Query 025023
Match_columns 259
No_of_seqs 59 out of 61
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 09:21:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025023.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025023hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3402 Uncharacterized conser 99.3 7.6E-12 1.7E-16 108.0 8.7 76 88-177 78-155 (161)
2 PF03703 bPH_2: Bacterial PH d 99.2 1.7E-11 3.8E-16 88.0 6.0 76 87-171 4-79 (80)
3 COG3428 Predicted membrane pro 98.6 1.2E-08 2.6E-13 100.4 2.7 86 52-158 45-130 (494)
4 COG3428 Predicted membrane pro 98.0 3.8E-05 8.3E-10 76.2 10.4 105 54-180 237-343 (494)
5 PF14470 bPH_3: Bacterial PH d 83.9 8.3 0.00018 28.4 7.5 65 88-170 25-89 (96)
6 PF06713 bPH_4: Bacterial PH d 65.9 29 0.00064 25.9 6.3 70 88-174 2-72 (74)
7 PF02893 GRAM: GRAM domain; I 54.6 34 0.00074 24.4 4.8 39 86-130 31-69 (69)
8 PF07263 DMP1: Dentin matrix p 50.5 6.8 0.00015 40.0 0.8 20 55-78 3-22 (514)
9 KOG3156 Uncharacterized membra 40.9 37 0.00081 31.5 3.9 27 44-70 192-218 (220)
10 PF15050 SCIMP: SCIMP protein 40.1 50 0.0011 28.6 4.3 29 52-83 9-38 (133)
11 PF07798 DUF1640: Protein of u 37.8 48 0.001 28.5 4.0 27 45-71 150-176 (177)
12 PRK10833 putative assembly pro 37.7 48 0.001 33.3 4.5 62 51-118 5-70 (617)
13 PF06459 RR_TM4-6: Ryanodine R 32.7 58 0.0012 30.7 3.9 18 56-73 175-192 (274)
14 PF06161 DUF975: Protein of un 31.7 85 0.0018 27.4 4.6 56 33-88 185-243 (243)
15 CHL00118 atpG ATP synthase CF0 30.1 76 0.0017 26.6 3.9 20 57-78 31-50 (156)
16 PF08512 Rtt106: Histone chape 29.3 1.6E+02 0.0036 22.9 5.4 59 88-163 14-74 (95)
17 PF10181 PIG-H: GPI-GlcNAc tra 28.9 93 0.002 23.4 3.8 25 108-132 20-44 (69)
18 PF10149 TM231: Transmembrane 28.5 59 0.0013 31.2 3.3 25 28-59 266-290 (320)
19 PRK00523 hypothetical protein; 27.8 1.1E+02 0.0024 24.0 4.1 16 49-64 4-19 (72)
20 PF08000 bPH_1: Bacterial PH d 27.2 3.5E+02 0.0077 22.6 7.3 79 88-175 43-122 (124)
21 PF11605 Vps36_ESCRT-II: Vacuo 27.1 81 0.0018 24.9 3.3 44 83-133 34-77 (89)
22 PRK13461 F0F1 ATP synthase sub 25.5 1.2E+02 0.0026 25.2 4.3 31 46-79 4-34 (159)
23 PF11014 DUF2852: Protein of u 25.0 91 0.002 26.3 3.4 20 54-73 14-33 (115)
24 PRK14471 F0F1 ATP synthase sub 24.6 1.2E+02 0.0026 25.4 4.1 30 47-79 8-37 (164)
25 PF10882 bPH_5: Bacterial PH d 24.4 66 0.0014 24.4 2.3 42 88-140 2-45 (100)
26 PF09624 DUF2393: Protein of u 23.9 1.6E+02 0.0034 24.2 4.6 42 77-121 38-79 (149)
27 PF06679 DUF1180: Protein of u 22.8 95 0.0021 27.4 3.2 32 60-91 99-131 (163)
28 KOG4838 Uncharacterized conser 22.3 1.4E+02 0.003 29.0 4.4 23 28-57 256-278 (312)
29 PF12955 DUF3844: Domain of un 21.6 1.2E+02 0.0027 25.0 3.5 40 30-69 51-90 (103)
30 smart00568 GRAM domain in gluc 21.1 1.7E+02 0.0037 20.2 3.7 35 87-127 24-58 (61)
31 PF05569 Peptidase_M56: BlaR1 20.9 2.4E+02 0.0052 25.5 5.5 21 101-121 165-186 (299)
32 PRK13453 F0F1 ATP synthase sub 20.9 1.5E+02 0.0033 25.2 4.1 30 47-79 18-47 (173)
33 PRK08455 fliL flagellar basal 20.4 62 0.0013 28.5 1.6 18 164-181 125-142 (182)
No 1
>COG3402 Uncharacterized conserved protein [Function unknown]
Probab=99.31 E-value=7.6e-12 Score=107.99 Aligned_cols=76 Identities=14% Similarity=0.239 Sum_probs=62.1
Q ss_pred eeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEeehhhhhhhcceeEEEEeccCCCCCCCCeeeecC--CCh
Q 025023 88 KLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQGYLQSLFGVYSLRIENVGVRRPPSDDVQIQGV--ANP 165 (259)
Q Consensus 88 kl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~QG~Lqr~FGl~slrIETAG~s~~~~~di~I~Gv--~~p 165 (259)
.|.+.|+++-- ..|++ ++.++.+|+-|||||+.+||||+|.||+.+++|.|||. +..|+|+ +.+
T Consensus 78 ry~v~~~el~i--q~GiL------v~~r~viP~~RVQhVDt~~GPL~R~~~La~vti~TAss------~~~IeaL~~~eA 143 (161)
T COG3402 78 RYEVEEDELDI--QHGIL------VRTRTVIPYVRVQHVDTEQGPLLRRYGLATVTITTASS------DHTIEALDREEA 143 (161)
T ss_pred eeecccceEEe--eccEE------EEEEEEeeEEEEEeeecccChHHHHhCcceEEEEeccc------cceecccCHHHH
Confidence 55555555555 49999 79999999999999999999999999999999999986 4555555 568
Q ss_pred hhHHHHHHHHHh
Q 025023 166 SDFRKAVLTRLS 177 (259)
Q Consensus 166 ~~fRk~Il~~~~ 177 (259)
+.+|+.+...+.
T Consensus 144 drlr~~l~~la~ 155 (161)
T COG3402 144 DRLRERLANLAR 155 (161)
T ss_pred HHHHHHHHHHHH
Confidence 888888766553
No 2
>PF03703 bPH_2: Bacterial PH domain; InterPro: IPR005182 A domain that is found in uncharacterised family of membrane proteins. 1-3 copies found in each protein, with each copy flanked by transmembrane helices.
Probab=99.24 E-value=1.7e-11 Score=87.95 Aligned_cols=76 Identities=17% Similarity=0.305 Sum_probs=63.6
Q ss_pred ceeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEeehhhhhhhcceeEEEEeccCCCCCCCCeeeecCCChh
Q 025023 87 RKLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQGYLQSLFGVYSLRIENVGVRRPPSDDVQIQGVANPS 166 (259)
Q Consensus 87 Rkl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~QG~Lqr~FGl~slrIETAG~s~~~~~di~I~Gv~~p~ 166 (259)
-+|.+|+..++.+ +|+| .+++..+|+++||+|.+.|||+||.||+.++++.++|+++.. ..+...++.+|+
T Consensus 4 ~~y~i~~~~l~i~--~G~~------~~~~~~i~~~~Iq~v~~~q~~~~r~~g~~~i~i~~~~~~~~~-~~i~~~~~~~a~ 74 (80)
T PF03703_consen 4 TGYTITDDRLIIR--SGLF------SKRTTIIPLDRIQSVSIKQNPLQRLFGLGTIKIDTAGGSGEK-IEIPFLSIEDAE 74 (80)
T ss_pred EEEEEECCEEEEE--ECeE------EEEEEEEEhhHeEEEEEEcCHHHHhCccEEEEEEECCCCCce-eEEecCCHHHHH
Confidence 4689999999997 7999 799999999999999999999999999999999999999542 345555555666
Q ss_pred hHHHH
Q 025023 167 DFRKA 171 (259)
Q Consensus 167 ~fRk~ 171 (259)
++++.
T Consensus 75 ~i~~~ 79 (80)
T PF03703_consen 75 EIYDW 79 (80)
T ss_pred HHHhh
Confidence 66553
No 3
>COG3428 Predicted membrane protein [Function unknown]
Probab=98.64 E-value=1.2e-08 Score=100.44 Aligned_cols=86 Identities=16% Similarity=0.300 Sum_probs=67.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhHhhhccccceeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEeeh
Q 025023 52 WVLYSLLLILAWGIGLFMLLYLPVRRYILRKDIRSRKLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQG 131 (259)
Q Consensus 52 wl~~slllilawgvGilmLL~lPirryi~~~d~~sRkl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~QG 131 (259)
|..+.+..+++|.|.- .+- | ..=+|.++++++.-+ +|++ +|+.+.+|++|||.|+..||
T Consensus 45 w~~~~~vv~vi~~i~~-ii~------w------~~~~Yried~~~~l~--~Gi~------~rk~r~i~~~RIQsVd~t~~ 103 (494)
T COG3428 45 WGGAALVVLVIFLILQ-IIK------W------ITFTYRIEDEEVRLQ--TGIF------SRKKRYIPIDRIQSVDTTAG 103 (494)
T ss_pred eeeehhhHHHHHHHHh-hhE------E------EEEEEEEecceEEEE--eeEE------eecceecchHhhhhhHHHHH
Confidence 7776666666666544 111 1 223678888888776 9999 89999999999999999999
Q ss_pred hhhhhhcceeEEEEeccCCCCCCCCee
Q 025023 132 YLQSLFGVYSLRIENVGVRRPPSDDVQ 158 (259)
Q Consensus 132 ~Lqr~FGl~slrIETAG~s~~~~~di~ 158 (259)
.++|+||+..++|||||+++.+.+++.
T Consensus 104 lv~rlfgl~~l~IeTaGg~~eae~~~~ 130 (494)
T COG3428 104 LVARLFGLVVLRIETAGGGGEAEAELV 130 (494)
T ss_pred HHHHhhccEEEEEEcCCCCCccceeee
Confidence 999999999999999998754455443
No 4
>COG3428 Predicted membrane protein [Function unknown]
Probab=98.01 E-value=3.8e-05 Score=76.23 Aligned_cols=105 Identities=23% Similarity=0.398 Sum_probs=71.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHhhhccccceeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEeehhh
Q 025023 54 LYSLLLILAWGIGLFMLLYLPVRRYILRKDIRSRKLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQGYL 133 (259)
Q Consensus 54 ~~slllilawgvGilmLL~lPirryi~~~d~~sRkl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~QG~L 133 (259)
++.++++.+|++++...++ ||- .|+-+|. +++.++ +||.+ -|++.|+|+.|||-|.++|.+|
T Consensus 237 ~~vl~llvaW~~s~~~tm~----rf~---~fq~~~~---~~~L~i--erGLl------err~~Tipl~RlqaV~l~esll 298 (494)
T COG3428 237 LAVLLLLVAWLLSIALTMF----RFY---GFQVMKE---NGVLHI--ERGLL------ERRKVTIPLRRLQAVTLRESLL 298 (494)
T ss_pred HHHHHHHHHHHHHHHHHhh----hhh---ceEEEec---CCEEEE--Eeeee------ecccceeehhheEEEEeechHH
Confidence 3444457788888765554 341 2222221 444444 59999 8999999999999999999999
Q ss_pred hhhhcceeEEEEeccCCC-C-CCCCeeeecCCChhhHHHHHHHHHhhcc
Q 025023 134 QSLFGVYSLRIENVGVRR-P-PSDDVQIQGVANPSDFRKAVLTRLSNMT 180 (259)
Q Consensus 134 qr~FGl~slrIETAG~s~-~-~~~di~I~Gv~~p~~fRk~Il~~~~~~~ 180 (259)
.|+||..++.++++|..+ . .+.+..+- |-.=|++++.-+.++.
T Consensus 299 rrl~G~~~v~v~~aG~~gd~~~sgs~~ll----P~~~k~~v~~~L~~~~ 343 (494)
T COG3428 299 RRLFGYAAVDVVTAGVHGDSQSSGSTPLL----PFIKKEAVLKLLRENT 343 (494)
T ss_pred HHhhccEEEEEEEecCCCCCcCCCceecc----ccccHHHHHHHHHHhC
Confidence 999999999999999332 2 33444433 3333566666666665
No 5
>PF14470 bPH_3: Bacterial PH domain
Probab=83.92 E-value=8.3 Score=28.44 Aligned_cols=65 Identities=20% Similarity=0.401 Sum_probs=44.6
Q ss_pred eeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEeehhhhhhhcceeEEEEeccCCCCCCCCeeeecCCChhh
Q 025023 88 KLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQGYLQSLFGVYSLRIENVGVRRPPSDDVQIQGVANPSD 167 (259)
Q Consensus 88 kl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~QG~Lqr~FGl~slrIETAG~s~~~~~di~I~Gv~~p~~ 167 (259)
-+++|..-+.+. +++.+ +| .....+||+.|++|....|.+. .+++|.+.| ..+++.-+ +.++
T Consensus 25 ~l~~TnkRlif~-~~~~~---~~--~~~~~i~y~~I~~v~~~~g~~~-----~~i~i~~~~------~~~~i~~i-~k~~ 86 (96)
T PF14470_consen 25 VLVLTNKRLIFY-SKGMF---GG--KKFESIPYDDITSVSFKKGILG-----GKITIETNG------EKIKIDNI-QKGD 86 (96)
T ss_pred EEEEeCCEEEEE-EcccC---CC--ceEEEEEhhheEEEEEEccccc-----cEEEEEECC------EEEEEEEc-CHHH
Confidence 577787777775 33322 23 6678999999999999999833 568888822 45666666 5555
Q ss_pred HHH
Q 025023 168 FRK 170 (259)
Q Consensus 168 fRk 170 (259)
+++
T Consensus 87 ~~~ 89 (96)
T PF14470_consen 87 VKE 89 (96)
T ss_pred HHH
Confidence 544
No 6
>PF06713 bPH_4: Bacterial PH domain; InterPro: IPR009589 This entry is represented by Bacteriophage SP-beta, YolF. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical proteins specific to Oceanobacillus and Bacillus species. Members of this family are typically around 130 residues in length. The function of this family is unknown.
Probab=65.85 E-value=29 Score=25.91 Aligned_cols=70 Identities=16% Similarity=0.177 Sum_probs=49.0
Q ss_pred eeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEeehhhhhhh-cceeEEEEeccCCCCCCCCeeeecCCChh
Q 025023 88 KLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQGYLQSLF-GVYSLRIENVGVRRPPSDDVQIQGVANPS 166 (259)
Q Consensus 88 kl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~QG~Lqr~F-Gl~slrIETAG~s~~~~~di~I~Gv~~p~ 166 (259)
+|.++++....| .| + +++. +|++.|+.|.=..+|+.+.. .+..|.|+..+. +.+.|. -.|.+
T Consensus 2 ~Y~i~~~~L~I~--~G-~------~~~~--I~i~~I~~I~~~~~~~~~~a~S~~rl~I~y~~~-----~~i~Is-P~~~~ 64 (74)
T PF06713_consen 2 KYIIEDDYLIIK--CG-F------FKKK--IPIEDIRSIRPTKNPLSSPALSLDRLEIYYGKY-----KSILIS-PKDKE 64 (74)
T ss_pred EEEEeCCEEEEE--EC-C------cccE--EEhHHccEEEecCCccccccccccEEEEEECCC-----CEEEEE-CCCHH
Confidence 355666666665 77 4 4655 99999999999999988655 467788887632 334444 67888
Q ss_pred hHHHHHHH
Q 025023 167 DFRKAVLT 174 (259)
Q Consensus 167 ~fRk~Il~ 174 (259)
+|-+++..
T Consensus 65 ~FI~~L~k 72 (74)
T PF06713_consen 65 EFIAELQK 72 (74)
T ss_pred HHHHHHHh
Confidence 88777654
No 7
>PF02893 GRAM: GRAM domain; InterPro: IPR004182 The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. It is normally about 70 amino acids in length. It is thought to be an intracellular protein-binding or lipid-binding signalling domain, which has an important function in membrane-associated processes. Mutations in the GRAM domain of myotubularins cause a muscle disease, which suggests that the domain is essential for the full function of the enzyme []. Myotubularin-related proteins are a large subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids [].; PDB: 1M7R_B 1LW3_A 1ZVR_A 1ZSQ_A.
Probab=54.63 E-value=34 Score=24.36 Aligned_cols=39 Identities=15% Similarity=0.205 Sum_probs=27.1
Q ss_pred cceeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEee
Q 025023 86 SRKLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQ 130 (259)
Q Consensus 86 sRkl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~Q 130 (259)
.=++|||++-+.|+-...-. ...-..+||..|.+|..+|
T Consensus 31 ~G~LyiT~~~lcF~s~~~~~------~~~~~~ipl~~I~~i~k~~ 69 (69)
T PF02893_consen 31 QGRLYITNNYLCFYSNKFGS------KTCKFVIPLSDIKSIEKET 69 (69)
T ss_dssp EEEEEEESSEEEEEESSSSS-------E-EEEEEGGGEEEEEEE-
T ss_pred eeEEEECCCEEEEEECCCCC------ceEEEEEEhHheeEEEEeC
Confidence 33899999999997212221 2236799999999998764
No 8
>PF07263 DMP1: Dentin matrix protein 1 (DMP1); InterPro: IPR009889 This family consists of several mammalian dentin matrix protein 1 (DMP1) sequences. The dentin matrix acidic phosphoprotein 1 (DMP1) gene has been mapped to human chromosome 4q21 []. DMP1 is a bone and teeth specific protein initially identified from mineralised dentin. DMP1 is primarily localised in the nuclear compartment of undifferentiated osteoblasts. In the nucleus, DMP1 acts as a transcriptional component for activation of osteoblast-specific genes like osteocalcin. During the early phase of osteoblast maturation, Ca2+ surges into the nucleus from the cytoplasm, triggering the phosphorylation of DMP1 by a nuclear isoform of casein kinase II. This phosphorylated DMP1 is then exported out into the extracellular matrix, where it regulates nucleation of hydroxyapatite. DMP1 is a unique molecule that initiates osteoblast differentiation by transcription in the nucleus and orchestrates mineralised matrix formation extracellularly, at later stages of osteoblast maturation []. The DMP1 gene has been found to be ectopically expressed in lung cancer although the reason for this is unknown [].; GO: 0001503 ossification, 0030198 extracellular matrix organization
Probab=50.51 E-value=6.8 Score=40.03 Aligned_cols=20 Identities=50% Similarity=1.026 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhh
Q 025023 55 YSLLLILAWGIGLFMLLYLPVRRY 78 (259)
Q Consensus 55 ~slllilawgvGilmLL~lPirry 78 (259)
++|||+++||+. +++|+.||
T Consensus 3 tsill~~lwgls----~alpvary 22 (514)
T PF07263_consen 3 TSILLMFLWGLS----CALPVARY 22 (514)
T ss_pred ceeHHHHHHHhh----cccchhhh
Confidence 578889999954 78899999
No 9
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=40.88 E-value=37 Score=31.54 Aligned_cols=27 Identities=26% Similarity=0.255 Sum_probs=20.2
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 025023 44 FVQYQTAQWVLYSLLLILAWGIGLFML 70 (259)
Q Consensus 44 ~vKY~tviwl~~slllilawgvGilmL 70 (259)
-+||+|++|+.-++.-++|.+++++-|
T Consensus 192 s~K~qt~qw~~g~v~~~~Al~La~~r~ 218 (220)
T KOG3156|consen 192 SVKTQTIQWLIGVVTGTSALVLAYLRL 218 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 469999999988776677766666544
No 10
>PF15050 SCIMP: SCIMP protein
Probab=40.06 E-value=50 Score=28.59 Aligned_cols=29 Identities=28% Similarity=0.657 Sum_probs=15.2
Q ss_pred HHHHHHHHHHH-HHHHHHHHHHhhhhhhHhhhc
Q 025023 52 WVLYSLLLILA-WGIGLFMLLYLPVRRYILRKD 83 (259)
Q Consensus 52 wl~~slllila-wgvGilmLL~lPirryi~~~d 83 (259)
|+..++..|++ .++|+++++.. |+.+|++
T Consensus 9 WiiLAVaII~vS~~lglIlyCvc---R~~lRqG 38 (133)
T PF15050_consen 9 WIILAVAIILVSVVLGLILYCVC---RWQLRQG 38 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH---HHHHHcc
Confidence 88887774332 34444444432 4444544
No 11
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=37.81 E-value=48 Score=28.47 Aligned_cols=27 Identities=15% Similarity=0.410 Sum_probs=19.5
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025023 45 VQYQTAQWVLYSLLLILAWGIGLFMLL 71 (259)
Q Consensus 45 vKY~tviwl~~slllilawgvGilmLL 71 (259)
+|++++.|+.-.++.+++.++|++-++
T Consensus 150 ~K~~~lr~~~g~i~~~~a~~la~~r~~ 176 (177)
T PF07798_consen 150 LKWDTLRWLVGVIFGCVALVLAILRLW 176 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 799999998765555667777765443
No 12
>PRK10833 putative assembly protein; Provisional
Probab=37.67 E-value=48 Score=33.33 Aligned_cols=62 Identities=21% Similarity=0.355 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhh--hhHh--hhccccceeEeeccceEeeecCCccccccccceeeEEE
Q 025023 51 QWVLYSLLLILAWGIGLFMLLYLPVR--RYIL--RKDIRSRKLFLTPNAIVYKVTRPVPFPCFGVLKKEKHV 118 (259)
Q Consensus 51 iwl~~slllilawgvGilmLL~lPir--ryi~--~~d~~sRkl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~V 118 (259)
.|++.+++++++.++..++++.-|=. ..|- =++-+-|.+.| ++||.+. +||..|+.-.+.++
T Consensus 5 l~~l~~l~~l~v~~~~al~~~id~n~~k~~i~~~v~~~tGr~l~I-~Gdi~ls-----~fP~lgv~l~~v~l 70 (617)
T PRK10833 5 LTTLMILLVVLVAGLSALVLLVNPNDFRAYMVKQVEARSGYQLQL-DGDLRWH-----VWPQLSILSGRMSL 70 (617)
T ss_pred HHHHHHHHHHHHHHHHHheEEEChHHhhHHHHHHHHHHhCCEEEE-cCceEEE-----EccceeEEeccEEE
Confidence 46666666666666666655544332 1121 22236678888 7888886 88988887666666
No 13
>PF06459 RR_TM4-6: Ryanodine Receptor TM 4-6; InterPro: IPR009460 The release of Ca2+ ions from intracellular stores is a key step in a wide variety of cellular functions. In striated muscle, the release of Ca2+ from the sarcoplasmic reticulum (SR) leads to muscle contraction. Ca2+ release occurs through large, high-conductance Ca2+ release channels, also known as ryanodine receptors (RyRs) because they bind the plant alkaloid ryanodine with high affinity and specificity []. This region covers TM regions 4-6 of the ryanodine receptor 1 family.; GO: 0005219 ryanodine-sensitive calcium-release channel activity, 0006874 cellular calcium ion homeostasis, 0016021 integral to membrane
Probab=32.73 E-value=58 Score=30.75 Aligned_cols=18 Identities=39% Similarity=0.693 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 025023 56 SLLLILAWGIGLFMLLYL 73 (259)
Q Consensus 56 slllilawgvGilmLL~l 73 (259)
-|.|++|++|=+++|||.
T Consensus 175 ~lALflAFaINFILLFYK 192 (274)
T PF06459_consen 175 FLALFLAFAINFILLFYK 192 (274)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 466799999999999995
No 14
>PF06161 DUF975: Protein of unknown function (DUF975); InterPro: IPR010380 This is a family of uncharacterised bacterial proteins.
Probab=31.73 E-value=85 Score=27.40 Aligned_cols=56 Identities=14% Similarity=0.134 Sum_probs=40.1
Q ss_pred eecccchhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh---Hhhhccccce
Q 025023 33 YTASFQEKEDNFVQYQTAQWVLYSLLLILAWGIGLFMLLYLPVRRY---ILRKDIRSRK 88 (259)
Q Consensus 33 y~AsF~e~~~~~vKY~tviwl~~slllilawgvGilmLL~lPirry---i~~~d~~sRk 88 (259)
-+.|++=|.++.-+++..+...++..++.+...|+..++..|+..- ..-.++++||
T Consensus 185 l~~S~~lmkg~k~~~f~l~Lsfigw~~L~~~t~gi~~l~~~pY~~~~~a~fY~~l~~~~ 243 (243)
T PF06161_consen 185 LKRSRKLMKGNKWRLFLLDLSFIGWYILGLLTFGIGLLWVIPYINTAQAEFYEELRKRK 243 (243)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4678889999999998888777776667777777777777787532 2355555554
No 15
>CHL00118 atpG ATP synthase CF0 B' subunit; Validated
Probab=30.06 E-value=76 Score=26.58 Aligned_cols=20 Identities=25% Similarity=0.451 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHHHhhhhhh
Q 025023 57 LLLILAWGIGLFMLLYLPVRRY 78 (259)
Q Consensus 57 lllilawgvGilmLL~lPirry 78 (259)
.+++++|.+ -.++|.|+...
T Consensus 31 nFliL~~lL--~k~l~~Pi~~~ 50 (156)
T CHL00118 31 QFLLLMVLL--NIILYKPLLKV 50 (156)
T ss_pred HHHHHHHHH--HHHHHHHHHHH
Confidence 344555554 35678888655
No 16
>PF08512 Rtt106: Histone chaperone Rttp106-like; InterPro: IPR013719 This is a domain of unknown function that is associated with a number of different protein families. It is found in Rtt106p, which is a histone chaperone involved in heterochromatin-mediated silencing []. It is also found in genes annotated as transcription factors/regulators. This domain is the C-terminal domain of yeast Spt16p P32558 from SWISSPROT, which is a subunit of the heterodimeric yeast FACT complex (Spt16p-Pob3p, IPR000969 from INTERPRO) []. In addition Spt16p and its relatives, in this entry, are described as non-peptidase homologues belonging to the MEROPS peptidase family M24. The FACT complex facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [, ]. ; PDB: 3TW1_A 3GYO_A 3TO1_A 3FSS_A 3TVV_B 3GYP_A 2GCJ_D 2GCL_A.
Probab=29.30 E-value=1.6e+02 Score=22.91 Aligned_cols=59 Identities=10% Similarity=0.194 Sum_probs=35.1
Q ss_pred eeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEeehhhhhhhcceeE--EEEeccCCCCCCCCeeeecCC
Q 025023 88 KLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQGYLQSLFGVYSL--RIENVGVRRPPSDDVQIQGVA 163 (259)
Q Consensus 88 kl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~QG~Lqr~FGl~sl--rIETAG~s~~~~~di~I~Gv~ 163 (259)
-||.+++.++|=+.+|.+ .+|++.|..|..++- +..+..++ .|.+-+.+ +.++.+.+|.
T Consensus 14 ~L~pl~~~l~f~~~kP~~-----------~i~~~dI~~v~feRv---~~~~~ktFDl~v~~k~~~---~~~~~fs~I~ 74 (95)
T PF08512_consen 14 FLYPLEKCLLFGLEKPPF-----------VIPLDDIESVEFERV---SSFSSKTFDLVVILKDYE---GPPHEFSSID 74 (95)
T ss_dssp EEEEESSEEEEECSSS-E-----------EEEGGGEEEEEEE-----ESSSSSEEEEEEEETT-T---S-EEEEEEEE
T ss_pred EEEEccceEEEecCCCeE-----------EEEhhHeeEEEEEec---ccCcceEEEEEEEEecCC---CCcEEEeeEC
Confidence 456666666664456666 899999999999985 33333333 34443323 5677887774
No 17
>PF10181 PIG-H: GPI-GlcNAc transferase complex, PIG-H component; InterPro: IPR019328 This entry represents a conserved domain found in PIG-H proteins. PIG-H is a family of conserved proteins that complexes with three other proteins to form the GPI-GnT (glycosylphosphatidylinositol anchor biosynthesis transferase) complex. It appears to be a peripheral membrane protein that faces the cytoplasm and which is involved in the first step in GPI anchor formation. ; GO: 0017176 phosphatidylinositol N-acetylglucosaminyltransferase activity
Probab=28.89 E-value=93 Score=23.36 Aligned_cols=25 Identities=24% Similarity=0.490 Sum_probs=20.9
Q ss_pred ccccceeeEEEeCCCeeeEEEeehh
Q 025023 108 CFGVLKKEKHVLLPSVQDIVIEQGY 132 (259)
Q Consensus 108 ~~gv~~~Ek~VPL~~IqdV~I~QG~ 132 (259)
++|-.++.+=+|.++|.||.|..|.
T Consensus 20 ~~g~~~~~~FIp~~~I~divInE~~ 44 (69)
T PF10181_consen 20 FSGRSSSRRFIPIDKIIDIVINEGF 44 (69)
T ss_pred EcCceeEEEEEEHHHeeEEEEEeeE
Confidence 3454467889999999999999997
No 18
>PF10149 TM231: Transmembrane protein 231; InterPro: IPR019306 The proteins in this entry belong to transmembrane protein family 231; they have no known function.
Probab=28.50 E-value=59 Score=31.25 Aligned_cols=25 Identities=24% Similarity=0.538 Sum_probs=22.1
Q ss_pred CcceeeecccchhhhhhhhhhHHHHHHHHHHH
Q 025023 28 DDDVLYTASFQEKEDNFVQYQTAQWVLYSLLL 59 (259)
Q Consensus 28 ~~~ily~AsF~e~~~~~vKY~tviwl~~slll 59 (259)
++.|+|..+|=|+.+.. |+.+...|
T Consensus 266 ~~~i~Y~p~~wE~lK~~-------WiQY~s~~ 290 (320)
T PF10149_consen 266 EEVILYRPGFWEMLKWA-------WIQYLSIF 290 (320)
T ss_pred ceEEEECccHHHHHHHH-------HHHHHHHH
Confidence 56999999999999999 99986655
No 19
>PRK00523 hypothetical protein; Provisional
Probab=27.79 E-value=1.1e+02 Score=24.04 Aligned_cols=16 Identities=13% Similarity=0.112 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHH
Q 025023 49 TAQWVLYSLLLILAWG 64 (259)
Q Consensus 49 tviwl~~slllilawg 64 (259)
+.+|+++.++.+++-+
T Consensus 4 ~~l~I~l~i~~li~G~ 19 (72)
T PRK00523 4 IGLALGLGIPLLIVGG 19 (72)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4556666555543333
No 20
>PF08000 bPH_1: Bacterial PH domain; InterPro: IPR012544 This family contains many bacterial hypothetical proteins.; PDB: 3DCX_E 3HSA_C 3B77_D.
Probab=27.19 E-value=3.5e+02 Score=22.63 Aligned_cols=79 Identities=15% Similarity=0.162 Sum_probs=47.1
Q ss_pred eeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEeeh-hhhhhhcceeEEEEeccCCCCCCCCeeeecCCChh
Q 025023 88 KLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQG-YLQSLFGVYSLRIENVGVRRPPSDDVQIQGVANPS 166 (259)
Q Consensus 88 kl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~QG-~Lqr~FGl~slrIETAG~s~~~~~di~I~Gv~~p~ 166 (259)
.+.+|.+.++.-=..|+- |-=+.-..+||.+|+++++|-. -++ ==+.|+|-..|+..+ -+..+.+-.|..
T Consensus 43 ~~vFTnkRlI~vD~QG~T----GkK~~~~siPY~~I~~~siETAG~~D---lD~Elki~i~~~~~~--i~~~f~k~~di~ 113 (124)
T PF08000_consen 43 EIVFTNKRLILVDKQGIT----GKKVEYKSIPYSSITHFSIETAGTFD---LDSELKIWISGQGFP--IEFEFKKKTDIY 113 (124)
T ss_dssp EEEEESSEEEEEEEESSS----SSEEEEEEEEGGGEEEEEEEECSSTT---SEEEEEEEETTESSE--EEEEEGTTSHHH
T ss_pred eEEEecChheEEecccCc----cceEEEEEEehhhccEEEEEeCCccc---CcccEEEEECCCcEE--EEEecCCCCCHH
Confidence 455566655554345655 3222234899999999888742 221 124566655555533 345677777777
Q ss_pred hHHHHHHHH
Q 025023 167 DFRKAVLTR 175 (259)
Q Consensus 167 ~fRk~Il~~ 175 (259)
++-+++...
T Consensus 114 ~i~k~L~~~ 122 (124)
T PF08000_consen 114 EIYKALAEY 122 (124)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 777777654
No 21
>PF11605 Vps36_ESCRT-II: Vacuolar protein sorting protein 36 Vps36; InterPro: IPR021648 Vps36 is a subunit of ESCRT-II, a protein involved in driving protein sorting from endosomes to lysosomes. The GLUE domain of Vps36 allows for a tight interaction to occur between the protein and Vps28, a subunit of ESCRT-I. This interaction is critical for ubiquitinated cargo progression from early to late endosomes []. ; PDB: 2HTH_B 2DX5_A 2CAY_B.
Probab=27.09 E-value=81 Score=24.88 Aligned_cols=44 Identities=20% Similarity=0.445 Sum_probs=31.4
Q ss_pred ccccceeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEeehhh
Q 025023 83 DIRSRKLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQGYL 133 (259)
Q Consensus 83 d~~sRkl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~QG~L 133 (259)
.|++=.+++|.|-|.|- ...-. -+.-..+||+.|.++....|.+
T Consensus 34 ~~q~G~l~LTsHRliw~-d~~~~------~~~s~~l~L~~i~~~e~~~gf~ 77 (89)
T PF11605_consen 34 NFQNGRLYLTSHRLIWV-DDSDP------SKHSIALPLSLISHIEYSAGFL 77 (89)
T ss_dssp T-SCEEEEEESSEEEEE-ESSGH------CHH-EEEEGGGEEEEEEE-STT
T ss_pred cccCCEEEEEeeEEEEE-cCCCC------ceeEEEEEchHeEEEEEEcccc
Confidence 56677999999999995 22222 2335699999999998888877
No 22
>PRK13461 F0F1 ATP synthase subunit B; Provisional
Probab=25.53 E-value=1.2e+02 Score=25.20 Aligned_cols=31 Identities=16% Similarity=0.189 Sum_probs=16.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhH
Q 025023 46 QYQTAQWVLYSLLLILAWGIGLFMLLYLPVRRYI 79 (259)
Q Consensus 46 KY~tviwl~~slllilawgvGilmLL~lPirryi 79 (259)
+..|++|-++. ++|++|. +..++|.|+..++
T Consensus 4 ~~~~~~~~~in-F~il~~i--L~~f~~kpi~~~l 34 (159)
T PRK13461 4 NIPTIIATIIN-FIILLLI--LKHFFFDKIKAVI 34 (159)
T ss_pred cHHHHHHHHHH-HHHHHHH--HHHHhHHHHHHHH
Confidence 34566665553 2233333 4466788987663
No 23
>PF11014 DUF2852: Protein of unknown function (DUF2852); InterPro: IPR021273 This bacterial family of proteins has no known function.
Probab=24.96 E-value=91 Score=26.33 Aligned_cols=20 Identities=35% Similarity=0.710 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 025023 54 LYSLLLILAWGIGLFMLLYL 73 (259)
Q Consensus 54 ~~slllilawgvGilmLL~l 73 (259)
+..+.||+.|-||+.||.|.
T Consensus 14 ~mVlGFi~fWPlGla~Lay~ 33 (115)
T PF11014_consen 14 AMVLGFIVFWPLGLALLAYM 33 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34556799999999999995
No 24
>PRK14471 F0F1 ATP synthase subunit B; Provisional
Probab=24.60 E-value=1.2e+02 Score=25.41 Aligned_cols=30 Identities=20% Similarity=0.287 Sum_probs=17.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhH
Q 025023 47 YQTAQWVLYSLLLILAWGIGLFMLLYLPVRRYI 79 (259)
Q Consensus 47 Y~tviwl~~slllilawgvGilmLL~lPirryi 79 (259)
|.++.|.++.+ +|++|. +-.++|.|+.+.+
T Consensus 8 ~~~~~~~~i~F-lil~~l--l~~~l~~pi~~~l 37 (164)
T PRK14471 8 FGLFFWQTILF-LILLLL--LAKFAWKPILGAV 37 (164)
T ss_pred HHHHHHHHHHH-HHHHHH--HHHHhHHHHHHHH
Confidence 45666666533 344444 3456788997663
No 25
>PF10882 bPH_5: Bacterial PH domain; InterPro: IPR020482 This entry contains membrane proteins with no known function.
Probab=24.36 E-value=66 Score=24.39 Aligned_cols=42 Identities=10% Similarity=0.226 Sum_probs=28.0
Q ss_pred eeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEEEeehh--hhhhhcce
Q 025023 88 KLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIVIEQGY--LQSLFGVY 140 (259)
Q Consensus 88 kl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~I~QG~--Lqr~FGl~ 140 (259)
++.++++.++=+ ++.. ..++|++.|++|...... -.|.||..
T Consensus 2 ~y~v~~~~l~I~--~~~~---------~~~Ip~~~I~~v~~~~~~~~~~R~~G~~ 45 (100)
T PF10882_consen 2 RYEVDDDGLIIR--WPFG---------KITIPLAEIESVELVDDLPPGIRTFGSG 45 (100)
T ss_pred EEEEECCEEEEE--Eccc---------cEEEEHHHcEEEEeccccCcceEEEEEc
Confidence 456666666664 3222 568999999999988764 35555544
No 26
>PF09624 DUF2393: Protein of unknown function (DUF2393); InterPro: IPR013417 The function of this protein is unknown. It is always found as part of a two-gene operon with IPR013416 from INTERPRO, a protein that appears to span the membrane seven times. It has so far been found in the bacteria Anabaena sp. (strain PCC 7120), Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus.
Probab=23.86 E-value=1.6e+02 Score=24.22 Aligned_cols=42 Identities=17% Similarity=0.225 Sum_probs=24.9
Q ss_pred hhHhhhccccceeEeeccceEeeecCCccccccccceeeEEEeCC
Q 025023 77 RYILRKDIRSRKLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLP 121 (259)
Q Consensus 77 ryi~~~d~~sRkl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~ 121 (259)
.+++.+..++..+.++...- ...+..+++| |.++++..-++.
T Consensus 38 ~~~l~~~~~~~~~~~~~~~~-l~~~~~~~v~--g~V~N~g~~~i~ 79 (149)
T PF09624_consen 38 YYWLDKYLKKIELTLTSQKR-LQYSESFYVD--GTVTNTGKFTIK 79 (149)
T ss_pred HHHHhhhcCCceEEEeeeee-eeeccEEEEE--EEEEECCCCEee
Confidence 44578888888888766555 4334555543 445555555543
No 27
>PF06679 DUF1180: Protein of unknown function (DUF1180); InterPro: IPR009565 This entry consists of several hypothetical eukaryotic proteins thought to be membrane proteins. Their function is unknown.
Probab=22.77 E-value=95 Score=27.41 Aligned_cols=32 Identities=25% Similarity=0.544 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHhhhhhhHhhh-ccccceeEe
Q 025023 60 ILAWGIGLFMLLYLPVRRYILRK-DIRSRKLFL 91 (259)
Q Consensus 60 ilawgvGilmLL~lPirryi~~~-d~~sRkl~v 91 (259)
++++|+..++.+|+-||.|=+++ .-+.|||-|
T Consensus 99 ~Vl~g~s~l~i~yfvir~~R~r~~~rktRkYgv 131 (163)
T PF06679_consen 99 YVLVGLSALAILYFVIRTFRLRRRNRKTRKYGV 131 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccccccceeecc
Confidence 55667777777777666442444 223355544
No 28
>KOG4838 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.25 E-value=1.4e+02 Score=29.05 Aligned_cols=23 Identities=26% Similarity=0.586 Sum_probs=20.2
Q ss_pred CcceeeecccchhhhhhhhhhHHHHHHHHH
Q 025023 28 DDDVLYTASFQEKEDNFVQYQTAQWVLYSL 57 (259)
Q Consensus 28 ~~~ily~AsF~e~~~~~vKY~tviwl~~sl 57 (259)
++.+.|+-+|-|+.+.| |+.+..
T Consensus 256 ~~~~~Y~~gfWE~lk~f-------Wiqy~s 278 (312)
T KOG4838|consen 256 EMEFIYKTGFWELLKWF-------WIQYLS 278 (312)
T ss_pred hhheeecccHHHHHHHH-------HHHHHH
Confidence 56899999999999999 998843
No 29
>PF12955 DUF3844: Domain of unknown function (DUF3844); InterPro: IPR024382 This presumed domain is found in fungal species. It contains 8 largely conserved cysteine residues. This domain is found in proteins thought to be located in the endoplasmic reticulum.
Probab=21.56 E-value=1.2e+02 Score=25.05 Aligned_cols=40 Identities=20% Similarity=0.247 Sum_probs=24.6
Q ss_pred ceeeecccchhhhhhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 025023 30 DVLYTASFQEKEDNFVQYQTAQWVLYSLLLILAWGIGLFM 69 (259)
Q Consensus 30 ~ily~AsF~e~~~~~vKY~tviwl~~slllilawgvGilm 69 (259)
++-|...==+..|--+.++-+.|.-+.++++++++|++|+
T Consensus 51 tt~W~G~aCqKkDvS~~F~L~~~~ti~lv~~~~~~I~lL~ 90 (103)
T PF12955_consen 51 TTHWGGPACQKKDVSVPFWLFAGFTIALVVLVAGAIGLLF 90 (103)
T ss_pred eeeecccccccccccchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444445666677777777777766666666666543
No 30
>smart00568 GRAM domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins.
Probab=21.13 E-value=1.7e+02 Score=20.19 Aligned_cols=35 Identities=17% Similarity=0.471 Sum_probs=24.6
Q ss_pred ceeEeeccceEeeecCCccccccccceeeEEEeCCCeeeEE
Q 025023 87 RKLFLTPNAIVYKVTRPVPFPCFGVLKKEKHVLLPSVQDIV 127 (259)
Q Consensus 87 Rkl~vt~~~IvYKv~rgv~fp~~gv~~~Ek~VPL~~IqdV~ 127 (259)
=++|+|++-+-|+ + ... |-...-..+||..|+.|.
T Consensus 24 G~lyiT~~~l~F~-S-~~~----~~~~~~~~ipl~~I~~i~ 58 (61)
T smart00568 24 GRLYISNYRLCFR-S-DLP----GKLTPKVVIPLADITRIE 58 (61)
T ss_pred EEEEEECCEEEEE-c-cCC----CCeeEEEEEEHHHeeEEE
Confidence 3899999999997 2 111 212336789999998875
No 31
>PF05569 Peptidase_M56: BlaR1 peptidase M56; InterPro: IPR008756 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 MEROPS peptidase family M56 (clan M-). The predicted active site residues for members of this family occur in the motif HEXXH. The type example is BlaR1 peptidase from Bacillus licheniformis. Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription.
Probab=20.92 E-value=2.4e+02 Score=25.48 Aligned_cols=21 Identities=19% Similarity=0.289 Sum_probs=11.9
Q ss_pred cCCccccc-cccceeeEEEeCC
Q 025023 101 TRPVPFPC-FGVLKKEKHVLLP 121 (259)
Q Consensus 101 ~rgv~fp~-~gv~~~Ek~VPL~ 121 (259)
+.++--|| +|.++....+|-.
T Consensus 165 s~~i~sP~~~G~~~p~I~lP~~ 186 (299)
T PF05569_consen 165 SSGISSPFVFGFLRPVIVLPES 186 (299)
T ss_pred cCCCCCCeeecCcceEEEecCc
Confidence 44444444 5766766666654
No 32
>PRK13453 F0F1 ATP synthase subunit B; Provisional
Probab=20.89 E-value=1.5e+02 Score=25.24 Aligned_cols=30 Identities=13% Similarity=0.226 Sum_probs=15.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhH
Q 025023 47 YQTAQWVLYSLLLILAWGIGLFMLLYLPVRRYI 79 (259)
Q Consensus 47 Y~tviwl~~slllilawgvGilmLL~lPirryi 79 (259)
+.|+.|.++. ++|++|. +..++|.|+..++
T Consensus 18 ~~t~~~~iIn-FliL~~l--L~~~l~~pi~~~l 47 (173)
T PRK13453 18 WGTVIVTVLT-FIVLLAL--LKKFAWGPLKDVM 47 (173)
T ss_pred HHHHHHHHHH-HHHHHHH--HHHHHHHHHHHHH
Confidence 5566665542 2233333 2355778886553
No 33
>PRK08455 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=20.41 E-value=62 Score=28.48 Aligned_cols=18 Identities=22% Similarity=0.229 Sum_probs=13.5
Q ss_pred ChhhHHHHHHHHHhhcch
Q 025023 164 NPSDFRKAVLTRLSNMTN 181 (259)
Q Consensus 164 ~p~~fRk~Il~~~~~~~~ 181 (259)
+-..+|++|+..++....
T Consensus 125 ~~p~IRD~ii~~Ls~kt~ 142 (182)
T PRK08455 125 KDPVIRDIIIRILSSKTV 142 (182)
T ss_pred hhhHHHHHHHHHHHcCCH
Confidence 445689999988887664
Done!