Query psy4241
Match_columns 305
No_of_seqs 255 out of 690
Neff 6.4
Searched_HMMs 46136
Date Fri Aug 16 20:26:08 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4241.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4241hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1340|consensus 99.8 3.5E-19 7.7E-24 160.5 10.0 142 88-232 34-206 (218)
2 smart00741 SapB Saposin (B) Do 99.5 5.1E-14 1.1E-18 104.7 6.7 75 92-167 2-76 (76)
3 KOG1340|consensus 99.3 2.6E-12 5.7E-17 116.1 6.0 117 54-172 86-208 (218)
4 smart00162 SAPA Saposin/surfac 99.2 2.8E-12 6.1E-17 82.5 -0.4 34 48-81 1-34 (34)
5 PF02199 SapA: Saposin A-type 99.0 2.1E-11 4.5E-16 79.0 -1.5 34 48-81 1-34 (34)
6 PF03489 SapB_2: Saposin-like 98.9 2.6E-09 5.5E-14 69.5 3.6 35 133-167 1-35 (35)
7 PF03489 SapB_2: Saposin-like 98.6 4.1E-08 8.9E-13 63.8 4.1 34 196-229 2-35 (35)
8 PF05184 SapB_1: Saposin-like 98.6 2.1E-08 4.5E-13 66.4 2.5 38 91-128 2-39 (39)
9 smart00741 SapB Saposin (B) Do 97.5 0.00011 2.4E-09 54.0 3.6 40 190-229 33-76 (76)
10 PF05184 SapB_1: Saposin-like 96.8 0.00015 3.2E-09 47.8 -1.3 32 256-287 2-33 (39)
11 KOG3770|consensus 85.7 1.1 2.3E-05 46.4 4.6 81 90-171 23-106 (577)
12 PF11938 DUF3456: TLR4 regulat 81.0 6.1 0.00013 33.8 6.8 73 91-163 2-145 (151)
13 PF10208 Armet: Degradation ar 50.6 5.4 0.00012 34.5 0.1 72 92-164 1-81 (154)
14 PF01034 Syndecan: Syndecan do 27.4 23 0.0005 26.2 0.3 13 3-17 33-45 (64)
15 PF13798 PCYCGC: Protein of un 27.4 83 0.0018 27.4 3.7 35 89-123 110-144 (158)
16 KOG4260|consensus 27.0 1.8E+02 0.0039 27.9 6.1 82 89-170 26-134 (350)
17 PF08006 DUF1700: Protein of u 26.9 1.1E+02 0.0024 26.4 4.6 49 113-165 3-51 (181)
18 KOG4154|consensus 25.8 1.3E+02 0.0029 25.7 4.5 77 88-165 27-112 (178)
19 TIGR02531 yecD_yerC TrpR-relat 24.0 1.6E+02 0.0035 22.9 4.5 61 100-169 5-65 (88)
No 1
>KOG1340|consensus
Probab=99.79 E-value=3.5e-19 Score=160.45 Aligned_cols=142 Identities=25% Similarity=0.448 Sum_probs=115.4
Q ss_pred CCCCcchhhHHHHHHHHHHhcccchHHHHHHHHHhccCcCCCcchhhhhHHHHHhhHHHHHHHHHcCCChhhhccccccc
Q psy4241 88 DGDDVCKICKNMVGQARDQLQSNETQQDLKAVFEGSCNLVPVKVIREGCDKLVDEFVPELIEVLSSQMNPDVVCSVAGLC 167 (305)
Q Consensus 88 ~~~~~C~~C~~vV~~v~~~L~~n~te~~I~~~L~~~C~~lP~~~~~~~C~~lV~~Y~p~II~~L~~~~~P~~IC~~lglC 167 (305)
..+..|+.|+.+|+.+..++.++ +.+|++.|+..|+.+|. ....+|..||+.|+|.||+.+.++++|+.||+.+++|
T Consensus 34 r~~~~C~lCe~~v~~i~~~~~~~--~~~i~~~l~~~Ckkl~~-~~~~~C~~fv~~y~~~ii~~l~~~~~P~~vC~~l~lC 110 (218)
T KOG1340|consen 34 RSAEVCELCELVVKRIQEYLDKN--QNELKEDLHAECKKLPK-AIPFECLSFVDSYLDPIIKELESGTAPEDVCKKLNLC 110 (218)
T ss_pred CccchhHHHHHHHHHHHHhhccc--HHHHHHHHHHHHHHhcc-cchHHHHHHHHHhhhHHHHHHHhccCHHHHHHHhccC
Confidence 34778999999999999999997 89999999999999996 3444999999999999999999999999999999999
Q ss_pred cCcchhhh-----------------hhhhccccccc-cc----------cccccc---hHHHHHHHHhhhchHHHHHhcC
Q psy4241 168 NNAAIDRL-----------------LLTAAGDHRDL-HS----------FPTRRL---KKKKKRCLLTEETVTPKVLSSQ 216 (305)
Q Consensus 168 ~~~~~~~~-----------------l~~~~~~~L~~-~~----------~~C~~l---~~~ck~~V~~Y~~~Ii~~L~~~ 216 (305)
+.+..... .+..+...|+. +. ..|..+ ...|++||+.|+|.||.+|.++
T Consensus 111 ~~~~~~~~~~~~~~~~~~~C~~C~~~V~~~~~~l~d~~~~k~~~~~~~~~~ck~l~~~~~~Ck~fV~~y~p~~i~~l~~~ 190 (218)
T KOG1340|consen 111 SASAGPVSEVFASQPAAGECELCRETVTEADTKLQDKPKTKGKIVSLLLKSCKSLPNYEQKCKQFVHEYGPQLITLLEEG 190 (218)
T ss_pred CcccchhhhhhhhcccccccHHHHHHHHHHHHhcccchhHHHHHHHHHHhhccCCccchhHHHHHHHHhccHHHHHHHHh
Confidence 96332110 01111112222 11 367666 4469999999999999999999
Q ss_pred CChHHHhhhcCCCccc
Q psy4241 217 MNPDVVCSVAGLCNNA 232 (305)
Q Consensus 217 ~~P~~VC~~iglC~~~ 232 (305)
++|++||+.+|.|+.+
T Consensus 191 ~~p~~vC~~l~~C~~~ 206 (218)
T KOG1340|consen 191 LDPHDVCTALGACPPA 206 (218)
T ss_pred hCchhHHHHhhcCCcc
Confidence 9999999999999953
No 2
>smart00741 SapB Saposin (B) Domains. Present in multiple copies in prosaposin and in pulmonary surfactant-associated protein B. In plant aspartic proteinases, a saposin domain is circularly permuted. This causes the prediction algorithm to predict two such domains, where only one is truly present.
Probab=99.49 E-value=5.1e-14 Score=104.71 Aligned_cols=75 Identities=32% Similarity=0.826 Sum_probs=72.7
Q ss_pred cchhhHHHHHHHHHHhcccchHHHHHHHHHhccCcCCCcchhhhhHHHHHhhHHHHHHHHHcCCChhhhccccccc
Q psy4241 92 VCKICKNMVGQARDQLQSNETQQDLKAVFEGSCNLVPVKVIREGCDKLVDEFVPELIEVLSSQMNPDVVCSVAGLC 167 (305)
Q Consensus 92 ~C~~C~~vV~~v~~~L~~n~te~~I~~~L~~~C~~lP~~~~~~~C~~lV~~Y~p~II~~L~~~~~P~~IC~~lglC 167 (305)
.|.+|+.+|+.++.++.++.+++.|.++++++|+.+|. .+...|+.+|+.|+|.|++.|.++++|++||..+|+|
T Consensus 2 ~C~~C~~~v~~~~~~~~~~~~~~~i~~~~~~~C~~~~~-~~~~~C~~~v~~~~~~ii~~i~~~~~p~~iC~~l~~C 76 (76)
T smart00741 2 LCELCEDVVKQLENLLKDNKTEEEIKKALEKVCKKLPK-SLSDQCKEFVDQYGPEIIDLLEQGLDPKDVCQKLGLC 76 (76)
T ss_pred cChHHHHHHHHHHHHHHhchHHHHHHHHHHHHHHHcCH-HHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHcCCC
Confidence 69999999999999999999999999999999999995 6899999999999999999999999999999999998
No 3
>KOG1340|consensus
Probab=99.30 E-value=2.6e-12 Score=116.08 Aligned_cols=117 Identities=24% Similarity=0.480 Sum_probs=95.7
Q ss_pred ccchhh---hccCccccccCcCCCCcchhhhcccc--CCCCCCcchhhHHHHHHHHHHhcc-cchHHHHHHHHHhccCcC
Q psy4241 54 RGQSFW---CEDLASAASCGATGHCIQAVWSHMKV--KEDGDDVCKICKNMVGQARDQLQS-NETQQDLKAVFEGSCNLV 127 (305)
Q Consensus 54 ~gP~~w---Cq~l~pa~iC~~l~lC~~~~w~~~~~--~~~~~~~C~~C~~vV~~v~~~L~~-n~te~~I~~~L~~~C~~l 127 (305)
|+|.+. =+...|..+|..+++|+........+ ....+..|..|...|+++...|.+ +.++..+.....+.|..+
T Consensus 86 y~~~ii~~l~~~~~P~~vC~~l~lC~~~~~~~~~~~~~~~~~~~C~~C~~~V~~~~~~l~d~~~~k~~~~~~~~~~ck~l 165 (218)
T KOG1340|consen 86 YLDPIIKELESGTAPEDVCKKLNLCSASAGPVSEVFASQPAAGECELCRETVTEADTKLQDKPKTKGKIVSLLLKSCKSL 165 (218)
T ss_pred hhhHHHHHHHhccCHHHHHHHhccCCcccchhhhhhhhcccccccHHHHHHHHHHHHhcccchhHHHHHHHHHHhhccCC
Confidence 667666 33467999999999999532111101 123378999999999999999999 778888888888999888
Q ss_pred CCcchhhhhHHHHHhhHHHHHHHHHcCCChhhhccccccccCcch
Q psy4241 128 PVKVIREGCDKLVDEFVPELIEVLSSQMNPDVVCSVAGLCNNAAI 172 (305)
Q Consensus 128 P~~~~~~~C~~lV~~Y~p~II~~L~~~~~P~~IC~~lglC~~~~~ 172 (305)
| .++..|+.||++|+|.||..+.++++|++||+.+|.|+++..
T Consensus 166 ~--~~~~~Ck~fV~~y~p~~i~~l~~~~~p~~vC~~l~~C~~~~~ 208 (218)
T KOG1340|consen 166 P--NYEQKCKQFVHEYGPQLITLLEEGLDPHDVCTALGACPPAAS 208 (218)
T ss_pred c--cchhHHHHHHHHhccHHHHHHHHhhCchhHHHHhhcCCcccc
Confidence 7 488899999999999999999999999999999999996543
No 4
>smart00162 SAPA Saposin/surfactant protein-B A-type DOMAIN. Present as four and three degenerate copies, respectively, in prosaposin and surfactant protein B. Single copies in acid sphingomyelinase, NK-lysin amoebapores and granulysin. Putative phospholipid membrane binding domains.
Probab=99.18 E-value=2.8e-12 Score=82.45 Aligned_cols=34 Identities=44% Similarity=1.116 Sum_probs=32.2
Q ss_pred CcccccccchhhhccCccccccCcCCCCcchhhh
Q psy4241 48 SSPECARGQSFWCEDLASAASCGATGHCIQAVWS 81 (305)
Q Consensus 48 g~~~C~~gP~~wCq~l~pa~iC~~l~lC~~~~w~ 81 (305)
|.++|++||+|||||++++..|++++||.+.+|+
T Consensus 1 G~~~CtwGPsyWC~~~~~A~~C~Av~hC~~~VW~ 34 (34)
T smart00162 1 GPKRCTWGPSVWCQNLETASQCNAVKHCLQRVWS 34 (34)
T ss_pred CcccccCCChhhcCCHHHHHHcCchhHHHhhccC
Confidence 6789999999999999999999999999999884
No 5
>PF02199 SapA: Saposin A-type domain; InterPro: IPR003119 Saposins are small lysosomal proteins that serve as activators of various lysosomal lipid-degrading enzymes []. They probably act by isolating the lipid substrate from the membrane surroundings, thus making it more accessible to the soluble degradative enzymes. All mammalian saposins are synthesized as a single precursor molecule (prosaposin) which contains four Saposin-B domains, yielding the active saposins after proteolytic cleavage, and two Saposin-A domains that are removed in the activation reaction. The Saposin-B domains also occur in other proteins, many of them active in the lysis of membranes [, ]. The saposin A-type domain may play a role in targeting, as propeptides containing the saposin A-type domain of the C terminus of prosaposin and of the N-terminal part of pulmonary surfactant-associated protein B are involved in the transport to the lysosome and to secretory granules (lamellar bodies, which are lysosomal-like organelles), respectively [].
Probab=99.02 E-value=2.1e-11 Score=78.98 Aligned_cols=34 Identities=44% Similarity=1.146 Sum_probs=32.4
Q ss_pred CcccccccchhhhccCccccccCcCCCCcchhhh
Q psy4241 48 SSPECARGQSFWCEDLASAASCGATGHCIQAVWS 81 (305)
Q Consensus 48 g~~~C~~gP~~wCq~l~pa~iC~~l~lC~~~~w~ 81 (305)
|.+.|++||+|||+|+++|..|++++||.+.+|+
T Consensus 1 G~~~C~~GP~yWC~~~~~A~~CgA~~hC~~~vW~ 34 (34)
T PF02199_consen 1 GPDQCTWGPSYWCQSLETAKECGAVKHCQQHVWN 34 (34)
T ss_pred CCCccCCCCCccccCHHHHHHcCHHHHHHHhhcC
Confidence 6789999999999999999999999999999984
No 6
>PF03489 SapB_2: Saposin-like type B, region 2; InterPro: IPR008138 Saposins are small lysosomal proteins that serve as activators of various lysosomal lipid-degrading enzymes []. They probably act by isolating the lipid substrate from the membrane surroundings, thus making it more accessible to the soluble degradative enzymes. All mammalian saposins are synthesized as a single precursor molecule (prosaposin) which contains four Saposin-B domains, yielding the active saposins after proteolytic cleavage, and two Saposin-A domains that are removed in the activation reaction. The Saposin-B domains also occur in other proteins, many of them active in the lysis of membranes [, ].; PDB: 3BQQ_A 2RB3_B 2R0R_A 3BQP_A 2R1Q_A 1NKL_A 1L9L_A 1QDM_C 3RFI_A 4DDJ_A ....
Probab=98.85 E-value=2.6e-09 Score=69.48 Aligned_cols=35 Identities=34% Similarity=0.974 Sum_probs=33.7
Q ss_pred hhhhHHHHHhhHHHHHHHHHcCCChhhhccccccc
Q psy4241 133 REGCDKLVDEFVPELIEVLSSQMNPDVVCSVAGLC 167 (305)
Q Consensus 133 ~~~C~~lV~~Y~p~II~~L~~~~~P~~IC~~lglC 167 (305)
+++|+.+|++|+|.||++|.++++|+.||+.+|+|
T Consensus 1 ~~~C~~~V~~y~~~ii~~l~~~~~p~~iC~~i~~C 35 (35)
T PF03489_consen 1 SDECKNFVDQYGPQIIQLLEKQLDPQQICTKIGLC 35 (35)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTSTHHHHHHHTTSS
T ss_pred CcHHHHHHHHHHHHHHHHHHhcCChHHHHHHcCCC
Confidence 46899999999999999999999999999999999
No 7
>PF03489 SapB_2: Saposin-like type B, region 2; InterPro: IPR008138 Saposins are small lysosomal proteins that serve as activators of various lysosomal lipid-degrading enzymes []. They probably act by isolating the lipid substrate from the membrane surroundings, thus making it more accessible to the soluble degradative enzymes. All mammalian saposins are synthesized as a single precursor molecule (prosaposin) which contains four Saposin-B domains, yielding the active saposins after proteolytic cleavage, and two Saposin-A domains that are removed in the activation reaction. The Saposin-B domains also occur in other proteins, many of them active in the lysis of membranes [, ].; PDB: 3BQQ_A 2RB3_B 2R0R_A 3BQP_A 2R1Q_A 1NKL_A 1L9L_A 1QDM_C 3RFI_A 4DDJ_A ....
Probab=98.63 E-value=4.1e-08 Score=63.76 Aligned_cols=34 Identities=24% Similarity=0.484 Sum_probs=32.4
Q ss_pred HHHHHHHHhhhchHHHHHhcCCChHHHhhhcCCC
Q psy4241 196 KKKKRCLLTEETVTPKVLSSQMNPDVVCSVAGLC 229 (305)
Q Consensus 196 ~~ck~~V~~Y~~~Ii~~L~~~~~P~~VC~~iglC 229 (305)
..|+.||++|+|.|+++|.++++|+.||+.+|+|
T Consensus 2 ~~C~~~V~~y~~~ii~~l~~~~~p~~iC~~i~~C 35 (35)
T PF03489_consen 2 DECKNFVDQYGPQIIQLLEKQLDPQQICTKIGLC 35 (35)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTSTHHHHHHHTTSS
T ss_pred cHHHHHHHHHHHHHHHHHHhcCChHHHHHHcCCC
Confidence 3589999999999999999999999999999999
No 8
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=98.62 E-value=2.1e-08 Score=66.42 Aligned_cols=38 Identities=37% Similarity=0.775 Sum_probs=36.7
Q ss_pred CcchhhHHHHHHHHHHhcccchHHHHHHHHHhccCcCC
Q psy4241 91 DVCKICKNMVGQARDQLQSNETQQDLKAVFEGSCNLVP 128 (305)
Q Consensus 91 ~~C~~C~~vV~~v~~~L~~n~te~~I~~~L~~~C~~lP 128 (305)
..|++|+++|++++++|++|.|+++|+++|+++|+.+|
T Consensus 2 ~~C~~C~~~v~~i~~~l~~~~t~~~I~~~l~~~C~~lP 39 (39)
T PF05184_consen 2 DECDICKFVVKEIEKLLKNNKTEEEIKKALEKACNKLP 39 (39)
T ss_dssp HHHHHHHHHHHHHHHHHHSTCHHHHHHHHHHHHHTTSC
T ss_pred CcchHHHHHHHHHHHHHHcCccHHHHHHHHHHHHhhCc
Confidence 46999999999999999999999999999999999998
No 9
>smart00741 SapB Saposin (B) Domains. Present in multiple copies in prosaposin and in pulmonary surfactant-associated protein B. In plant aspartic proteinases, a saposin domain is circularly permuted. This causes the prediction algorithm to predict two such domains, where only one is truly present.
Probab=97.49 E-value=0.00011 Score=54.01 Aligned_cols=40 Identities=23% Similarity=0.407 Sum_probs=35.6
Q ss_pred ccccc----hHHHHHHHHhhhchHHHHHhcCCChHHHhhhcCCC
Q psy4241 190 PTRRL----KKKKKRCLLTEETVTPKVLSSQMNPDVVCSVAGLC 229 (305)
Q Consensus 190 ~C~~l----~~~ck~~V~~Y~~~Ii~~L~~~~~P~~VC~~iglC 229 (305)
.|..+ ...|+.+++.|+|.|++.+.+.++|+.||+.+|+|
T Consensus 33 ~C~~~~~~~~~~C~~~v~~~~~~ii~~i~~~~~p~~iC~~l~~C 76 (76)
T smart00741 33 VCKKLPKSLSDQCKEFVDQYGPEIIDLLEQGLDPKDVCQKLGLC 76 (76)
T ss_pred HHHHcCHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHcCCC
Confidence 46555 34689999999999999999999999999999998
No 10
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=96.84 E-value=0.00015 Score=47.76 Aligned_cols=32 Identities=9% Similarity=0.313 Sum_probs=29.7
Q ss_pred CCCcchHHHHHHHHHHHhhhchhhhhcCCCCc
Q psy4241 256 SDCKNCASFADLVTKKFNAASKQDVTNDPFGS 287 (305)
Q Consensus 256 ~~C~~Ce~vV~~v~~~L~~n~ted~~~~~~~~ 287 (305)
..|.+|+++|+++++.|.+|.|++.|.++|++
T Consensus 2 ~~C~~C~~~v~~i~~~l~~~~t~~~I~~~l~~ 33 (39)
T PF05184_consen 2 DECDICKFVVKEIEKLLKNNKTEEEIKKALEK 33 (39)
T ss_dssp HHHHHHHHHHHHHHHHHHSTCHHHHHHHHHHH
T ss_pred CcchHHHHHHHHHHHHHHcCccHHHHHHHHHH
Confidence 47999999999999999999999999998875
No 11
>KOG3770|consensus
Probab=85.72 E-value=1.1 Score=46.38 Aligned_cols=81 Identities=19% Similarity=0.402 Sum_probs=70.4
Q ss_pred CCcchhhHHHHHHHHHHhcccchHHHHHHHHHhccCcCCCcchhhhhHHHHHhhHHHHHHHHHcCC-Chhhhcccc-c-c
Q psy4241 90 DDVCKICKNMVGQARDQLQSNETQQDLKAVFEGSCNLVPVKVIREGCDKLVDEFVPELIEVLSSQM-NPDVVCSVA-G-L 166 (305)
Q Consensus 90 ~~~C~~C~~vV~~v~~~L~~n~te~~I~~~L~~~C~~lP~~~~~~~C~~lV~~Y~p~II~~L~~~~-~P~~IC~~l-g-l 166 (305)
...|..|+..++.++..++...+...|...+-.+|+.+.. .-...|+.+++.|...++..+.... +|.+||..+ + -
T Consensus 23 ~~~c~~c~~~~~~~~~~~~~~~~~~~v~v~~~~~c~~~~~-~~~~vc~~~~~~f~~~f~~v~~r~~~~~~~icg~~l~~~ 101 (577)
T KOG3770|consen 23 KAQCTFCEKELSNAQKFPARISTNCTVIVFAVAVCELFVI-EPTPVCTWIIDEFNDEFFDVFVRSANSPEEICGHFLPDT 101 (577)
T ss_pred cchhhhhhhhhhhHHhhhhcccccchhhhhHHHHhccccc-cCcchhhHHHHHHHHHHHHHHHHHhcCHHHHhhcccCCc
Confidence 3489999999999999999999999999999999998775 4578999999999999999887755 899999764 4 6
Q ss_pred ccCcc
Q psy4241 167 CNNAA 171 (305)
Q Consensus 167 C~~~~ 171 (305)
|....
T Consensus 102 c~~~~ 106 (577)
T KOG3770|consen 102 CGDIV 106 (577)
T ss_pred ccccc
Confidence 87654
No 12
>PF11938 DUF3456: TLR4 regulator and MIR-interacting MSAP; InterPro: IPR021852 This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 182 to 356 amino acids in length.
Probab=81.02 E-value=6.1 Score=33.76 Aligned_cols=73 Identities=22% Similarity=0.471 Sum_probs=53.5
Q ss_pred CcchhhHHHHHHHHHHhcc---------------------------cchHHHHHHHHHhccCcCCC--------------
Q psy4241 91 DVCKICKNMVGQARDQLQS---------------------------NETQQDLKAVFEGSCNLVPV-------------- 129 (305)
Q Consensus 91 ~~C~~C~~vV~~v~~~L~~---------------------------n~te~~I~~~L~~~C~~lP~-------------- 129 (305)
..|..|+.+|..++..|.. ..++..+.++|+++|+.+..
T Consensus 2 ~~C~~C~~l~~el~~~l~~~~~~~~v~~~~~r~d~~g~~~~~~~~y~~SE~~l~EvlE~vC~~~~~Y~~~~~~~~~~~~~ 81 (151)
T PF11938_consen 2 LKCSACRALVEELEHRLAKTDPKKFVDVGGFRLDPDGERKKKKIPYARSELRLVEVLENVCEKMKDYVLHKDKSTGKRVY 81 (151)
T ss_pred CcchHHHHHHHHHHHHHHHhCCcCceeccccccccccccccccCccccchhHHHHHHHHHccCcccceeeecCCCCceEE
Confidence 4699999999988876643 13556778999999986430
Q ss_pred --------------------------cchhhhhHHHHHhhHHHHHHHHHcCCC----hhhhccc
Q psy4241 130 --------------------------KVIREGCDKLVDEFVPELIEVLSSQMN----PDVVCSV 163 (305)
Q Consensus 130 --------------------------~~~~~~C~~lV~~Y~p~II~~L~~~~~----P~~IC~~ 163 (305)
+.+...|..+|+.|...|++++.+... -+.+|..
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~C~~ilEe~Ed~i~~~~~~~~~~~~l~~~LC~~ 145 (151)
T PF11938_consen 82 KRMSTTGGTNPELSEKDVKVDPSDENKRLKFYCERILEEYEDEIEEWFFSEQDEDDLEEWLCSE 145 (151)
T ss_pred EecCCCcCcccccccccceeecHHHHhHHHHHHHHHHHHhHHHHHHHHHhcCCccCHHHHhhhc
Confidence 013568999999999999999998653 1345653
No 13
>PF10208 Armet: Degradation arginine-rich protein for mis-folding; InterPro: IPR019345 This entry represents Armet proteins (aka mesencephalic astrocyte-derived neurotrophic factor or arginine-rich protein). Armet is a small protein of approximately 170 residues which contains four di-sulphide bridges that are highly conserved from nematodes to humans. Armet is a soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress []. Armet from Rattus norvegicus (Rat) selectively promotes the survival of dopaminergic neurons of the ventral mid-brain. It modulates GABAergic transmission to the dopaminergic neurons of the substantia nigra, and enhances spontaneous, as well as evoked, GABAergic inhibitory postsynaptic currents in dopaminergic neurons [].; PDB: 2KVE_A 2KVD_A 2W51_A 2W50_B 2RQY_A.
Probab=50.57 E-value=5.4 Score=34.54 Aligned_cols=72 Identities=15% Similarity=0.315 Sum_probs=51.5
Q ss_pred cchhhHHHHHHHHHHhcccc---hHHHHHHHHHhccCcCCCcchhhhhHHHHHh------hHHHHHHHHHcCCChhhhcc
Q psy4241 92 VCKICKNMVGQARDQLQSNE---TQQDLKAVFEGSCNLVPVKVIREGCDKLVDE------FVPELIEVLSSQMNPDVVCS 162 (305)
Q Consensus 92 ~C~~C~~vV~~v~~~L~~n~---te~~I~~~L~~~C~~lP~~~~~~~C~~lV~~------Y~p~II~~L~~~~~P~~IC~ 162 (305)
.|.+|..+++.+.+.|.... +...|+++|.+.|...-++ -...|-.+-.. -...+.+-|.-++.++.||.
T Consensus 1 ~CEVCv~~l~~f~~sl~~~~~~~~~~~ie~~l~~~C~~~k~k-enr~CYyig~~~dsat~il~evs~Pls~~mP~~KICe 79 (154)
T PF10208_consen 1 ECEVCVKFLDRFYASLKDKDVKFDPDKIEKELRKFCKKAKGK-ENRFCYYIGATEDSATGILNEVSKPLSWHMPVEKICE 79 (154)
T ss_dssp STHHHHCCHHHHHHHHHHTTS-SSCCHHHHHHHHHHCTS-CH-HHHHHHHTT-STTTSHCCCHHHHHHHCTTSSCCCHHH
T ss_pred CCcchHHHHHHHHHHhhcccccCCHHHHHHHHHHHHHhccCc-ccceEeeecccchHHHHHHHhhccccccCCCHHHHHH
Confidence 49999999999999884433 5578999999999988763 45566443221 12346677777888899997
Q ss_pred cc
Q psy4241 163 VA 164 (305)
Q Consensus 163 ~l 164 (305)
.+
T Consensus 80 kL 81 (154)
T PF10208_consen 80 KL 81 (154)
T ss_dssp HH
T ss_pred HH
Confidence 65
No 14
>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]. Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.
Probab=27.42 E-value=23 Score=26.23 Aligned_cols=13 Identities=69% Similarity=1.140 Sum_probs=1.7
Q ss_pred eeeeccccCCCCCCC
Q psy4241 3 IYRVRKKKTDNGSLQ 17 (305)
Q Consensus 3 ~~~~~~~~~~~~~~~ 17 (305)
|||.||| |.||.+
T Consensus 33 iyR~rkk--dEGSY~ 45 (64)
T PF01034_consen 33 IYRMRKK--DEGSYD 45 (64)
T ss_dssp ----S--------SS
T ss_pred HHHHHhc--CCCCcc
Confidence 6887655 778764
No 15
>PF13798 PCYCGC: Protein of unknown function with PCYCGC motif
Probab=27.41 E-value=83 Score=27.44 Aligned_cols=35 Identities=14% Similarity=0.395 Sum_probs=31.3
Q ss_pred CCCcchhhHHHHHHHHHHhcccchHHHHHHHHHhc
Q psy4241 89 GDDVCKICKNMVGQARDQLQSNETQQDLKAVFEGS 123 (305)
Q Consensus 89 ~~~~C~~C~~vV~~v~~~L~~n~te~~I~~~L~~~ 123 (305)
-+..|.+|..+..+.-.+.++..+..+|++++++-
T Consensus 110 Hg~~C~vCl~ia~~a~~~~~~Gks~~eIR~~ID~k 144 (158)
T PF13798_consen 110 HGTRCGVCLDIAVQAVQMYQEGKSPKEIRQYIDEK 144 (158)
T ss_pred cccccHHHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 35679999999999999999999999999999863
No 16
>KOG4260|consensus
Probab=27.03 E-value=1.8e+02 Score=27.88 Aligned_cols=82 Identities=20% Similarity=0.468 Sum_probs=58.1
Q ss_pred CCCcchhhHHHHHHHHHHhcc---------------------cchHHHHHHHHHhccCcCCCcchhhhhHHHHHhhHHHH
Q psy4241 89 GDDVCKICKNMVGQARDQLQS---------------------NETQQDLKAVFEGSCNLVPVKVIREGCDKLVDEFVPEL 147 (305)
Q Consensus 89 ~~~~C~~C~~vV~~v~~~L~~---------------------n~te~~I~~~L~~~C~~lP~~~~~~~C~~lV~~Y~p~I 147 (305)
.+..|-.|..+|..+..-|.. ..++..+.+.|+++|+.-..+...-.|..+++.....|
T Consensus 26 kp~pCrtC~~LVssFn~GlerT~r~hfaGGdTAWEEknL~kYk~SE~RLvEilEglCsks~~~n~DfeCh~lle~hEell 105 (350)
T KOG4260|consen 26 KPEPCRTCRGLVSSFNEGLERTARHHFAGGDTAWEEKNLSKYKTSETRLVEILEGLCSKSSLPNMDFECHTLLEKHEELL 105 (350)
T ss_pred CCCCchHHHHHHHHHHHHHHHHhhhccCCCchhhhhhhhhhccccchhHHHHHHHhhhccCCCCCChHHHHHHHHHHHHH
Confidence 457799999999988765543 23455678999999998533234559999999988888
Q ss_pred HHHHHcCC--Chhh---hcc-ccccccCc
Q psy4241 148 IEVLSSQM--NPDV---VCS-VAGLCNNA 170 (305)
Q Consensus 148 I~~L~~~~--~P~~---IC~-~lglC~~~ 170 (305)
-++...+. .|+. +|. .+.+|-+.
T Consensus 106 E~w~~hkq~e~Pdl~~WlCvdqLkvCCp~ 134 (350)
T KOG4260|consen 106 EEWWYHKQHESPDLFNWLCVDQLKVCCPD 134 (350)
T ss_pred HHHHHHhhcCCchHHhHhhhhhheeccCC
Confidence 77766543 4553 564 46776544
No 17
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=26.89 E-value=1.1e+02 Score=26.43 Aligned_cols=49 Identities=8% Similarity=0.163 Sum_probs=36.7
Q ss_pred HHHHHHHHHhccCcCCCcchhhhhHHHHHhhHHHHHHHHHcCCChhhhccccc
Q psy4241 113 QQDLKAVFEGSCNLVPVKVIREGCDKLVDEFVPELIEVLSSQMNPDVVCSVAG 165 (305)
Q Consensus 113 e~~I~~~L~~~C~~lP~~~~~~~C~~lV~~Y~p~II~~L~~~~~P~~IC~~lg 165 (305)
+++..+.|++.=+.+| ..+-+.+++.|...+-+..+++.+-++++..+|
T Consensus 3 k~efL~~L~~~L~~lp----~~e~~e~l~~Y~e~f~d~~~~G~sEeeii~~LG 51 (181)
T PF08006_consen 3 KNEFLNELEKYLKKLP----EEEREEILEYYEEYFDDAGEEGKSEEEIIAELG 51 (181)
T ss_pred HHHHHHHHHHHHHcCC----HHHHHHHHHHHHHHHHHhhhCCCCHHHHHHHcC
Confidence 3444444444334577 457888899999999999988899999999887
No 18
>KOG4154|consensus
Probab=25.81 E-value=1.3e+02 Score=25.68 Aligned_cols=77 Identities=17% Similarity=0.407 Sum_probs=50.9
Q ss_pred CCCCcchhhHHHHHHHHHHhcccc---hHHHHHHHHHhccCcCCCcchhhhhHHH--HHhhHHHHH----HHHHcCCChh
Q psy4241 88 DGDDVCKICKNMVGQARDQLQSNE---TQQDLKAVFEGSCNLVPVKVIREGCDKL--VDEFVPELI----EVLSSQMNPD 158 (305)
Q Consensus 88 ~~~~~C~~C~~vV~~v~~~L~~n~---te~~I~~~L~~~C~~lP~~~~~~~C~~l--V~~Y~p~II----~~L~~~~~P~ 158 (305)
.....|.+|-..++.+-+-|.+.. .-.+|+.++-++|..--++ -...|-.+ .+.-...|| .-|..++..+
T Consensus 27 lk~~dcevci~~l~rf~~~l~d~d~~~~~~~ie~~~~kfck~~k~k-e~r~cyyig~~ddaat~iinelskpla~~ip~e 105 (178)
T KOG4154|consen 27 LKEEDCEVCIKTLGRFADDLDDRDTKFDPAQIENAFIKFCKAAKGK-EHRFCYYIGALDDAATGIINELSKPLAHHIPAE 105 (178)
T ss_pred CCcccchHHHHHHHHHHHhhccccccCCHHHHHHHHHHHHHHhcCC-cceeeeeeccchHHHHHHHHHhcchhhccCcHH
Confidence 345679999999999988888763 3478999998888776553 33444332 122233344 4455577888
Q ss_pred hhccccc
Q psy4241 159 VVCSVAG 165 (305)
Q Consensus 159 ~IC~~lg 165 (305)
.||.++.
T Consensus 106 kiceklk 112 (178)
T KOG4154|consen 106 KICEKLK 112 (178)
T ss_pred HHHHHHH
Confidence 9998663
No 19
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=24.00 E-value=1.6e+02 Score=22.92 Aligned_cols=61 Identities=8% Similarity=0.176 Sum_probs=47.3
Q ss_pred HHHHHHHhcccchHHHHHHHHHhccCcCCCcchhhhhHHHHHhhHHHHHHHHHcCCChhhhccccccccC
Q psy4241 100 VGQARDQLQSNETQQDLKAVFEGSCNLVPVKVIREGCDKLVDEFVPELIEVLSSQMNPDVVCSVAGLCNN 169 (305)
Q Consensus 100 V~~v~~~L~~n~te~~I~~~L~~~C~~lP~~~~~~~C~~lV~~Y~p~II~~L~~~~~P~~IC~~lglC~~ 169 (305)
++.+-+.+.+..+.+++..+++.+|..-.. + .+-+. -.|..++.++.+..+|...+|.=.+
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~l~t~~e~---~----~Ls~R--~~I~~ll~~G~S~~eIA~~LgISrs 65 (88)
T TIGR02531 5 LDELFDAILTLKNREECYRFFDDIATINEI---Q----SLAQR--LQVAKMLKQGKTYSDIEAETGASTA 65 (88)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHhCCHHHH---H----hhhHH--HHHHHHHHCCCCHHHHHHHHCcCHH
Confidence 445556677778999999999999986542 3 25555 6788899999999999999987654
Done!