Query T0605 3NMD, , 72 residues
Match_columns 72
No_of_seqs 11 out of 13
Neff 2.0
Searched_HMMs 11830
Date Mon Jul 5 08:53:11 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0605.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0605.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04859 DUF641: Plant protein 75.4 2.5 0.00021 20.6 5.7 34 33-66 88-121 (132)
2 PF04880 NUDE_C: NUDE protein, 74.5 2 0.00017 21.3 4.6 41 20-67 1-44 (166)
3 PF12240 Angiomotin_C: Angiomo 74.2 1.2 0.0001 22.6 3.4 25 38-62 141-165 (205)
4 PF05983 Med7: MED7 protein; 62.4 4.8 0.00041 18.9 6.3 53 18-70 103-161 (162)
5 PF03882 KicB: KicB killing fa 48.4 8.2 0.0007 17.5 6.5 54 16-69 210-266 (440)
6 PF09862 DUF2089: Protein of u 45.4 7.8 0.00066 17.7 3.3 48 14-61 45-100 (113)
7 PF10018 Med4: Vitamin-D-recep 41.2 11 0.0009 16.9 7.2 47 25-71 11-60 (190)
8 PF09036 Bcr-Abl_Oligo: Bcr-Ab 40.9 11 0.00091 16.8 3.6 23 45-67 31-53 (79)
9 PF12329 TMF_DNA_bd: TATA elem 40.5 11 0.00093 16.8 4.8 34 34-67 6-39 (74)
10 PF05667 DUF812: Protein of un 40.4 11 0.00093 16.8 5.9 38 28-65 442-479 (594)
11 PF09457 RBD-FIP: FIP domain ; 39.5 11 0.00096 16.7 4.9 30 21-50 2-31 (48)
12 PF07544 Med9: RNA polymerase 35.3 13 0.0011 16.3 3.2 29 42-70 38-66 (67)
13 PF10390 ELL: RNA polymerase I 33.8 12 0.001 16.5 2.8 35 37-71 197-237 (282)
14 PF11731 Cdd1: Pathogenicity l 33.7 4.5 0.00038 19.1 0.5 50 17-71 21-72 (93)
15 PF09710 Trep_dent_lipo: Trepo 25.6 20 0.0016 15.3 2.8 30 40-70 59-88 (394)
16 PF08614 ATG16: Autophagy prot 25.0 20 0.0017 15.2 6.6 30 35-64 125-154 (194)
17 PF05739 SNARE: SNARE domain; 24.7 20 0.0017 15.2 7.6 50 19-68 11-60 (63)
18 PF12418 AcylCoA_DH_N: Acyl-Co 22.9 15 0.0013 15.9 1.7 15 18-32 4-18 (34)
19 PF08687 ASD2: Apx/Shroom doma 22.7 22 0.0019 15.0 5.8 14 57-70 133-146 (264)
20 PF08172 CASP_C: CASP C termin 21.6 23 0.002 14.8 4.4 29 40-68 94-122 (249)
No 1
>PF04859 DUF641: Plant protein of unknown function (DUF641); InterPro: IPR006943 This conserved region is found in a number of plant proteins of unknown function.
Probab=75.43 E-value=2.5 Score=20.61 Aligned_cols=34 Identities=32% Similarity=0.532 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9998899999999998733999999999889989
Q T0605 33 EELRQRDALIDELELELDQKDELIQMLQNELDKY 66 (72)
Q Consensus 33 eElr~rDe~I~~LE~ELdeKD~lIr~LqnELDKy 66 (72)
+-++-.+.+++.|+.+++.||+=|-.|...|+--
T Consensus 88 sll~~yE~~~~kL~~e~~~KDseI~~Lr~~L~e~ 121 (132)
T PF04859_consen 88 SLLRTYEIMVKKLESEIDAKDSEIDRLREKLEEL 121 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999999988889999999999999
No 2
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Aspergillus nidulans NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei . It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function. ; PDB: 2v66_E 2v71_A.
Probab=74.46 E-value=2 Score=21.26 Aligned_cols=41 Identities=39% Similarity=0.494 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH
Q ss_conf 1899999998889999889999999999873399999---99998899898
Q T0605 20 SLRDLQYALQEKIEELRQRDALIDELELELDQKDELI---QMLQNELDKYR 67 (72)
Q Consensus 20 slrdLq~aL~~K~eElr~rDe~I~~LE~ELdeKD~lI---r~LqnELDKyR 67 (72)
||-|+.-.+++-|| .-.+||.||+||+.|. |+|.-|+--.|
T Consensus 1 SLeD~EskyN~AiE-------r~alLE~El~EKE~L~ie~QRLkDElrDLk 44 (166)
T PF04880_consen 1 SLEDFESKYNQAIE-------RNALLEEELDEKENLRIENQRLKDELRDLK 44 (166)
T ss_dssp HHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHCH-----------
T ss_pred CHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 98899999999999-------878899999999999999999999999999
No 3
>PF12240 Angiomotin_C: Angiomotin C terminal
Probab=74.24 E-value=1.2 Score=22.57 Aligned_cols=25 Identities=28% Similarity=0.526 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999873399999999988
Q T0605 38 RDALIDELELELDQKDELIQMLQNE 62 (72)
Q Consensus 38 rDe~I~~LE~ELdeKD~lIr~LqnE 62 (72)
-+..|+.|+..+-|||+.|+-||-.
T Consensus 141 mE~riK~L~aqi~EKDAmIkvLqq~ 165 (205)
T PF12240_consen 141 MEGRIKNLHAQIAEKDAMIKVLQQR 165 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999889999999711
No 4
>PF05983 Med7: MED7 protein; InterPro: IPR009244 This family consists of several eukaryotic proteins, which are homologues of the yeast MED7 protein. Activation of gene transcription in metazoans is a multistep process that is triggered by factors that recognise transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus .; GO: 0003713 transcription coactivator activity, 0045941 positive regulation of transcription, 0005634 nucleus; PDB: 3fbi_C 3fbn_C 1ykh_A 1yke_C.
Probab=62.43 E-value=4.8 Score=18.94 Aligned_cols=53 Identities=23% Similarity=0.398 Sum_probs=40.0
Q ss_pred CCCHHHHHHHH---HHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 10189999999---888---999988999999999987339999999998899898651
Q T0605 18 RGSLRDLQYAL---QEK---IEELRQRDALIDELELELDQKDELIQMLQNELDKYRSVI 70 (72)
Q Consensus 18 ~gslrdLq~aL---~~K---~eElr~rDe~I~~LE~ELdeKD~lIr~LqnELDKyRsvv 70 (72)
...+.++..++ +-- .+.---|+.+|.+||.-+++|-+.|..++.-+++.++++
T Consensus 103 ~~ki~~i~~L~~N~hHlLN~yRPhQAre~Li~~me~Ql~~kr~~i~~i~~~~~~~~~~l 161 (162)
T PF05983_consen 103 ERKIEDIRLLFINMHHLLNEYRPHQARESLIMMMEEQLEQKREEIEQIRKALEEVREKL 161 (162)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 88999999999999999987187989999999999999999999999999999999773
No 5
>PF03882 KicB: KicB killing factor; InterPro: IPR005582 This family contains MukF, which are proteins involved in the segregation and condensation of prokaryotic chromosomes. MukE (IPR007385 from INTERPRO) along with MukF interact with MukB (IPR007406 from INTERPRO) in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli . The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC . ScpA (IPR003768 from INTERPRO) and ScpB (IPR005234 from INTERPRO) have little sequence similarity to MukE or MukF, though they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. ; PDB: 3euh_B 1t98_A 3euj_B 3euk_E.
Probab=48.41 E-value=8.2 Score=17.54 Aligned_cols=54 Identities=37% Similarity=0.434 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 11101899999998889999889999999999---8733999999999889989865
Q T0605 16 EGRGSLRDLQYALQEKIEELRQRDALIDELEL---ELDQKDELIQMLQNELDKYRSV 69 (72)
Q Consensus 16 ~~~gslrdLq~aL~~K~eElr~rDe~I~~LE~---ELdeKD~lIr~LqnELDKyRsv 69 (72)
|--||+||||-.|.-....+-.-=..|++.-. +++--|.++..||+.||+-+|-
T Consensus 210 etsgtLRELqdtL~aagD~lqa~Ll~IQe~~~~~~~l~~vd~l~~~Lq~kLDrI~sW 266 (440)
T PF03882_consen 210 ETSGTLRELQDTLEAAGDKLQAQLLRIQECVMGRDDLDFVDNLIFDLQSKLDRIISW 266 (440)
T ss_dssp HH---HHHHHHHHHH---HHHHHHHHHHHHHHCSSS-HHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 987569999999997268999999999999716751789999999999999999999
No 6
>PF09862 DUF2089: Protein of unknown function(DUF2089)
Probab=45.44 E-value=7.8 Score=17.68 Aligned_cols=48 Identities=27% Similarity=0.520 Sum_probs=36.0
Q ss_pred HCCCCCCHHHHHHHHHHHHHHHHHH-HHHHHHHHH-------HHHHHHHHHHHHHH
Q ss_conf 1011101899999998889999889-999999999-------87339999999998
Q T0605 14 SIEGRGSLRDLQYALQEKIEELRQR-DALIDELEL-------ELDQKDELIQMLQN 61 (72)
Q Consensus 14 ~~~~~gslrdLq~aL~~K~eElr~r-De~I~~LE~-------ELdeKD~lIr~Lqn 61 (72)
-+.-||+++++...|.-+--++|.| |.+|+.|.. +-+++.+++..|.+
T Consensus 45 Fl~~~GnlKe~ak~lgiSYpTvR~rLd~ii~~lg~~~~~~~~~~~~~~~IL~~L~~ 100 (113)
T PF09862_consen 45 FLKCRGNLKEVAKELGISYPTVRNRLDRIIEKLGYEEEEEEEENDERKEILDKLEK 100 (113)
T ss_pred HHHHCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 99918989999999788828999999999998179877665444469999999990
No 7
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 17t
Probab=41.20 E-value=11 Score=16.86 Aligned_cols=47 Identities=26% Similarity=0.355 Sum_probs=36.4
Q ss_pred HHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99998889---999889999999999873399999999988998986515
Q T0605 25 QYALQEKI---EELRQRDALIDELELELDQKDELIQMLQNELDKYRSVIR 71 (72)
Q Consensus 25 q~aL~~K~---eElr~rDe~I~~LE~ELdeKD~lIr~LqnELDKyRsvvr 71 (72)
+-.|..-+ .+.......|..|..|....|.-|+.+..+|-.+++.+.
T Consensus 11 d~~L~~~l~~l~~hq~~~~~I~~L~~e~~~lD~~ik~~~~~L~~~~~eL~ 60 (190)
T PF10018_consen 11 DDELKSALEELQEHQENQARILQLRAEVESLDEQIKDIVKELKEARKELE 60 (190)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999999999999999999999999999999999999
No 8
>PF09036 Bcr-Abl_Oligo: Bcr-Abl oncoprotein oligomerisation domain; InterPro: IPR015123 The Bcr-Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein . ; PDB: 1k1f_B.
Probab=40.92 E-value=11 Score=16.84 Aligned_cols=23 Identities=35% Similarity=0.499 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99987339999999998899898
Q T0605 45 LELELDQKDELIQMLQNELDKYR 67 (72)
Q Consensus 45 LE~ELdeKD~lIr~LqnELDKyR 67 (72)
+|++|+.--+-|++|+-|+.|-|
T Consensus 31 ~eqele~Cr~sirrLeqEvNkER 53 (79)
T PF09036_consen 31 IEQELERCRASIRRLEQEVNKER 53 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 79999999999999999985989
No 9
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding
Probab=40.47 E-value=11 Score=16.79 Aligned_cols=34 Identities=24% Similarity=0.290 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9988999999999987339999999998899898
Q T0605 34 ELRQRDALIDELELELDQKDELIQMLQNELDKYR 67 (72)
Q Consensus 34 Elr~rDe~I~~LE~ELdeKD~lIr~LqnELDKyR 67 (72)
.|+.+|+.|..|-.|...=-...-.+.+-|.|.|
T Consensus 6 ~l~EKDe~Ia~L~~EGe~Lsk~el~~~~~IKkLr 39 (74)
T PF12329_consen 6 KLKEKDEQIAQLMEEGEKLSKQELKHNNTIKKLR 39 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9884799999999989998887876167999999
No 10
>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function.
Probab=40.40 E-value=11 Score=16.79 Aligned_cols=38 Identities=37% Similarity=0.546 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 98889999889999999999873399999999988998
Q T0605 28 LQEKIEELRQRDALIDELELELDQKDELIQMLQNELDK 65 (72)
Q Consensus 28 L~~K~eElr~rDe~I~~LE~ELdeKD~lIr~LqnELDK 65 (72)
..++..+++.--.-|+.++.|+..|++.++.|..|+.+
T Consensus 442 ~~~kl~~vk~~r~~i~~~~~el~~Kee~~~~L~~e~e~ 479 (594)
T PF05667_consen 442 SQQKLQEVKEVRQKIQEIEEELQTKEEQHKQLESELEK 479 (594)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 89999999999999999999999889999999999984
No 11
>PF09457 RBD-FIP: FIP domain ; PDB: 2d7c_D 2hv8_D 2k6s_B 2gzd_D 2gzh_B.
Probab=39.54 E-value=11 Score=16.71 Aligned_cols=30 Identities=37% Similarity=0.391 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 899999998889999889999999999873
Q T0605 21 LRDLQYALQEKIEELRQRDALIDELELELD 50 (72)
Q Consensus 21 lrdLq~aL~~K~eElr~rDe~I~~LE~ELd 50 (72)
--+|..+|+..-++++++|..|++|+.=+|
T Consensus 2 ~deL~~~l~k~e~e~~~~~~~v~eLe~YiD 31 (48)
T PF09457_consen 2 RDELIEALQKQEEENSRKDQHVKELEDYID 31 (48)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 888999999869999988887889999999
No 12
>PF07544 Med9: RNA polymerase II transcription mediator complex subunit 9; InterPro: IPR011425 These proteins include CSE2 (P33308 from SWISSPROT) and a subunit of the Mediator complex . CSE2, or chromosome segregation protein, has a microtubule-related role in chromosome segregation.; GO: 0005634 nucleus
Probab=35.30 E-value=13 Score=16.30 Aligned_cols=29 Identities=28% Similarity=0.415 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999987339999999998899898651
Q T0605 42 IDELELELDQKDELIQMLQNELDKYRSVI 70 (72)
Q Consensus 42 I~~LE~ELdeKD~lIr~LqnELDKyRsvv 70 (72)
+++-+.++.+...-|+.++.-|++|++.+
T Consensus 38 ~eEq~~~i~~le~~i~~k~~vL~~~k~~~ 66 (67)
T PF07544_consen 38 VEEQEQEIEELEEQIARKREVLRKLKSMC 66 (67)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999999999998651
No 13
>PF10390 ELL: RNA polymerase II elongation factor ELL ; PDB: 2doa_A 2e5n_A.
Probab=33.81 E-value=12 Score=16.53 Aligned_cols=35 Identities=31% Similarity=0.414 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHC
Q ss_conf 8999999999987339999999998------8998986515
Q T0605 37 QRDALIDELELELDQKDELIQMLQN------ELDKYRSVIR 71 (72)
Q Consensus 37 ~rDe~I~~LE~ELdeKD~lIr~Lqn------ELDKyRsvvr 71 (72)
-|+-+|-.|.++...|.++|.+|++ +-|..++++.
T Consensus 197 ~RkRvIHLLALkpykk~El~~rL~~dgl~~~dk~~l~~iL~ 237 (282)
T PF10390_consen 197 LRKRVIHLLALKPYKKPELLLRLQKDGLSDKDKNCLRSILQ 237 (282)
T ss_dssp HHHHHHHHHHHS-B-HHHHHHHHCC----HHHHHHH--HCC
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 12201346643633367999876306886356889999999
No 14
>PF11731 Cdd1: Pathogenicity locus
Probab=33.68 E-value=4.5 Score=19.12 Aligned_cols=50 Identities=24% Similarity=0.251 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf 110189999999888999988999--9999999873399999999988998986515
Q T0605 17 GRGSLRDLQYALQEKIEELRQRDA--LIDELELELDQKDELIQMLQNELDKYRSVIR 71 (72)
Q Consensus 17 ~~gslrdLq~aL~~K~eElr~rDe--~I~~LE~ELdeKD~lIr~LqnELDKyRsvvr 71 (72)
|..+.+||..+=...+++|+.+|. +-+-|+.-.+. ++=-|.||-||++|+
T Consensus 21 G~a~a~DL~~lGi~s~~~L~g~dP~elY~~l~~~~G~-----~~DpCvldvfr~~v~ 72 (93)
T PF11731_consen 21 GPATAKDLRLLGIHSPEQLAGADPEELYERLCALTGQ-----RHDPCVLDVFRCAVY 72 (93)
T ss_pred CHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHHHHCC-----CCCCHHHHHHHHHHH
T ss_conf 7999999999189989999269999999999998489-----778599999999999
No 15
>PF09710 Trep_dent_lipo: Treponema clustered lipoprotein (Trep_dent_lipo)
Probab=25.57 E-value=20 Score=15.29 Aligned_cols=30 Identities=43% Similarity=0.574 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999987339999999998899898651
Q T0605 40 ALIDELELELDQKDELIQMLQNELDKYRSVI 70 (72)
Q Consensus 40 e~I~~LE~ELdeKD~lIr~LqnELDKyRsvv 70 (72)
|+|++||.- ..--.-.+.|+-|||+|--|.
T Consensus 59 E~ik~le~k-k~~~e~Lk~l~~elD~~d~v~ 88 (394)
T PF09710_consen 59 EQIKELEEK-KAYEESLKQLQLELDKYDDVL 88 (394)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHH
T ss_conf 897543555-666766666663221344432
No 16
>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway .
Probab=25.03 E-value=20 Score=15.23 Aligned_cols=30 Identities=40% Similarity=0.520 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 988999999999987339999999998899
Q T0605 35 LRQRDALIDELELELDQKDELIQMLQNELD 64 (72)
Q Consensus 35 lr~rDe~I~~LE~ELdeKD~lIr~LqnELD 64 (72)
+..-.+-|+.|+.+|.+|...+.-|+.|+.
T Consensus 125 ~~~l~~~~~~l~eel~ek~k~~e~l~DE~~ 154 (194)
T PF08614_consen 125 LTQLQEKIKDLEEELKEKNKALETLQDELL 154 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 999999999999999999988999998999
No 17
>PF05739 SNARE: SNARE domain; InterPro: IPR000727 The process of vesicular fusion with target membranes depends on a set of SNAREs (SNAP-Receptors), which are associated with the fusing membranes , . Target SNAREs (t-SNAREs) are localised on the target membrane and belong to two different families, the syntaxin-like family and the SNAP-25 like family. One member of each family, together with a v-SNARE localised on the vesicular membrane, are required for fusion. The Syntaxins are type-I transmembrane proteins that contain several regions with coiled-coil propensity in their cytosolic part, the SNARE motif. SNAP-25 (IPR000928 from INTERPRO) is a protein consisting of two coiled-coil regions, which is associated with the membrane by lipid anchors. SNARE motifs assemble into parallel four helix bundles stabilised by the burial of these hydrophobic helix faces in the bundle core. Monomeric SNARE motifs are disordered so this assembly reaction is accompanied by a dramatic increase in alpha-helical secondary structure . The parallel arrangement of SNARE motifs within complexes bring the transmembrane anchors, and the two membranes, into close proximity. Recently, it was shown that the two coiled-coil regions of SNAP-25 and one of the coiled-coil regions of the syntaxins are related . This domain is found in both Syntaxin and SNAP-25 families as well as in other proteins.; PDB: 1gl2_B 2nps_B 3b5n_F 1fio_A 1l4a_B 1hvv_B 1jth_B 3c98_B 1sfc_F 1urq_B ....
Probab=24.70 E-value=20 Score=15.19 Aligned_cols=50 Identities=20% Similarity=0.370 Sum_probs=45.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 01899999998889999889999999999873399999999988998986
Q T0605 19 GSLRDLQYALQEKIEELRQRDALIDELELELDQKDELIQMLQNELDKYRS 68 (72)
Q Consensus 19 gslrdLq~aL~~K~eElr~rDe~I~~LE~ELdeKD~lIr~LqnELDKyRs 68 (72)
.++.+|+-++..=-.++..-.++|+.++-.++.-..-++.-..+|.|+..
T Consensus 11 ~~i~~l~~~~~~i~~ev~~Q~~~ld~i~~~~~~~~~~l~~~~~~L~k~~~ 60 (63)
T PF05739_consen 11 QSIQELKQMFQDIGTEVEEQNEMLDRIENNVDNANENLKRANKKLKKALK 60 (63)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999999999813568999999899999999999999999987
No 18
>PF12418 AcylCoA_DH_N: Acyl-CoA dehydrogenase N terminal
Probab=22.85 E-value=15 Score=15.92 Aligned_cols=15 Identities=40% Similarity=0.771 Sum_probs=12.1
Q ss_pred CCCHHHHHHHHHHHH
Q ss_conf 101899999998889
Q T0605 18 RGSLRDLQYALQEKI 32 (72)
Q Consensus 18 ~gslrdLq~aL~~K~ 32 (72)
++.+||++|.|++-.
T Consensus 4 ~ap~rD~~F~L~evl 18 (34)
T PF12418_consen 4 KAPLRDMQFVLYEVL 18 (34)
T ss_pred CCCHHHHHHHHHHHH
T ss_conf 876889998999998
No 19
>PF08687 ASD2: Apx/Shroom domain ASD2; InterPro: IPR014799 This region is found in the actin binding protein Shroom, which mediates apical constriction in epithelial cells and is required for neural tube closure.
Probab=22.74 E-value=22 Score=14.96 Aligned_cols=14 Identities=36% Similarity=0.622 Sum_probs=10.8
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 99998899898651
Q T0605 57 QMLQNELDKYRSVI 70 (72)
Q Consensus 57 r~LqnELDKyRsvv 70 (72)
.|--||+||||..+
T Consensus 133 ~c~P~E~~Kfr~fi 146 (264)
T PF08687_consen 133 KCKPNEFEKFRMFI 146 (264)
T ss_pred HCCHHHHHHHHHHH
T ss_conf 63877899999999
No 20
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport .; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=21.55 E-value=23 Score=14.82 Aligned_cols=29 Identities=24% Similarity=0.298 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999873399999999988998986
Q T0605 40 ALIDELELELDQKDELIQMLQNELDKYRS 68 (72)
Q Consensus 40 e~I~~LE~ELdeKD~lIr~LqnELDKyRs 68 (72)
....+||.|+..--..|.-|+.|+++.+.
T Consensus 94 ~Rn~ELEeelr~~~~~~~~Lr~Ev~~Lk~ 122 (249)
T PF08172_consen 94 QRNAELEEELRKLYQEVSSLRQEVESLKA 122 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999999988789999999999998
Done!