Query psy414
Match_columns 176
No_of_seqs 120 out of 145
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 17:55:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy414.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/414hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05821 NDUF_B8: NADH-ubiquin 100.0 2.9E-70 6.3E-75 448.3 12.9 155 16-174 13-167 (179)
2 KOG4040|consensus 100.0 4E-62 8.7E-67 393.8 11.3 152 21-175 23-175 (186)
3 PF00446 GnRH: Gonadotropin-re 76.4 1.4 3.1E-05 20.6 0.8 9 29-37 2-10 (10)
4 PF05821 NDUF_B8: NADH-ubiquin 68.6 8.3 0.00018 32.1 4.2 47 124-173 121-179 (179)
5 PF05920 Homeobox_KN: Homeobox 67.4 4.2 9E-05 25.8 1.7 20 37-57 8-27 (40)
6 PF06392 Asr: Acid shock prote 52.6 8.1 0.00017 21.1 0.9 12 41-52 8-19 (19)
7 PF13807 GNVR: G-rich domain o 44.1 31 0.00066 24.3 3.2 25 123-147 52-76 (82)
8 PF06166 DUF979: Protein of un 35.8 38 0.00082 30.7 3.1 25 32-56 67-92 (308)
9 COG3817 Predicted membrane pro 30.0 49 0.0011 29.7 2.8 25 32-56 71-96 (313)
10 smart00389 HOX Homeodomain. DN 29.7 59 0.0013 20.4 2.5 21 37-58 22-42 (56)
11 PF14147 Spore_YhaL: Sporulati 27.5 75 0.0016 21.7 2.7 21 125-145 1-21 (52)
12 PF01102 Glycophorin_A: Glycop 26.8 61 0.0013 25.4 2.6 17 129-145 65-81 (122)
13 COG3765 WzzB Chain length dete 24.4 98 0.0021 28.5 3.8 43 103-147 289-334 (347)
14 PF09098 Dehyd-heme_bind: Quin 24.0 57 0.0012 27.1 2.0 23 40-62 50-76 (167)
15 COG4957 Predicted transcriptio 23.7 27 0.00058 28.4 0.0 30 46-78 90-119 (148)
16 PF08628 Nexin_C: Sorting nexi 23.1 1.8E+02 0.004 21.4 4.5 23 30-52 52-75 (113)
17 TIGR00669 asnA aspartate--ammo 23.0 61 0.0013 29.6 2.2 17 38-54 176-194 (330)
18 PF15183 MRAP: Melanocortin-2 22.8 2.2E+02 0.0047 21.4 4.7 38 108-149 27-64 (90)
19 KOG4075|consensus 22.8 70 0.0015 26.6 2.3 10 96-105 82-91 (167)
20 PRK05425 asparagine synthetase 22.3 64 0.0014 29.5 2.2 17 38-54 178-196 (327)
21 PF01282 Ribosomal_S24e: Ribos 22.3 66 0.0014 23.4 1.9 24 35-58 7-31 (84)
22 PF14990 DUF4516: Domain of un 22.1 2.5E+02 0.0054 18.7 4.5 32 123-154 3-34 (47)
23 PF11821 DUF3341: Protein of u 22.1 1.2E+02 0.0026 25.0 3.6 34 102-143 37-70 (173)
24 PHA02284 hypothetical protein 21.9 74 0.0016 27.4 2.3 43 10-60 89-133 (251)
25 PTZ00213 asparagine synthetase 21.8 67 0.0014 29.6 2.2 17 38-54 179-197 (348)
26 PF11293 DUF3094: Protein of u 21.6 1.7E+02 0.0037 20.2 3.6 38 112-149 15-52 (55)
27 cd00645 AsnA Asparagine synthe 21.0 72 0.0015 29.0 2.2 17 38-54 168-186 (309)
28 PF13721 SecD-TM1: SecD export 20.9 1.2E+02 0.0027 22.5 3.1 18 124-141 3-20 (101)
No 1
>PF05821 NDUF_B8: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); InterPro: IPR008699 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=100.00 E-value=2.9e-70 Score=448.30 Aligned_cols=155 Identities=35% Similarity=0.548 Sum_probs=147.2
Q ss_pred HHHHhhhhhhhcccCCCCCCCCCCCCCHHHHHHHHHHcCCCCCCcccCCCCCCCCCCCCCCCCCCcccCCCCCCCCCcCC
Q psy414 16 VLSLQQNSVRTAFVYTPDWLPGERPKTEEERRKAAKKYNLLPEEYEVQPDDGFATGDYPHLPHTHYDSRDPFYPWDYPMF 95 (176)
Q Consensus 16 ~~~~~~~~~r~~~~~~~d~~PgpyP~t~eer~aaAkKY~l~~edY~P~~ddg~~~GDYP~lP~~s~q~RDPy~~WDdpq~ 95 (176)
...++.++||+||+|||||+|||||||+|||+||||||||+||||+||+|||+++||||+||.+|+|+||||++|||||+
T Consensus 13 ~~~~~~~~~r~~~~~~kd~~PgpyP~t~eer~aaAkKY~l~pedY~P~pDDg~~~GDYP~lp~~s~q~RDPy~~WDdpq~ 92 (179)
T PF05821_consen 13 NPAVLPLGARTASGWNKDWKPGPYPKTPEERAAAAKKYGLRPEDYEPYPDDGMGYGDYPKLPDISQQERDPYYDWDDPQE 92 (179)
T ss_pred hhhhhhhhhhhhccCCccCCCCCCCCCHHHHHHHHHHcCCCHHHcCCCCCCCcccCCCCCCCccchhhcCCCCCcCChhh
Confidence 44456899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCccCccccCCCCCCCccccCHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCCCCCCCccccccc
Q psy414 96 RTNYGEPLPNDFAISHYGMGFNEQPVNQRISVWEQLAYMVGILGTISLVLKYFCWEKRYYYPKFDSPKYQKGVVHYGYH 174 (176)
Q Consensus 96 RRNfgEPvH~d~d~Dm~s~dr~d~~~~~~vs~~~~l~~~~g~l~g~~~~~~~l~~~y~~~~Pv~prqYP~~GL~Hytfe 174 (176)
|||||||||+ |+|||++||+|++ ++.++|.+++.+|++|+ ||+++++||++++++++||+|||||+|||.|+++.
T Consensus 93 RRNfgEPvH~--d~Dm~s~dr~d~~-~~~~~w~~~~~~l~~fl-g~~~~~~~~~~~~~~~~P~~pKqYP~~gL~~e~gg 167 (179)
T PF05821_consen 93 RRNFGEPVHE--DFDMYSPDRYDTS-PTPVSWQSMLKQLFGFL-GFMLFMFYLGEMYPPYRPVMPKQYPYNGLYLELGG 167 (179)
T ss_pred hcCCCCCCcc--cccceeecccccC-CCcccHHHHHHHHHHHH-HHHHHHHHHhhhccCCCCCCcccCCCCCeecccCC
Confidence 9999999999 9999999999987 56778999999999999 99999999998999999999999999999998875
No 2
>KOG4040|consensus
Probab=100.00 E-value=4e-62 Score=393.78 Aligned_cols=152 Identities=34% Similarity=0.535 Sum_probs=142.8
Q ss_pred hhhhhhcccCCCCCCCCCCCCCHHHHHHHHHHcCCCCCCcccCCCCCCCCCCCCCCCCCCcccCCCCCCCCCcCCCCCCC
Q psy414 21 QNSVRTAFVYTPDWLPGERPKTEEERRKAAKKYNLLPEEYEVQPDDGFATGDYPHLPHTHYDSRDPFYPWDYPMFRTNYG 100 (176)
Q Consensus 21 ~~~~r~~~~~~~d~~PgpyP~t~eer~aaAkKY~l~~edY~P~~ddg~~~GDYP~lP~~s~q~RDPy~~WDdpq~RRNfg 100 (176)
..+.|++++|+||++|||||+|||||+||||||||+|||||||+|||+++||||+|+.+++++||||+.||+||+|||||
T Consensus 23 ~~g~rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEdY~py~dDg~gyGDYPkLg~~~~~~kDpyy~Wd~p~~rrNwg 102 (186)
T KOG4040|consen 23 PRGPRTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPEDYQPYDDDGVGYGDYPKLGVITYDHKDPYYAWDDPQNRRNWG 102 (186)
T ss_pred ccccccccccccccCCCCCCCCHHHHHHHHHHhCCCHhhcCcCCcCCcccCCCCcCcccccccCCCccccCChhhhcccC
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCccCccccCCCCCCC-ccccCHHHHHHHHHHHHHHHHHHHHHhhcccccCCCCCCCCCCCCCcccccccc
Q psy414 101 EPLPNDFAISHYGMGFNEQPV-NQRISVWEQLAYMVGILGTISLVLKYFCWEKRYYYPKFDSPKYQKGVVHYGYHQ 175 (176)
Q Consensus 101 EPvH~d~d~Dm~s~dr~d~~~-~~~vs~~~~l~~~~g~l~g~~~~~~~l~~~y~~~~Pv~prqYP~~GL~Hytfe~ 175 (176)
||||+ |+|+|+.||++..+ ++.++|..+|.+|+|+| .++++++|+...++.++||+|||||++|+.||+|+.
T Consensus 103 Epv~~--d~d~Y~~dR~t~~e~p~y~~w~~~~mcl~g~~-~~~l~~~y~~d~~p~ykPv~pKQYpy~~~~~y~f~d 175 (186)
T KOG4040|consen 103 EPVPI--DMDRYRGDRFTGLEAPDYTTWNSIVMCLRGLV-PMALLAWYFTDEHPRYKPVMPKQYPYDFYRAYPFDD 175 (186)
T ss_pred CCcch--hHhhhccccccccCCCCcccHHHHHHHHHHHH-HHHHHHHHHcccccccccCCcccCCCCCeeeccCCC
Confidence 99999 99999999988643 66789999999999999 666667788889999999999999999999999984
No 3
>PF00446 GnRH: Gonadotropin-releasing hormone; InterPro: IPR002012 The gonadotropin-releasing hormones (GnRH) (gonadoliberin) [] are a family of peptides that play a pivotal role in reproduction. The main function of GnRH is to act on the pituitary to stimulate the synthesis and secretion of luteinizing and follicle-stimulating hormones, but GnRH also acts on the brain, retina, sympathetic nervous system, gonads and placenta in certain species. There seems to be at least three forms of GnRH. The second form is expressed in midbrain and seems to be widespread. The third form has only been found so far in fish. GnRH is a C-terminal amidated decapeptide processed from a larger precursor protein. Four of the ten residues are perfectly conserved in all species where GnRH has been sequenced.; GO: 0005179 hormone activity, 0007275 multicellular organismal development, 0005576 extracellular region
Probab=76.43 E-value=1.4 Score=20.63 Aligned_cols=9 Identities=33% Similarity=1.069 Sum_probs=8.0
Q ss_pred cCCCCCCCC
Q psy414 29 VYTPDWLPG 37 (176)
Q Consensus 29 ~~~~d~~Pg 37 (176)
+|+.+|+||
T Consensus 2 HwS~~w~PG 10 (10)
T PF00446_consen 2 HWSHGWKPG 10 (10)
T ss_pred ccccccCCC
Confidence 699999998
No 4
>PF05821 NDUF_B8: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); InterPro: IPR008699 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=68.61 E-value=8.3 Score=32.08 Aligned_cols=47 Identities=21% Similarity=0.155 Sum_probs=28.3
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHhh--c-----cccc-----CCCCCCCCCCCCCcccccc
Q psy414 124 RISVWEQLAYMVGILGTISLVLKYFC--W-----EKRY-----YYPKFDSPKYQKGVVHYGY 173 (176)
Q Consensus 124 ~vs~~~~l~~~~g~l~g~~~~~~~l~--~-----~y~~-----~~Pv~prqYP~~GL~Hytf 173 (176)
..+...+++.|+||+++++.++.... + -|+. +.---|+..| ++||+|
T Consensus 121 w~~~~~~l~~flg~~~~~~~~~~~~~~~~P~~pKqYP~~gL~~e~ggdp~k~p---~~~y~~ 179 (179)
T PF05821_consen 121 WQSMLKQLFGFLGFMLFMFYLGEMYPPYRPVMPKQYPYNGLYLELGGDPSKEP---VVHYEI 179 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCCCCCcccCCCCCeecccCCCCccCC---cCCccC
Confidence 34566789999999977666653322 1 1211 1223455566 899997
No 5
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=67.43 E-value=4.2 Score=25.77 Aligned_cols=20 Identities=30% Similarity=0.423 Sum_probs=14.3
Q ss_pred CCCCCCHHHHHHHHHHcCCCC
Q psy414 37 GERPKTEEERRKAAKKYNLLP 57 (176)
Q Consensus 37 gpyP~t~eer~aaAkKY~l~~ 57 (176)
-||| |+||+...|++-||..
T Consensus 8 nPYP-s~~ek~~L~~~tgls~ 27 (40)
T PF05920_consen 8 NPYP-SKEEKEELAKQTGLSR 27 (40)
T ss_dssp SGS---HHHHHHHHHHHTS-H
T ss_pred CCCC-CHHHHHHHHHHcCCCH
Confidence 4786 6788999999999864
No 6
>PF06392 Asr: Acid shock protein repeat ; InterPro: IPR009435 The Asr protein is synthesised as a precursor and the cleavage is essential for moderate to high acid tolerance []. Enterobacteria have developed numerous constitutive and inducible strategies to sense and adapt to external acidity. These molecular responses require many specific acid shock proteins (ASPs) [].; GO: 0010447 response to acidity, 0042597 periplasmic space
Probab=52.56 E-value=8.1 Score=21.15 Aligned_cols=12 Identities=50% Similarity=0.661 Sum_probs=10.3
Q ss_pred CCHHHHHHHHHH
Q psy414 41 KTEEERRKAAKK 52 (176)
Q Consensus 41 ~t~eer~aaAkK 52 (176)
+|.|+++.||||
T Consensus 8 ~~~eqkaqaakk 19 (19)
T PF06392_consen 8 KATEQKAQAAKK 19 (19)
T ss_pred ccHHHHHHHhcC
Confidence 588999999986
No 7
>PF13807 GNVR: G-rich domain on putative tyrosine kinase
Probab=44.06 E-value=31 Score=24.29 Aligned_cols=25 Identities=16% Similarity=0.194 Sum_probs=17.3
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHH
Q psy414 123 QRISVWEQLAYMVGILGTISLVLKY 147 (176)
Q Consensus 123 ~~vs~~~~l~~~~g~l~g~~~~~~~ 147 (176)
.++++.+.+...+|+++|+++.+.+
T Consensus 52 ~P~~P~~~lil~l~~~~Gl~lgi~~ 76 (82)
T PF13807_consen 52 KPVSPKRALILALGLFLGLILGIGL 76 (82)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHHHH
Confidence 3677777777777777777765533
No 8
>PF06166 DUF979: Protein of unknown function (DUF979); InterPro: IPR009323 This family consists of several putative bacterial membrane proteins. The function of this family is unclear.
Probab=35.84 E-value=38 Score=30.66 Aligned_cols=25 Identities=28% Similarity=0.229 Sum_probs=19.3
Q ss_pred CCCCCCCCCC-CHHHHHHHHHHcCCC
Q psy414 32 PDWLPGERPK-TEEERRKAAKKYNLL 56 (176)
Q Consensus 32 ~d~~PgpyP~-t~eer~aaAkKY~l~ 56 (176)
+.-+.|.++. |+|||++.|||+|.+
T Consensus 67 ~~v~~g~~~~~s~e~r~~~a~rlGnk 92 (308)
T PF06166_consen 67 GQVGIGSYKEPSEEEREASAKRLGNK 92 (308)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHhcCe
Confidence 4456777776 688999999999854
No 9
>COG3817 Predicted membrane protein [Function unknown]
Probab=30.01 E-value=49 Score=29.74 Aligned_cols=25 Identities=28% Similarity=0.320 Sum_probs=20.4
Q ss_pred CCCCCCCCCC-CHHHHHHHHHHcCCC
Q psy414 32 PDWLPGERPK-TEEERRKAAKKYNLL 56 (176)
Q Consensus 32 ~d~~PgpyP~-t~eer~aaAkKY~l~ 56 (176)
+.-++|.+|+ ++|||++-|++||-+
T Consensus 71 ~~v~~G~~~~~~~e~re~~A~rlgnr 96 (313)
T COG3817 71 GQVKIGALPELSPEEREKSANRLGNR 96 (313)
T ss_pred CCcccCCCCCCCHHHHHHHHHHhcCE
Confidence 4568899988 788999999999843
No 10
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=29.72 E-value=59 Score=20.36 Aligned_cols=21 Identities=33% Similarity=0.434 Sum_probs=16.9
Q ss_pred CCCCCCHHHHHHHHHHcCCCCC
Q psy414 37 GERPKTEEERRKAAKKYNLLPE 58 (176)
Q Consensus 37 gpyP~t~eer~aaAkKY~l~~e 58 (176)
.+|| |.+++...|+..||..+
T Consensus 22 ~~~P-~~~~~~~la~~~~l~~~ 42 (56)
T smart00389 22 NPYP-SREEREELAAKLGLSER 42 (56)
T ss_pred CCCC-CHHHHHHHHHHHCcCHH
Confidence 3477 88999999999998743
No 11
>PF14147 Spore_YhaL: Sporulation protein YhaL
Probab=27.47 E-value=75 Score=21.66 Aligned_cols=21 Identities=19% Similarity=0.139 Sum_probs=13.5
Q ss_pred cCHHHHHHHHHHHHHHHHHHH
Q psy414 125 ISVWEQLAYMVGILGTISLVL 145 (176)
Q Consensus 125 vs~~~~l~~~~g~l~g~~~~~ 145 (176)
++||..+..++.++.|+|++-
T Consensus 1 ~PwWvY~vi~gI~~S~ym~v~ 21 (52)
T PF14147_consen 1 IPWWVYFVIAGIIFSGYMAVK 21 (52)
T ss_pred CcchHHHHHHHHHHHHHHHHH
Confidence 468877766666666666543
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=26.83 E-value=61 Score=25.41 Aligned_cols=17 Identities=6% Similarity=0.354 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy414 129 EQLAYMVGILGTISLVL 145 (176)
Q Consensus 129 ~~l~~~~g~l~g~~~~~ 145 (176)
.+..++||+|+|+.+.+
T Consensus 65 ~i~~Ii~gv~aGvIg~I 81 (122)
T PF01102_consen 65 AIIGIIFGVMAGVIGII 81 (122)
T ss_dssp CHHHHHHHHHHHHHHHH
T ss_pred ceeehhHHHHHHHHHHH
Confidence 35666677776666543
No 13
>COG3765 WzzB Chain length determinant protein [Cell envelope biogenesis, outer membrane]
Probab=24.41 E-value=98 Score=28.52 Aligned_cols=43 Identities=16% Similarity=-0.022 Sum_probs=26.9
Q ss_pred CCCCCccCccccCCCCCC--Cc-cccCHHHHHHHHHHHHHHHHHHHHH
Q psy414 103 LPNDFAISHYGMGFNEQP--VN-QRISVWEQLAYMVGILGTISLVLKY 147 (176)
Q Consensus 103 vH~d~d~Dm~s~dr~d~~--~~-~~vs~~~~l~~~~g~l~g~~~~~~~ 147 (176)
++. ..+-.+.-|++.+ .| .+.++.++|..++|+++|+|+.++.
T Consensus 289 l~v--~d~~~~~yRYl~~P~~Pvkrd~PrrA~ilil~~LiGgm~g~g~ 334 (347)
T COG3765 289 LKV--LDERFSTYRYLQKPTLPVKRDSPRRAIILILGALIGGMLGAGV 334 (347)
T ss_pred ccC--cccceeEEEecCCCCCCCcCCCcchHHHHHHHHHHHHHHHHHH
Confidence 455 4555566667643 12 2567778887777777777776644
No 14
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=24.01 E-value=57 Score=27.12 Aligned_cols=23 Identities=39% Similarity=0.508 Sum_probs=13.8
Q ss_pred CCCHHHHHHH----HHHcCCCCCCccc
Q psy414 40 PKTEEERRKA----AKKYNLLPEEYEV 62 (176)
Q Consensus 40 P~t~eer~aa----AkKY~l~~edY~P 62 (176)
+-|++||+|+ |++|||-|+|-++
T Consensus 50 ~Is~eer~avVkYLAd~~GLap~Et~~ 76 (167)
T PF09098_consen 50 PISPEERRAVVKYLADTQGLAPSETAP 76 (167)
T ss_dssp ---HHHHHHHHHHHHHHT---CGGCTT
T ss_pred CCCHHHHHHHHHHHHHccCCCchhhcc
Confidence 4588999886 6799999998654
No 15
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=23.69 E-value=27 Score=28.41 Aligned_cols=30 Identities=33% Similarity=0.705 Sum_probs=20.6
Q ss_pred HHHHHHHcCCCCCCcccCCCCCCCCCCCCCCCC
Q psy414 46 RRKAAKKYNLLPEEYEVQPDDGFATGDYPHLPH 78 (176)
Q Consensus 46 r~aaAkKY~l~~edY~P~~ddg~~~GDYP~lP~ 78 (176)
++-..-+|||.||||.- .=|+ -.|||.+-+
T Consensus 90 KRHL~t~~gmTPd~YR~--KW~L-P~dYPMvAP 119 (148)
T COG4957 90 KRHLTTHYGLTPDEYRA--KWGL-PPDYPMVAP 119 (148)
T ss_pred HHHHhcccCCCHHHHHH--hcCC-CCCCCccch
Confidence 44566789999999981 1122 379998754
No 16
>PF08628 Nexin_C: Sorting nexin C terminal; InterPro: IPR013937 This region is found at the C terminus of proteins belonging to the nexin family. It is found on proteins which also contain IPR001683 from INTERPRO.
Probab=23.12 E-value=1.8e+02 Score=21.37 Aligned_cols=23 Identities=22% Similarity=0.400 Sum_probs=13.8
Q ss_pred CCCC-CCCCCCCCCHHHHHHHHHH
Q psy414 30 YTPD-WLPGERPKTEEERRKAAKK 52 (176)
Q Consensus 30 ~~~d-~~PgpyP~t~eer~aaAkK 52 (176)
|.-. +.+.+-|+|+|||++.+++
T Consensus 52 wP~g~~~~~~~~Rt~~ek~~tr~~ 75 (113)
T PF08628_consen 52 WPNGKLAEPPPPRTEEEKLRTRQE 75 (113)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHH
Confidence 5444 2233338999998776553
No 17
>TIGR00669 asnA aspartate--ammonia ligase, AsnA-type. The fact that the protein from the H. influenzae is more than 70 % identical to that from the spirochete Treponema pallidum, but less than 65 % identical to that from the closely related E. coli, strongly suggests lateral transfer.
Probab=23.03 E-value=61 Score=29.62 Aligned_cols=17 Identities=18% Similarity=0.325 Sum_probs=13.6
Q ss_pred CCCC-CHHHHH-HHHHHcC
Q psy414 38 ERPK-TEEERR-KAAKKYN 54 (176)
Q Consensus 38 pyP~-t~eer~-aaAkKY~ 54 (176)
.||. |++||+ ++||+||
T Consensus 176 ~YP~lt~keRE~~i~ke~g 194 (330)
T TIGR00669 176 RYPDLDSKGRERAICKELG 194 (330)
T ss_pred HCCCCCHHHHHHHHHHHhC
Confidence 3554 899998 8889888
No 18
>PF15183 MRAP: Melanocortin-2 receptor accessory protein family
Probab=22.85 E-value=2.2e+02 Score=21.40 Aligned_cols=38 Identities=21% Similarity=0.152 Sum_probs=23.7
Q ss_pred ccCccccCCCCCCCccccCHHHHHHHHHHHHHHHHHHHHHhh
Q psy414 108 AISHYGMGFNEQPVNQRISVWEQLAYMVGILGTISLVLKYFC 149 (176)
Q Consensus 108 d~Dm~s~dr~d~~~~~~vs~~~~l~~~~g~l~g~~~~~~~l~ 149 (176)
|+.-+...+++. .|-.|..++.|.+|+|-++++|.+-+
T Consensus 27 d~~~Lka~kysI----VI~FWv~LA~FV~~lF~iL~~ms~sg 64 (90)
T PF15183_consen 27 DEEKLKANKYSI----VIAFWVSLAAFVVFLFLILLYMSWSG 64 (90)
T ss_pred CHHHhcccceee----ehhHHHHHHHHHHHHHHHHHHHhccC
Confidence 334444544443 46778888888888876666665543
No 19
>KOG4075|consensus
Probab=22.83 E-value=70 Score=26.62 Aligned_cols=10 Identities=30% Similarity=0.786 Sum_probs=6.2
Q ss_pred CCCCCCCCCC
Q psy414 96 RTNYGEPLPN 105 (176)
Q Consensus 96 RRNfgEPvH~ 105 (176)
|=-|||+.-+
T Consensus 82 risF~et~ae 91 (167)
T KOG4075|consen 82 RISFGETFAE 91 (167)
T ss_pred HHHhcccccc
Confidence 4457776665
No 20
>PRK05425 asparagine synthetase AsnA; Provisional
Probab=22.33 E-value=64 Score=29.45 Aligned_cols=17 Identities=41% Similarity=0.636 Sum_probs=13.7
Q ss_pred CCCC-CHHHHH-HHHHHcC
Q psy414 38 ERPK-TEEERR-KAAKKYN 54 (176)
Q Consensus 38 pyP~-t~eer~-aaAkKY~ 54 (176)
-||. |++||+ ++||+||
T Consensus 178 ~YP~l~~keRE~~i~ke~g 196 (327)
T PRK05425 178 RYPDLTPKEREDAIAKEYG 196 (327)
T ss_pred HCCCCCHHHHHHHHHHHhC
Confidence 4564 899998 8889888
No 21
>PF01282 Ribosomal_S24e: Ribosomal protein S24e; InterPro: IPR001976 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the S24e ribosomal proteins from eukaryotes and archaebacteria. These proteins have 101 to 148 amino acids.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2V94_B 1YWX_A 2G1D_A 3IZ6_U 1XN9_A 2XZM_P 2XZN_P 3U5G_Y 3J16_D 3IZB_U ....
Probab=22.31 E-value=66 Score=23.35 Aligned_cols=24 Identities=38% Similarity=0.567 Sum_probs=18.0
Q ss_pred CCC-CCCCCHHHHHHHHHHcCCCCC
Q psy414 35 LPG-ERPKTEEERRKAAKKYNLLPE 58 (176)
Q Consensus 35 ~Pg-pyP~t~eer~aaAkKY~l~~e 58 (176)
-|| +.|...|=|.+.|+.||..++
T Consensus 7 h~g~~Tpsr~ei~~klA~~~~~~~~ 31 (84)
T PF01282_consen 7 HPGKPTPSRKEIREKLAAMLNVDPD 31 (84)
T ss_dssp -SSSSS--HHHHHHHHHHHHTSTGC
T ss_pred CCCCCCCCHHHHHHHHHHHhCCCCC
Confidence 367 889999999999999998554
No 22
>PF14990 DUF4516: Domain of unknown function (DUF4516)
Probab=22.08 E-value=2.5e+02 Score=18.69 Aligned_cols=32 Identities=13% Similarity=-0.139 Sum_probs=17.2
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHhhccccc
Q psy414 123 QRISVWEQLAYMVGILGTISLVLKYFCWEKRY 154 (176)
Q Consensus 123 ~~vs~~~~l~~~~g~l~g~~~~~~~l~~~y~~ 154 (176)
..++|.+.++.+...++..++..-.+-..|++
T Consensus 3 ~Gv~~~~yl~~~~~s~~sM~aGA~vVH~~ykP 34 (47)
T PF14990_consen 3 AGVSWPSYLKSLVASLLSMLAGASVVHNIYKP 34 (47)
T ss_pred CCCcHHHHHHHHHHHHHHHHhhhHHHHHHhCc
Confidence 35788877776665554444433333324444
No 23
>PF11821 DUF3341: Protein of unknown function (DUF3341); InterPro: IPR021776 This family of proteins are functionally uncharacterised. This family is found in bacteria. Proteins in this family are about 170 amino acids in length.
Probab=22.07 E-value=1.2e+02 Score=25.00 Aligned_cols=34 Identities=15% Similarity=0.228 Sum_probs=20.6
Q ss_pred CCCCCCccCccccCCCCCCCccccCHHHHHHHHHHHHHHHHH
Q psy414 102 PLPNDFAISHYGMGFNEQPVNQRISVWEQLAYMVGILGTISL 143 (176)
Q Consensus 102 PvH~d~d~Dm~s~dr~d~~~~~~vs~~~~l~~~~g~l~g~~~ 143 (176)
|||. =.+.++. .+++++|..-+.-++|+++|+++
T Consensus 37 Pvhg--ld~alg~------~~s~l~~~~l~~Gl~G~~~~~~l 70 (173)
T PF11821_consen 37 PVHG--LDEALGL------KRSRLPWIALVGGLTGFATAFLL 70 (173)
T ss_pred cCcC--HHHHhCC------CCCchHHHHHHHHHHHHHHHHHH
Confidence 6776 4455543 25688877666666666655554
No 24
>PHA02284 hypothetical protein
Probab=21.89 E-value=74 Score=27.42 Aligned_cols=43 Identities=30% Similarity=0.312 Sum_probs=30.7
Q ss_pred ccchHHHHHHhhhhhhhcccCCCCCCCCCCCC-CHHHHHHHHHHcCCCC-CCc
Q psy414 10 VKSLGKVLSLQQNSVRTAFVYTPDWLPGERPK-TEEERRKAAKKYNLLP-EEY 60 (176)
Q Consensus 10 ~~~~~~~~~~~~~~~r~~~~~~~d~~PgpyP~-t~eer~aaAkKY~l~~-edY 60 (176)
|.+=||.-||+++++-- .|.|||+ |+|....|.+=||..- |||
T Consensus 89 VDs~~K~~SLL~Q~~EL--------~~~~~~~~~~~~~K~~T~YYNF~~f~D~ 133 (251)
T PHA02284 89 VDSDRKYYSLLQQITEL--------SKDPFPKWVEDDAKGLTKYYNFQDFEDV 133 (251)
T ss_pred eccchhHHHHHHHHHHh--------CcccchhhhHHHHhhhhhhcccccHHHh
Confidence 55678999999888754 4789998 5555556666677665 554
No 25
>PTZ00213 asparagine synthetase A; Provisional
Probab=21.81 E-value=67 Score=29.58 Aligned_cols=17 Identities=35% Similarity=0.601 Sum_probs=13.8
Q ss_pred CCCC-CHHHHH-HHHHHcC
Q psy414 38 ERPK-TEEERR-KAAKKYN 54 (176)
Q Consensus 38 pyP~-t~eer~-aaAkKY~ 54 (176)
.||. |++||+ ++||+||
T Consensus 179 ~YP~lt~keRE~~i~ke~g 197 (348)
T PTZ00213 179 MYPNLSPKEREREIVKKYG 197 (348)
T ss_pred HCCCCCHHHHHHHHHHHhC
Confidence 4665 899998 8889887
No 26
>PF11293 DUF3094: Protein of unknown function (DUF3094); InterPro: IPR021444 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=21.62 E-value=1.7e+02 Score=20.15 Aligned_cols=38 Identities=13% Similarity=0.212 Sum_probs=24.8
Q ss_pred cccCCCCCCCccccCHHHHHHHHHHHHHHHHHHHHHhh
Q psy414 112 YGMGFNEQPVNQRISVWEQLAYMVGILGTISLVLKYFC 149 (176)
Q Consensus 112 ~s~dr~d~~~~~~vs~~~~l~~~~g~l~g~~~~~~~l~ 149 (176)
|..-..+..+..++-++..+..+++++.|+.++..+++
T Consensus 15 yL~a~~~~VER~PFrP~~Ll~~li~Vv~gl~llS~ll~ 52 (55)
T PF11293_consen 15 YLQAGVNQVERKPFRPWRLLIVLIVVVIGLGLLSRLLS 52 (55)
T ss_pred HHhCCCCccccCCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333444456677777777788888878777665555
No 27
>cd00645 AsnA Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II aminoacyl-tRNA synthetases. Ammonia-dependent AsnA is not homologous to the glutamine-dependent asparagine synthetase AsnB.
Probab=21.02 E-value=72 Score=28.95 Aligned_cols=17 Identities=29% Similarity=0.403 Sum_probs=13.7
Q ss_pred CCCC-CHHHHH-HHHHHcC
Q psy414 38 ERPK-TEEERR-KAAKKYN 54 (176)
Q Consensus 38 pyP~-t~eer~-aaAkKY~ 54 (176)
.||. |++||+ ++||+||
T Consensus 168 ~YP~l~~keRE~~i~ke~g 186 (309)
T cd00645 168 RYPDLTPKEREDAICKEHG 186 (309)
T ss_pred HCCCCCHHHHHHHHHHHhC
Confidence 4554 899998 8889888
No 28
>PF13721 SecD-TM1: SecD export protein N-terminal TM region
Probab=20.88 E-value=1.2e+02 Score=22.54 Aligned_cols=18 Identities=28% Similarity=0.471 Sum_probs=11.9
Q ss_pred ccCHHHHHHHHHHHHHHH
Q psy414 124 RISVWEQLAYMVGILGTI 141 (176)
Q Consensus 124 ~vs~~~~l~~~~g~l~g~ 141 (176)
+++.||.++.++.+++|+
T Consensus 3 ~yp~WKyllil~vl~~~~ 20 (101)
T PF13721_consen 3 RYPLWKYLLILVVLLLGA 20 (101)
T ss_pred CcchHHHHHHHHHHHHHH
Confidence 678888887665554333
Done!