Query 033319
Match_columns 122
No_of_seqs 104 out of 186
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 12:27:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033319.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033319hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4455 Uncharacterized conser 100.0 2.9E-36 6.2E-41 211.8 7.8 105 15-119 6-110 (110)
2 PF07019 Rab5ip: Rab5-interact 100.0 2E-28 4.3E-33 164.3 6.7 81 33-113 1-81 (81)
3 KOG3415 Putative Rab5-interact 99.6 2.5E-16 5.4E-21 112.7 6.1 87 32-118 42-128 (129)
4 PF01102 Glycophorin_A: Glycop 78.1 2.7 5.8E-05 30.4 3.1 14 41-54 66-79 (122)
5 PRK13682 hypothetical protein; 60.2 36 0.00078 21.2 4.9 21 41-61 6-26 (51)
6 COG5487 Small integral membran 51.9 57 0.0012 20.4 4.9 19 43-61 8-26 (54)
7 PF02439 Adeno_E3_CR2: Adenovi 51.4 29 0.00063 20.3 3.2 32 40-85 4-35 (38)
8 PF07043 DUF1328: Protein of u 47.8 57 0.0012 19.1 4.7 20 44-63 4-23 (39)
9 PF12650 DUF3784: Domain of un 37.8 1.2E+02 0.0026 20.1 5.6 30 19-48 33-62 (97)
10 PF10112 Halogen_Hydrol: 5-bro 37.1 1.1E+02 0.0025 22.9 5.6 31 39-72 10-40 (199)
11 TIGR00383 corA magnesium Mg(2+ 34.7 2.3E+02 0.005 22.4 7.6 35 42-76 267-309 (318)
12 COG2149 Predicted membrane pro 33.8 1.3E+02 0.0027 21.9 4.9 26 24-49 15-41 (120)
13 PF14015 DUF4231: Protein of u 33.3 1.4E+02 0.003 19.8 5.0 23 33-55 15-37 (112)
14 PHA00024 IX minor coat protein 30.1 24 0.00052 20.1 0.6 17 101-117 8-24 (33)
15 PLN03211 ABC transporter G-25; 29.5 1.5E+02 0.0032 26.8 5.8 34 35-68 408-448 (659)
16 PRK12872 ubiA prenyltransferas 28.6 2.6E+02 0.0056 21.8 6.5 14 98-111 271-284 (285)
17 PF03419 Peptidase_U4: Sporula 24.6 93 0.002 24.9 3.3 54 35-88 31-86 (293)
18 COG3619 Predicted membrane pro 24.5 2.7E+02 0.0058 22.1 5.8 45 27-71 164-208 (226)
19 PF04906 Tweety: Tweety; Inte 23.0 3.9E+02 0.0084 22.7 6.9 19 22-40 168-186 (406)
20 PF10112 Halogen_Hydrol: 5-bro 22.5 2.2E+02 0.0048 21.3 4.9 22 35-56 9-30 (199)
21 PF04829 PT-VENN: Pre-toxin do 22.1 1.2E+02 0.0025 18.9 2.7 21 36-56 11-31 (55)
22 PLN02953 phosphatidate cytidyl 21.6 1.5E+02 0.0032 25.8 4.1 34 35-70 97-130 (403)
23 COG5000 NtrY Signal transducti 20.9 69 0.0015 29.6 2.0 33 25-57 355-388 (712)
24 PF14927 Neurensin: Neurensin 20.3 2.3E+02 0.005 21.0 4.4 31 16-47 77-107 (140)
No 1
>KOG4455 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=2.9e-36 Score=211.85 Aligned_cols=105 Identities=38% Similarity=0.616 Sum_probs=100.6
Q ss_pred CCCCCccccChHHHHhhHHHHHHHHHHHHHHHHHHhhhhcccchhHHHHHHHHHHHHHHHHHHHhCCcccccccccchhc
Q 033319 15 DVSNDLQIFNAENLQSNMKVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMAKAKFSVHSYFDSWNRIL 94 (122)
Q Consensus 15 ~~~~~~~~~~~~~v~~N~~~l~~~r~~~s~l~Gi~AGILGLtg~~GFlfy~~~~~~~sll~~~k~~~~~~~yF~s~~~i~ 94 (122)
++..++|+++.+|++.|++++++||+++|+++|++||||||||+.||++|+++.++.++++..|++++|.+||+++.++|
T Consensus 6 ~~~~~~~~~s~aav~nN~kvl~f~Rt~~s~i~G~aAGILGltg~~GFi~Y~l~~~i~~il~~~K~~~~~~kyf~s~~~~f 85 (110)
T KOG4455|consen 6 AEEVFIPIYSTAAVRNNKKVLEFVRTSSSAIAGCAAGILGLTGLHGFIFYFLSVLILSILLVLKAGGQWGKYFQSRRNLF 85 (110)
T ss_pred hhhcCCcchhHHHHhcCHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHCCCHHhhcCchhHHH
Confidence 34567799999999999999999999999999999999999999999999999888888888899999999999999999
Q ss_pred ccccccchhhhhhHhhhhccceeee
Q 033319 95 LDGFLGGLMSFVLFWTYPSKNSKYL 119 (122)
Q Consensus 95 ~~g~~~~l~~FvL~Wtl~Y~lv~~~ 119 (122)
++++++++++|||+||+.|+++|+|
T Consensus 86 ~~~f~~Gl~tyVl~Wtf~Y~lv~~~ 110 (110)
T KOG4455|consen 86 TESFLGGLTTYVLAWTFFYGLVHVY 110 (110)
T ss_pred HHHHhchHHHHHHHHHHHhhhhccC
Confidence 9999999999999999999999987
No 2
>PF07019 Rab5ip: Rab5-interacting protein (Rab5ip)
Probab=99.95 E-value=2e-28 Score=164.33 Aligned_cols=81 Identities=44% Similarity=0.857 Sum_probs=79.1
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcccchhHHHHHHHHHHHHHHHHHHHhCCcccccccccchhcccccccchhhhhhHhhhh
Q 033319 33 KVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMAKAKFSVHSYFDSWNRILLDGFLGGLMSFVLFWTYP 112 (122)
Q Consensus 33 ~~l~~~r~~~s~l~Gi~AGILGLtg~~GFlfy~~~~~~~sll~~~k~~~~~~~yF~s~~~i~~~g~~~~l~~FvL~Wtl~ 112 (122)
|+++|+||++|+++|++||||||||+.||++|++++++++.+++.|+++++++||.+++|+++||+++++++|||+||++
T Consensus 1 dvi~~~r~~~a~~~Gi~aGILgLtg~~Gf~~f~~~~~~~s~~~~~~~~~~~~~~f~~~~~i~~~g~~~~l~~Fvl~Wtl~ 80 (81)
T PF07019_consen 1 DVIYWCRQIIALLAGIAAGILGLTGLYGFIFFFLSSFLVSLLYYAKAGFPDEDYFGGPWEIFTEGFFSGLSTFVLFWTLF 80 (81)
T ss_pred CHHHHHHHHHHHHHHHHhhhcccccHHHHHHHHHHHHHHHHHHHHHhcCChhhhcCCHHHHHHhhhhchHHHHHHHhhee
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred c
Q 033319 113 S 113 (122)
Q Consensus 113 Y 113 (122)
|
T Consensus 81 Y 81 (81)
T PF07019_consen 81 Y 81 (81)
T ss_pred C
Confidence 8
No 3
>KOG3415 consensus Putative Rab5-interacting protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.65 E-value=2.5e-16 Score=112.66 Aligned_cols=87 Identities=24% Similarity=0.440 Sum_probs=81.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcccchhHHHHHHHHHHHHHHHHHHHhCCcccccccccchhcccccccchhhhhhHhhh
Q 033319 32 MKVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMAKAKFSVHSYFDSWNRILLDGFLGGLMSFVLFWTY 111 (122)
Q Consensus 32 ~~~l~~~r~~~s~l~Gi~AGILGLtg~~GFlfy~~~~~~~sll~~~k~~~~~~~yF~s~~~i~~~g~~~~l~~FvL~Wtl 111 (122)
.++++|.||+.+++.|++.||++|+|..|.+.|+..+..+..+++.+-.+-.++-|.+-+|+..||++.++.+|++.|++
T Consensus 42 lDViyW~rQVi~l~lGviwGi~pL~G~l~iv~f~~issgIvy~y~~~~~~VDEee~GG~weL~kEGf~asfa~FlvtWIi 121 (129)
T KOG3415|consen 42 LDVIYWIRQVIGLILGVIWGIIPLVGFLGIVLFLGISSGIVYLYYANFLKVDEEEYGGHWELLKEGFMASFALFLVTWII 121 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHhhchhhhHHHHHHHHHhhhhHHHHHHHHHHhcCHHHhCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 38899999999999999999999999999999999999888888887777778888889999999999999999999999
Q ss_pred hccceee
Q 033319 112 PSKNSKY 118 (122)
Q Consensus 112 ~Y~lv~~ 118 (122)
+|++.||
T Consensus 122 ~Yt~~hy 128 (129)
T KOG3415|consen 122 FYTLAHY 128 (129)
T ss_pred HHhhhcc
Confidence 9999997
No 4
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=78.05 E-value=2.7 Score=30.44 Aligned_cols=14 Identities=50% Similarity=0.975 Sum_probs=12.6
Q ss_pred HHHHHHHHHhhhhc
Q 033319 41 FLSIIGGVIAGILG 54 (122)
Q Consensus 41 ~~s~l~Gi~AGILG 54 (122)
+..+++|+.|||+|
T Consensus 66 i~~Ii~gv~aGvIg 79 (122)
T PF01102_consen 66 IIGIIFGVMAGVIG 79 (122)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred eeehhHHHHHHHHH
Confidence 58899999999987
No 5
>PRK13682 hypothetical protein; Provisional
Probab=60.17 E-value=36 Score=21.17 Aligned_cols=21 Identities=33% Similarity=0.702 Sum_probs=17.2
Q ss_pred HHHHHHHHHhhhhcccchhHH
Q 033319 41 FLSIIGGVIAGILGFTGLMGF 61 (122)
Q Consensus 41 ~~s~l~Gi~AGILGLtg~~GF 61 (122)
+.-++..++||++|.+|..|-
T Consensus 6 liFliiA~iA~~lGF~GiAg~ 26 (51)
T PRK13682 6 IIFLVIALIAAVLGFGGIAGA 26 (51)
T ss_pred HHHHHHHHHHHHhccchHHHH
Confidence 344677899999999999984
No 6
>COG5487 Small integral membrane protein [Function unknown]
Probab=51.94 E-value=57 Score=20.41 Aligned_cols=19 Identities=42% Similarity=0.747 Sum_probs=15.0
Q ss_pred HHHHHHHhhhhcccchhHH
Q 033319 43 SIIGGVIAGILGFTGLMGF 61 (122)
Q Consensus 43 s~l~Gi~AGILGLtg~~GF 61 (122)
=++.-++||.||..|+.|-
T Consensus 8 FlvialIa~~lGFgGiaga 26 (54)
T COG5487 8 FLVIALIAGALGFGGIAGA 26 (54)
T ss_pred HHHHHHHHHHhCcccHHHH
Confidence 3566788999999999874
No 7
>PF02439 Adeno_E3_CR2: Adenovirus E3 region protein CR2; InterPro: IPR003470 Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host []. This region called CR1 (conserved region 1) [] is found three times in Human adenovirus 19 (a subgroup D adenovirus) 49 kDa protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain.
Probab=51.39 E-value=29 Score=20.34 Aligned_cols=32 Identities=19% Similarity=0.230 Sum_probs=18.6
Q ss_pred HHHHHHHHHHhhhhcccchhHHHHHHHHHHHHHHHHHHHhCCcccc
Q 033319 40 TFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMAKAKFSVHS 85 (122)
Q Consensus 40 ~~~s~l~Gi~AGILGLtg~~GFlfy~~~~~~~sll~~~k~~~~~~~ 85 (122)
+..|++.|+++|+. .+++..++|..|-++++.
T Consensus 4 s~IaIIv~V~vg~~--------------iiii~~~~YaCcykk~~~ 35 (38)
T PF02439_consen 4 STIAIIVAVVVGMA--------------IIIICMFYYACCYKKHRR 35 (38)
T ss_pred chhhHHHHHHHHHH--------------HHHHHHHHHHHHHccccc
Confidence 45677788877643 344455566655545443
No 8
>PF07043 DUF1328: Protein of unknown function (DUF1328); InterPro: IPR009760 This entry represents several hypothetical bacterial proteins of around 50 residues in length. The function of this family is unknown but is thought to be a membrane protein.; GO: 0005886 plasma membrane
Probab=47.80 E-value=57 Score=19.15 Aligned_cols=20 Identities=45% Similarity=0.801 Sum_probs=16.7
Q ss_pred HHHHHHhhhhcccchhHHHH
Q 033319 44 IIGGVIAGILGFTGLMGFVF 63 (122)
Q Consensus 44 ~l~Gi~AGILGLtg~~GFlf 63 (122)
++..++||++|.+|..|-..
T Consensus 4 liiAliAg~lGF~Giag~a~ 23 (39)
T PF07043_consen 4 LIIALIAGVLGFGGIAGTAA 23 (39)
T ss_pred HHHHHHHHHcCcccHHHHHH
Confidence 56788999999999998743
No 9
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=37.83 E-value=1.2e+02 Score=20.10 Aligned_cols=30 Identities=17% Similarity=0.311 Sum_probs=16.0
Q ss_pred CccccChHHHHhhHHHHHHHHHHHHHHHHH
Q 033319 19 DLQIFNAENLQSNMKVIYYSRTFLSIIGGV 48 (122)
Q Consensus 19 ~~~~~~~~~v~~N~~~l~~~r~~~s~l~Gi 48 (122)
|.+.+|.+.+.++......+=.+..++.++
T Consensus 33 Ek~~~D~~~l~r~~g~~~~~~~i~~li~~l 62 (97)
T PF12650_consen 33 EKEKYDKKKLCRFMGKFMLIIGIILLIGGL 62 (97)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334566666666665555544444444444
No 10
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=37.14 E-value=1.1e+02 Score=22.85 Aligned_cols=31 Identities=23% Similarity=0.421 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHhhhhcccchhHHHHHHHHHHHHH
Q 033319 39 RTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITS 72 (122)
Q Consensus 39 r~~~s~l~Gi~AGILGLtg~~GFlfy~~~~~~~s 72 (122)
|.+++++.+++++++ .+.|+-.+++.+++++
T Consensus 10 ~~~~~~~~~~~~~~~---~~~~~~~~~~l~~l~~ 40 (199)
T PF10112_consen 10 RWILGVLIAAITFLV---SFFGFDHSFLLSLLIG 40 (199)
T ss_pred HHHHHHHHHHHHHHH---HHHHhhHHHHHHHHHH
Confidence 445555544444444 4444444444444444
No 11
>TIGR00383 corA magnesium Mg(2+) and cobalt Co(2+) transport protein (corA). The article in Microb Comp Genomics 1998;3(3):151-69 (Medline:98448512) discusses this family and suggests that some members may have functions other than Mg2+ transport.
Probab=34.73 E-value=2.3e+02 Score=22.40 Aligned_cols=35 Identities=26% Similarity=0.386 Sum_probs=22.5
Q ss_pred HHHHHHHHhhhhccc--------chhHHHHHHHHHHHHHHHHH
Q 033319 42 LSIIGGVIAGILGFT--------GLMGFVFYFLIMAITSVCLM 76 (122)
Q Consensus 42 ~s~l~Gi~AGILGLt--------g~~GFlfy~~~~~~~sll~~ 76 (122)
.-+..-++||+.|.- .-+||...++.+++++++.+
T Consensus 267 IflP~t~IaGiyGMNf~~mP~l~~~~gy~~~l~~m~~i~~~~~ 309 (318)
T TIGR00383 267 IFIPLTFIAGIYGMNFKFMPELNWKYGYPAVLIVMAVIALGPL 309 (318)
T ss_pred HHHHHHHHHHHHhCCcccCccccchhHHHHHHHHHHHHHHHHH
Confidence 334456788888843 34688877777777775443
No 12
>COG2149 Predicted membrane protein [Function unknown]
Probab=33.80 E-value=1.3e+02 Score=21.93 Aligned_cols=26 Identities=15% Similarity=0.170 Sum_probs=20.1
Q ss_pred ChHHHHhhHHH-HHHHHHHHHHHHHHH
Q 033319 24 NAENLQSNMKV-IYYSRTFLSIIGGVI 49 (122)
Q Consensus 24 ~~~~v~~N~~~-l~~~r~~~s~l~Gi~ 49 (122)
|+.+-+-|.+. +-|+|+..+++++-+
T Consensus 15 d~R~~lAnERTFLAWiRTsLallafGv 41 (120)
T COG2149 15 DYRFTLANERTFLAWIRTSLALLAFGV 41 (120)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46666777765 899999999987654
No 13
>PF14015 DUF4231: Protein of unknown function (DUF4231)
Probab=33.33 E-value=1.4e+02 Score=19.82 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcc
Q 033319 33 KVIYYSRTFLSIIGGVIAGILGF 55 (122)
Q Consensus 33 ~~l~~~r~~~s~l~Gi~AGILGL 55 (122)
+..++.-....++.++.++++++
T Consensus 15 q~~~~~~~~~~i~~~~~~a~i~~ 37 (112)
T PF14015_consen 15 QRRYRRLRIASIILSVLGAVIPV 37 (112)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555666665555555554
No 14
>PHA00024 IX minor coat protein
Probab=30.10 E-value=24 Score=20.08 Aligned_cols=17 Identities=12% Similarity=0.057 Sum_probs=13.0
Q ss_pred chhhhhhHhhhhcccee
Q 033319 101 GLMSFVLFWTYPSKNSK 117 (122)
Q Consensus 101 ~l~~FvL~Wtl~Y~lv~ 117 (122)
-+..|+|-|++.|++..
T Consensus 8 ffgA~ilG~~l~~~Il~ 24 (33)
T PHA00024 8 FFGAYILGWALFYGILV 24 (33)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 35678999999988653
No 15
>PLN03211 ABC transporter G-25; Provisional
Probab=29.47 E-value=1.5e+02 Score=26.75 Aligned_cols=34 Identities=24% Similarity=0.550 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHhhhh-------cccchhHHHHHHHHH
Q 033319 35 IYYSRTFLSIIGGVIAGIL-------GFTGLMGFVFYFLIM 68 (122)
Q Consensus 35 l~~~r~~~s~l~Gi~AGIL-------GLtg~~GFlfy~~~~ 68 (122)
+.+.|.+.+++.|++.|.+ ++.+..|++||.+..
T Consensus 408 ~~~~r~~~~i~~~ll~G~lf~~~~~~~~~~r~g~lff~~~~ 448 (659)
T PLN03211 408 FNTLRVFQVIAAALLAGLMWWHSDFRDVQDRLGLLFFISIF 448 (659)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence 4568889999999998876 344577888887554
No 16
>PRK12872 ubiA prenyltransferase; Reviewed
Probab=28.64 E-value=2.6e+02 Score=21.81 Aligned_cols=14 Identities=36% Similarity=0.373 Sum_probs=8.8
Q ss_pred cccchhhhhhHhhh
Q 033319 98 FLGGLMSFVLFWTY 111 (122)
Q Consensus 98 ~~~~l~~FvL~Wtl 111 (122)
++.++..+.+.|.+
T Consensus 271 ~~~g~~~~~~~~~~ 284 (285)
T PRK12872 271 MLLGLISMLLGLLV 284 (285)
T ss_pred HHHHHHHHHHHHHh
Confidence 45667777766653
No 17
>PF03419 Peptidase_U4: Sporulation factor SpoIIGA This family belongs to family U4 of the peptidase classification.; InterPro: IPR005081 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. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to the MEROPS peptidase family U4 (SpoIIGA peptidase family, clan U-). Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the putative processing enzyme SpoIIGA []. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0030436 asexual sporulation
Probab=24.63 E-value=93 Score=24.87 Aligned_cols=54 Identities=17% Similarity=0.204 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHhhhhcccchhHHHHHHHHHHHHHHHHHH--HhCCccccccc
Q 033319 35 IYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAITSVCLMA--KAKFSVHSYFD 88 (122)
Q Consensus 35 l~~~r~~~s~l~Gi~AGILGLtg~~GFlfy~~~~~~~sll~~~--k~~~~~~~yF~ 88 (122)
..+.|-+.+..+|....++-+..-.+++..++..++++.+... ...++++++++
T Consensus 31 ~~~~Rll~~A~~Gal~~~~~~~p~~~~~~~~~~k~l~s~lmv~iaf~~~~~~~~~k 86 (293)
T PF03419_consen 31 ASRWRLLLGAAIGALYSLLIFFPPLSFLYSILFKLLISVLMVLIAFGPKRWRQFIK 86 (293)
T ss_pred CcHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHHHHHHHHHHHHHhCCCcHHHHHH
Confidence 5677888888888888877777777877777777777765543 22333444444
No 18
>COG3619 Predicted membrane protein [Function unknown]
Probab=24.45 E-value=2.7e+02 Score=22.10 Aligned_cols=45 Identities=20% Similarity=0.129 Sum_probs=31.0
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHhhhhcccchhHHHHHHHHHHHH
Q 033319 27 NLQSNMKVIYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAIT 71 (122)
Q Consensus 27 ~v~~N~~~l~~~r~~~s~l~Gi~AGILGLtg~~GFlfy~~~~~~~ 71 (122)
+-+++.+.+.+.--..+.+.|.++|.+.=.=+.+........+++
T Consensus 164 ~~~~~~~~~~~~~~il~f~~GAi~g~ll~~~~g~~al~~~~~~i~ 208 (226)
T COG3619 164 DKEKLRDWLIYLSLILSFIVGAICGALLTLFFGLKALWVVAALIL 208 (226)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 345556677778888899999999988665555665555444444
No 19
>PF04906 Tweety: Tweety; InterPro: IPR006990 None of the members of the tweety (tty) family have been functionally characterised. However, they are considered to be transmembrane proteins with five potential membrane-spanning regions. A number of potential functions have been suggested on the basis of homology to the yeast FTR1 and FTH1 iron transporter proteins and the mammalian neurotensin receptors 1 and 2 in that they have a similar hydrophobicity profiles although there is no detectable sequence homology to the tweety-related proteins. It has been proposed that the tweety-related proteins could be involved in transport of iron or other divalent cations or alternatively that they may be membrane-bound receptors [].
Probab=22.95 E-value=3.9e+02 Score=22.72 Aligned_cols=19 Identities=21% Similarity=0.254 Sum_probs=14.7
Q ss_pred ccChHHHHhhHHHHHHHHH
Q 033319 22 IFNAENLQSNMKVIYYSRT 40 (122)
Q Consensus 22 ~~~~~~v~~N~~~l~~~r~ 40 (122)
..+.+.+.+..+..++.|-
T Consensus 168 ~~~l~~~~~~~~~~E~yRw 186 (406)
T PF04906_consen 168 SLSLEQLAEQVSFYEYYRW 186 (406)
T ss_pred CCCHHHHHHHHHHHHHHHH
Confidence 5677888888888888883
No 20
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=22.47 E-value=2.2e+02 Score=21.30 Aligned_cols=22 Identities=14% Similarity=0.203 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHhhhhccc
Q 033319 35 IYYSRTFLSIIGGVIAGILGFT 56 (122)
Q Consensus 35 l~~~r~~~s~l~Gi~AGILGLt 56 (122)
+.|+-.....++.....++++.
T Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~ 30 (199)
T PF10112_consen 9 FRWILGVLIAAITFLVSFFGFD 30 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHHhh
Confidence 3555555555555555555444
No 21
>PF04829 PT-VENN: Pre-toxin domain with VENN motif; InterPro: IPR006914 This group of proteins, mainly from Neisseria meningitidis, may have haemagglutinin or haemolysin activity. A number of them have a second conserved domain, IPR006915 from INTERPRO, which is found in possible Pseudomonas aeruginosa haemagglutinins []. Filamentous haemagglutinin (FHA) is a major virulence attachment factor produced by certain bacterial species that functions as both a primary adhesin and an immunomodulator. Haemolysin is pore-forming toxin.
Probab=22.13 E-value=1.2e+02 Score=18.87 Aligned_cols=21 Identities=14% Similarity=0.207 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHhhhhccc
Q 033319 36 YYSRTFLSIIGGVIAGILGFT 56 (122)
Q Consensus 36 ~~~r~~~s~l~Gi~AGILGLt 56 (122)
+.+..+..++.|+++|+.|=.
T Consensus 11 ~~v~~ls~l~ag~ag~~~g~~ 31 (55)
T PF04829_consen 11 QKVSALSQLAAGVAGALAGGS 31 (55)
T ss_pred HHHHHHHHHHHHHHHHHHcCc
Confidence 345667778888888887754
No 22
>PLN02953 phosphatidate cytidylyltransferase
Probab=21.57 E-value=1.5e+02 Score=25.75 Aligned_cols=34 Identities=21% Similarity=0.231 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHhhhhcccchhHHHHHHHHHHH
Q 033319 35 IYYSRTFLSIIGGVIAGILGFTGLMGFVFYFLIMAI 70 (122)
Q Consensus 35 l~~~r~~~s~l~Gi~AGILGLtg~~GFlfy~~~~~~ 70 (122)
-.+.|..++++++..+..+=+ +.|..|.++..++
T Consensus 97 ~l~~RIiSglvl~~l~l~vV~--~GGw~F~~~va~i 130 (403)
T PLN02953 97 QLKKRVIFGIGIGLPVGCVVL--AGGWFFTVALAAS 130 (403)
T ss_pred cHHHHHHHHHHHHHHHHheee--eCcHHHHHHHHHH
Confidence 346788888887766544433 3444444444433
No 23
>COG5000 NtrY Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]
Probab=20.86 E-value=69 Score=29.56 Aligned_cols=33 Identities=30% Similarity=0.660 Sum_probs=25.6
Q ss_pred hHHHHhhHHHHHHHHHHH-HHHHHHHhhhhcccc
Q 033319 25 AENLQSNMKVIYYSRTFL-SIIGGVIAGILGFTG 57 (122)
Q Consensus 25 ~~~v~~N~~~l~~~r~~~-s~l~Gi~AGILGLtg 57 (122)
++.+..|++.++.-|.++ +++.|++||++|+..
T Consensus 355 q~~l~~ak~~~e~rr~f~E~VLsgvtaGVi~~d~ 388 (712)
T COG5000 355 QEALERAKDALEQRRRFLEAVLSGLTAGVIGFDN 388 (712)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCceeEEEEcC
Confidence 566667777787766655 789999999998864
No 24
>PF14927 Neurensin: Neurensin
Probab=20.30 E-value=2.3e+02 Score=20.96 Aligned_cols=31 Identities=6% Similarity=0.046 Sum_probs=22.6
Q ss_pred CCCCccccChHHHHhhHHHHHHHHHHHHHHHH
Q 033319 16 VSNDLQIFNAENLQSNMKVIYYSRTFLSIIGG 47 (122)
Q Consensus 16 ~~~~~~~~~~~~v~~N~~~l~~~r~~~s~l~G 47 (122)
+..+.+..++++++.| +.+..||..-.+++.
T Consensus 77 ~~~~~~~vD~~a~~~n-~~Ld~c~laG~~L~~ 107 (140)
T PF14927_consen 77 EAGEFVVVDSQAARFN-NALDTCKLAGLILLC 107 (140)
T ss_pred ccccccccchHHHHHh-hhHHHHHHHHHHHHH
Confidence 3478899999999999 567778765444443
Done!