Query 034548
Match_columns 91
No_of_seqs 111 out of 518
Neff 7.9
Searched_HMMs 46136
Date Fri Mar 29 04:00:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034548.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034548hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0959 N-arginine dibasic con 99.9 1.7E-22 3.8E-27 158.4 6.9 91 1-91 349-439 (974)
2 COG1025 Ptr Secreted/periplasm 99.8 7.6E-19 1.7E-23 137.0 7.6 91 1-91 344-434 (937)
3 PRK15101 protease3; Provisiona 99.6 8.7E-15 1.9E-19 115.3 7.2 90 2-91 366-455 (961)
4 PTZ00432 falcilysin; Provision 96.0 0.0034 7.4E-08 51.7 1.7 70 2-73 466-541 (1119)
5 PF11044 TMEMspv1-c74-12: Plec 68.1 14 0.0003 19.3 3.4 12 4-15 13-24 (49)
6 PF05193 Peptidase_M16_C: Pept 66.9 13 0.00028 22.8 4.0 29 2-30 154-182 (184)
7 TIGR02110 PQQ_syn_pqqF coenzym 57.0 18 0.00038 29.1 3.8 46 2-49 314-359 (696)
8 PHA02898 virion envelope prote 45.9 25 0.00055 20.9 2.4 27 4-30 23-49 (92)
9 PF11517 Nab2: Nuclear abundan 43.8 73 0.0016 19.5 4.2 30 3-32 68-97 (107)
10 PHA02680 ORF090 IMV phosphoryl 38.6 51 0.0011 19.6 2.9 27 4-30 23-50 (91)
11 KOG1235 Predicted unusual prot 37.7 54 0.0012 25.7 3.7 67 4-73 207-273 (538)
12 cd04383 RhoGAP_srGAP RhoGAP_sr 36.3 27 0.00058 23.1 1.7 30 4-33 75-104 (188)
13 PF13053 DUF3914: Protein of u 36.1 47 0.001 19.6 2.5 19 12-30 66-84 (92)
14 PF05767 Pox_A14: Poxvirus vir 35.0 63 0.0014 19.4 2.9 26 4-29 23-48 (92)
15 PF08621 RPAP1_N: RPAP1-like, 32.1 6.3 0.00014 20.8 -1.5 30 55-84 12-42 (49)
16 COG3383 Uncharacterized anaero 31.1 48 0.001 27.5 2.6 50 5-54 716-765 (978)
17 PF12627 PolyA_pol_RNAbd: Prob 31.0 62 0.0013 17.0 2.4 29 4-33 8-36 (64)
18 COG4304 Uncharacterized protei 30.3 27 0.00058 22.8 0.9 22 68-89 111-133 (166)
19 cd04384 RhoGAP_CdGAP RhoGAP_Cd 29.7 24 0.00053 23.5 0.7 79 4-89 75-153 (195)
20 PF06743 FAST_1: FAST kinase-l 28.3 21 0.00044 19.9 0.1 36 48-83 26-64 (71)
21 PF07939 DUF1685: Protein of u 28.1 75 0.0016 17.7 2.3 17 25-41 6-22 (64)
22 PF02998 Lentiviral_Tat: Lenti 27.0 1.2E+02 0.0027 17.7 3.2 21 10-30 41-61 (86)
23 PF07521 RMMBL: RNA-metabolisi 23.7 53 0.0012 16.3 1.2 19 72-90 17-35 (43)
24 PF10239 DUF2465: Protein of u 23.4 1.6E+02 0.0035 21.4 4.0 63 22-84 38-102 (318)
25 cd04398 RhoGAP_fRGD1 RhoGAP_fR 22.4 45 0.00097 21.8 0.9 29 4-32 76-104 (192)
26 KOG0181 20S proteasome, regula 22.3 42 0.00092 23.1 0.8 23 37-59 100-122 (233)
27 PHA03048 IMV membrane protein; 21.9 1.3E+02 0.0027 18.0 2.6 29 4-36 23-51 (93)
28 cd04400 RhoGAP_fBEM3 RhoGAP_fB 20.8 38 0.00082 22.3 0.3 30 4-33 81-110 (190)
No 1
>KOG0959 consensus N-arginine dibasic convertase NRD1 and related Zn2+-dependent endopeptidases, insulinase superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=99.87 E-value=1.7e-22 Score=158.36 Aligned_cols=91 Identities=44% Similarity=0.915 Sum_probs=89.3
Q ss_pred ChHHHHHHHHHHHHHHhCCCchHHHHHHHHhHhhccccCCCCChHHHHHHHHHhCCCCCcccccccCCCCCCCCHHHHHH
Q 034548 1 MQDVVGLLFKYINLLQQSGASKWIFDELSAVCEVTFHYQDKVPPIDYVVTVAANMETYPPQDWLVGESLPSNFNPEIIQM 80 (91)
Q Consensus 1 ~~~Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~~~F~f~~~~~~~~~~~~la~~m~~~p~edvL~~~~l~~~~d~~~i~~ 80 (91)
+++|++++|+||++|+..|+++|+|+|++.+++..|+|+++.+|+++++++|.+|+.||++|||.|++++.+|||+.|++
T Consensus 349 ~~~ii~~~f~yi~~l~~~~~~~~i~~E~~~~~~~~Frf~~k~~p~~~~~~~~~nlq~~P~~~il~~~~ll~~~~p~~i~~ 428 (974)
T KOG0959|consen 349 VDEIIGLVFNYIKLLQSAGPEKWIFKELQLISEVKFRFQDKEPPMEYASEIASNLQYYPVEDVLTGSYLLTEFDPDLIQE 428 (974)
T ss_pred HHHHHHHHHHHHHHHHhcCchhHHHHHHHHhhhhheeecccCCcHHHHHHHHhhcccCChHHhhcchhhhhhcChHHHHH
Confidence 37999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhccCCCcCC
Q 034548 81 TLKELSPKTVR 91 (91)
Q Consensus 81 ~l~~l~p~N~r 91 (91)
+++.|+|.|+|
T Consensus 429 ~~~~L~p~n~~ 439 (974)
T KOG0959|consen 429 VLSSLVPSNMR 439 (974)
T ss_pred HHHhcCcccce
Confidence 99999999986
No 2
>COG1025 Ptr Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]
Probab=99.77 E-value=7.6e-19 Score=137.01 Aligned_cols=91 Identities=36% Similarity=0.660 Sum_probs=89.4
Q ss_pred ChHHHHHHHHHHHHHHhCCCchHHHHHHHHhHhhccccCCCCChHHHHHHHHHhCCCCCcccccccCCCCCCCCHHHHHH
Q 034548 1 MQDVVGLLFKYINLLQQSGASKWIFDELSAVCEVTFHYQDKVPPIDYVVTVAANMETYPPQDWLVGESLPSNFNPEIIQM 80 (91)
Q Consensus 1 ~~~Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~~~F~f~~~~~~~~~~~~la~~m~~~p~edvL~~~~l~~~~d~~~i~~ 80 (91)
|++||.++|+|+++++.+|++.|.|+|++.+.++.|+|.++.+|++++++++.+|+.+|+++++.+..++..||+..++.
T Consensus 344 ~~~VI~~~F~yl~~l~~~~~~~~~f~Elq~v~~l~f~y~~~t~~~~~~~~l~~~m~~~p~~~~~~~~~~~~~yd~~~~~~ 423 (937)
T COG1025 344 YDRVIALTFQYLNLLREKGIPKYTFDELQNVLDLDFRYPSKTRPMDYVSWLADNMEREPVEHTLYASLVLPRYDPKAIQE 423 (937)
T ss_pred HHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHhhhcccccCChHHHHHHHHHhcccCChhhhhchhhcccccCHHHHHH
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhccCCCcCC
Q 034548 81 TLKELSPKTVR 91 (91)
Q Consensus 81 ~l~~l~p~N~r 91 (91)
+|..|+|+|+|
T Consensus 424 ~l~~~~pen~R 434 (937)
T COG1025 424 RLALMTPENAR 434 (937)
T ss_pred HHHhhCccceE
Confidence 99999999987
No 3
>PRK15101 protease3; Provisional
Probab=99.56 E-value=8.7e-15 Score=115.33 Aligned_cols=90 Identities=31% Similarity=0.584 Sum_probs=87.5
Q ss_pred hHHHHHHHHHHHHHHhCCCchHHHHHHHHhHhhccccCCCCChHHHHHHHHHhCCCCCcccccccCCCCCCCCHHHHHHH
Q 034548 2 QDVVGLLFKYINLLQQSGASKWIFDELSAVCEVTFHYQDKVPPIDYVVTVAANMETYPPQDWLVGESLPSNFNPEIIQMT 81 (91)
Q Consensus 2 ~~Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~~~F~f~~~~~~~~~~~~la~~m~~~p~edvL~~~~l~~~~d~~~i~~~ 81 (91)
++|++.+|++|+.|++.|+.+|.+++.+++...+|+|+++..+++++..+|.+|+.+|+++++.+.++++++|++.|+++
T Consensus 366 ~~v~~~i~~~i~~l~~~g~~~~el~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~i~~~ 445 (961)
T PRK15101 366 DQVVAAIFSYLNLLREKGIDKSYFDELAHVLDLDFRYPSITRDMDYIEWLADTMLRVPVEHTLDAPYIADRYDPKAIKAR 445 (961)
T ss_pred HHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHhccccCCCCCChHHHHHHHHHHhhhCCHHHheeCchhhhcCCHHHHHHH
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhccCCCcCC
Q 034548 82 LKELSPKTVR 91 (91)
Q Consensus 82 l~~l~p~N~r 91 (91)
+++|+|+|++
T Consensus 446 ~~~l~~~n~~ 455 (961)
T PRK15101 446 LAEMTPQNAR 455 (961)
T ss_pred HhhcCHhHEE
Confidence 9999999974
No 4
>PTZ00432 falcilysin; Provisional
Probab=96.01 E-value=0.0034 Score=51.69 Aligned_cols=70 Identities=10% Similarity=0.152 Sum_probs=58.7
Q ss_pred hHHHHHHHHHHHHHHhCCCchHHHHHHHHhHhhccccCCCCC-----hHHHHHHHHHhCCC-CCcccccccCCCCCCC
Q 034548 2 QDVVGLLFKYINLLQQSGASKWIFDELSAVCEVTFHYQDKVP-----PIDYVVTVAANMET-YPPQDWLVGESLPSNF 73 (91)
Q Consensus 2 ~~Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~~~F~f~~~~~-----~~~~~~~la~~m~~-~p~edvL~~~~l~~~~ 73 (91)
++|.+.|+++|+.+++.|+.+|.++ +.+.++.|++++... ...++..++..+++ .+|.++|..+..+++.
T Consensus 466 ~ev~~~I~~~L~~l~~eGi~~eele--~a~~qlef~~rE~~~~~~p~gl~~~~~~~~~~~~g~dp~~~l~~~~~l~~l 541 (1119)
T PTZ00432 466 YTFEKVVLNALTKVVTEGFNKSAVE--ASLNNIEFVMKELNLGTYPKGLMLIFLMQSRLQYGKDPFEILRFEKLLNEL 541 (1119)
T ss_pred HHHHHHHHHHHHHHHHhCCCHHHHH--HHHHHHHHHhhhccCCCCCcHHHHHHHHHHHHhcCCCHHHHHhhHHHHHHH
Confidence 4799999999999999999999997 778889999988753 58999999999876 8899988876655433
No 5
>PF11044 TMEMspv1-c74-12: Plectrovirus spv1-c74 ORF 12 transmembrane protein; InterPro: IPR022743 This is a group of proteins expressed by Plectroviruses. The Plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. This entry represents putative transmembrane proteins of unknown function.
Probab=68.13 E-value=14 Score=19.26 Aligned_cols=12 Identities=25% Similarity=0.479 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHH
Q 034548 4 VVGLLFKYINLL 15 (91)
Q Consensus 4 Vi~~vF~yi~ll 15 (91)
|+-.+|.|+.|+
T Consensus 13 Iil~If~~iGl~ 24 (49)
T PF11044_consen 13 IILGIFAWIGLS 24 (49)
T ss_pred HHHHHHHHHHHH
Confidence 567789999987
No 6
>PF05193 Peptidase_M16_C: Peptidase M16 inactive domain; InterPro: IPR007863 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 []. These metallopeptidases belong to MEROPS peptidase family M16 (clan ME). They include proteins, which are classified as non-peptidase homologues either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity. The peptidases in this group of sequences include: Insulinase, insulin-degrading enzyme (3.4.24.56 from EC) Mitochondrial processing peptidase alpha subunit, (Alpha-MPP, 3.4.24.64 from EC) Pitrlysin, Protease III precursor (3.4.24.55 from EC) Nardilysin, (3.4.24.61 from EC) Ubiquinol-cytochrome C reductase complex core protein I,mitochondrial precursor (1.10.2.2 from EC) Coenzyme PQQ synthesis protein F (3.4.99 from EC) These proteins do not share many regions of sequence similarity; the most noticeable is in the N-terminal section. This region includes a conserved histidine followed, two residues later by a glutamate and another histidine. In pitrilysin, it has been shown [] that this H-x-x-E-H motif is involved in enzymatic activity; the two histidines bind zinc and the glutamate is necessary for catalytic activity. The mitochondrial processing peptidase consists of two structurally related domains. One is the active peptidase whereas the other, the C-terminal region, is inactive. The two domains hold the substrate like a clamp [].; GO: 0004222 metalloendopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 1BE3_B 1PP9_B 2A06_B 1SQB_B 1SQP_B 1L0N_B 1SQX_B 1NU1_B 1L0L_B 2FYU_B ....
Probab=66.88 E-value=13 Score=22.84 Aligned_cols=29 Identities=10% Similarity=0.270 Sum_probs=24.7
Q ss_pred hHHHHHHHHHHHHHHhCCCchHHHHHHHH
Q 034548 2 QDVVGLLFKYINLLQQSGASKWIFDELSA 30 (91)
Q Consensus 2 ~~Vi~~vF~yi~llk~~~~~~~~~~E~~~ 30 (91)
+++++.+++.++.|++.|+.++-++..++
T Consensus 154 ~~~~~~~~~~l~~l~~~~~s~~el~~~k~ 182 (184)
T PF05193_consen 154 DEAIEAILQELKRLREGGISEEELERAKN 182 (184)
T ss_dssp HHHHHHHHHHHHHHHHHCS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 57899999999999999999998887765
No 7
>TIGR02110 PQQ_syn_pqqF coenzyme PQQ biosynthesis probable peptidase PqqF. In a subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone), this probable peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA (TIGR02107), a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases.
Probab=57.00 E-value=18 Score=29.12 Aligned_cols=46 Identities=13% Similarity=0.272 Sum_probs=34.5
Q ss_pred hHHHHHHHHHHHHHHhCCCchHHHHHHHHhHhhccccCCCCChHHHHH
Q 034548 2 QDVVGLLFKYINLLQQSGASKWIFDELSAVCEVTFHYQDKVPPIDYVV 49 (91)
Q Consensus 2 ~~Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~~~F~f~~~~~~~~~~~ 49 (91)
++|+..++++|+.|++.+... ..+|..++.+.+|.|..- +|.+.+.
T Consensus 314 ~~v~~~i~~~L~~L~~~~~~~-~~eel~rlk~~~~~~~~~-~~l~~~r 359 (696)
T TIGR02110 314 QQIEQLLTQWLGALAEQTWAE-QLEHYAQLAQRRFQTLAL-SPLAQLR 359 (696)
T ss_pred HHHHHHHHHHHHHHHhcCCCC-CHHHHHHHHHhhhhhccc-ChHHHHh
Confidence 579999999999999884221 467889999998886543 3555555
No 8
>PHA02898 virion envelope protein; Provisional
Probab=45.95 E-value=25 Score=20.95 Aligned_cols=27 Identities=19% Similarity=0.327 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHhCCCchHHHHHHHH
Q 034548 4 VVGLLFKYINLLQQSGASKWIFDELSA 30 (91)
Q Consensus 4 Vi~~vF~yi~llk~~~~~~~~~~E~~~ 30 (91)
++..+|+|+++=|+..+....|.-+..
T Consensus 23 ~~ACIfAfidfSK~~~~~~~~wRalSi 49 (92)
T PHA02898 23 IVACICAYIELSKSEKPADSALRSISI 49 (92)
T ss_pred HHHHHHheehhhcCCCcchhHHHHHHH
Confidence 567899999998888776777755443
No 9
>PF11517 Nab2: Nuclear abundant poly(A) RNA-bind protein 2 (Nab2); InterPro: IPR021083 Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N-terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1 []. The N-terminal domain of Nab2 shows a structure of a helical fold. The N-terminal domain of Nab2 is thought to mediate protein:protein interactions that facilitate the nuclear export of mRNA []. An essential hydrophobic Phe73 patch on the N-terminal domain is thought to be an important component of the interface between Nab2 and Mlp1 [].; PDB: 3LCN_B 2V75_A 2JPS_A.
Probab=43.78 E-value=73 Score=19.49 Aligned_cols=30 Identities=27% Similarity=0.300 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHhCCCchHHHHHHHHhH
Q 034548 3 DVVGLLFKYINLLQQSGASKWIFDELSAVC 32 (91)
Q Consensus 3 ~Vi~~vF~yi~llk~~~~~~~~~~E~~~i~ 32 (91)
.|++..|.-+..|+....-+-++.-++.+.
T Consensus 68 ~VVQtaF~ale~Lq~Ge~~e~iv~Ki~~~~ 97 (107)
T PF11517_consen 68 DVVQTAFFALEALQQGETVENIVSKIRGMN 97 (107)
T ss_dssp HHHHHHHHHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCCCcHHHHHHHHHccC
Confidence 467777777777777666666776666543
No 10
>PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional
Probab=38.56 E-value=51 Score=19.63 Aligned_cols=27 Identities=11% Similarity=0.504 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHhC-CCchHHHHHHHH
Q 034548 4 VVGLLFKYINLLQQS-GASKWIFDELSA 30 (91)
Q Consensus 4 Vi~~vF~yi~llk~~-~~~~~~~~E~~~ 30 (91)
++..+|+|+++=|.. ++....|.-+..
T Consensus 23 ~~ACIFAfidFSK~~s~~~~~~wRalSi 50 (91)
T PHA02680 23 TAACVFAFVDFSKNTSNVTDYVWRALSV 50 (91)
T ss_pred HHHHHHhhhhhhccCCCCcchhHHHHHH
Confidence 567899999998876 566777754443
No 11
>KOG1235 consensus Predicted unusual protein kinase [General function prediction only]
Probab=37.70 E-value=54 Score=25.70 Aligned_cols=67 Identities=10% Similarity=0.196 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHhCCCchHHHHHHHHhHhhccccCCCCChHHHHHHHHHhCCCCCcccccccCCCCCCC
Q 034548 4 VVGLLFKYINLLQQSGASKWIFDELSAVCEVTFHYQDKVPPIDYVVTVAANMETYPPQDWLVGESLPSNF 73 (91)
Q Consensus 4 Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~~~F~f~~~~~~~~~~~~la~~m~~~p~edvL~~~~l~~~~ 73 (91)
.+..++.|++.+--...-.|+.||++.-.-..++|..... .+.+.+.++..++...-+.-|.+++++
T Consensus 207 ~~~~~~~~l~k~~p~~~~~~lvdE~~~~L~~ELDF~~EA~---Nae~~~~~f~~~~~~~~V~VP~Vy~~~ 273 (538)
T KOG1235|consen 207 NLRLLAKVLQKFFPDFDLVWLVDEIAKSLPQELDFTKEAK---NAERFRENFKDFSLLTYVLVPKVYWDL 273 (538)
T ss_pred HHHHHHHHHHHhCcCCchhhHHHHHHhhhHhhcchHHHHH---hHHHHHHHHHhcccccceeCCeehhhc
Confidence 3566777777765555678999999887666666655443 566666666555533333334444443
No 12
>cd04383 RhoGAP_srGAP RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an N-terminal FCH domain, a central RhoGAP domain and a C-terminal SH3 domain; this SH3 domain interacts with the intracellular proline-rich-tail of the Roundabout receptor (Robo). This interaction with Robo then activates the rhoGAP domain which in turn inhibits Cdc42 activity. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific group
Probab=36.34 E-value=27 Score=23.09 Aligned_cols=30 Identities=27% Similarity=0.329 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHhCCCchHHHHHHHHhHh
Q 034548 4 VVGLLFKYINLLQQSGASKWIFDELSAVCE 33 (91)
Q Consensus 4 Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~ 33 (91)
|.+++=.|+.-|.+.-.+...|+++.....
T Consensus 75 va~lLK~fLReLPepLip~~~~~~~~~~~~ 104 (188)
T cd04383 75 VAGVLKLYFRGLENPLFPKERFEDLMSCVK 104 (188)
T ss_pred HHHHHHHHHHhCCCccCCHHHHHHHHHHHh
Confidence 444555676666655567788888876654
No 13
>PF13053 DUF3914: Protein of unknown function (DUF3914)
Probab=36.06 E-value=47 Score=19.62 Aligned_cols=19 Identities=26% Similarity=0.573 Sum_probs=16.0
Q ss_pred HHHHHhCCCchHHHHHHHH
Q 034548 12 INLLQQSGASKWIFDELSA 30 (91)
Q Consensus 12 i~llk~~~~~~~~~~E~~~ 30 (91)
-++||..|++-|+-=|+-+
T Consensus 66 WkmLkdKGVPlWiIlemL~ 84 (92)
T PF13053_consen 66 WKMLKDKGVPLWIILEMLQ 84 (92)
T ss_pred HHHHHhcCCcHHHHHHHHH
Confidence 4789999999999888764
No 14
>PF05767 Pox_A14: Poxvirus virion envelope protein A14; InterPro: IPR008785 This family consists of several Poxvirus virion envelope protein A14-like sequences. A14 is a component of the virion membrane and has been found to be an H1 phosphatase substrate in vivo and in vitro. A14 is hyperphosphorylated on serine residues in the absence of H1 expression [].; GO: 0019031 viral envelope
Probab=35.00 E-value=63 Score=19.35 Aligned_cols=26 Identities=15% Similarity=0.522 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHhCCCchHHHHHHH
Q 034548 4 VVGLLFKYINLLQQSGASKWIFDELS 29 (91)
Q Consensus 4 Vi~~vF~yi~llk~~~~~~~~~~E~~ 29 (91)
+++.+|+|+++=|...+....|.-+.
T Consensus 23 ~~aCIfAfidfsK~~~~~~~~wRalS 48 (92)
T PF05767_consen 23 IAACIFAFIDFSKNTKPTDYTWRALS 48 (92)
T ss_pred HHHHHHHhhhhccCCCCchhHHHHHH
Confidence 56789999999888877676664433
No 15
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=32.15 E-value=6.3 Score=20.80 Aligned_cols=30 Identities=20% Similarity=0.436 Sum_probs=23.4
Q ss_pred CCCCCccccccc-CCCCCCCCHHHHHHHHhc
Q 034548 55 METYPPQDWLVG-ESLPSNFNPEIIQMTLKE 84 (91)
Q Consensus 55 m~~~p~edvL~~-~~l~~~~d~~~i~~~l~~ 84 (91)
|....+++|+.. ..++..+||.+|.-+++.
T Consensus 12 L~~MS~eEI~~er~eL~~~LdP~li~~L~~R 42 (49)
T PF08621_consen 12 LASMSPEEIEEEREELLESLDPKLIEFLKKR 42 (49)
T ss_pred HHhCCHHHHHHHHHHHHHhCCHHHHHHHHHh
Confidence 445678888887 578888999999888764
No 16
>COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only]
Probab=31.09 E-value=48 Score=27.51 Aligned_cols=50 Identities=16% Similarity=0.268 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHhCCCchHHHHHHHHhHhhccccCCCCChHHHHHHHHHh
Q 034548 5 VGLLFKYINLLQQSGASKWIFDELSAVCEVTFHYQDKVPPIDYVVTVAAN 54 (91)
Q Consensus 5 i~~vF~yi~llk~~~~~~~~~~E~~~i~~~~F~f~~~~~~~~~~~~la~~ 54 (91)
++.+++.+.=+-..-+..||+.++++.....|+|.-.+.-|+.+.+|+-.
T Consensus 716 iQrlykvleP~gdsrpDW~Iiq~vA~~lG~~wnY~hpSeIm~EiA~l~P~ 765 (978)
T COG3383 716 IQRLYKVLEPLGDSRPDWEIIQEVANALGAGWNYSHPSEIMDEIAALTPS 765 (978)
T ss_pred HHHHHHHhccccCCCccHHHHHHHHHHhcCCCCCCCHHHHHHHHHhhCcc
Confidence 45566666666556678899999999999999998877777877777644
No 17
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=31.05 E-value=62 Score=17.02 Aligned_cols=29 Identities=17% Similarity=0.196 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHhCCCchHHHHHHHHhHh
Q 034548 4 VVGLLFKYINLLQQSGASKWIFDELSAVCE 33 (91)
Q Consensus 4 Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~ 33 (91)
...++-+...+|+.. +.+++++|+.++-.
T Consensus 8 t~~ai~~~~~~L~~i-s~ERi~~El~kil~ 36 (64)
T PF12627_consen 8 TEEAIKENAELLSKI-SKERIREELEKILS 36 (64)
T ss_dssp HHHHHHHHGGGGGGS--HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhcC-CHHHHHHHHHHHHc
Confidence 344455555555433 56899999998754
No 18
>COG4304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.35 E-value=27 Score=22.82 Aligned_cols=22 Identities=27% Similarity=0.540 Sum_probs=17.5
Q ss_pred CCCCCCC-HHHHHHHHhccCCCc
Q 034548 68 SLPSNFN-PEIIQMTLKELSPKT 89 (91)
Q Consensus 68 ~l~~~~d-~~~i~~~l~~l~p~N 89 (91)
-++.+|| |+.|.+++++|.|.|
T Consensus 111 ~iYaDFdYPe~iEsFvAYMP~kd 133 (166)
T COG4304 111 KIYADFDYPEEIESFVAYMPPKD 133 (166)
T ss_pred HHHHhcCChHHHHHHHHhCCccc
Confidence 4556777 899999999998876
No 19
>cd04384 RhoGAP_CdGAP RhoGAP_CdGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of CdGAP-like proteins; CdGAP contains an N-terminal RhoGAP domain and a C-terminal proline-rich region, and it is active on both Cdc42 and Rac1 but not RhoA. CdGAP is recruited to focal adhesions via the interaction with the scaffold protein actopaxin (alpha-parvin). Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=29.70 E-value=24 Score=23.47 Aligned_cols=79 Identities=13% Similarity=0.181 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHhCCCchHHHHHHHHhHhhccccCCCCChHHHHHHHHHhCCCCCcccccccCCCCCCCCHHHHHHHHh
Q 034548 4 VVGLLFKYINLLQQSGASKWIFDELSAVCEVTFHYQDKVPPIDYVVTVAANMETYPPQDWLVGESLPSNFNPEIIQMTLK 83 (91)
Q Consensus 4 Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~~~F~f~~~~~~~~~~~~la~~m~~~p~edvL~~~~l~~~~d~~~i~~~l~ 83 (91)
|.+.+=.|+.-|.+.=.+...|+++....+. .++..-+..+-.-+...|+.+.-.-.+++.-+..-.-.+-.+
T Consensus 75 va~lLK~flReLPePLi~~~~y~~~~~~~~~-------~~~~~~~~~l~~li~~LP~~n~~~L~~L~~~L~~V~~~s~~N 147 (195)
T cd04384 75 VSSLCKLYFRELPNPLLTYQLYEKFSEAVSA-------ASDEERLEKIHDVIQQLPPPHYRTLEFLMRHLSRLAKYCSIT 147 (195)
T ss_pred HHHHHHHHHHhCCCccCCHHHHHHHHHHHhc-------CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 4444446776665544667788887766543 122233333333334455554433333333332222233344
Q ss_pred ccCCCc
Q 034548 84 ELSPKT 89 (91)
Q Consensus 84 ~l~p~N 89 (91)
.||+.|
T Consensus 148 kM~~~N 153 (195)
T cd04384 148 NMHAKN 153 (195)
T ss_pred CCCHHH
Confidence 555544
No 20
>PF06743 FAST_1: FAST kinase-like protein, subdomain 1; InterPro: IPR010622 This entry represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis []. Note that many family members are hypothetical proteins.; GO: 0004672 protein kinase activity
Probab=28.35 E-value=21 Score=19.89 Aligned_cols=36 Identities=14% Similarity=0.355 Sum_probs=23.1
Q ss_pred HHHHHHhCCCCCccccccc---CCCCCCCCHHHHHHHHh
Q 034548 48 VVTVAANMETYPPQDWLVG---ESLPSNFNPEIIQMTLK 83 (91)
Q Consensus 48 ~~~la~~m~~~p~edvL~~---~~l~~~~d~~~i~~~l~ 83 (91)
+..+..++..++|++++.. =.+++.|.++.|+++++
T Consensus 26 ~~~L~~~l~~~~p~~ll~~v~Sl~~l~~~p~~~l~~vf~ 64 (71)
T PF06743_consen 26 IERLESYLDEFSPEDLLDLVWSLCLLQRFPEDLLNKVFS 64 (71)
T ss_pred HHHHHHhcccCCHHHHHHHHHHHHHHhhCCHHHHHHHcC
Confidence 4455555556677765554 34667788888887764
No 21
>PF07939 DUF1685: Protein of unknown function (DUF1685); InterPro: IPR012881 The members of this family are hypothetical eukaryotic proteins of unknown function. The region in question is approximately 100 amino acid residues long.
Probab=28.10 E-value=75 Score=17.75 Aligned_cols=17 Identities=24% Similarity=0.642 Sum_probs=14.7
Q ss_pred HHHHHHhHhhccccCCC
Q 034548 25 FDELSAVCEVTFHYQDK 41 (91)
Q Consensus 25 ~~E~~~i~~~~F~f~~~ 41 (91)
.+|+|..-++.|.|.+.
T Consensus 6 ldELkGc~dLGFgF~~~ 22 (64)
T PF07939_consen 6 LDELKGCIDLGFGFDEE 22 (64)
T ss_pred HHHHhhhhhhccccCcc
Confidence 68999999999999554
No 22
>PF02998 Lentiviral_Tat: Lentiviral Tat protein; InterPro: IPR004247 This family contains retroviral transactivating (Tat) proteins, from a variety of lentiviruses. The Tat protein may have a role in trans-activation of the viral long terminal repeat [].; GO: 0045893 positive regulation of transcription, DNA-dependent
Probab=26.95 E-value=1.2e+02 Score=17.72 Aligned_cols=21 Identities=10% Similarity=0.485 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCchHHHHHHHH
Q 034548 10 KYINLLQQSGASKWIFDELSA 30 (91)
Q Consensus 10 ~yi~llk~~~~~~~~~~E~~~ 30 (91)
.+++||+....-..++.|.++
T Consensus 41 rWLAML~~~~~R~kV~rEmQk 61 (86)
T PF02998_consen 41 RWLAMLRNGRNRRKVYREMQK 61 (86)
T ss_pred HHHHHHHccchHHHHHHHHHH
Confidence 588999998888889988876
No 23
>PF07521 RMMBL: RNA-metabolising metallo-beta-lactamase; InterPro: IPR011108 The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in IPR001279 from INTERPRO and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism [].; PDB: 3ZQ4_D 2I7T_A 2I7V_A 2YCB_B 3BK1_A 3T3N_A 3BK2_A 3T3O_A 3AF5_A 3AF6_A ....
Probab=23.68 E-value=53 Score=16.33 Aligned_cols=19 Identities=21% Similarity=0.396 Sum_probs=13.8
Q ss_pred CCCHHHHHHHHhccCCCcC
Q 034548 72 NFNPEIIQMTLKELSPKTV 90 (91)
Q Consensus 72 ~~d~~~i~~~l~~l~p~N~ 90 (91)
--|.+.+.++++.+.|.++
T Consensus 17 Had~~~L~~~i~~~~p~~v 35 (43)
T PF07521_consen 17 HADREELLEFIEQLNPRKV 35 (43)
T ss_dssp S-BHHHHHHHHHHHCSSEE
T ss_pred CCCHHHHHHHHHhcCCCEE
Confidence 4567888888888888654
No 24
>PF10239 DUF2465: Protein of unknown function (DUF2465); InterPro: IPR018797 FAM98A, B and C are glycine-rich proteins found from worms to humans whose function is unknown.
Probab=23.37 E-value=1.6e+02 Score=21.42 Aligned_cols=63 Identities=13% Similarity=0.215 Sum_probs=40.0
Q ss_pred hHHHHHHHHhHhhccccCCCCChHHHHHHHHHhCCC--CCcccccccCCCCCCCCHHHHHHHHhc
Q 034548 22 KWIFDELSAVCEVTFHYQDKVPPIDYVVTVAANMET--YPPQDWLVGESLPSNFNPEIIQMTLKE 84 (91)
Q Consensus 22 ~~~~~E~~~i~~~~F~f~~~~~~~~~~~~la~~m~~--~p~edvL~~~~l~~~~d~~~i~~~l~~ 84 (91)
.|+=.|++.+..++=.-....+.-.+..+++.-+.. ||...+.+|+..-.--+++.--.+|.+
T Consensus 38 ~wL~~EL~~l~~leE~v~~~dd~~~f~~Els~~L~El~CPy~~L~~G~~~~rl~~~~~~l~LL~f 102 (318)
T PF10239_consen 38 AWLASELKTLCKLEESVSSPDDAESFLLELSGFLKELGCPYSALTSGDISDRLQSKEDRLLLLEF 102 (318)
T ss_pred HHHHHHHHHHhccccccCCCchHHHHHHHHHHHHHhcCCCcHHHcCCcchhhhcCHHHHHHHHHH
Confidence 478899999988833322333344688888888865 899988888664444444333333333
No 25
>cd04398 RhoGAP_fRGD1 RhoGAP_fRGD1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD1-like proteins. Yeast Rgd1 is a GAP protein for Rho3 and Rho4 and plays a role in low-pH response. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=22.40 E-value=45 Score=21.82 Aligned_cols=29 Identities=21% Similarity=0.181 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHhCCCchHHHHHHHHhH
Q 034548 4 VVGLLFKYINLLQQSGASKWIFDELSAVC 32 (91)
Q Consensus 4 Vi~~vF~yi~llk~~~~~~~~~~E~~~i~ 32 (91)
|.+.+=.|+.-|...=.+...|+++....
T Consensus 76 va~~LK~fLreLp~pLi~~~~~~~~~~~~ 104 (192)
T cd04398 76 VASLLKLFFRELPEPLLTKALSREFIEAA 104 (192)
T ss_pred HHHHHHHHHHhCCCccCCHHHHHHHHHHH
Confidence 44444466666655556677888776654
No 26
>KOG0181 consensus 20S proteasome, regulatory subunit alpha type PSMA2/PRE8 [Posttranslational modification, protein turnover, chaperones]
Probab=22.33 E-value=42 Score=23.11 Aligned_cols=23 Identities=30% Similarity=0.556 Sum_probs=19.5
Q ss_pred ccCCCCChHHHHHHHHHhCCCCC
Q 034548 37 HYQDKVPPIDYVVTVAANMETYP 59 (91)
Q Consensus 37 ~f~~~~~~~~~~~~la~~m~~~p 59 (91)
-|++..+...++.++|+-||.|.
T Consensus 100 vY~e~~pt~qlv~~~asvmQEyT 122 (233)
T KOG0181|consen 100 VYGEPIPTTQLVQEVASVMQEYT 122 (233)
T ss_pred HhcCCCCHHHHHHHHHHHHHHHh
Confidence 47888888999999999999654
No 27
>PHA03048 IMV membrane protein; Provisional
Probab=21.92 E-value=1.3e+02 Score=18.05 Aligned_cols=29 Identities=10% Similarity=0.444 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHhCCCchHHHHHHHHhHhhcc
Q 034548 4 VVGLLFKYINLLQQSGASKWIFDELSAVCEVTF 36 (91)
Q Consensus 4 Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~~~F 36 (91)
++..+|+|+++=|.++ ....|. .++-+.|
T Consensus 23 ~~aCIfAfidfsK~k~-~~~~wR---alsii~F 51 (93)
T PHA03048 23 AASCIFAFVDFSKNKA-TVTVWR---ALSGIAF 51 (93)
T ss_pred HHHHHHhhhhhhcCCC-cchhHH---HHHHHHH
Confidence 5678999999988754 455554 4444444
No 28
>cd04400 RhoGAP_fBEM3 RhoGAP_fBEM3: RhoGAP (GTPase-activator [GAP] protein for Rho-like small GTPases) domain of fungal BEM3-like proteins. Bem3 is a GAP protein of Cdc42, and is specifically involved in the control of the initial assembly of the septin ring in yeast bud formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=20.81 E-value=38 Score=22.28 Aligned_cols=30 Identities=23% Similarity=0.294 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHhCCCchHHHHHHHHhHh
Q 034548 4 VVGLLFKYINLLQQSGASKWIFDELSAVCE 33 (91)
Q Consensus 4 Vi~~vF~yi~llk~~~~~~~~~~E~~~i~~ 33 (91)
|...+=.|++-|.+.-++...|+++..+.+
T Consensus 81 va~lLK~flreLP~PLi~~~~~~~~~~~~~ 110 (190)
T cd04400 81 VAGLLKLYLRELPTLILGGELHNDFKRLVE 110 (190)
T ss_pred HHHHHHHHHHhCCcccCCHHHHHHHHHHHh
Confidence 444445666666555566778887776554
Done!