Query 039804
Match_columns 95
No_of_seqs 109 out of 1016
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 13:22:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039804.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039804hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02164 sulfotransferase 99.9 1.8E-25 4E-30 163.9 7.2 90 1-90 254-345 (346)
2 KOG1584 Sulfotransferase [Gene 99.9 6.6E-24 1.4E-28 152.2 4.5 85 1-90 210-296 (297)
3 PF00685 Sulfotransfer_1: Sulf 99.2 4.6E-11 9.9E-16 82.3 5.6 77 1-85 191-267 (267)
4 PF13788 DUF4180: Domain of un 70.4 3.9 8.4E-05 25.9 2.0 38 52-92 69-106 (113)
5 PF11952 DUF3469: Protein of u 64.4 4.9 0.00011 24.2 1.5 19 2-25 47-65 (87)
6 PRK11753 DNA-binding transcrip 58.6 4.8 0.0001 26.8 0.8 27 3-34 3-29 (211)
7 TIGR01565 homeo_ZF_HD homeobox 53.1 20 0.00043 19.9 2.6 20 62-81 5-24 (58)
8 PF12123 Amidase02_C: N-acetyl 51.9 17 0.00037 19.3 2.1 18 63-80 22-39 (45)
9 PF02750 Synapsin_C: Synapsin, 49.8 8.3 0.00018 26.9 0.9 34 48-81 109-148 (203)
10 PRK10363 cpxP periplasmic repr 48.6 18 0.0004 24.4 2.4 25 60-84 119-143 (166)
11 PHA02902 putative IMV membrane 44.5 24 0.00053 20.2 2.1 18 60-77 49-66 (70)
12 PRK10455 periplasmic protein; 43.9 20 0.00044 23.9 2.0 26 59-84 124-149 (161)
13 PF04719 TAFII28: hTAFII28-lik 43.2 10 0.00022 23.1 0.4 21 63-83 6-26 (90)
14 PRK12751 cpxP periplasmic stre 40.5 29 0.00062 23.3 2.4 23 61-83 126-148 (162)
15 PF00046 Homeobox: Homeobox do 38.9 48 0.001 17.3 2.8 18 62-79 4-21 (57)
16 PF12174 RST: RCD1-SRO-TAF4 (R 37.7 8.4 0.00018 22.2 -0.5 43 16-60 13-57 (70)
17 KOG0856 Predicted pilin-like t 37.0 17 0.00038 23.9 0.9 21 60-80 20-40 (146)
18 KOG3895 Synaptic vesicle prote 37.0 19 0.00042 27.6 1.2 39 48-86 298-345 (488)
19 smart00874 B5 tRNA synthetase 36.9 26 0.00057 19.4 1.5 23 2-29 13-35 (71)
20 PF07813 LTXXQ: LTXXQ motif fa 36.1 37 0.00081 19.7 2.2 18 59-76 82-99 (100)
21 COG1949 Orn Oligoribonuclease 36.1 37 0.0008 23.2 2.3 25 63-87 48-72 (184)
22 PF05572 Peptidase_M43: Pregna 36.0 34 0.00074 22.4 2.2 17 62-78 138-154 (154)
23 PF15138 Syncollin: Syncollin 35.3 12 0.00026 23.5 -0.1 15 52-66 92-106 (112)
24 PHA02681 ORF089 virion membran 34.6 40 0.00088 20.3 2.1 22 60-81 47-68 (92)
25 PF05088 Bac_GDH: Bacterial NA 32.3 60 0.0013 29.2 3.5 45 49-93 329-381 (1528)
26 PRK12750 cpxP periplasmic repr 32.3 26 0.00056 23.6 1.1 24 61-84 133-156 (170)
27 PF03484 B5: tRNA synthetase B 31.4 27 0.00058 19.6 1.0 25 2-31 13-37 (70)
28 PF07858 LEH: Limonene-1,2-epo 31.1 21 0.00045 22.9 0.5 20 53-72 102-121 (125)
29 KOG0278 Serine/threonine kinas 30.0 21 0.00046 26.2 0.4 18 48-65 38-55 (334)
30 KOG3242 Oligoribonuclease (3'- 29.0 52 0.0011 22.8 2.2 28 60-87 65-92 (208)
31 TIGR01346 isocit_lyase isocitr 29.0 72 0.0016 25.5 3.2 31 57-89 417-447 (527)
32 PLN00410 U5 snRNP protein, DIM 28.5 1.1E+02 0.0023 20.0 3.6 39 52-90 84-133 (142)
33 cd04275 ZnMc_pappalysin_like Z 28.4 50 0.0011 23.1 2.1 17 61-77 208-224 (225)
34 PRK14565 triosephosphate isome 27.5 72 0.0016 22.7 2.8 26 56-81 4-29 (237)
35 PRK15063 isocitrate lyase; Pro 27.4 78 0.0017 24.6 3.1 31 58-90 316-346 (428)
36 PRK15492 triosephosphate isome 27.1 78 0.0017 22.7 2.9 24 57-80 6-29 (260)
37 cd00311 TIM Triosephosphate is 27.0 70 0.0015 22.6 2.7 26 57-82 3-28 (242)
38 PF10925 DUF2680: Protein of u 26.6 87 0.0019 17.3 2.5 17 65-81 1-17 (59)
39 KOG0844 Transcription factor E 25.2 33 0.00072 25.7 0.8 23 57-79 180-202 (408)
40 PRK15117 ABC transporter perip 24.2 77 0.0017 21.8 2.4 31 51-82 71-102 (211)
41 smart00389 HOX Homeodomain. DN 24.1 97 0.0021 15.8 2.4 20 62-81 4-23 (56)
42 KOG1379 Serine/threonine prote 23.9 39 0.00084 25.3 0.9 24 57-80 111-140 (330)
43 PF09832 DUF2059: Uncharacteri 23.7 45 0.00097 18.1 1.0 26 56-81 8-33 (64)
44 PF00121 TIM: Triosephosphate 23.6 67 0.0015 22.8 2.0 26 57-82 3-28 (244)
45 PF02130 UPF0054: Uncharacteri 22.7 1.1E+02 0.0023 19.8 2.7 27 65-91 42-69 (145)
46 PRK14566 triosephosphate isome 22.1 1E+02 0.0022 22.3 2.7 26 57-82 8-33 (260)
47 PF07818 HCNGP: HCNGP-like pro 21.8 56 0.0012 19.9 1.2 18 13-30 41-58 (96)
48 TIGR03481 HpnM hopanoid biosyn 21.0 1E+02 0.0022 21.1 2.4 30 52-82 68-98 (198)
49 PF14794 DUF4479: Domain of un 21.0 1E+02 0.0022 17.8 2.1 22 59-80 42-63 (73)
50 PF13227 DUF4035: Protein of u 20.8 27 0.00059 19.2 -0.3 22 51-72 2-23 (53)
51 PF06047 SynMuv_product: Ras-i 20.5 95 0.0021 19.4 2.0 20 51-75 26-45 (104)
52 smart00678 WWE Domain in Delte 20.1 1.2E+02 0.0026 16.8 2.3 24 56-80 7-30 (73)
53 PRK14905 triosephosphate isome 20.0 1.3E+02 0.0027 22.7 2.9 25 57-81 7-31 (355)
No 1
>PLN02164 sulfotransferase
Probab=99.92 E-value=1.8e-25 Score=163.93 Aligned_cols=90 Identities=47% Similarity=0.779 Sum_probs=75.8
Q ss_pred CcccCCCCChHHHhhHHHHHHHHhCChhHhhhhHhhcccccccc--ccccCcceeeccccCCcccCCCHHHHHHHHHHHH
Q 039804 1 AEFLSQPFTSEEEEAGVVQEIVKLRSFENMSNLEVTKSRINRVN--IEIKNDVYFRQGKVGAWKNHLTAEMLQCLDQIVQ 78 (95)
Q Consensus 1 A~FLg~~~~~~~~~~~~~~~iv~~ssf~~Mk~~~~~~~~~~~~~--~~~~~~~f~RkG~vG~Wk~~ft~eq~~~~~~~~~ 78 (95)
|+|||+++++++++++++++|+++|||++||++++|........ .......|||||+|||||||||++|+++|+++++
T Consensus 254 a~FLG~~~s~ee~~~~~v~~ive~~SFe~Mk~~e~n~~~~~~~~~~~~~~~~~FfRKG~vGdWkn~lt~e~~~r~d~~~~ 333 (346)
T PLN02164 254 AEFMGYGFTAEEEEKGVVEKVVKLCSFETLKNLEANKGEKDREDRPAVYANSAYFRKGKVGDWQNYLTPEMAARIDGLME 333 (346)
T ss_pred HHHhCCCCchhhcchHHHHHHHHHCCHHHHhhhHhhccccccccccccccCcceeeccCCCCCcccCCHHHHHHHHHHHH
Confidence 68999999998888899999999999999999877654321011 0123457999999999999999999999999999
Q ss_pred hHhCCCCceeec
Q 039804 79 QKFKDSGFVTLK 90 (95)
Q Consensus 79 ~~l~~~~l~f~~ 90 (95)
++|+|+||.|-.
T Consensus 334 ekl~gsgl~~~~ 345 (346)
T PLN02164 334 EKFKGTGLLEHD 345 (346)
T ss_pred HHhcCCCCcccC
Confidence 999999999854
No 2
>KOG1584 consensus Sulfotransferase [General function prediction only]
Probab=99.89 E-value=6.6e-24 Score=152.19 Aligned_cols=85 Identities=38% Similarity=0.452 Sum_probs=68.9
Q ss_pred CcccCCCCChHHHhhHHHHHHHHhCChhHhhhh-HhhccccccccccccCcceeeccccCCcccCCCHHHHHHHHHHHHh
Q 039804 1 AEFLSQPFTSEEEEAGVVQEIVKLRSFENMSNL-EVTKSRINRVNIEIKNDVYFRQGKVGAWKNHLTAEMLQCLDQIVQQ 79 (95)
Q Consensus 1 A~FLg~~~~~~~~~~~~~~~iv~~ssf~~Mk~~-~~~~~~~~~~~~~~~~~~f~RkG~vG~Wk~~ft~eq~~~~~~~~~~ 79 (95)
|+|||+++++++ +++++.|.+|+.|+.+ .+|.+..+..........|||||+|||||||||++|+++||.++++
T Consensus 210 aeFLg~~~~~Ee-----~~~~~~~~~~~~~~~n~l~nle~n~~~~~~~~~~~F~RKG~vGDWKn~~T~~~~ekfD~~~ee 284 (297)
T KOG1584|consen 210 AEFLGCPFTKEE-----EDKGVVHLSFELCSLNPLSNLEVNKTEKLLHKISPFFRKGEVGDWKNYLTPEMNEKFDKIYEE 284 (297)
T ss_pred HHHhCCCCCHHH-----HhhhhHHHHHHHHhhccccCceecccccccccchhhhcCCCcccccccCCHHHHHHHHHHHHH
Confidence 789999999999 8888888888888875 4554433211112233889999999999999999999999999999
Q ss_pred HhCC-CCceeec
Q 039804 80 KFKD-SGFVTLK 90 (95)
Q Consensus 80 ~l~~-~~l~f~~ 90 (95)
+|+| +||.|..
T Consensus 285 km~g~sgL~F~~ 296 (297)
T KOG1584|consen 285 KMEGCSGLKFRT 296 (297)
T ss_pred HhcCCCCccccc
Confidence 9999 7898864
No 3
>PF00685 Sulfotransfer_1: Sulfotransferase domain; InterPro: IPR000863 This family includes a range of sulphotransferase proteins including flavonyl 3-sulphotransferase, aryl sulphotransferase, alcohol sulphotransferase, oestrogen sulphotransferase and phenol-sulphating phenol sulphotransferase. These enzymes are responsible for the transfer of sulphate groups to specific compounds.; GO: 0008146 sulfotransferase activity; PDB: 3MGC_A 3MGB_A 3MG9_A 1G3M_B 1HY3_B 2QP4_A 3F3Y_C 1EFH_A 1OV4_A 1J99_A ....
Probab=99.18 E-value=4.6e-11 Score=82.31 Aligned_cols=77 Identities=31% Similarity=0.620 Sum_probs=59.4
Q ss_pred CcccCCCCChHHHhhHHHHHHHHhCChhHhhhhHhhccccccccccccCcceeeccccCCcccCCCHHHHHHHHHHHHhH
Q 039804 1 AEFLSQPFTSEEEEAGVVQEIVKLRSFENMSNLEVTKSRINRVNIEIKNDVYFRQGKVGAWKNHLTAEMLQCLDQIVQQK 80 (95)
Q Consensus 1 A~FLg~~~~~~~~~~~~~~~iv~~ssf~~Mk~~~~~~~~~~~~~~~~~~~~f~RkG~vG~Wk~~ft~eq~~~~~~~~~~~ 80 (95)
++|||.+++++. ++.+++++++++|+......... ........++|+|.+|+||++||+++++.+++++.+.
T Consensus 191 ~~FLgl~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~W~~~l~~e~~~~i~~~~~~~ 262 (267)
T PF00685_consen 191 CDFLGLPFSDEP-----LDKIVEKSSFDNMRSKEARNKSK---LSDGSSSRFFRKGKSGRWKNELSPEQIDRIERICGDA 262 (267)
T ss_dssp HHHTTSS--HHH-----HHHHHHHTSHHHHHHETTTSSTT---SCTTTTSTSSEET-STGGGGTSBHHHHHHHHHHHHHH
T ss_pred HHHHhhccchhh-----hHHHHHhhhhhhhcccccccccc---cccCCcceeeeecccCcccccCCHHHHHHHHHHHHHH
Confidence 369999999999 99999999999999753221110 0011346799999999999999999999999999999
Q ss_pred hCCCC
Q 039804 81 FKDSG 85 (95)
Q Consensus 81 l~~~~ 85 (95)
|...|
T Consensus 263 m~~~~ 267 (267)
T PF00685_consen 263 MRELG 267 (267)
T ss_dssp HTTSS
T ss_pred HccCC
Confidence 98765
No 4
>PF13788 DUF4180: Domain of unknown function (DUF4180)
Probab=70.39 E-value=3.9 Score=25.93 Aligned_cols=38 Identities=11% Similarity=0.140 Sum_probs=33.3
Q ss_pred eeeccccCCcccCCCHHHHHHHHHHHHhHhCCCCceeeccc
Q 039804 52 YFRQGKVGAWKNHLTAEMLQCLDQIVQQKFKDSGFVTLKMF 92 (95)
Q Consensus 52 f~RkG~vG~Wk~~ft~eq~~~~~~~~~~~l~~~~l~f~~~~ 92 (95)
-+|-.+|||+..| ..++++.+.+.|--+|..+.|.++.
T Consensus 69 ~iklAivGD~s~~---~~S~~l~dfi~EsN~G~~~~F~~~~ 106 (113)
T PF13788_consen 69 RIKLAIVGDFSAY---ATSKSLRDFIYESNRGNHFFFVPDE 106 (113)
T ss_pred ceeEEEEEccccc---ccchhHHHHHHHhcCCCeEEEECCH
Confidence 3677899999999 7889999999999999999998764
No 5
>PF11952 DUF3469: Protein of unknown function (DUF3469); InterPro: IPR021859 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 108 to 439 amino acids in length.
Probab=64.42 E-value=4.9 Score=24.18 Aligned_cols=19 Identities=21% Similarity=0.555 Sum_probs=15.7
Q ss_pred cccCCCCChHHHhhHHHHHHHHhC
Q 039804 2 EFLSQPFTSEEEEAGVVQEIVKLR 25 (95)
Q Consensus 2 ~FLg~~~~~~~~~~~~~~~iv~~s 25 (95)
.||||.|+.+. +++|.+.+
T Consensus 47 ~fLGC~Yp~~~-----m~~v~ema 65 (87)
T PF11952_consen 47 EFLGCRYPPEV-----MEKVMEMA 65 (87)
T ss_pred HHHhcCCCHHH-----HHHHHHHh
Confidence 49999999987 88887654
No 6
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=58.59 E-value=4.8 Score=26.77 Aligned_cols=27 Identities=11% Similarity=0.143 Sum_probs=23.9
Q ss_pred ccCCCCChHHHhhHHHHHHHHhCChhHhhhhH
Q 039804 3 FLSQPFTSEEEEAGVVQEIVKLRSFENMSNLE 34 (95)
Q Consensus 3 FLg~~~~~~~~~~~~~~~iv~~ssf~~Mk~~~ 34 (95)
.||+|+++++ ++.+++++....+++..
T Consensus 3 ~~~~~~~~~~-----~~~l~~~~~~~~~~kg~ 29 (211)
T PRK11753 3 VLGKPQTDPT-----LEWFLSHCHIHKYPAKS 29 (211)
T ss_pred cccCCCCHHH-----HHHHHhhCeEEEeCCCC
Confidence 4899999999 99999999988888753
No 7
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=53.09 E-value=20 Score=19.92 Aligned_cols=20 Identities=15% Similarity=0.177 Sum_probs=16.7
Q ss_pred ccCCCHHHHHHHHHHHHhHh
Q 039804 62 KNHLTAEMLQCLDQIVQQKF 81 (95)
Q Consensus 62 k~~ft~eq~~~~~~~~~~~l 81 (95)
|..||++|.++|++.++..-
T Consensus 5 RT~Ft~~Q~~~Le~~fe~~~ 24 (58)
T TIGR01565 5 RTKFTAEQKEKMRDFAEKLG 24 (58)
T ss_pred CCCCCHHHHHHHHHHHHHcC
Confidence 56899999999998887643
No 8
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=51.87 E-value=17 Score=19.25 Aligned_cols=18 Identities=11% Similarity=0.252 Sum_probs=13.2
Q ss_pred cCCCHHHHHHHHHHHHhH
Q 039804 63 NHLTAEMLQCLDQIVQQK 80 (95)
Q Consensus 63 ~~ft~eq~~~~~~~~~~~ 80 (95)
+.++..|+++|.+|+.++
T Consensus 22 ~~~s~~~L~k~~~wld~r 39 (45)
T PF12123_consen 22 DPLSDAELDKFTAWLDER 39 (45)
T ss_dssp ----HHHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHHHHHHhc
Confidence 467899999999999986
No 9
>PF02750 Synapsin_C: Synapsin, ATP binding domain; InterPro: IPR020898 The synapsins are a family of neuron-specific phosphoproteins that coat synaptic vesicles and are involved in the binding between these vesicles and the cytoskeleton (including actin filaments). The family comprises 5 homologous proteins Ia, Ib, IIa, IIb and III. Synapsins I, II, and III are encoded by 3 different genes. The a and b isoforms of synapsin I and II are splice variants of the primary transcripts []. Synapsin I is mainly associated with regulation of neurotransmitter release from presynaptic neuron terminals []. Synapsin II, as well as being involved in neurotransmitter release, has a role in the synaptogenesis and synaptic plasticity responsible for long term potentiation []. Recent studies implicate synapsin III with a developmental role in neurite elongation and synapse formation that is distinct from the functions of synapsins I and II []. Structurally, synapsins are multidomain proteins, of which 3 domains are common to all the mammalian forms. The N-terminal `A' domain is ~30 residues long and contains a serine residue that serves as an acceptor site for protein kinase-mediated phosphorylation. This is followed by the `B' linker domain, which is ~80 residues long and is relatively poorly conserved. Domain `C' is the longest, spanning approximately 300 residues. This domain is highly conserved across all the synapsins (including those from Drosophila) and is possessed by all splice variants. The remaining six domains, D-I, are not shared by all the synapsins and differ both between the primary transcripts and the splice variants. This entry represent the ATP-grasp fold found in synapsins, which is responsible for Ca dependent ATP binding. ; PDB: 1PX2_A 1PK8_F 1AUV_B 1AUX_A 2P0A_A 1I7N_A 1I7L_A.
Probab=49.82 E-value=8.3 Score=26.87 Aligned_cols=34 Identities=21% Similarity=0.349 Sum_probs=22.9
Q ss_pred cCcceeeccccCCcccCC-C-----HHHHHHHHHHHHhHh
Q 039804 48 KNDVYFRQGKVGAWKNHL-T-----AEMLQCLDQIVQQKF 81 (95)
Q Consensus 48 ~~~~f~RkG~vG~Wk~~f-t-----~eq~~~~~~~~~~~l 81 (95)
.-..|+|+++.|.||.-= | .++.+|+..|+.+..
T Consensus 109 ~ykA~~R~sis~nWK~N~gsa~lEqi~~~~ryk~Wvd~~s 148 (203)
T PF02750_consen 109 NYKAYMRTSISGNWKANTGSAMLEQIAMTERYKLWVDECS 148 (203)
T ss_dssp EEEEEEEEESSSTSSTTSSSEEEEEE---HHHHHHHHHHG
T ss_pred eEEEEEEccccccccccccchheeecCCChHHHHHHHHHH
Confidence 345799999999999632 2 246678888887653
No 10
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=48.58 E-value=18 Score=24.42 Aligned_cols=25 Identities=24% Similarity=0.218 Sum_probs=21.3
Q ss_pred CcccCCCHHHHHHHHHHHHhHhCCC
Q 039804 60 AWKNHLTAEMLQCLDQIVQQKFKDS 84 (95)
Q Consensus 60 ~Wk~~ft~eq~~~~~~~~~~~l~~~ 84 (95)
.--+.|||||-..|++.+++++..+
T Consensus 119 qmy~lLTPEQKaq~~~~~~~rm~~~ 143 (166)
T PRK10363 119 QMYRLLTPEQQAVLNEKHQQRMEQL 143 (166)
T ss_pred HHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 3456899999999999999998764
No 11
>PHA02902 putative IMV membrane protein; Provisional
Probab=44.53 E-value=24 Score=20.23 Aligned_cols=18 Identities=28% Similarity=0.612 Sum_probs=15.3
Q ss_pred CcccCCCHHHHHHHHHHH
Q 039804 60 AWKNHLTAEMLQCLDQIV 77 (95)
Q Consensus 60 ~Wk~~ft~eq~~~~~~~~ 77 (95)
-.++.+||+|++.+.+.+
T Consensus 49 ~F~D~lTpDQirAlHrlv 66 (70)
T PHA02902 49 LFKDSLTPDQIKALHRLV 66 (70)
T ss_pred hhhccCCHHHHHHHHHHH
Confidence 378999999999998765
No 12
>PRK10455 periplasmic protein; Reviewed
Probab=43.86 E-value=20 Score=23.88 Aligned_cols=26 Identities=15% Similarity=0.208 Sum_probs=22.0
Q ss_pred CCcccCCCHHHHHHHHHHHHhHhCCC
Q 039804 59 GAWKNHLTAEMLQCLDQIVQQKFKDS 84 (95)
Q Consensus 59 G~Wk~~ft~eq~~~~~~~~~~~l~~~ 84 (95)
..+-+.|||||-+.|++.+++++...
T Consensus 124 ~qiy~vLTPEQr~q~~~~~ekr~~~~ 149 (161)
T PRK10455 124 NKIYNVLTPEQKKQFNANFEKRLTER 149 (161)
T ss_pred HHHHHhCCHHHHHHHHHHHHHHHHhc
Confidence 35668999999999999999888763
No 13
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=43.16 E-value=10 Score=23.06 Aligned_cols=21 Identities=14% Similarity=0.335 Sum_probs=11.2
Q ss_pred cCCCHHHHHHHHHHHHhHhCC
Q 039804 63 NHLTAEMLQCLDQIVQQKFKD 83 (95)
Q Consensus 63 ~~ft~eq~~~~~~~~~~~l~~ 83 (95)
+.||++|..|++.+=+..+..
T Consensus 6 ~~f~~eQ~~Rye~fRRs~~~k 26 (90)
T PF04719_consen 6 SNFDEEQLDRYEAFRRSSFNK 26 (90)
T ss_dssp ----HHHHHHHHHHHH----H
T ss_pred HcCCHHHHHHHHHHHHccCCH
Confidence 479999999999887766544
No 14
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=40.53 E-value=29 Score=23.26 Aligned_cols=23 Identities=26% Similarity=0.316 Sum_probs=19.9
Q ss_pred cccCCCHHHHHHHHHHHHhHhCC
Q 039804 61 WKNHLTAEMLQCLDQIVQQKFKD 83 (95)
Q Consensus 61 Wk~~ft~eq~~~~~~~~~~~l~~ 83 (95)
--+.|||||-+.|.+.+++++..
T Consensus 126 my~lLTPEQra~l~~~~e~r~~~ 148 (162)
T PRK12751 126 MYNLLTPEQKEALNKKHQERIEK 148 (162)
T ss_pred HHHcCCHHHHHHHHHHHHHHHHH
Confidence 34689999999999999988865
No 15
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=38.92 E-value=48 Score=17.29 Aligned_cols=18 Identities=28% Similarity=0.523 Sum_probs=15.7
Q ss_pred ccCCCHHHHHHHHHHHHh
Q 039804 62 KNHLTAEMLQCLDQIVQQ 79 (95)
Q Consensus 62 k~~ft~eq~~~~~~~~~~ 79 (95)
+..||++|...+++.+..
T Consensus 4 r~~~t~~q~~~L~~~f~~ 21 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQE 21 (57)
T ss_dssp SSSSSHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHH
Confidence 457999999999999986
No 16
>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=37.70 E-value=8.4 Score=22.23 Aligned_cols=43 Identities=16% Similarity=0.184 Sum_probs=25.5
Q ss_pred HHHHHHHHhCChhHhhhhHhhccccccccccccCcceee--ccccCC
Q 039804 16 GVVQEIVKLRSFENMSNLEVTKSRINRVNIEIKNDVYFR--QGKVGA 60 (95)
Q Consensus 16 ~~~~~iv~~ssf~~Mk~~~~~~~~~~~~~~~~~~~~f~R--kG~vG~ 60 (95)
.|+..|..+.+-+.|......|... .....+...|+| +++|||
T Consensus 13 ~L~~~l~~~l~~~~~~~l~~~Y~~~--k~~kIsR~~fvr~lR~IVGD 57 (70)
T PF12174_consen 13 MLFSALSKHLPPSKMDLLQKHYEEF--KKKKISREEFVRKLRQIVGD 57 (70)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHH--HHCCCCHHHHHHHHHHHHHH
Confidence 4588888888888887644434333 122234556666 366664
No 17
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=37.02 E-value=17 Score=23.94 Aligned_cols=21 Identities=19% Similarity=0.509 Sum_probs=17.5
Q ss_pred CcccCCCHHHHHHHHHHHHhH
Q 039804 60 AWKNHLTAEMLQCLDQIVQQK 80 (95)
Q Consensus 60 ~Wk~~ft~eq~~~~~~~~~~~ 80 (95)
.||..|||+|-+.+++.--++
T Consensus 20 EWr~~LsPeQ~~v~RekgTE~ 40 (146)
T KOG0856|consen 20 EWRKVLSPEQFRVLREKGTER 40 (146)
T ss_pred HHHhhcCHHHhhhhHhhcccC
Confidence 899999999999988765443
No 18
>KOG3895 consensus Synaptic vesicle protein Synapsin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=36.99 E-value=19 Score=27.57 Aligned_cols=39 Identities=21% Similarity=0.377 Sum_probs=26.1
Q ss_pred cCcceeeccccCCcccCCCHHH------HHHHHHHHH---hHhCCCCc
Q 039804 48 KNDVYFRQGKVGAWKNHLTAEM------LQCLDQIVQ---QKFKDSGF 86 (95)
Q Consensus 48 ~~~~f~RkG~vG~Wk~~ft~eq------~~~~~~~~~---~~l~~~~l 86 (95)
+-..|+|.|+.|.||.---..+ .+|+..|+. +.+.+.+|
T Consensus 298 nYKaymRtsIsgnWKtNtGSamLEQIamseRyklwvdtcse~fGgldI 345 (488)
T KOG3895|consen 298 NYKAYMRTSISGNWKTNTGSAMLEQIAMSERYKLWVDTCSEMFGGLDI 345 (488)
T ss_pred hHHHHhhhhhccCcccCchHHHHHHHHHHHHHHHHHHHHHHhcCCcce
Confidence 4567999999999998765443 345555554 45555554
No 19
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=36.93 E-value=26 Score=19.38 Aligned_cols=23 Identities=35% Similarity=0.553 Sum_probs=19.0
Q ss_pred cccCCCCChHHHhhHHHHHHHHhCChhH
Q 039804 2 EFLSQPFTSEEEEAGVVQEIVKLRSFEN 29 (95)
Q Consensus 2 ~FLg~~~~~~~~~~~~~~~iv~~ssf~~ 29 (95)
+.||.+++.++ +..++....|+.
T Consensus 13 ~llG~~i~~~e-----i~~~L~~lg~~~ 35 (71)
T smart00874 13 RLLGLDLSAEE-----IEEILKRLGFEV 35 (71)
T ss_pred HHHCCCCCHHH-----HHHHHHHCCCeE
Confidence 46899999888 899998888754
No 20
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=36.10 E-value=37 Score=19.65 Aligned_cols=18 Identities=33% Similarity=0.266 Sum_probs=13.5
Q ss_pred CCcccCCCHHHHHHHHHH
Q 039804 59 GAWKNHLTAEMLQCLDQI 76 (95)
Q Consensus 59 G~Wk~~ft~eq~~~~~~~ 76 (95)
-.-.+.|||+|.+++++.
T Consensus 82 ~~~~~vLt~eQk~~~~~l 99 (100)
T PF07813_consen 82 HALYAVLTPEQKEKFDQL 99 (100)
T ss_dssp HHHHTTS-HHHHHHHHHH
T ss_pred HHHHhcCCHHHHHHHHHh
Confidence 345678999999999875
No 21
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=36.08 E-value=37 Score=23.21 Aligned_cols=25 Identities=24% Similarity=0.304 Sum_probs=22.3
Q ss_pred cCCCHHHHHHHHHHHHhHhCCCCce
Q 039804 63 NHLTAEMLQCLDQIVQQKFKDSGFV 87 (95)
Q Consensus 63 ~~ft~eq~~~~~~~~~~~l~~~~l~ 87 (95)
=|-+++++..|++|..+.-..+||.
T Consensus 48 Ihq~~e~L~~Mdew~~~~H~~sGL~ 72 (184)
T COG1949 48 IHQSDEQLAKMDEWNTETHGRSGLT 72 (184)
T ss_pred EeCCHHHHHHHHHHHHHccccccHH
Confidence 3889999999999999998888874
No 22
>PF05572 Peptidase_M43: Pregnancy-associated plasma protein-A; InterPro: IPR008754 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase M43 (cytophagalysin family, clan MA(M)), subfamily M43. The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example of this family is the pregnancy-associated plasma protein A (PAPP-A), which cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the Homo sapiens ovary and the cardiovascular system [, , , ].; PDB: 3LUN_A 3LUM_B 2J83_A 2CKI_A.
Probab=36.00 E-value=34 Score=22.44 Aligned_cols=17 Identities=12% Similarity=0.245 Sum_probs=12.3
Q ss_pred ccCCCHHHHHHHHHHHH
Q 039804 62 KNHLTAEMLQCLDQIVQ 78 (95)
Q Consensus 62 k~~ft~eq~~~~~~~~~ 78 (95)
.+.||+.|..||...++
T Consensus 138 ~~~FT~gQ~~RM~~~l~ 154 (154)
T PF05572_consen 138 MNMFTPGQVARMRAVLE 154 (154)
T ss_dssp --B-BHHHHHHHHHHHH
T ss_pred ccccCHHHHHHHHHHhC
Confidence 57899999999998764
No 23
>PF15138 Syncollin: Syncollin
Probab=35.30 E-value=12 Score=23.51 Aligned_cols=15 Identities=27% Similarity=0.893 Sum_probs=12.1
Q ss_pred eeeccccCCcccCCC
Q 039804 52 YFRQGKVGAWKNHLT 66 (95)
Q Consensus 52 f~RkG~vG~Wk~~ft 66 (95)
-+|+|..|+|-|..+
T Consensus 92 e~r~GiFg~WndaIs 106 (112)
T PF15138_consen 92 EYRRGIFGDWNDAIS 106 (112)
T ss_pred HHhcccccchhhhhh
Confidence 388999999987654
No 24
>PHA02681 ORF089 virion membrane protein; Provisional
Probab=34.64 E-value=40 Score=20.31 Aligned_cols=22 Identities=9% Similarity=0.366 Sum_probs=17.7
Q ss_pred CcccCCCHHHHHHHHHHHHhHh
Q 039804 60 AWKNHLTAEMLQCLDQIVQQKF 81 (95)
Q Consensus 60 ~Wk~~ft~eq~~~~~~~~~~~l 81 (95)
-+++.+|++|++.+.+.+----
T Consensus 47 ~F~D~lTpDQVrAlHRlvTsSp 68 (92)
T PHA02681 47 SFEDKMTDDQVRAFHALVTSSP 68 (92)
T ss_pred hhhccCCHHHHHHHHHHHhCCC
Confidence 4788999999999998776433
No 25
>PF05088 Bac_GDH: Bacterial NAD-glutamate dehydrogenase
Probab=32.30 E-value=60 Score=29.22 Aligned_cols=45 Identities=16% Similarity=0.393 Sum_probs=40.5
Q ss_pred CcceeeccccCCc--------ccCCCHHHHHHHHHHHHhHhCCCCceeecccc
Q 039804 49 NDVYFRQGKVGAW--------KNHLTAEMLQCLDQIVQQKFKDSGFVTLKMFS 93 (95)
Q Consensus 49 ~~~f~RkG~vG~W--------k~~ft~eq~~~~~~~~~~~l~~~~l~f~~~~~ 93 (95)
-..|+|++.-|.+ |+.|+.+...++...+.+.+.+..+.|.+.++
T Consensus 329 vRlf~R~D~~grfvs~LVyvPrd~y~t~~r~~i~~~l~~~~~~~~~~~~~~~~ 381 (1528)
T PF05088_consen 329 VRLFLRRDPFGRFVSCLVYVPRDRYNTELRERIQDILMEAFGGTSSEFYTYFS 381 (1528)
T ss_pred eeEEEEEcCCCCEEEEEEEEehhhCCHHHHHHHHHHHHHHhCCEEEEEEEEec
Confidence 3469999999997 99999999999999999999999999887764
No 26
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=32.26 E-value=26 Score=23.57 Aligned_cols=24 Identities=17% Similarity=0.263 Sum_probs=20.4
Q ss_pred cccCCCHHHHHHHHHHHHhHhCCC
Q 039804 61 WKNHLTAEMLQCLDQIVQQKFKDS 84 (95)
Q Consensus 61 Wk~~ft~eq~~~~~~~~~~~l~~~ 84 (95)
.-+.|||||.+.|.+..++++.++
T Consensus 133 ~~~vLTpEQRak~~e~~~~r~~~~ 156 (170)
T PRK12750 133 MLSILTPEQKAKFQELQQERMQEC 156 (170)
T ss_pred HHHhCCHHHHHHHHHHHHHHHHHH
Confidence 478999999999999998887643
No 27
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=31.37 E-value=27 Score=19.63 Aligned_cols=25 Identities=24% Similarity=0.356 Sum_probs=16.0
Q ss_pred cccCCCCChHHHhhHHHHHHHHhCChhHhh
Q 039804 2 EFLSQPFTSEEEEAGVVQEIVKLRSFENMS 31 (95)
Q Consensus 2 ~FLg~~~~~~~~~~~~~~~iv~~ssf~~Mk 31 (95)
+.||..++.++ +.++++...|+.=.
T Consensus 13 ~~lG~~i~~~~-----i~~~L~~lg~~~~~ 37 (70)
T PF03484_consen 13 KLLGIDISPEE-----IIKILKRLGFKVEK 37 (70)
T ss_dssp HHHTS---HHH-----HHHHHHHTT-EEEE
T ss_pred HHhCCCCCHHH-----HHHHHHHCCCEEEE
Confidence 46888888888 89999888875443
No 28
>PF07858 LEH: Limonene-1,2-epoxide hydrolase catalytic domain; InterPro: IPR013100 Epoxide hydrolases catalyse the hydrolysis of epoxides to corresponding diols, which is important in detoxification, synthesis of signal molecules, or metabolism. Limonene-1,2- epoxide hydrolase (LEH) differs from many other epoxide hydrolases in its structure and its novel one-step catalytic mechanism. Its main fold consists of a six-stranded mixed beta-sheet, with three N-terminal alpha helices packed to one side to create a pocket that extends into the protein core. A fourth helix lies in such a way that it acts as a rim to this pocket. Although mainly lined by hydrophobic residues, this pocket features a cluster of polar groups that lie at its deepest point and constitute the enzymes active site []. ; PDB: 2BNG_C 1NWW_A 1NU3_B.
Probab=31.05 E-value=21 Score=22.89 Aligned_cols=20 Identities=20% Similarity=0.478 Sum_probs=14.2
Q ss_pred eeccccCCcccCCCHHHHHH
Q 039804 53 FRQGKVGAWKNHLTAEMLQC 72 (95)
Q Consensus 53 ~RkG~vG~Wk~~ft~eq~~~ 72 (95)
|+-|++=-||+||+.....+
T Consensus 102 v~dGkI~~WRDYFD~~~~~~ 121 (125)
T PF07858_consen 102 VRDGKITLWRDYFDLADFLK 121 (125)
T ss_dssp EETTEEEEEEEE--HHHHHH
T ss_pred EECCEEEEEeccCCHHHHHH
Confidence 77889999999999765544
No 29
>KOG0278 consensus Serine/threonine kinase receptor-associated protein [Lipid transport and metabolism]
Probab=30.04 E-value=21 Score=26.20 Aligned_cols=18 Identities=22% Similarity=0.637 Sum_probs=15.4
Q ss_pred cCcceeeccccCCcccCC
Q 039804 48 KNDVYFRQGKVGAWKNHL 65 (95)
Q Consensus 48 ~~~~f~RkG~vG~Wk~~f 65 (95)
...+++|.|..|||-..|
T Consensus 38 d~~pmlr~g~tgdwigtf 55 (334)
T KOG0278|consen 38 DGKPMLRNGDTGDWIGTF 55 (334)
T ss_pred CCCchhccCCCCCcEEee
Confidence 567899999999998766
No 30
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=29.01 E-value=52 Score=22.79 Aligned_cols=28 Identities=18% Similarity=0.276 Sum_probs=24.0
Q ss_pred CcccCCCHHHHHHHHHHHHhHhCCCCce
Q 039804 60 AWKNHLTAEMLQCLDQIVQQKFKDSGFV 87 (95)
Q Consensus 60 ~Wk~~ft~eq~~~~~~~~~~~l~~~~l~ 87 (95)
+--=+.++++...|++|+.+....+||+
T Consensus 65 d~vI~~~~evld~MneWc~ehhg~SGLt 92 (208)
T KOG3242|consen 65 DLVIHQPKEVLDKMNEWCIEHHGNSGLT 92 (208)
T ss_pred cchhcCCHHHHHHHHHHHHHhccchhHH
Confidence 4445788999999999999999999875
No 31
>TIGR01346 isocit_lyase isocitrate lyase. Isocitrate lyase and malate synthase are the enzymes of the glyoxylate shunt, a pathway associated with the TCA cycle.
Probab=29.01 E-value=72 Score=25.48 Aligned_cols=31 Identities=10% Similarity=0.146 Sum_probs=23.4
Q ss_pred ccCCcccCCCHHHHHHHHHHHHhHhCCCCceee
Q 039804 57 KVGAWKNHLTAEMLQCLDQIVQQKFKDSGFVTL 89 (95)
Q Consensus 57 ~vG~Wk~~ft~eq~~~~~~~~~~~l~~~~l~f~ 89 (95)
-.=+|+.+|++++++.|...+.+ .|.-++|.
T Consensus 417 PSFNW~~~~~d~~~~~F~~~L~~--lGy~~QfI 447 (527)
T TIGR01346 417 PSFNWSAHMEDDEIAKFIQELGD--LGYKWQFI 447 (527)
T ss_pred CCccccccCCHHHHHHHHHHHHh--cCceEEEE
Confidence 44579999999999999877776 44445554
No 32
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=28.55 E-value=1.1e+02 Score=19.99 Aligned_cols=39 Identities=21% Similarity=0.459 Sum_probs=29.7
Q ss_pred eeeccc------cCC-----cccCCCHHHHHHHHHHHHhHhCCCCceeec
Q 039804 52 YFRQGK------VGA-----WKNHLTAEMLQCLDQIVQQKFKDSGFVTLK 90 (95)
Q Consensus 52 f~RkG~------vG~-----Wk~~ft~eq~~~~~~~~~~~l~~~~l~f~~ 90 (95)
|+|.|. +|+ |.-.--.+....++..++..++|.+|-..|
T Consensus 84 ffk~g~~~vd~~tG~~~k~~~~~~~k~~l~~~i~~~~~~a~~g~~~~~~~ 133 (142)
T PLN00410 84 FFRNKHIMIDLGTGNNNKINWALKDKQEFIDIVETVYRGARKGRGLVISP 133 (142)
T ss_pred EEECCeEEEEEecccccccccccCCHHHHHHHHHHHHHHHhcCCeEEECC
Confidence 888888 673 544555688889999999999998876544
No 33
>cd04275 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved.
Probab=28.41 E-value=50 Score=23.15 Aligned_cols=17 Identities=12% Similarity=0.163 Sum_probs=14.5
Q ss_pred cccCCCHHHHHHHHHHH
Q 039804 61 WKNHLTAEMLQCLDQIV 77 (95)
Q Consensus 61 Wk~~ft~eq~~~~~~~~ 77 (95)
-.++||+.|..||...+
T Consensus 208 C~~~FT~~Q~~RM~~~~ 224 (225)
T cd04275 208 CMNEFTPGQVTRMRSYL 224 (225)
T ss_pred hhcccCHHHHHHHHHHh
Confidence 56899999999998764
No 34
>PRK14565 triosephosphate isomerase; Provisional
Probab=27.50 E-value=72 Score=22.66 Aligned_cols=26 Identities=15% Similarity=0.217 Sum_probs=20.5
Q ss_pred cccCCcccCCCHHHHHHHHHHHHhHh
Q 039804 56 GKVGAWKNHLTAEMLQCLDQIVQQKF 81 (95)
Q Consensus 56 G~vG~Wk~~ft~eq~~~~~~~~~~~l 81 (95)
=.+|.||-+++..+...+-+.+...+
T Consensus 4 ~v~~NWKmn~~~~~~~~~~~~l~~~~ 29 (237)
T PRK14565 4 LIVANWKMNGDFSLFSSFLKELSNKL 29 (237)
T ss_pred EEEEECccccCHHHHHHHHHHHHhhc
Confidence 35799999999988888777776554
No 35
>PRK15063 isocitrate lyase; Provisional
Probab=27.38 E-value=78 Score=24.62 Aligned_cols=31 Identities=13% Similarity=0.217 Sum_probs=23.5
Q ss_pred cCCcccCCCHHHHHHHHHHHHhHhCCCCceeec
Q 039804 58 VGAWKNHLTAEMLQCLDQIVQQKFKDSGFVTLK 90 (95)
Q Consensus 58 vG~Wk~~ft~eq~~~~~~~~~~~l~~~~l~f~~ 90 (95)
.=.|+.+|++++++.|.+.+.+ -|..++|.|
T Consensus 316 sfnW~~~~~~~~~~~f~~eL~~--~Gy~~~~~~ 346 (428)
T PRK15063 316 SFNWKKNLDDATIAKFQRELGA--MGYKFQFIT 346 (428)
T ss_pred CcccccccCHHHHHHHHHHHHH--cCceEEEec
Confidence 3479999999999999877776 455555543
No 36
>PRK15492 triosephosphate isomerase; Provisional
Probab=27.09 E-value=78 Score=22.72 Aligned_cols=24 Identities=4% Similarity=-0.330 Sum_probs=19.3
Q ss_pred ccCCcccCCCHHHHHHHHHHHHhH
Q 039804 57 KVGAWKNHLTAEMLQCLDQIVQQK 80 (95)
Q Consensus 57 ~vG~Wk~~ft~eq~~~~~~~~~~~ 80 (95)
.+|.||=+++..+...+-+.+...
T Consensus 6 i~~NWKmn~~~~~~~~~~~~~~~~ 29 (260)
T PRK15492 6 FGTNLKMYKGIADATDFLAKLSEL 29 (260)
T ss_pred EEEECCcCCCHHHHHHHHHHHHhh
Confidence 458999999999988877777554
No 37
>cd00311 TIM Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually homodimeric, but in some organisms tetrameric, is ubiqitous and conserved in function across eukaryotes, bacteria and archaea.
Probab=26.96 E-value=70 Score=22.64 Aligned_cols=26 Identities=23% Similarity=0.263 Sum_probs=21.0
Q ss_pred ccCCcccCCCHHHHHHHHHHHHhHhC
Q 039804 57 KVGAWKNHLTAEMLQCLDQIVQQKFK 82 (95)
Q Consensus 57 ~vG~Wk~~ft~eq~~~~~~~~~~~l~ 82 (95)
.+|.||-+.+.++...+-+.+...+.
T Consensus 3 i~~NwKmn~~~~~~~~~~~~l~~~~~ 28 (242)
T cd00311 3 VAGNWKMNGTLAEALELAKALNAVLK 28 (242)
T ss_pred EEEECCcccCHHHHHHHHHHHHhhcc
Confidence 36899999999998888777776664
No 38
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=26.56 E-value=87 Score=17.34 Aligned_cols=17 Identities=24% Similarity=0.278 Sum_probs=11.4
Q ss_pred CCHHHHHHHHHHHHhHh
Q 039804 65 LTAEMLQCLDQIVQQKF 81 (95)
Q Consensus 65 ft~eq~~~~~~~~~~~l 81 (95)
||++|...++.++.+.+
T Consensus 1 lT~~Qk~el~~l~~qm~ 17 (59)
T PF10925_consen 1 LTDQQKKELKALYKQML 17 (59)
T ss_pred CCHHHHHHHHHHHHHHH
Confidence 56777777777766544
No 39
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=25.20 E-value=33 Score=25.72 Aligned_cols=23 Identities=13% Similarity=0.296 Sum_probs=18.7
Q ss_pred ccCCcccCCCHHHHHHHHHHHHh
Q 039804 57 KVGAWKNHLTAEMLQCLDQIVQQ 79 (95)
Q Consensus 57 ~vG~Wk~~ft~eq~~~~~~~~~~ 79 (95)
.+-.+|..||-||+.|+++-+.+
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyr 202 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYR 202 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHH
Confidence 44458999999999999987664
No 40
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=24.18 E-value=77 Score=21.85 Aligned_cols=31 Identities=16% Similarity=0.149 Sum_probs=23.8
Q ss_pred ceeeccccC-CcccCCCHHHHHHHHHHHHhHhC
Q 039804 51 VYFRQGKVG-AWKNHLTAEMLQCLDQIVQQKFK 82 (95)
Q Consensus 51 ~f~RkG~vG-~Wk~~ft~eq~~~~~~~~~~~l~ 82 (95)
.++-+...| -|++ +|++|.++|-+.+.+-|.
T Consensus 71 ~~~s~~vLG~~wr~-as~eQr~~F~~~F~~~Lv 102 (211)
T PRK15117 71 KYAGALVLGRYYKD-ATPAQREAYFAAFREYLK 102 (211)
T ss_pred HHHHHHHhhhhhhh-CCHHHHHHHHHHHHHHHH
Confidence 345566777 5876 999999999988887664
No 41
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=24.13 E-value=97 Score=15.81 Aligned_cols=20 Identities=25% Similarity=0.333 Sum_probs=16.1
Q ss_pred ccCCCHHHHHHHHHHHHhHh
Q 039804 62 KNHLTAEMLQCLDQIVQQKF 81 (95)
Q Consensus 62 k~~ft~eq~~~~~~~~~~~l 81 (95)
+..|+++++..++.++...-
T Consensus 4 r~~~~~~~~~~L~~~f~~~~ 23 (56)
T smart00389 4 RTSFTPEQLEELEKEFQKNP 23 (56)
T ss_pred CCcCCHHHHHHHHHHHHhCC
Confidence 34599999999999987654
No 42
>KOG1379 consensus Serine/threonine protein phosphatase [Signal transduction mechanisms]
Probab=23.90 E-value=39 Score=25.30 Aligned_cols=24 Identities=25% Similarity=0.623 Sum_probs=19.0
Q ss_pred ccCCcccC------CCHHHHHHHHHHHHhH
Q 039804 57 KVGAWKNH------LTAEMLQCLDQIVQQK 80 (95)
Q Consensus 57 ~vG~Wk~~------ft~eq~~~~~~~~~~~ 80 (95)
-||+|++| |+-+..+.+++.++.-
T Consensus 111 GVGGWa~~GiDpg~fS~eLM~~ce~~v~~~ 140 (330)
T KOG1379|consen 111 GVGGWAEYGIDPGAFSRELMSNCERLVQNS 140 (330)
T ss_pred ccchHhhcCcCHHHHHHHHHHHHHHHhccc
Confidence 57999987 8888888888777653
No 43
>PF09832 DUF2059: Uncharacterized protein conserved in bacteria (DUF2059); InterPro: IPR018637 This entry contains proteins that have no known function. ; PDB: 2X3O_B 3OAO_A.
Probab=23.66 E-value=45 Score=18.13 Aligned_cols=26 Identities=15% Similarity=0.248 Sum_probs=19.0
Q ss_pred cccCCcccCCCHHHHHHHHHHHHhHh
Q 039804 56 GKVGAWKNHLTAEMLQCLDQIVQQKF 81 (95)
Q Consensus 56 G~vG~Wk~~ft~eq~~~~~~~~~~~l 81 (95)
..+.-|..+||.++++.+-.+|..-+
T Consensus 8 ~~~~~y~~~ft~~El~~i~~FY~Sp~ 33 (64)
T PF09832_consen 8 QMAPIYAEHFTEEELDAILAFYESPL 33 (64)
T ss_dssp HHHHHHHHHS-HHHHHHHHHHHHSHH
T ss_pred HHHHHHHHHCCHHHHHHHHHHHCCHH
Confidence 34456778999999999998887544
No 44
>PF00121 TIM: Triosephosphate isomerase; InterPro: IPR000652 Triosephosphate isomerase (5.3.1.1 from EC) (TIM) [] is the glycolytic enzyme that catalyses the reversible interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. TIM plays an important role in several metabolic pathways and is essential for efficient energy production. It is present in eukaryotes as well as in prokaryotes. TIM is a dimer of identical subunits, each of which is made up of about 250 amino-acid residues. A glutamic acid residue is involved in the catalytic mechanism [, ]. The tertiary structure of TIM has eight beta/alpha motifs folded into a barrel structure. The TIM barrel fold occurs ubiquitously and is found in numerous other enzymes that can be involved in energy metabolism, macromolecule metabolism, or small molecule metabolism []. The sequence around the active site residue is perfectly conserved in all known TIM's. Deficiencies in TIM are associated with haemolytic anaemia coupled with a progressive, severe neurological disorder [].; GO: 0004807 triose-phosphate isomerase activity, 0008152 metabolic process; PDB: 2YPI_A 1YPI_A 1NEY_B 1NF0_B 1I45_A 7TIM_A 3YPI_B 2H6R_H 2Y63_A 1N55_A ....
Probab=23.59 E-value=67 Score=22.76 Aligned_cols=26 Identities=19% Similarity=0.130 Sum_probs=20.8
Q ss_pred ccCCcccCCCHHHHHHHHHHHHhHhC
Q 039804 57 KVGAWKNHLTAEMLQCLDQIVQQKFK 82 (95)
Q Consensus 57 ~vG~Wk~~ft~eq~~~~~~~~~~~l~ 82 (95)
.+|+||-+.+.++...+-+.+.....
T Consensus 3 i~~NwKmn~~~~~~~~~~~~l~~~~~ 28 (244)
T PF00121_consen 3 IIGNWKMNGTGEEALEFLKELLNAKL 28 (244)
T ss_dssp EEEEETBSGSHHHHHHHHHHHHHHHC
T ss_pred EEEehhhCcCHHHHHHHHHHHHhccc
Confidence 46899999999999888887555444
No 45
>PF02130 UPF0054: Uncharacterized protein family UPF0054; InterPro: IPR002036 These, as yet, uncharacterised proteins are of 17 to 21 kDa. They contain a conserved region with three histidines at the C terminus. The protein family is represented by a single member sequence only in nearly every bacterium. The crystal structure of the protein from the hyperthermophilic bacteria Aquifex aeolicus has been determined. The overall fold consists of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices. Structure-based homology analysis reveals a good resemblance to the metal-dependent proteinases such as collagenases and gelatinases. However, experimental tests for collagenase and gelatinase-type function show no detectable activity under standard assay conditions [].; GO: 0046872 metal ion binding; PDB: 1TVI_A 1OZ9_A 1XM5_A 1XAX_A.
Probab=22.65 E-value=1.1e+02 Score=19.83 Aligned_cols=27 Identities=11% Similarity=-0.016 Sum_probs=19.8
Q ss_pred CCHHHHHHHHHHHHhHhCCCC-ceeecc
Q 039804 65 LTAEMLQCLDQIVQQKFKDSG-FVTLKM 91 (95)
Q Consensus 65 ft~eq~~~~~~~~~~~l~~~~-l~f~~~ 91 (95)
-+++.+++++..+..+-..|| |+|+..
T Consensus 42 v~~~~i~~LN~~yr~~d~pTDVLSFp~~ 69 (145)
T PF02130_consen 42 VDDEEIRELNKQYRGKDYPTDVLSFPYD 69 (145)
T ss_dssp E-HHHHHHHHHHHHS-SSS-SEEEEE--
T ss_pred ECHHHHHHHHHHHcCCCCCCeEEeECCC
Confidence 468999999999999999999 888653
No 46
>PRK14566 triosephosphate isomerase; Provisional
Probab=22.11 E-value=1e+02 Score=22.29 Aligned_cols=26 Identities=27% Similarity=0.340 Sum_probs=20.9
Q ss_pred ccCCcccCCCHHHHHHHHHHHHhHhC
Q 039804 57 KVGAWKNHLTAEMLQCLDQIVQQKFK 82 (95)
Q Consensus 57 ~vG~Wk~~ft~eq~~~~~~~~~~~l~ 82 (95)
.+|.||-+.+..+...+-+.+...+.
T Consensus 8 i~gNWKmn~~~~~~~~~~~~l~~~~~ 33 (260)
T PRK14566 8 VAGNWKMNGSAALAQELFKKFAGKLQ 33 (260)
T ss_pred EEEECCcCcCHHHHHHHHHHHHhhcC
Confidence 57999999999998887777766553
No 47
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=21.77 E-value=56 Score=19.91 Aligned_cols=18 Identities=0% Similarity=0.381 Sum_probs=14.5
Q ss_pred HhhHHHHHHHHhCChhHh
Q 039804 13 EEAGVVQEIVKLRSFENM 30 (95)
Q Consensus 13 ~~~~~~~~iv~~ssf~~M 30 (95)
.++.++++|++++.++-.
T Consensus 41 rNP~i~ekLi~~~~Ide~ 58 (96)
T PF07818_consen 41 RNPSILEKLIEFFGIDEY 58 (96)
T ss_pred CChHHHHHHHHHcCCCcc
Confidence 467889999999998763
No 48
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here have anything to do with toluene per-se.
Probab=21.05 E-value=1e+02 Score=21.07 Aligned_cols=30 Identities=13% Similarity=0.212 Sum_probs=22.0
Q ss_pred eeeccccC-CcccCCCHHHHHHHHHHHHhHhC
Q 039804 52 YFRQGKVG-AWKNHLTAEMLQCLDQIVQQKFK 82 (95)
Q Consensus 52 f~RkG~vG-~Wk~~ft~eq~~~~~~~~~~~l~ 82 (95)
.+-+...| .|+. +|++|.++|-+.+..-+.
T Consensus 68 ~mar~vLG~~W~~-~s~~Qr~~F~~~F~~~l~ 98 (198)
T TIGR03481 68 AMARLTLGSSWTS-LSPEQRRRFIGAFRELSI 98 (198)
T ss_pred HHHHHHhhhhhhh-CCHHHHHHHHHHHHHHHH
Confidence 34455666 5766 999999999988876443
No 49
>PF14794 DUF4479: Domain of unknown function (DUF4479); PDB: 3BU2_C.
Probab=20.97 E-value=1e+02 Score=17.80 Aligned_cols=22 Identities=32% Similarity=0.351 Sum_probs=12.7
Q ss_pred CCcccCCCHHHHHHHHHHHHhH
Q 039804 59 GAWKNHLTAEMLQCLDQIVQQK 80 (95)
Q Consensus 59 G~Wk~~ft~eq~~~~~~~~~~~ 80 (95)
|.=.=.||++|++.+++.+.+.
T Consensus 42 ~~G~V~Lt~eqv~~LN~~l~~~ 63 (73)
T PF14794_consen 42 GNGQVFLTEEQVAKLNQALQKA 63 (73)
T ss_dssp --------HHHHHHHHHHHHHT
T ss_pred CCcCEEcCHHHHHHHHHHHHHc
Confidence 3444499999999999998874
No 50
>PF13227 DUF4035: Protein of unknown function (DUF4035)
Probab=20.80 E-value=27 Score=19.16 Aligned_cols=22 Identities=18% Similarity=0.514 Sum_probs=18.7
Q ss_pred ceeeccccCCcccCCCHHHHHH
Q 039804 51 VYFRQGKVGAWKNHLTAEMLQC 72 (95)
Q Consensus 51 ~f~RkG~vG~Wk~~ft~eq~~~ 72 (95)
.|-|.--+|+||.-+-..|+..
T Consensus 2 ~fdr~~P~G~~R~D~~~Aqia~ 23 (53)
T PF13227_consen 2 AFDREQPFGDWRGDYRAAQIAA 23 (53)
T ss_pred cccccCCcchHHHHHHHHHHHH
Confidence 4678888999999999888877
No 51
>PF06047 SynMuv_product: Ras-induced vulval development antagonist; InterPro: IPR009269 This is a family of eukaryotic proteins with undetermined function.
Probab=20.49 E-value=95 Score=19.37 Aligned_cols=20 Identities=30% Similarity=0.579 Sum_probs=15.5
Q ss_pred ceeeccccCCcccCCCHHHHHHHHH
Q 039804 51 VYFRQGKVGAWKNHLTAEMLQCLDQ 75 (95)
Q Consensus 51 ~f~RkG~vG~Wk~~ft~eq~~~~~~ 75 (95)
.-=|+|.|| +|.++++.|+.
T Consensus 26 RIPRRGEIG-----ltseeI~~~E~ 45 (104)
T PF06047_consen 26 RIPRRGEIG-----LTSEEIASFED 45 (104)
T ss_pred CCCCCcccC-----CCHHHHHHHHh
Confidence 445789996 88999988874
No 52
>smart00678 WWE Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis.
Probab=20.07 E-value=1.2e+02 Score=16.83 Aligned_cols=24 Identities=13% Similarity=0.327 Sum_probs=19.2
Q ss_pred cccCCcccCCCHHHHHHHHHHHHhH
Q 039804 56 GKVGAWKNHLTAEMLQCLDQIVQQK 80 (95)
Q Consensus 56 G~vG~Wk~~ft~eq~~~~~~~~~~~ 80 (95)
+..|.|..| +++.+..+++.+...
T Consensus 7 ~~~g~W~~Y-~~~~~~~IE~ay~~~ 30 (73)
T smart00678 7 GRNGKWWPY-DPRVSEDIEEAYAAG 30 (73)
T ss_pred CCCCCeeeC-ChHHHHHHHHHHHcC
Confidence 445889987 778899999988874
No 53
>PRK14905 triosephosphate isomerase/PTS system glucose/sucrose-specific transporter subunit IIB; Provisional
Probab=20.02 E-value=1.3e+02 Score=22.73 Aligned_cols=25 Identities=4% Similarity=-0.443 Sum_probs=19.6
Q ss_pred ccCCcccCCCHHHHHHHHHHHHhHh
Q 039804 57 KVGAWKNHLTAEMLQCLDQIVQQKF 81 (95)
Q Consensus 57 ~vG~Wk~~ft~eq~~~~~~~~~~~l 81 (95)
.+|.||-++|......+-..+...+
T Consensus 7 v~gNWKmn~~~~~~~~~~~~l~~~~ 31 (355)
T PRK14905 7 FGTNLKMYKGNAETVDYLSELLAFA 31 (355)
T ss_pred EEEECCcCCCHHHHHHHHHHHHHhh
Confidence 5799999999988877776665544
Done!