Query psy1331
Match_columns 157
No_of_seqs 200 out of 1178
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 16:14:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1331.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1331hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1471|consensus 99.9 9.5E-25 2E-29 178.6 6.7 94 1-98 167-260 (317)
2 PF00650 CRAL_TRIO: CRAL/TRIO 99.9 1.7E-24 3.7E-29 159.5 4.7 91 1-94 69-159 (159)
3 smart00516 SEC14 Domain in hom 99.8 3.4E-21 7.4E-26 141.7 7.8 88 1-95 70-157 (158)
4 cd00170 SEC14 Sec14p-like lipi 99.8 1.9E-20 4.1E-25 135.9 8.0 88 1-94 70-157 (157)
5 KOG1470|consensus 99.8 1.7E-19 3.7E-24 147.3 6.2 88 1-97 158-245 (324)
6 PF13716 CRAL_TRIO_2: Divergen 98.6 3.5E-09 7.5E-14 77.6 -1.2 80 12-96 64-145 (149)
7 KOG4406|consensus 96.9 0.0016 3.4E-08 55.5 5.0 69 12-85 145-213 (467)
8 PF04838 Baculo_LEF5: Baculovi 48.5 13 0.00029 27.6 1.9 67 18-85 17-97 (159)
9 PF03641 Lysine_decarbox: Poss 45.4 46 0.001 23.7 4.3 42 35-81 86-132 (133)
10 PF06280 DUF1034: Fn3-like dom 44.9 23 0.0005 24.3 2.6 19 133-151 62-80 (112)
11 COG0052 RpsB Ribosomal protein 41.3 30 0.00065 27.9 3.0 68 27-97 30-103 (252)
12 PF14310 Fn3-like: Fibronectin 38.2 43 0.00094 21.0 2.9 19 132-150 24-42 (71)
13 PF04378 RsmJ: Ribosomal RNA s 34.7 30 0.00065 27.8 2.1 28 34-61 206-233 (245)
14 COG2961 ComJ Protein involved 34.1 34 0.00075 27.8 2.3 26 34-59 237-262 (279)
15 PRK04020 rps2P 30S ribosomal p 24.7 99 0.0021 24.1 3.4 70 28-99 35-108 (204)
16 PF07454 SpoIIP: Stage II spor 24.4 87 0.0019 25.5 3.1 33 8-40 197-229 (268)
17 KOG0534|consensus 23.7 43 0.00093 27.5 1.2 39 17-58 201-239 (286)
18 TIGR01011 rpsB_bact ribosomal 22.7 1E+02 0.0022 24.3 3.1 67 29-98 30-102 (225)
19 TIGR02867 spore_II_P stage II 21.4 1.2E+02 0.0026 23.5 3.2 33 8-40 119-151 (196)
20 PF14900 DUF4493: Domain of un 20.8 1.5E+02 0.0033 23.0 3.8 80 61-156 34-113 (235)
21 PRK05299 rpsB 30S ribosomal pr 20.7 92 0.002 25.1 2.6 68 29-98 32-104 (258)
No 1
>KOG1471|consensus
Probab=99.91 E-value=9.5e-25 Score=178.58 Aligned_cols=94 Identities=36% Similarity=0.628 Sum_probs=89.4
Q ss_pred CCCCccCCcccchhHHHHHHHHHHHHhhcccccCcEEEEeCChHHHHHHHHHHhhcChhhhceeEEccCCCCCcHHHHHc
Q psy1331 1 MSDFSMKQYAWRPAAELVLCMLQMYEANYPEILKNCYVINAPKVFTLAWRVVKKFLHEYTISKIHLYRAEPAKWRPILLE 80 (157)
Q Consensus 1 l~g~s~~~~~~~~~~~~~~~~~~~~~~~yPe~l~~i~iiNaP~~~~~~~~~vk~fl~~~t~~Ki~~~~~~~~~~~~~L~~ 80 (157)
|+|++|+|+ +++....+++++.++|++|||+++++||||+|++|+++|++++|||+++|++||++++ ++|.++|.+
T Consensus 167 l~G~~~~~~-~~~~~~~~~~~~~~~q~~yPe~l~~~~iIN~P~~f~~~~~~ikpfL~~kt~~ki~~~~---~~~~~~L~k 242 (317)
T KOG1471|consen 167 LKGVSLSHL-LKPAPTLLKKILKILQDNYPERLKRIHIINAPTIFSALWKVVKPFLDEKTRKKIHVLH---SKDKESLLK 242 (317)
T ss_pred CCCCcchhH-HHHHHHHHHHHHHHHHHhCHHhhceEEEEcCchhHHHHHHHHhccCCHHHHhhheecC---CCchhhhhh
Confidence 689999999 8999999999999999999999999999999999999999999999999999999665 568999999
Q ss_pred cCCCCCCCccCCCCCCCC
Q psy1331 81 QMEEDMWPASMGGAGRDP 98 (157)
Q Consensus 81 ~i~~~~LP~~yGG~~~~~ 98 (157)
+|+++.||++|||++.+.
T Consensus 243 ~i~~~~LP~~yGG~~~~~ 260 (317)
T KOG1471|consen 243 YIPPEVLPEEYGGTCGDL 260 (317)
T ss_pred hCCHhhCccccCCCcccc
Confidence 999999999999998874
No 2
>PF00650 CRAL_TRIO: CRAL/TRIO domain; InterPro: IPR001251 This entry defines the C-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1OLM_E 1O6U_E 3Q8G_A 3B7Q_B 3B7Z_A ....
Probab=99.90 E-value=1.7e-24 Score=159.47 Aligned_cols=91 Identities=33% Similarity=0.711 Sum_probs=79.6
Q ss_pred CCCCccCCcccchhHHHHHHHHHHHHhhcccccCcEEEEeCChHHHHHHHHHHhhcChhhhceeEEccCCCCCcHHHHHc
Q psy1331 1 MSDFSMKQYAWRPAAELVLCMLQMYEANYPEILKNCYVINAPKVFTLAWRVVKKFLHEYTISKIHLYRAEPAKWRPILLE 80 (157)
Q Consensus 1 l~g~s~~~~~~~~~~~~~~~~~~~~~~~yPe~l~~i~iiNaP~~~~~~~~~vk~fl~~~t~~Ki~~~~~~~~~~~~~L~~ 80 (157)
++|++++++++.+ ++.++.++++++++||+|++++||||+|++|.++|+++++||+++|++||+++++ .+|.++|.+
T Consensus 69 ~~g~~~~~~~~~~-~~~~k~~~~~~~~~yP~rl~~i~iin~p~~~~~~~~~~~~~l~~~~~~ki~~~~~--~~~~~~l~~ 145 (159)
T PF00650_consen 69 LSGFSLSNFDWWP-ISFLKKIIQLLQDHYPERLGKIYIINAPWFFRVLWKIVKPFLSPKTREKIVFHSG--SDWKAKLKE 145 (159)
T ss_dssp -TT--HHHHHCHH-HHHHHHHHHHHHHHSTTTEEEEEEES--TTHHHHHHHHGGGS-HHHHCTEEEECT--TCHCHHHCC
T ss_pred CCCceEeccccch-hhhhhhhhhhhcccCCccceeEEEEecChhhhhhHhHHHhhcCHhhheeEEEECC--cccHHHHHh
Confidence 5789999986555 8999999999999999999999999999999999999999999999999999973 677789999
Q ss_pred cCCCCCCCccCCCC
Q psy1331 81 QMEEDMWPASMGGA 94 (157)
Q Consensus 81 ~i~~~~LP~~yGG~ 94 (157)
+||+++||++|||+
T Consensus 146 ~i~~~~lP~~~GG~ 159 (159)
T PF00650_consen 146 YIDPEQLPVEYGGT 159 (159)
T ss_dssp CSTGGGSBGGGTSS
T ss_pred hCCHhHCchhcCCC
Confidence 99999999999996
No 3
>smart00516 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.84 E-value=3.4e-21 Score=141.69 Aligned_cols=88 Identities=28% Similarity=0.536 Sum_probs=81.5
Q ss_pred CCCCccCCcccchhHHHHHHHHHHHHhhcccccCcEEEEeCChHHHHHHHHHHhhcChhhhceeEEccCCCCCcHHHHHc
Q psy1331 1 MSDFSMKQYAWRPAAELVLCMLQMYEANYPEILKNCYVINAPKVFTLAWRVVKKFLHEYTISKIHLYRAEPAKWRPILLE 80 (157)
Q Consensus 1 l~g~s~~~~~~~~~~~~~~~~~~~~~~~yPe~l~~i~iiNaP~~~~~~~~~vk~fl~~~t~~Ki~~~~~~~~~~~~~L~~ 80 (157)
++|++++|++ ++.+++++++++++||++++++||+|+|+++.++|+++++|+++++++||++++ +++.+.|.+
T Consensus 70 ~~~~~~~~~~----~~~lk~~~~~~~~~yp~~l~~i~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~---~~~~~~L~~ 142 (158)
T smart00516 70 LKGLSMSNPD----LSVLRKILKILQDHYPERLGKVLIINPPWFFRVLWKIIKPFLDEKTREKIRFVG---NDSKEELLE 142 (158)
T ss_pred CCCCCccccc----HHHHHHHHHHHHHHhHHHhCeEEEECCCHHHHHHHHHHHhhcChhhhccEEEeC---CCCHHHHHh
Confidence 4678888763 578999999999999999999999999999999999999999999999999999 456899999
Q ss_pred cCCCCCCCccCCCCC
Q psy1331 81 QMEEDMWPASMGGAG 95 (157)
Q Consensus 81 ~i~~~~LP~~yGG~~ 95 (157)
+||+++||++|||++
T Consensus 143 ~i~~~~lP~~~GG~~ 157 (158)
T smart00516 143 YIDPEQLPEELGGTL 157 (158)
T ss_pred hCCHhhCcHhhCCCC
Confidence 999999999999986
No 4
>cd00170 SEC14 Sec14p-like lipid-binding domain. Found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits.
Probab=99.83 E-value=1.9e-20 Score=135.89 Aligned_cols=88 Identities=33% Similarity=0.650 Sum_probs=81.7
Q ss_pred CCCCccCCcccchhHHHHHHHHHHHHhhcccccCcEEEEeCChHHHHHHHHHHhhcChhhhceeEEccCCCCCcHHHHHc
Q psy1331 1 MSDFSMKQYAWRPAAELVLCMLQMYEANYPEILKNCYVINAPKVFTLAWRVVKKFLHEYTISKIHLYRAEPAKWRPILLE 80 (157)
Q Consensus 1 l~g~s~~~~~~~~~~~~~~~~~~~~~~~yPe~l~~i~iiNaP~~~~~~~~~vk~fl~~~t~~Ki~~~~~~~~~~~~~L~~ 80 (157)
++|++++++ . +..+.+++++++++++||++++++||+|+|+++..+|+++++|+++++++||++++ ++ .++|.+
T Consensus 70 ~~~~~~~~~-~-~~~~~~k~~~~~~~~~yp~~l~~v~ivn~p~~~~~~~~~~~~~l~~~~~~ki~~~~---~~-~~~L~~ 143 (157)
T cd00170 70 LKGLSLSHL-L-PDPSLLKKILKILQDNYPERLKAVYIINPPWFFKVLWKIVKPFLSEKTRKKIVFLG---SD-KEELLK 143 (157)
T ss_pred CCCCChhcc-c-hhHHHHHHHHHHHHHhChHhhCeEEEECCCHhHHHHHHHHHHhcCHhhhhhEEEec---CC-HHHHHh
Confidence 568888888 3 56789999999999999999999999999999999999999999999999999998 33 789999
Q ss_pred cCCCCCCCccCCCC
Q psy1331 81 QMEEDMWPASMGGA 94 (157)
Q Consensus 81 ~i~~~~LP~~yGG~ 94 (157)
++|+++||.+|||+
T Consensus 144 ~i~~~~Lp~~~GG~ 157 (157)
T cd00170 144 YIDKEQLPEEYGGT 157 (157)
T ss_pred hCChhhCcHhhCCC
Confidence 99999999999996
No 5
>KOG1470|consensus
Probab=99.78 E-value=1.7e-19 Score=147.35 Aligned_cols=88 Identities=28% Similarity=0.510 Sum_probs=80.9
Q ss_pred CCCCccCCcccchhHHHHHHHHHHHHhhcccccCcEEEEeCChHHHHHHHHHHhhcChhhhceeEEccCCCCCcHHHHHc
Q psy1331 1 MSDFSMKQYAWRPAAELVLCMLQMYEANYPEILKNCYVINAPKVFTLAWRVVKKFLHEYTISKIHLYRAEPAKWRPILLE 80 (157)
Q Consensus 1 l~g~s~~~~~~~~~~~~~~~~~~~~~~~yPe~l~~i~iiNaP~~~~~~~~~vk~fl~~~t~~Ki~~~~~~~~~~~~~L~~ 80 (157)
+.||||++++ ++..+.++.++|+||||||+.++++|+||+|..+|+++||||+++|++||.|... ...|.+
T Consensus 158 ~~~fs~sN~d----~~~~k~~~~~lq~hYPErLg~a~l~~~P~iF~~~wkiikpflDp~t~~Kv~F~~~-----~~~l~~ 228 (324)
T KOG1470|consen 158 LTGFSMSNPD----IKFLKELLHILQDHYPERLGKALLVNAPWIFQPFWKIIKPFLDPKTASKVKFVEP-----KDDLSE 228 (324)
T ss_pred cccCcccCCC----cHHHHHHHHHHHHhChHHhhhhhhcCChHHHHHHHHHhhhccChhhhceeEEecC-----hhHHHh
Confidence 5799999885 5678999999999999999999999999999999999999999999999999983 456999
Q ss_pred cCCCCCCCccCCCCCCC
Q psy1331 81 QMEEDMWPASMGGAGRD 97 (157)
Q Consensus 81 ~i~~~~LP~~yGG~~~~ 97 (157)
+||+++||..+||+...
T Consensus 229 ~~d~~~l~s~~GG~~~~ 245 (324)
T KOG1470|consen 229 YFDESQLPSLFGGKLLF 245 (324)
T ss_pred hCCccccchhhCCCccc
Confidence 99999999999997655
No 6
>PF13716 CRAL_TRIO_2: Divergent CRAL/TRIO domain; PDB: 2D4Q_B 3PG7_B 2E2X_B 3P7Z_B 3PEG_A.
Probab=98.63 E-value=3.5e-09 Score=77.65 Aligned_cols=80 Identities=14% Similarity=0.272 Sum_probs=59.6
Q ss_pred chhHHHHHHHHHHHHhhcccccCcEEEEeCChHHHHHH-HHHHhhcChhh-hceeEEccCCCCCcHHHHHccCCCCCCCc
Q psy1331 12 RPAAELVLCMLQMYEANYPEILKNCYVINAPKVFTLAW-RVVKKFLHEYT-ISKIHLYRAEPAKWRPILLEQMEEDMWPA 89 (157)
Q Consensus 12 ~~~~~~~~~~~~~~~~~yPe~l~~i~iiNaP~~~~~~~-~~vk~fl~~~t-~~Ki~~~~~~~~~~~~~L~~~i~~~~LP~ 89 (157)
.|....++++.+.+...|+..++++||||+.+++..+. .+.+++.+.+. ..||.++.+ .++|.++||+++||+
T Consensus 64 ~~~~~~l~~~~~~l~~~~~~nl~~vyiv~p~~~~k~~~~~~~~~~~~~~~~~~kv~~~~s-----l~~L~~~i~~~qL~~ 138 (149)
T PF13716_consen 64 EPSLSWLKQLYKLLPRKYKKNLKKVYIVHPNWFLKKILATLLRPFVSSKFWKKKVVYVSS-----LSELSKHIDPSQLPE 138 (149)
T ss_dssp ---HHHHHHTTTSS-HHHHHTEEEEEEES--HHHHHHHHHTTTTGGGGTT--TTEEEESS-----TCGGGGTSGGGG---
T ss_pred CCchHHHHHHHHHHHHHHhhceEEEEEECCCHHHHHHHHHHhcccccccccceEEEEECC-----HHHHHhhCCHHHhcc
Confidence 35578899999999999999999999999999999999 55577788888 899999873 889999999999999
Q ss_pred cCCCCCC
Q psy1331 90 SMGGAGR 96 (157)
Q Consensus 90 ~yGG~~~ 96 (157)
++||..+
T Consensus 139 ~lp~~~~ 145 (149)
T PF13716_consen 139 SLPGVLQ 145 (149)
T ss_dssp ---HHH-
T ss_pred cCCCEEe
Confidence 9998764
No 7
>KOG4406|consensus
Probab=96.90 E-value=0.0016 Score=55.49 Aligned_cols=69 Identities=19% Similarity=0.349 Sum_probs=59.9
Q ss_pred chhHHHHHHHHHHHHhhcccccCcEEEEeCChHHHHHHHHHHhhcChhhhceeEEccCCCCCcHHHHHccCCCC
Q psy1331 12 RPAAELVLCMLQMYEANYPEILKNCYVINAPKVFTLAWRVVKKFLHEYTISKIHLYRAEPAKWRPILLEQMEED 85 (157)
Q Consensus 12 ~~~~~~~~~~~~~~~~~yPe~l~~i~iiNaP~~~~~~~~~vk~fl~~~t~~Ki~~~~~~~~~~~~~L~~~i~~~ 85 (157)
+|.+.++.....-+..+|=--++.+|+|..-|+..++|+++|||++.|..+||+-++ ..++|.+++.-+
T Consensus 145 kp~l~~l~~aYke~Dr~~~KNlKalYvvHptwfikvi~n~~kplIS~KF~rKi~Y~n-----~lseL~~~l~l~ 213 (467)
T KOG4406|consen 145 KPYLQLLFDAYKELDRNFKKNLKALYVVHPTWFIKVIWNLFKPLISLKFTRKIIYFN-----SLSELFEALKLN 213 (467)
T ss_pred cchHHHHHHHHHHHHHHHhhhhhheEEecHHHHHHHHHHHHhhhcchhhhceeEEee-----hHHHHHHhhhhh
Confidence 466777777777778888888999999999999999999999999999999999998 388998876533
No 8
>PF04838 Baculo_LEF5: Baculoviridae late expression factor 5 ; InterPro: IPR006923 This is a family of Baculoviridae late expression factor 5, required for late and very late gene expression.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=48.53 E-value=13 Score=27.64 Aligned_cols=67 Identities=15% Similarity=0.258 Sum_probs=49.5
Q ss_pred HHHHHHHHHhhcccccC--cEEEEeCChHHHHHHHHHHhhcCh--hhhceeEE--------ccCCCCC--cHHHHHccCC
Q psy1331 18 VLCMLQMYEANYPEILK--NCYVINAPKVFTLAWRVVKKFLHE--YTISKIHL--------YRAEPAK--WRPILLEQME 83 (157)
Q Consensus 18 ~~~~~~~~~~~yPe~l~--~i~iiNaP~~~~~~~~~vk~fl~~--~t~~Ki~~--------~~~~~~~--~~~~L~~~i~ 83 (157)
...++.++-.+||.-++ -.-++|..-.|.++|+-+- -++. +.|+.|+. +.++..+ ..++|.+.|+
T Consensus 17 y~~LI~fL~~nyp~nVKNkTFNF~nTGHlFHsLYAYvP-~~s~~~kERKQIRLs~dcI~kL~~nT~NdfKLY~Elf~~i~ 95 (159)
T PF04838_consen 17 YKELIDFLITNYPKNVKNKTFNFANTGHLFHSLYAYVP-SVSNVEKERKQIRLSEDCIEKLFVNTINDFKLYEELFDMID 95 (159)
T ss_pred HHHHHHHHHhhcccccccCeeecCCCchhhhhhhhccC-CCchHhHHHHHhhhhHHHHHHHHHhcCchHHHHHHHHHHHH
Confidence 57789999999999998 8999999999999998774 4444 67777776 2211123 3377777776
Q ss_pred CC
Q psy1331 84 ED 85 (157)
Q Consensus 84 ~~ 85 (157)
.+
T Consensus 96 ~~ 97 (159)
T PF04838_consen 96 DN 97 (159)
T ss_pred cc
Confidence 43
No 9
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=45.35 E-value=46 Score=23.70 Aligned_cols=42 Identities=12% Similarity=0.178 Sum_probs=32.8
Q ss_pred cEEEEeCChHHHHHHHHH-----HhhcChhhhceeEEccCCCCCcHHHHHcc
Q psy1331 35 NCYVINAPKVFTLAWRVV-----KKFLHEYTISKIHLYRAEPAKWRPILLEQ 81 (157)
Q Consensus 35 ~i~iiNaP~~~~~~~~~v-----k~fl~~~t~~Ki~~~~~~~~~~~~~L~~~ 81 (157)
.++++|..-++.-++.++ ..|++++..+.+.+..+ .+++.++
T Consensus 86 Piil~~~~g~w~~l~~~l~~~~~~g~i~~~~~~~~~~~d~-----~~e~~~~ 132 (133)
T PF03641_consen 86 PIILLNIDGFWDPLLEFLDRMIEEGFISPDDLDLLHFVDD-----PEEALEY 132 (133)
T ss_dssp EEEEEECGGCCHHHHHHHHHHHHTTSSSHHHHCCEEEESS-----HHHHHHH
T ss_pred CEEEeCCcchHHHHHHHHHHHHHCCCCCHHHCCeEEEeCC-----HHHHHhh
Confidence 699999887777777766 46888899999999873 6666554
No 10
>PF06280 DUF1034: Fn3-like domain (DUF1034); InterPro: IPR010435 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain of unknown function is present in bacterial and plant peptidases belonging to MEROPS peptidase family S8 (subfamily S8A subtilisin, clan SB). It is C-terminal to and adjacent to the S8 peptidase domain and can be found in conjunction with the PA (Protease associated) domain (IPR003137 from INTERPRO) and additionally in Gram-positive bacteria with the surface protein anchor domain (IPR001899 from INTERPRO).; GO: 0004252 serine-type endopeptidase activity, 0005618 cell wall, 0016020 membrane; PDB: 3EIF_A 1XF1_B.
Probab=44.87 E-value=23 Score=24.28 Aligned_cols=19 Identities=11% Similarity=0.181 Sum_probs=15.7
Q ss_pred eEEEEeCCCcEEEEEEecC
Q psy1331 133 TQACVKKGEKLSLDFIAPQ 151 (157)
Q Consensus 133 ~~~~V~~g~~~~i~~~v~~ 151 (157)
.+++|+||++.+|.+.+.-
T Consensus 62 ~~vTV~ag~s~~v~vti~~ 80 (112)
T PF06280_consen 62 DTVTVPAGQSKTVTVTITP 80 (112)
T ss_dssp EEEEE-TTEEEEEEEEEE-
T ss_pred CeEEECCCCEEEEEEEEEe
Confidence 4899999999999999975
No 11
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=41.30 E-value=30 Score=27.94 Aligned_cols=68 Identities=13% Similarity=0.120 Sum_probs=43.9
Q ss_pred hhcccccCcEEEEeCChHHH---HHHHHHHhhcChhhhceeEEccCCC--CCcHHHHHccCCCCCCCccC-CCCCCC
Q psy1331 27 ANYPEILKNCYVINAPKVFT---LAWRVVKKFLHEYTISKIHLYRAEP--AKWRPILLEQMEEDMWPASM-GGAGRD 97 (157)
Q Consensus 27 ~~yPe~l~~i~iiNaP~~~~---~~~~~vk~fl~~~t~~Ki~~~~~~~--~~~~~~L~~~i~~~~LP~~y-GG~~~~ 97 (157)
-.|.+| ..+||||.-+-.. .++++++.... --.+|-|+++.. .+...+..+..+.-.+...| ||++++
T Consensus 30 fIf~~R-ngihIIDL~kT~~~l~~A~~~v~~~~~--~~g~ILfVgTK~~a~~~V~~~A~r~g~~yV~~RwLgG~LTN 103 (252)
T COG0052 30 FIFGER-NGIHIIDLQKTLERLREAYKFLRRIAA--NGGKILFVGTKKQAQEPVKEFAERTGAYYVNGRWLGGMLTN 103 (252)
T ss_pred cceeec-CCcEEEEHHHHHHHHHHHHHHHHHHHc--CCCEEEEEechHHHHHHHHHHHHHhCCceecCcccCccccC
Confidence 358899 9999999876544 34444444431 257899999621 11223444566777777776 999987
No 12
>PF14310 Fn3-like: Fibronectin type III-like domain; PDB: 3ABZ_D 3AC0_D 2X40_A 2X41_A 2X42_A.
Probab=38.22 E-value=43 Score=20.99 Aligned_cols=19 Identities=21% Similarity=0.567 Sum_probs=14.7
Q ss_pred ceEEEEeCCCcEEEEEEec
Q psy1331 132 YTQACVKKGEKLSLDFIAP 150 (157)
Q Consensus 132 ~~~~~V~~g~~~~i~~~v~ 150 (157)
.+.+.+.+|++..+++.+.
T Consensus 24 F~rv~l~pGes~~v~~~l~ 42 (71)
T PF14310_consen 24 FERVSLAPGESKTVSFTLP 42 (71)
T ss_dssp EEEEEE-TT-EEEEEEEEE
T ss_pred eEEEEECCCCEEEEEEEEC
Confidence 3478899999999999985
No 13
>PF04378 RsmJ: Ribosomal RNA small subunit methyltransferase D, RsmJ; InterPro: IPR007473 This is a bacterial protein of unknown function, possibly secreted.; PDB: 2OO3_A.
Probab=34.70 E-value=30 Score=27.78 Aligned_cols=28 Identities=18% Similarity=0.224 Sum_probs=20.3
Q ss_pred CcEEEEeCChHHHHHHHHHHhhcChhhh
Q psy1331 34 KNCYVINAPKVFTLAWRVVKKFLHEYTI 61 (157)
Q Consensus 34 ~~i~iiNaP~~~~~~~~~vk~fl~~~t~ 61 (157)
..++|||+||-+.-...-+-++|.+...
T Consensus 206 SGm~iiNPPw~l~~~l~~~l~~L~~~L~ 233 (245)
T PF04378_consen 206 SGMLIINPPWTLDEELEEILPWLAETLA 233 (245)
T ss_dssp EEEEEES--TTHHHHHHHHHHHHHHHSS
T ss_pred ceEEEEcCCccHHHHHHHHHHHHHHHhC
Confidence 4689999999999888888877765443
No 14
>COG2961 ComJ Protein involved in catabolism of external DNA [General function prediction only]
Probab=34.14 E-value=34 Score=27.84 Aligned_cols=26 Identities=23% Similarity=0.300 Sum_probs=22.1
Q ss_pred CcEEEEeCChHHHHHHHHHHhhcChh
Q psy1331 34 KNCYVINAPKVFTLAWRVVKKFLHEY 59 (157)
Q Consensus 34 ~~i~iiNaP~~~~~~~~~vk~fl~~~ 59 (157)
..++|||+||-+.--...+-|+|...
T Consensus 237 SGMivINPPwtle~ql~~~LP~L~~~ 262 (279)
T COG2961 237 SGMIVINPPWTLEQQLRAALPWLTTL 262 (279)
T ss_pred eeEEEECCCccHHHHHHHHHHHHHHH
Confidence 46899999999999998888888654
No 15
>PRK04020 rps2P 30S ribosomal protein S2; Provisional
Probab=24.69 E-value=99 Score=24.12 Aligned_cols=70 Identities=19% Similarity=0.185 Sum_probs=39.2
Q ss_pred hcccccCcEEEEeCChHHHHHHHHHHhhcChhhhceeEEccCCCCCcH---HHHHccCCCCCCCccC-CCCCCCCC
Q psy1331 28 NYPEILKNCYVINAPKVFTLAWRVVKKFLHEYTISKIHLYRAEPAKWR---PILLEQMEEDMWPASM-GGAGRDPD 99 (157)
Q Consensus 28 ~yPe~l~~i~iiNaP~~~~~~~~~vk~fl~~~t~~Ki~~~~~~~~~~~---~~L~~~i~~~~LP~~y-GG~~~~~~ 99 (157)
.|..|-..+||||.-.....+-. ...|+......+|-|+++. .... .+..+..+...+-..| ||++++..
T Consensus 35 Iyg~r~~gi~IIdL~kT~~~L~~-A~~~i~~~~~~~ILfVgTk-~~~~~~v~k~A~~~g~~~v~~RWlgG~LTN~~ 108 (204)
T PRK04020 35 IYRVRPDGLYVLDVRKTDERIRI-AAKFLSRYEPEKILVVSSR-QYGQKPVQKFAEVVGAKAITGRFIPGTLTNPS 108 (204)
T ss_pred EeeecCCCCEEEcHHHHHHHHHH-HHHHHHHhcCCeEEEEeCC-HHHHHHHHHHHHHhCCeeecCccCCCcCcCcc
Confidence 45666678899997654432222 2233333356789999862 1122 2233345555555555 99988643
No 16
>PF07454 SpoIIP: Stage II sporulation protein P (SpoIIP); InterPro: IPR010897 This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation []. SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, [, , ]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers [].
Probab=24.42 E-value=87 Score=25.46 Aligned_cols=33 Identities=15% Similarity=0.371 Sum_probs=27.9
Q ss_pred CcccchhHHHHHHHHHHHHhhcccccCcEEEEe
Q psy1331 8 QYAWRPAAELVLCMLQMYEANYPEILKNCYVIN 40 (157)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~yPe~l~~i~iiN 40 (157)
|=.|+-..++..++...++..||...+.|++=+
T Consensus 197 np~~~~N~~fA~~l~~~~~~~yPGl~rgI~~k~ 229 (268)
T PF07454_consen 197 NPNWEKNLAFAKQLHAKLEKKYPGLSRGIFVKD 229 (268)
T ss_pred CCCHHHHHHHHHHHHHHHHhHCCCccceeeecC
Confidence 334777789999999999999999999888755
No 17
>KOG0534|consensus
Probab=23.71 E-value=43 Score=27.54 Aligned_cols=39 Identities=28% Similarity=0.514 Sum_probs=31.4
Q ss_pred HHHHHHHHHHhhcccccCcEEEEeCChHHHHHHHHHHhhcCh
Q psy1331 17 LVLCMLQMYEANYPEILKNCYVINAPKVFTLAWRVVKKFLHE 58 (157)
Q Consensus 17 ~~~~~~~~~~~~yPe~l~~i~iiNaP~~~~~~~~~vk~fl~~ 58 (157)
++++-+.-++.+||++++--|.++.|. -.|+--.+|+++
T Consensus 201 Llr~eL~~la~~~p~rf~~~y~v~~~~---~~w~~~~g~It~ 239 (286)
T KOG0534|consen 201 LLREELEELASKYPERFKVWYVVDQPP---EIWDGSVGFITK 239 (286)
T ss_pred chHHHHHHHHhhCcceEEEEEEEcCCc---ccccCccCccCH
Confidence 478888999999999999999999998 566655555543
No 18
>TIGR01011 rpsB_bact ribosomal protein S2, bacterial type. TIGR01012 describes the archaeal and cytosolic forms.
Probab=22.71 E-value=1e+02 Score=24.30 Aligned_cols=67 Identities=15% Similarity=0.105 Sum_probs=39.5
Q ss_pred cccccCcEEEEeCChHHHHHHHHHHhhcC--hhhhceeEEccCCCCCcH---HHHHccCCCCCCCcc-CCCCCCCC
Q psy1331 29 YPEILKNCYVINAPKVFTLAWRVVKKFLH--EYTISKIHLYRAEPAKWR---PILLEQMEEDMWPAS-MGGAGRDP 98 (157)
Q Consensus 29 yPe~l~~i~iiNaP~~~~~~~~~vk~fl~--~~t~~Ki~~~~~~~~~~~---~~L~~~i~~~~LP~~-yGG~~~~~ 98 (157)
|-+| ..++|||.-.....+-...+ |+. .+...+|-|+++. .... +++.+..+...+-.. +||++++.
T Consensus 30 yg~r-~g~~IIdL~~T~~~L~~A~~-~i~~~~~~~g~iLfV~tk-~~~~~~v~~~a~~~~~~yv~~rWlgG~LTN~ 102 (225)
T TIGR01011 30 FGER-NGIHIIDLQKTLQLLKEAYN-FVKDVAANGGKILFVGTK-KQAKEIIKEEAERCGMFYVNQRWLGGMLTNF 102 (225)
T ss_pred eeee-CCeEEEcHHHHHHHHHHHHH-HHHHHHhCCCEEEEEeCC-HHHHHHHHHHHHHhCCcccCCeecCeeccCH
Confidence 6666 78999998776554433333 333 2357889999963 2222 233334444444444 59999863
No 19
>TIGR02867 spore_II_P stage II sporulation protein P. Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members.
Probab=21.39 E-value=1.2e+02 Score=23.47 Aligned_cols=33 Identities=12% Similarity=0.238 Sum_probs=26.9
Q ss_pred CcccchhHHHHHHHHHHHHhhcccccCcEEEEe
Q psy1331 8 QYAWRPAAELVLCMLQMYEANYPEILKNCYVIN 40 (157)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~yPe~l~~i~iiN 40 (157)
+=.|+...++..++...++..||...+.|++=|
T Consensus 119 np~~~~N~~fA~~l~~~~~~~yPgl~rgi~~k~ 151 (196)
T TIGR02867 119 NPHFEKNLQLANKLHAKLEKKYPGLSRGIFYKD 151 (196)
T ss_pred CCCHHHHHHHHHHHHHHHHhhCCCcccceEEcc
Confidence 333666788999999999999999999888744
No 20
>PF14900 DUF4493: Domain of unknown function (DUF4493)
Probab=20.84 E-value=1.5e+02 Score=23.00 Aligned_cols=80 Identities=15% Similarity=0.111 Sum_probs=45.8
Q ss_pred hceeEEccCCCCCcHHHHHccCCCCCCCccCCCCCCCCCCCcccccccCCCCCCCcccccCCCCCCCccCcceEEEEeCC
Q psy1331 61 ISKIHLYRAEPAKWRPILLEQMEEDMWPASMGGAGRDPDGNPRCLTKIPQIGKVPKSMYMKKPIDKSLEENYTQACVKKG 140 (157)
Q Consensus 61 ~~Ki~~~~~~~~~~~~~L~~~i~~~~LP~~yGG~~~~~~gd~~c~~~i~~gg~vP~s~y~~~~~~~~~~~~~~~~~V~~g 140 (157)
.-+|+|++. + ....++-+...+| |+.+..+-|.-.-. ..+|...... |-. +.-... +.++|.+|
T Consensus 34 ~~~v~I~~~---~--~~~~~~~~~~~~~---~~~i~L~~G~Ytv~--A~~g~~~~~~-~d~--pyy~G~---~~f~I~~g 97 (235)
T PF14900_consen 34 DFTVEIYNA---D--GTVVKYWKYSEMP---GESIELPVGSYTVK--ASYGDNVAAG-FDK--PYYEGS---TTFTIEKG 97 (235)
T ss_pred ceEEEEEeC---C--CcEEEecchhccc---cceEeecCCcEEEE--EEcCCCcccc-ccC--ceeecc---eeEEEecC
Confidence 456777772 2 4455555666666 67777777753222 2233222211 110 000122 38999999
Q ss_pred CcEEEEEEecCCCccc
Q psy1331 141 EKLSLDFIAPQEGYFL 156 (157)
Q Consensus 141 ~~~~i~~~v~~~g~~l 156 (157)
+...+.+.+.-+++++
T Consensus 98 ~~t~v~v~C~laN~~V 113 (235)
T PF14900_consen 98 ETTTVSVTCKLANAKV 113 (235)
T ss_pred CcEEEEEEEEeeeeEE
Confidence 9999999998777654
No 21
>PRK05299 rpsB 30S ribosomal protein S2; Provisional
Probab=20.70 E-value=92 Score=25.10 Aligned_cols=68 Identities=12% Similarity=0.009 Sum_probs=38.8
Q ss_pred cccccCcEEEEeCChHHHHHHHHHHhhcC-hhhhceeEEccCCCCCcH---HHHHccCCCCCCCc-cCCCCCCCC
Q psy1331 29 YPEILKNCYVINAPKVFTLAWRVVKKFLH-EYTISKIHLYRAEPAKWR---PILLEQMEEDMWPA-SMGGAGRDP 98 (157)
Q Consensus 29 yPe~l~~i~iiNaP~~~~~~~~~vk~fl~-~~t~~Ki~~~~~~~~~~~---~~L~~~i~~~~LP~-~yGG~~~~~ 98 (157)
|-+| ..+||||.-.....+-..++-+-. .+...+|-|+++. .... ....+..+.-.+-. .+||++++.
T Consensus 32 yg~r-~gi~IIdL~kT~~~L~~A~~~i~~~~~~~g~iLfVgTk-~~~~~~V~~~A~~~~~~yv~~rWlgG~LTN~ 104 (258)
T PRK05299 32 FGER-NGIHIIDLQKTVPMLDEAYNFVRDVAANGGKILFVGTK-KQAQEAIAEEAERCGMPYVNHRWLGGMLTNF 104 (258)
T ss_pred eccc-CCeEEEcHHHHHHHHHHHHHHHHHHHhCCCEEEEEECc-HHHHHHHHHHHHHhCCeeeCCeecCeeccCH
Confidence 5566 889999987765544433333222 2457889999963 2222 22233344434433 459999863
Done!