Query 040093
Match_columns 48
No_of_seqs 54 out of 56
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 05:03:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040093.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040093hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4267 Predicted membrane pro 99.4 2.9E-13 6.4E-18 85.3 4.0 36 2-37 75-110 (110)
2 PF03647 Tmemb_14: Transmembra 98.5 9.3E-08 2E-12 57.2 2.1 26 2-27 71-96 (96)
3 PF06103 DUF948: Bacterial pro 42.1 48 0.001 18.6 3.2 20 11-30 2-21 (90)
4 cd04411 Ribosomal_P1_P2_L12p R 41.7 19 0.00042 22.0 1.6 15 21-35 1-16 (105)
5 PF05283 MGC-24: Multi-glycosy 41.1 32 0.0007 23.2 2.7 21 11-31 165-185 (186)
6 PLN02356 phosphateglycerate ki 40.9 41 0.00089 24.9 3.4 25 10-34 7-31 (423)
7 PF04588 HIG_1_N: Hypoxia indu 40.8 53 0.0011 17.5 3.1 25 4-28 2-26 (54)
8 PF06522 B12D: NADH-ubiquinone 37.3 62 0.0013 18.3 3.1 24 7-30 5-28 (73)
9 COG4858 Uncharacterized membra 36.8 26 0.00056 24.8 1.7 14 11-24 105-118 (226)
10 PTZ00233 variable surface prot 35.8 27 0.00059 26.9 1.9 31 9-41 440-470 (509)
11 COG5548 Small integral membran 35.2 28 0.00061 22.1 1.6 25 2-28 74-98 (105)
12 PF09777 OSTMP1: Osteopetrosis 35.0 59 0.0013 22.1 3.2 20 19-38 201-220 (237)
13 PTZ00234 variable surface prot 32.8 34 0.00074 25.6 1.9 27 14-41 371-400 (433)
14 PF10661 EssA: WXG100 protein 32.5 65 0.0014 20.6 2.9 26 6-31 115-141 (145)
15 PF10206 WRW: Mitochondrial F1 31.6 58 0.0012 20.3 2.5 19 11-29 77-95 (104)
16 PF07423 DUF1510: Protein of u 31.2 61 0.0013 22.2 2.8 34 5-40 12-45 (217)
17 PF13197 DUF4013: Protein of u 28.5 1E+02 0.0022 18.9 3.3 26 13-38 9-39 (169)
18 PF12273 RCR: Chitin synthesis 24.7 1.1E+02 0.0024 18.4 2.9 16 12-27 7-22 (130)
19 PRK11235 bifunctional antitoxi 24.5 1.1E+02 0.0023 18.0 2.7 22 17-38 27-48 (80)
20 PF14019 DUF4235: Protein of u 24.3 1.5E+02 0.0032 16.9 4.4 25 13-38 10-34 (78)
21 PF11337 DUF3139: Protein of u 24.2 84 0.0018 17.8 2.2 19 23-41 18-36 (85)
22 PF12270 Cyt_c_ox_IV: Cytochro 24.1 2.1E+02 0.0046 18.5 4.2 33 9-41 34-70 (137)
23 PF04678 DUF607: Protein of un 23.6 1.4E+02 0.003 19.2 3.3 24 16-39 129-152 (180)
24 PF02468 PsbN: Photosystem II 23.5 1.4E+02 0.0029 16.1 3.2 28 16-43 10-37 (43)
25 cd07468 CRD_TK_ROR2 Cysteine-r 23.0 47 0.001 21.6 1.0 22 18-39 58-81 (140)
26 PF02439 Adeno_E3_CR2: Adenovi 22.9 1.3E+02 0.0029 15.8 2.8 18 11-28 10-27 (38)
27 TIGR03685 L21P_arch 50S riboso 22.8 63 0.0014 19.7 1.6 15 21-35 1-16 (105)
28 PRK12573 putative monovalent c 22.1 2.1E+02 0.0047 18.1 3.9 26 11-36 9-34 (140)
29 PF06939 DUF1286: Protein of u 21.5 1.2E+02 0.0026 19.4 2.7 24 2-25 2-26 (114)
30 PF06679 DUF1180: Protein of u 21.4 1.4E+02 0.0031 19.7 3.1 26 13-38 100-125 (163)
31 PRK13183 psbN photosystem II r 21.1 1.3E+02 0.0028 16.5 2.4 28 16-43 13-40 (46)
32 KOG4697 Integral membrane prot 21.1 1.2E+02 0.0025 20.5 2.7 27 14-40 25-51 (160)
No 1
>KOG4267 consensus Predicted membrane protein [Function unknown]
Probab=99.40 E-value=2.9e-13 Score=85.27 Aligned_cols=36 Identities=53% Similarity=1.103 Sum_probs=34.9
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHHHhcCCCCCC
Q 040093 2 WMQTKKLFPTGFYAAISAAMLCFYSYVVASGGNPPP 37 (48)
Q Consensus 2 y~~T~kifPaG~va~iS~~M~~FY~y~l~~ggNp~p 37 (48)
|+.|+|+||+|+++.+|++|+|||.|++++++||+|
T Consensus 75 ~~~s~K~mPaglva~~s~~m~~~Y~y~~~~~~~~~~ 110 (110)
T KOG4267|consen 75 FYRSRKIMPAGLVAGISLLMTCFYLYVVLRGGNPPP 110 (110)
T ss_pred hhccCCccchHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 789999999999999999999999999999999986
No 2
>PF03647 Tmemb_14: Transmembrane proteins 14C; InterPro: IPR005349 This family of short membrane proteins is as yet uncharacterised.; GO: 0016020 membrane; PDB: 2LOS_A 2LOO_A 2LOP_A.
Probab=98.46 E-value=9.3e-08 Score=57.25 Aligned_cols=26 Identities=46% Similarity=0.964 Sum_probs=23.4
Q ss_pred cccccccchhHHHHHHHHHHHHHHHH
Q 040093 2 WMQTKKLFPTGFYAAISAAMLCFYSY 27 (48)
Q Consensus 2 y~~T~kifPaG~va~iS~~M~~FY~y 27 (48)
|.+|+|+||+|+++++|++|++||.|
T Consensus 71 ~~~t~k~~Pagl~~~~s~~~~~~y~Y 96 (96)
T PF03647_consen 71 YIKTRKFMPAGLMALLSGAMLAFYYY 96 (96)
T ss_dssp S-SSSSSCCCHHHHHHHHHHHHHHC-
T ss_pred HHHcCCCccHHHHHHHHHHHHHHhcC
Confidence 78999999999999999999999987
No 3
>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins.
Probab=42.10 E-value=48 Score=18.62 Aligned_cols=20 Identities=35% Similarity=0.466 Sum_probs=16.8
Q ss_pred hHHHHHHHHHHHHHHHHHHh
Q 040093 11 TGFYAAISAAMLCFYSYVVA 30 (48)
Q Consensus 11 aG~va~iS~~M~~FY~y~l~ 30 (48)
+++++.++.+.++.|+-..+
T Consensus 2 a~lI~Aiaf~vLvi~l~~~l 21 (90)
T PF06103_consen 2 AGLIAAIAFAVLVIFLIKVL 21 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 68899999999998887665
No 4
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=41.73 E-value=19 Score=21.97 Aligned_cols=15 Identities=27% Similarity=0.530 Sum_probs=12.1
Q ss_pred HHHHHHHHHh-cCCCC
Q 040093 21 MLCFYSYVVA-SGGNP 35 (48)
Q Consensus 21 M~~FY~y~l~-~ggNp 35 (48)
|-|-|+|-|+ .+||.
T Consensus 1 m~~v~A~Lll~~~g~~ 16 (105)
T cd04411 1 MEYVAAYLLLHKGGKE 16 (105)
T ss_pred CHHHHHHHHHHhcCCC
Confidence 6789999999 66665
No 5
>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=41.12 E-value=32 Score=23.19 Aligned_cols=21 Identities=14% Similarity=0.393 Sum_probs=18.5
Q ss_pred hHHHHHHHHHHHHHHHHHHhc
Q 040093 11 TGFYAAISAAMLCFYSYVVAS 31 (48)
Q Consensus 11 aG~va~iS~~M~~FY~y~l~~ 31 (48)
-|||-.+++.-.+|++|+..+
T Consensus 165 GGIVL~LGv~aI~ff~~KF~k 185 (186)
T PF05283_consen 165 GGIVLTLGVLAIIFFLYKFCK 185 (186)
T ss_pred hHHHHHHHHHHHHHHHhhhcc
Confidence 589999999999999999764
No 6
>PLN02356 phosphateglycerate kinase
Probab=40.86 E-value=41 Score=24.92 Aligned_cols=25 Identities=28% Similarity=0.356 Sum_probs=21.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHhcCCC
Q 040093 10 PTGFYAAISAAMLCFYSYVVASGGN 34 (48)
Q Consensus 10 PaG~va~iS~~M~~FY~y~l~~ggN 34 (48)
--.+++.-|++|++-|.+.+....+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~ 31 (423)
T PLN02356 7 TGAVVAAASLLMLLSYSFLLCNSRK 31 (423)
T ss_pred hhHHHHHHHHHHHHHHHHHhhcccc
Confidence 3468899999999999999986655
No 7
>PF04588 HIG_1_N: Hypoxia induced protein conserved region; InterPro: IPR007667 The hypoxia induced gene 1 (HIG1) or hypoglycemia/hypoxia inducible mitochondrial protein (HIMP1) is up-regulated by stresses of the microenvironment such as low oxygen or low glucose conditions. HIG1 is a mitochondrial inner membrane protein, which is ubiquitously expressed. It is predicted to be an integral membrane protein consisting of two hydrophobic helices, 21-23 residues in length that might tend to form a hairpin-like loop across the bilayer. HIG1 could be implied in apoptotic or cytoprotective signals. HIG1 is a member of a well conserved eukaryote protein family. The predicted transmembrane helice (TMH) and loop regions represent the most highly conserved regions in these proteins [, ]. The profile we developed covers the predicted TMH and loop regions. This domain is found in proteins thought to be involved in the response to hypoxia []. It is also found in altered inheritance of mitochondria proteins.; PDB: 2LOM_A 2LON_A.
Probab=40.84 E-value=53 Score=17.52 Aligned_cols=25 Identities=24% Similarity=0.530 Sum_probs=17.2
Q ss_pred cccccchhHHHHHHHHHHHHHHHHH
Q 040093 4 QTKKLFPTGFYAAISAAMLCFYSYV 28 (48)
Q Consensus 4 ~T~kifPaG~va~iS~~M~~FY~y~ 28 (48)
+-+.++|-|..+...++....|.+.
T Consensus 2 ke~plv~ig~~~~~~~l~~g~~~~~ 26 (54)
T PF04588_consen 2 KENPLVPIGMLATVGALAYGLYNFR 26 (54)
T ss_dssp -S--CHHHHHHHHHHHHHHHHHHHT
T ss_pred CcccHHHHHHHHHHHHHHHHHHHhc
Confidence 3467889999988888777766654
No 8
>PF06522 B12D: NADH-ubiquinone reductase complex 1 MLRQ subunit; InterPro: IPR010530 The MLRQ subunit of mitochondrial NADH-ubiquinone reductase complex I is nuclear [] and is found in plants [], insects, fungi and higher metazoans []. It appears to act within the membrane and, in mammals, is highly expressed in muscle and neural tissue, indicative of a role in ATP generation [].
Probab=37.32 E-value=62 Score=18.25 Aligned_cols=24 Identities=21% Similarity=0.419 Sum_probs=20.2
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHh
Q 040093 7 KLFPTGFYAAISAAMLCFYSYVVA 30 (48)
Q Consensus 7 kifPaG~va~iS~~M~~FY~y~l~ 30 (48)
-++|=.++..+.+.|++||++..+
T Consensus 5 el~PL~~~vg~a~~~a~~~~~r~l 28 (73)
T PF06522_consen 5 ELYPLFVIVGVAVGGATFYLYRLL 28 (73)
T ss_pred cccchHHHHHHHHHHHHHHHHHHH
Confidence 467888888899999999999866
No 9
>COG4858 Uncharacterized membrane-bound protein conserved in bacteria [Function unknown]
Probab=36.82 E-value=26 Score=24.78 Aligned_cols=14 Identities=29% Similarity=0.313 Sum_probs=6.6
Q ss_pred hHHHHHHHHHHHHH
Q 040093 11 TGFYAAISAAMLCF 24 (48)
Q Consensus 11 aG~va~iS~~M~~F 24 (48)
-|+++++|++|+.|
T Consensus 105 lg~~aLlsgitaff 118 (226)
T COG4858 105 LGAMALLSGITAFF 118 (226)
T ss_pred HHHHHHHHHHHHHH
Confidence 34445555444443
No 10
>PTZ00233 variable surface protein Vir18; Provisional
Probab=35.80 E-value=27 Score=26.85 Aligned_cols=31 Identities=19% Similarity=0.132 Sum_probs=24.7
Q ss_pred chhHHHHHHHHHHHHHHHHHHhcCCCCCCcccc
Q 040093 9 FPTGFYAAISAAMLCFYSYVVASGGNPPPKKLK 41 (48)
Q Consensus 9 fPaG~va~iS~~M~~FY~y~l~~ggNp~pkk~~ 41 (48)
+|=|||.+|+++.=-==+|.+|+.-| +||-+
T Consensus 440 aPmGIvLLLGLLFKyTPLWRvLTKkn--RKk~a 470 (509)
T PTZ00233 440 MPIGIALLLGLLFKYTPLWRVLTKKN--RKKGA 470 (509)
T ss_pred cchhHHHHHHHhhccchhHHhhhhcc--ccccc
Confidence 69999999976655556999999988 67655
No 11
>COG5548 Small integral membrane protein [Function unknown]
Probab=35.15 E-value=28 Score=22.07 Aligned_cols=25 Identities=32% Similarity=0.616 Sum_probs=18.6
Q ss_pred cccccccchhHHHHHHHHHHHHHHHHH
Q 040093 2 WMQTKKLFPTGFYAAISAAMLCFYSYV 28 (48)
Q Consensus 2 y~~T~kifPaG~va~iS~~M~~FY~y~ 28 (48)
+++++|.+|++..++.. |.-.|.|+
T Consensus 74 ~~~sRKpvP~~Lt~lgg--~~s~y~y~ 98 (105)
T COG5548 74 LVRSRKPVPAGLTTLGG--MLSLYVYV 98 (105)
T ss_pred ccccCCCcchHHHHHhh--hhhhhhee
Confidence 56899999999988754 55556554
No 12
>PF09777 OSTMP1: Osteopetrosis-associated transmembrane protein 1 precursor; InterPro: IPR019172 Osteopetrosis-associated transmembrane protein 1 (OSTM1) is required for osteoclast and melanocyte maturation and function. Mutations in OSTM1 give rise to autosomal recessive osteopetrosis, also called autosomal recessive Albers-Schonberg disease [, ].
Probab=35.02 E-value=59 Score=22.14 Aligned_cols=20 Identities=15% Similarity=0.047 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHhcCCCCCCc
Q 040093 19 AAMLCFYSYVVASGGNPPPK 38 (48)
Q Consensus 19 ~~M~~FY~y~l~~ggNp~pk 38 (48)
++.++||+-..+.|+...++
T Consensus 201 ~lpv~FY~~s~~~~~~~~r~ 220 (237)
T PF09777_consen 201 FLPVLFYLSSYLHSERKKRK 220 (237)
T ss_pred HHHHHHHHhheeeecccccc
Confidence 45679999999988774444
No 13
>PTZ00234 variable surface protein Vir12; Provisional
Probab=32.75 E-value=34 Score=25.57 Aligned_cols=27 Identities=15% Similarity=0.228 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHhcCCC---CCCcccc
Q 040093 14 YAAISAAMLCFYSYVVASGGN---PPPKKLK 41 (48)
Q Consensus 14 va~iS~~M~~FY~y~l~~ggN---p~pkk~~ 41 (48)
+|+|..+..+|| |++.++=. |.+|+++
T Consensus 371 ~ailGtifFlfy-yn~ss~lks~~~krkrkk 400 (433)
T PTZ00234 371 ASIIGVLVFLFF-FFKSTPIRSQTNKGEKKK 400 (433)
T ss_pred HHHHHHHHHhhh-hhcccchhccccchhhcc
Confidence 355666666777 67765433 4444433
No 14
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=32.46 E-value=65 Score=20.61 Aligned_cols=26 Identities=27% Similarity=0.227 Sum_probs=17.4
Q ss_pred cccchhHHHHH-HHHHHHHHHHHHHhc
Q 040093 6 KKLFPTGFYAA-ISAAMLCFYSYVVAS 31 (48)
Q Consensus 6 ~kifPaG~va~-iS~~M~~FY~y~l~~ 31 (48)
..+.|.=++++ ..++|+|+=+|.+++
T Consensus 115 ~~~~~~i~~~i~g~ll~i~~giy~~~r 141 (145)
T PF10661_consen 115 KPISPTILLSIGGILLAICGGIYVVLR 141 (145)
T ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566544444 356888999999875
No 15
>PF10206 WRW: Mitochondrial F1F0-ATP synthase, subunit f; InterPro: IPR019344 This entry represents small proteins of approximately 110 amino acids, which are highly conserved from nematodes to humans. Some have been annotated in Swiss-Prot as being the f subunit of mitochondrial F1F0-ATP synthase but this could not be confirmed. The sequence has a well-conserved WRW motif. The exact function of the protein is not known.
Probab=31.63 E-value=58 Score=20.27 Aligned_cols=19 Identities=16% Similarity=0.345 Sum_probs=15.5
Q ss_pred hHHHHHHHHHHHHHHHHHH
Q 040093 11 TGFYAAISAAMLCFYSYVV 29 (48)
Q Consensus 11 aG~va~iS~~M~~FY~y~l 29 (48)
+|+.-++.+.|++||+++-
T Consensus 77 a~~~~v~~g~~~~~Y~~~Y 95 (104)
T PF10206_consen 77 APFFQVLAGYMVFSYCINY 95 (104)
T ss_pred chhHHHHHHHHHHHHHHhh
Confidence 5677788899999999864
No 16
>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=31.22 E-value=61 Score=22.24 Aligned_cols=34 Identities=21% Similarity=0.383 Sum_probs=21.7
Q ss_pred ccccchhHHHHHHHHHHHHHHHHHHhcCCCCCCccc
Q 040093 5 TKKLFPTGFYAAISAAMLCFYSYVVASGGNPPPKKL 40 (48)
Q Consensus 5 T~kifPaG~va~iS~~M~~FY~y~l~~ggNp~pkk~ 40 (48)
+++|+=. .+++++ +..+|.+|.|+.|+++.++..
T Consensus 12 ~N~iLNi-aI~IV~-lLIiiva~~lf~~~~~~~~~~ 45 (217)
T PF07423_consen 12 TNKILNI-AIGIVS-LLIIIVAYQLFFGGDDSPAAS 45 (217)
T ss_pred hhhhHHH-HHHHHH-HHHHHHhhhheecCCCchhhh
Confidence 3444433 334444 667889999999888666533
No 17
>PF13197 DUF4013: Protein of unknown function (DUF4013)
Probab=28.51 E-value=1e+02 Score=18.91 Aligned_cols=26 Identities=23% Similarity=0.276 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHhcCC-----CCCCc
Q 040093 13 FYAAISAAMLCFYSYVVASGG-----NPPPK 38 (48)
Q Consensus 13 ~va~iS~~M~~FY~y~l~~gg-----Np~pk 38 (48)
.+..+-..-...|.++++++. +++|+
T Consensus 9 ~i~ii~~~~~~GY~~~v~~~~~~g~~~~lP~ 39 (169)
T PF13197_consen 9 IIPIIGLFLLLGYLVRVIRSTAIGGSDPLPE 39 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhccCCCCCCC
Confidence 456677777889999998655 66665
No 18
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=24.75 E-value=1.1e+02 Score=18.39 Aligned_cols=16 Identities=25% Similarity=0.266 Sum_probs=7.3
Q ss_pred HHHHHHHHHHHHHHHH
Q 040093 12 GFYAAISAAMLCFYSY 27 (48)
Q Consensus 12 G~va~iS~~M~~FY~y 27 (48)
.||.++-++.++||++
T Consensus 7 iii~~i~l~~~~~~~~ 22 (130)
T PF12273_consen 7 IIIVAILLFLFLFYCH 22 (130)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444444444444444
No 19
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=24.54 E-value=1.1e+02 Score=18.01 Aligned_cols=22 Identities=27% Similarity=0.326 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHhcCCCCCCc
Q 040093 17 ISAAMLCFYSYVVASGGNPPPK 38 (48)
Q Consensus 17 iS~~M~~FY~y~l~~ggNp~pk 38 (48)
.|.++..||-+.+..++-|-..
T Consensus 27 ~S~Ai~~fl~qi~~~~~iPF~~ 48 (80)
T PRK11235 27 PSEALRLLLQYVAENGRLPFKT 48 (80)
T ss_pred HHHHHHHHHHHHHHhCCCCCCC
Confidence 5889999999999999997653
No 20
>PF14019 DUF4235: Protein of unknown function (DUF4235)
Probab=24.32 E-value=1.5e+02 Score=16.90 Aligned_cols=25 Identities=24% Similarity=0.329 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCc
Q 040093 13 FYAAISAAMLCFYSYVVASGGNPPPK 38 (48)
Q Consensus 13 ~va~iS~~M~~FY~y~l~~ggNp~pk 38 (48)
+.+.+-+-...=.+|...+| ++||+
T Consensus 10 ~~ag~~a~k~~~~~W~~~tg-~~~P~ 34 (78)
T PF14019_consen 10 LAAGFLAGKVFEQVWKKVTG-REPPK 34 (78)
T ss_pred HHHHHHHHHHHHHHHHHHcC-CCCCC
Confidence 34444444556678999988 65564
No 21
>PF11337 DUF3139: Protein of unknown function (DUF3139); InterPro: IPR021486 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=24.19 E-value=84 Score=17.81 Aligned_cols=19 Identities=21% Similarity=0.135 Sum_probs=14.0
Q ss_pred HHHHHHHhcCCCCCCcccc
Q 040093 23 CFYSYVVASGGNPPPKKLK 41 (48)
Q Consensus 23 ~FY~y~l~~ggNp~pkk~~ 41 (48)
+|.++.+...|||-.+..+
T Consensus 18 li~~~~~~~~~~~~~k~~~ 36 (85)
T PF11337_consen 18 LIIGIYYFFNGNPYQKHKA 36 (85)
T ss_pred HHHHHHHhhcCchhhHHHH
Confidence 6777777778988776554
No 22
>PF12270 Cyt_c_ox_IV: Cytochrome c oxidase subunit IV; InterPro: IPR021050 This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. This family is the fourth subunit of the cytochrome c oxidase complex. This subunit does not have a catalytic capacity but instead, is required for assembly and/or stability of the complex []. ; GO: 0004129 cytochrome-c oxidase activity, 0055114 oxidation-reduction process, 0016021 integral to membrane
Probab=24.10 E-value=2.1e+02 Score=18.53 Aligned_cols=33 Identities=27% Similarity=0.264 Sum_probs=22.9
Q ss_pred chhHHHHHH----HHHHHHHHHHHHhcCCCCCCcccc
Q 040093 9 FPTGFYAAI----SAAMLCFYSYVVASGGNPPPKKLK 41 (48)
Q Consensus 9 fPaG~va~i----S~~M~~FY~y~l~~ggNp~pkk~~ 41 (48)
=|+|.++++ =++|.+||++...+--.+.|+--.
T Consensus 34 E~~Gt~aL~ls~~l~~mig~yl~~~~rr~~~rPED~~ 70 (137)
T PF12270_consen 34 EWVGTVALVLSGGLALMIGFYLRFTARRIGPRPEDRE 70 (137)
T ss_pred CcchHHHHHHHHHHHHHHHHHHHHHHhhCCCCCcccc
Confidence 467776654 457889999999976666665444
No 23
>PF04678 DUF607: Protein of unknown function, DUF607; InterPro: IPR006769 This entry represents the C-terminal domain of coiled-coil domain containing protein 109.
Probab=23.57 E-value=1.4e+02 Score=19.19 Aligned_cols=24 Identities=8% Similarity=0.027 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCcc
Q 040093 16 AISAAMLCFYSYVVASGGNPPPKK 39 (48)
Q Consensus 16 ~iS~~M~~FY~y~l~~ggNp~pkk 39 (48)
+.++.+.++|+|-+.++..+.+..
T Consensus 129 v~~~~~i~~y~yfl~t~re~sy~~ 152 (180)
T PF04678_consen 129 VGYGTSILGYAYFLYTRREYSYES 152 (180)
T ss_pred HhHHHHHHHHHHHHHhCCCCChHH
Confidence 334445578999999988876653
No 24
>PF02468 PsbN: Photosystem II reaction centre N protein (psbN); InterPro: IPR003398 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 PsbN found in PSII. PsbN may have a role in PSII stability, however its actual function unknown. PsbN does not appear to be essential for photoautotrophic growth or normal PSII function.; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane
Probab=23.46 E-value=1.4e+02 Score=16.12 Aligned_cols=28 Identities=25% Similarity=0.489 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCcccccc
Q 040093 16 AISAAMLCFYSYVVASGGNPPPKKLKSS 43 (48)
Q Consensus 16 ~iS~~M~~FY~y~l~~ggNp~pkk~~~~ 43 (48)
.++.+..++=.|.+-++=.||.|++++.
T Consensus 10 ~i~~~lv~~Tgy~iYtaFGppSk~LrDP 37 (43)
T PF02468_consen 10 FISCLLVSITGYAIYTAFGPPSKELRDP 37 (43)
T ss_pred HHHHHHHHHHhhhhhheeCCCccccCCc
Confidence 3455555666677776666888988763
No 25
>cd07468 CRD_TK_ROR2 Cysteine-rich domain of tyrosine kinase-like orphan receptor 2. The cysteine-rich domain (CRD) is an essential part of the tyrosine kinase-like orphan receptor (Ror2), a conserved family of tyrosine kinases that function in various processes, including neuronal and skeletal development, cell polarity, and cell movement. Ror proteins are receptors of Wnt proteins, which are key players in a number of fundamental cellular processes in embryogenesis and postnatal development. In different cellular contexts, Ror proteins can either activate or repress transcription of Wnt target genes, and can modulate Wnt signaling by sequestering Wnt ligands. In addition, a number of Wnt-independent functions have been proposed for both Ror1 and Ror2.
Probab=23.00 E-value=47 Score=21.63 Aligned_cols=22 Identities=14% Similarity=0.614 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHh--cCCCCCCcc
Q 040093 18 SAAMLCFYSYVVA--SGGNPPPKK 39 (48)
Q Consensus 18 S~~M~~FY~y~l~--~ggNp~pkk 39 (48)
+.-++|+|++-+- +++.|+|++
T Consensus 58 A~~~LC~~~Fp~C~~~~~~p~pr~ 81 (140)
T cd07468 58 AIPSFCHFVFPLCDDRSRTPKPRE 81 (140)
T ss_pred HHHHHHHHcCCCCCCCCCCCCCcc
Confidence 4568999999988 466676654
No 26
>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []. This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Probab=22.94 E-value=1.3e+02 Score=15.84 Aligned_cols=18 Identities=11% Similarity=0.586 Sum_probs=9.5
Q ss_pred hHHHHHHHHHHHHHHHHH
Q 040093 11 TGFYAAISAAMLCFYSYV 28 (48)
Q Consensus 11 aG~va~iS~~M~~FY~y~ 28 (48)
+|+++.++.+.+|+..|-
T Consensus 10 v~V~vg~~iiii~~~~Ya 27 (38)
T PF02439_consen 10 VAVVVGMAIIIICMFYYA 27 (38)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 355555555555555543
No 27
>TIGR03685 L21P_arch 50S ribosomal protein L12P. This model represents the L12P protein of the large (50S) subunit of the archaeal ribosome.
Probab=22.83 E-value=63 Score=19.73 Aligned_cols=15 Identities=27% Similarity=0.461 Sum_probs=11.1
Q ss_pred HHHHHHHHHh-cCCCC
Q 040093 21 MLCFYSYVVA-SGGNP 35 (48)
Q Consensus 21 M~~FY~y~l~-~ggNp 35 (48)
|=|-|+|-|+ .+||+
T Consensus 1 M~yvyA~Lll~~~g~~ 16 (105)
T TIGR03685 1 MEYIYAALLLHSAGKE 16 (105)
T ss_pred CHHHHHHHHHHhcCCC
Confidence 5688999999 55553
No 28
>PRK12573 putative monovalent cation/H+ antiporter subunit B; Reviewed
Probab=22.14 E-value=2.1e+02 Score=18.11 Aligned_cols=26 Identities=19% Similarity=0.373 Sum_probs=18.7
Q ss_pred hHHHHHHHHHHHHHHHHHHhcCCCCC
Q 040093 11 TGFYAAISAAMLCFYSYVVASGGNPP 36 (48)
Q Consensus 11 aG~va~iS~~M~~FY~y~l~~ggNp~ 36 (48)
.-+.-++.-.+..|=+|.+++|-|.|
T Consensus 9 r~~~r~l~p~i~l~s~yv~l~GH~~P 34 (140)
T PRK12573 9 RTVAKIVTFIILLFSVFLFLAGHNEP 34 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCCCCC
Confidence 33445666778888888888888855
No 29
>PF06939 DUF1286: Protein of unknown function (DUF1286); InterPro: IPR009705 This entry is represented by Sulfolobus virus STSV1, Orf8. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical archaeal proteins of around 120 residues in length. All members of this family seem to be Sulfolobus species specific. The function of this family is unknown.
Probab=21.49 E-value=1.2e+02 Score=19.42 Aligned_cols=24 Identities=33% Similarity=0.610 Sum_probs=20.0
Q ss_pred cccccccchhHHHHHHHHHHH-HHH
Q 040093 2 WMQTKKLFPTGFYAAISAAML-CFY 25 (48)
Q Consensus 2 y~~T~kifPaG~va~iS~~M~-~FY 25 (48)
=++|+-+|-+|++++++.... -||
T Consensus 2 kL~tHyVFs~GlLtLl~s~~~~~f~ 26 (114)
T PF06939_consen 2 KLRTHYVFSTGLLTLLSSFFLSNFY 26 (114)
T ss_pred ceeeeehhhhhHHHHHHHHHHhhHH
Confidence 367899999999999998777 555
No 30
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=21.45 E-value=1.4e+02 Score=19.67 Aligned_cols=26 Identities=12% Similarity=0.091 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCc
Q 040093 13 FYAAISAAMLCFYSYVVASGGNPPPK 38 (48)
Q Consensus 13 ~va~iS~~M~~FY~y~l~~ggNp~pk 38 (48)
|+.++|++..+..+.+..+-+++..|
T Consensus 100 Vl~g~s~l~i~yfvir~~R~r~~~rk 125 (163)
T PF06679_consen 100 VLVGLSALAILYFVIRTFRLRRRNRK 125 (163)
T ss_pred HHHHHHHHHHHHHHHHHHhhcccccc
Confidence 45566666666677778877775554
No 31
>PRK13183 psbN photosystem II reaction center protein N; Provisional
Probab=21.13 E-value=1.3e+02 Score=16.52 Aligned_cols=28 Identities=25% Similarity=0.444 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCcccccc
Q 040093 16 AISAAMLCFYSYVVASGGNPPPKKLKSS 43 (48)
Q Consensus 16 ~iS~~M~~FY~y~l~~ggNp~pkk~~~~ 43 (48)
.++.+..++=.|.|-++=.||.|.+.+.
T Consensus 13 ~i~~lL~~~TgyaiYtaFGppSk~LrDP 40 (46)
T PRK13183 13 TILAILLALTGFGIYTAFGPPSKELDDP 40 (46)
T ss_pred HHHHHHHHHhhheeeeccCCcccccCCc
Confidence 4666777777888888888888888753
No 32
>KOG4697 consensus Integral membrane protein involved in transport between the late Golgi and endosome [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.11 E-value=1.2e+02 Score=20.55 Aligned_cols=27 Identities=19% Similarity=0.173 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHhcCCCCCCccc
Q 040093 14 YAAISAAMLCFYSYVVASGGNPPPKKL 40 (48)
Q Consensus 14 va~iS~~M~~FY~y~l~~ggNp~pkk~ 40 (48)
..+.+++.++||+++.+++.|-..+.+
T Consensus 25 ~~vy~t~~ll~~~~~kL~~d~~~~e~L 51 (160)
T KOG4697|consen 25 IFVYTTAILLFYCWAKLAYDLNIKEWL 51 (160)
T ss_pred hHHHHHHHHHHHHHHHHhhhhcchhhh
Confidence 567899999999999999888655443
Done!