.89 E-value=1.6e+02 Score=27.08 Aligned_cols=68 Identities=6% Similarity=0.028 Sum_probs=43.9
Q ss_pred HHHHHHhhHHHHHHHHHHHHHHHHhhcC------hhHHHHHHHHHHHHhhhchHHHHHHHHHHHHHHHHHHhhC
Q 027666 130 LVNCIIAPLLEEAVYRGFLLTSLASTMS------WRNAVVISSAIFSVAHFSIDNFLQLFIIGCVLGSSYCWSG 197 (220)
Q Consensus 130 ~~~~i~~pi~EEl~fRg~l~~~l~~~~~------~~~ail~ss~iF~~~H~~~~~~~~~~~~gl~~~~~y~~t~ 197 (220)
+.+.+-+++.--++|-|.--....-..+ .-....-.+.-++..|........+.+.|+.++|.++|+|
T Consensus 92 ~aMlf~aG~G~gllfwgvaEP~~h~~~PP~g~e~~s~~A~~~A~~~~~fHWG~~aWaiY~~~~la~ay~~y~~~ 165 (504)
T PRK03356 92 IFMMFASCTSAAVLFWGSIEIYYYISTPPFGLEPNSTGAKELGLAYSLFHWGPLPWATYSFLSVAFGYFFFVRK 165 (504)
T ss_pred HHHHHHHhhhhhhhhhhhhhHHHHcCCCCCCCCCCcHHHHHHHHHHHHHHhcHHHHHHHHHHHHHHHHHHHhcC
Confidence 3444445555555555544332211111 1234567789999999988888889999999999887655
No 17
>TIGR02359 thiW thiW protein. Levels of thiamine pyrophosphate (TPP) or thiamine regulate transcription or translation of a number of thiamine biosynthesis, salvage, or transport genes in a wide range of prokaryotes. The mechanism involves direct binding, with no protein involved,to a structural element called THI found in the untranslated upstream region of thiamine metabolism gene operons. This element is called a riboswitch and is seen also for other metabolites such as FMN and glycine. This protein family consists of proteins identified in operons controlled by the THI riboswitch and designated ThiW. The hydrophobic nature of this protein and reconstructed metabolic background suggests that this protein acts in transport of a thiazole precursor of thiamine.
Probab=21.78 E-value=3.8e+02 Score=20.59 Aligned_cols=27 Identities=7% Similarity=-0.160 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHhhCCchHHHHHHH
Q 027666 181 QLFIIGCVLGSSYCWSGNLISSIAIHS 207 (220)
Q Consensus 181 ~~~~~gl~~~~~y~~t~~l~~~i~~H~ 207 (220)
.....+++-|++|+|+++.+.++....
T Consensus 74 g~~~~a~laGliyrk~~~~~~a~~ge~ 100 (160)
T TIGR02359 74 GGMPGALLAGLLYRFGRKHYWASLGEI 100 (160)
T ss_pred HHHHHHHHHHHHHHHccccHHHHHHHH
Confidence 334567777788888777765554443
No 18
>PRK09400 secE preprotein translocase subunit SecE; Reviewed
Probab=21.21 E-value=2.3e+02 Score=17.96 Aligned_cols=18 Identities=22% Similarity=0.455 Sum_probs=7.6
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 027666 81 ASALGFAVLTSLVFLASL 98 (220)
Q Consensus 81 ~~~~g~~~~~~~~~~~~~ 98 (220)
...+|.++...+.++..+
T Consensus 38 ~~~iG~~i~G~iGf~Ikl 55 (61)
T PRK09400 38 VTGLGILLIGLIGFIIYL 55 (61)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 334444444444444433
No 19
>PTZ00370 STEVOR; Provisional
Probab=20.45 E-value=1.4e+02 Score=25.37 Aligned_cols=12 Identities=25% Similarity=0.324 Sum_probs=5.8
Q ss_pred HHHHHhhcCCCc
Q 027666 51 FLLSRTIKPEYD 62 (220)
Q Consensus 51 ~~~~~~~~~~~~ 62 (220)
++++||||+.++
T Consensus 276 iwlyrrRK~swk 287 (296)
T PTZ00370 276 IWLYRRRKNSWK 287 (296)
T ss_pred HHHHHhhcchhH
Confidence 344455555444
Done!