Query psy14865
Match_columns 98
No_of_seqs 94 out of 103
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 22:46:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14865.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14865hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1826|consensus 99.4 2.2E-14 4.7E-19 132.4 0.8 86 12-97 1841-1927(2724)
2 PF14228 MOR2-PAG1_mid: Cell m 98.0 6.2E-06 1.3E-10 75.0 4.3 86 12-97 561-652 (1120)
3 KOG1826|consensus 97.6 6E-05 1.3E-09 71.6 3.6 81 13-97 2012-2092(2724)
4 cd04865 LigD_Pol_like_2 LigD_P 78.4 4.1 9E-05 31.6 4.3 56 13-68 119-185 (228)
5 cd04863 MtLigD_Pol_like MtLigD 78.3 3.9 8.5E-05 31.8 4.2 52 13-64 122-183 (231)
6 cd04864 LigD_Pol_like_1 LigD_P 78.2 4.2 9.1E-05 31.6 4.3 51 13-63 119-179 (228)
7 TIGR02778 ligD_pol DNA polymer 77.7 4.4 9.5E-05 31.8 4.4 55 13-67 134-199 (245)
8 cd04861 LigD_Pol_like LigD_Pol 73.4 6.7 0.00015 30.4 4.3 56 13-68 118-184 (227)
9 cd04862 PaeLigD_Pol_like PaeLi 73.4 6.8 0.00015 30.4 4.3 56 13-68 118-184 (227)
10 TIGR02776 NHEJ_ligase_prk DNA 73.3 6 0.00013 34.1 4.4 51 13-63 411-472 (552)
11 cd04866 LigD_Pol_like_3 LigD_P 70.9 8.2 0.00018 29.9 4.3 56 13-68 113-180 (223)
12 COG3285 Predicted eukaryotic-t 61.8 13 0.00028 30.2 3.9 50 13-62 145-204 (299)
13 PRK09633 ligD ATP-dependent DN 60.9 15 0.00032 32.1 4.4 55 13-67 452-518 (610)
14 PRK09632 ATP-dependent DNA lig 54.0 22 0.00047 32.1 4.4 52 13-64 155-216 (764)
15 PRK05972 ligD ATP-dependent DN 51.9 24 0.00051 32.3 4.3 55 13-67 704-769 (860)
16 cd01785 PDZ_GEF_RA Ubiquitin-l 42.6 11 0.00024 25.4 0.6 22 8-29 19-40 (85)
17 PLN03220 uncharacterized prote 42.3 48 0.001 23.1 3.8 39 13-55 66-104 (105)
18 cd00015 ALBUMIN Albumin domain 37.2 48 0.001 24.2 3.3 47 31-77 116-164 (185)
19 cd08816 CARD_RIG-I_1 Caspase a 37.0 10 0.00023 25.7 -0.2 27 67-95 8-34 (89)
20 PLN03219 uncharacterized prote 33.2 76 0.0016 22.2 3.6 36 15-54 70-105 (108)
21 smart00103 ALBUMIN serum album 31.8 55 0.0012 24.0 2.9 51 27-77 119-171 (187)
22 PF00273 Serum_albumin: Serum 28.9 67 0.0015 23.2 2.9 35 43-77 130-164 (178)
23 TIGR03342 dsrC_tusE_dsvC sulfu 25.8 1.5E+02 0.0032 20.5 4.0 47 32-78 7-60 (108)
24 PF11732 Thoc2: Transcription- 25.6 15 0.00033 24.0 -0.9 42 56-98 34-77 (77)
25 KOG0953|consensus 24.6 1.5E+02 0.0033 26.7 4.7 60 15-77 541-604 (700)
26 PF11903 DUF3423: Protein of u 23.9 72 0.0016 20.5 2.1 29 48-77 32-60 (72)
27 KOG0460|consensus 22.1 94 0.002 26.5 2.9 60 18-91 196-258 (449)
28 PRK13679 hypothetical protein; 21.1 24 0.00053 24.9 -0.6 8 59-66 32-39 (168)
29 COG2442 Uncharacterized conser 20.8 1E+02 0.0022 20.1 2.3 23 53-75 47-69 (79)
30 KOG4088|consensus 20.5 59 0.0013 24.2 1.3 57 3-73 95-152 (167)
31 PF02519 Auxin_inducible: Auxi 20.4 1.7E+02 0.0037 19.6 3.5 30 15-50 65-95 (100)
32 PF13876 Phage_gp49_66: Phage 20.2 76 0.0016 20.9 1.6 31 25-58 31-62 (81)
33 PF07684 NODP: NOTCH protein; 20.2 1.4E+02 0.003 18.6 2.8 37 6-42 21-59 (63)
No 1
>KOG1826|consensus
Probab=99.43 E-value=2.2e-14 Score=132.35 Aligned_cols=86 Identities=36% Similarity=0.509 Sum_probs=83.6
Q ss_pred hHHHHHHHHhhhhccCC-CceeeeccceeecCChhHHHHHHhHHhhccCCCCcHHHHHHHHhccccCchhhhhHHHhhhc
Q psy14865 12 EEAQRVLRLSLDEFALP-KFYLLFGVSLCIPANNTIFIKSISETLAKNEPHLTLEFLEECISGFKQSTIVLKHLCLEYMT 90 (98)
Q Consensus 12 ~~ay~lL~~~~~~F~L~-k~~Ll~s~~l~vP~d~t~Fi~~IS~~LA~~~P~LTl~Fl~e~~~g~~~~~~~~k~~~L~Ym~ 90 (98)
..||++++++.--|.|- .++.+..-|+|+|.+++.|++.+|+.||.++||+|++|++|+|.|+.++..+-+++|+.||+
T Consensus 1841 ksa~nl~caLt~~fdlrve~~~i~~~~lcip~~n~v~lk~~~q~L~~n~ph~~leflee~~sg~~~s~~eishLcl~yvs 1920 (2724)
T KOG1826|consen 1841 KSAGNLGCALTVLFDLRVELHDITLYDLCIPRFNPVSLKIYFQVLHENPPHYKLEFLEELFSGKFNSVYEISHLCLVYVS 1920 (2724)
T ss_pred HHHHhhcchheeeeeeeEeeeeeeeccccccCCCceeehhHHHHHhcCCCcceeehhhhhhhhhhhhHHHHHHHHHHHhc
Confidence 36899999999999999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCC
Q psy14865 91 PWLPNLV 97 (98)
Q Consensus 91 PWl~NL~ 97 (98)
||+.|++
T Consensus 1921 pw~~~lv 1927 (2724)
T KOG1826|consen 1921 PWTGVLV 1927 (2724)
T ss_pred hhhHhHH
Confidence 9999986
No 2
>PF14228 MOR2-PAG1_mid: Cell morphogenesis central region
Probab=98.00 E-value=6.2e-06 Score=74.96 Aligned_cols=86 Identities=24% Similarity=0.304 Sum_probs=63.8
Q ss_pred hHHHHHHHHhhhhccCC-C----ceeeeccceeecCChhHHHHHHhHHhhccCCCCcHHHHHHHHhc-cccCchhhhhHH
Q psy14865 12 EEAQRVLRLSLDEFALP-K----FYLLFGVSLCIPANNTIFIKSISETLAKNEPHLTLEFLEECISG-FKQSTIVLKHLC 85 (98)
Q Consensus 12 ~~ay~lL~~~~~~F~L~-k----~~Ll~s~~l~vP~d~t~Fi~~IS~~LA~~~P~LTl~Fl~e~~~g-~~~~~~~~k~~~ 85 (98)
+.|.+||+.+..-|--. + ..+..+..--.|.---..-..||++||+.+|+||++++.||..- ++..+...|.-.
T Consensus 561 ~~A~qLL~~Le~R~~~~s~~~~~~~f~~si~s~l~~vYk~aQ~eLS~~LA~~hPELs~~ifSEi~~R~~~~~~~~~rr~m 640 (1120)
T PF14228_consen 561 SKAMQLLRALEERFFSSSGSEKSGDFRESISSKLPAVYKKAQFELSKRLAKQHPELSFPIFSEISQRFFNAVPPDARRDM 640 (1120)
T ss_pred HHHHHHHHHHHHHhhcccccccccceehhccCCcHHHHHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHhcCChhHHHHH
Confidence 46888998876544222 1 12333444446666667788999999999999999999999864 555566677789
Q ss_pred HhhhcccCCCCC
Q psy14865 86 LEYMTPWLPNLV 97 (98)
Q Consensus 86 L~Ym~PWl~NL~ 97 (98)
|.||.|||+||.
T Consensus 641 L~~LlPWvqnle 652 (1120)
T PF14228_consen 641 LAYLLPWVQNLE 652 (1120)
T ss_pred HHHHHHHHhhce
Confidence 999999999973
No 3
>KOG1826|consensus
Probab=97.57 E-value=6e-05 Score=71.65 Aligned_cols=81 Identities=21% Similarity=0.294 Sum_probs=76.4
Q ss_pred HHHHHHHHhhhhccCCCceeeeccceeecCChhHHHHHHhHHhhccCCCCcHHHHHHHHhccccCchhhhhHHHhhhccc
Q psy14865 13 EAQRVLRLSLDEFALPKFYLLFGVSLCIPANNTIFIKSISETLAKNEPHLTLEFLEECISGFKQSTIVLKHLCLEYMTPW 92 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~~Ll~s~~l~vP~d~t~Fi~~IS~~LA~~~P~LTl~Fl~e~~~g~~~~~~~~k~~~L~Ym~PW 92 (98)
-+|+|++++...|+++=.+...+.+-.+|-|+++|..+|-..|+.+.|++|...+.+.|+|.+ .-.+.-+|+|.| |
T Consensus 2012 vS~nlI~~~c~~~d~~~t~p~~s~Eq~v~wD~~t~L~r~~~mlS~sn~~~~a~~~pYl~h~lt-fli~tg~~sl~~---~ 2087 (2724)
T KOG1826|consen 2012 VSYNLIAATCASFDLNFTHPHRSPEQYVPWDTTTFLGRIGKMLSESNPELTAYMFPYLLHALT-FLIPTGICSLSY---W 2087 (2724)
T ss_pred hHHHHHHHHHHHhccccCCCCCCHhHhCCcccHHHHHHHHHHHcccChhhHHHHHHHHHhhee-eeecccceeeee---c
Confidence 379999999999999977888889999999999999999999999999999999999999996 889999999999 9
Q ss_pred CCCCC
Q psy14865 93 LPNLV 97 (98)
Q Consensus 93 l~NL~ 97 (98)
++||.
T Consensus 2088 t~~L~ 2092 (2724)
T KOG1826|consen 2088 TPNLY 2092 (2724)
T ss_pred cCcce
Confidence 99984
No 4
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=78.37 E-value=4.1 Score=31.63 Aligned_cols=56 Identities=23% Similarity=0.306 Sum_probs=42.6
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCCh-------hHHHHHHhHHhhccCCCC-cHHHHH
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPANN-------TIFIKSISETLAKNEPHL-TLEFLE 68 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d~-------t~Fi~~IS~~LA~~~P~L-Tl~Fl~ 68 (98)
++-++++..|++.+|..+ +.--++|+ ++|-.+ -.|...|.+.|++..|++ |.+..+
T Consensus 119 ~~A~~vr~~L~~lgL~sf~KTSG~kGlHv~vPl~~~~~~~~~r~fa~~iA~~l~~~~P~~~t~~~~k 185 (228)
T cd04865 119 EVALLVREVLDELGLRGYPKTSGARGLHIYVPIAPRYTFEEVRRFAELLAREVERRLPDLATTERWK 185 (228)
T ss_pred HHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhhH
Confidence 577899999999999976 44455554 677654 568999999999999995 444443
No 5
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=78.31 E-value=3.9 Score=31.81 Aligned_cols=52 Identities=23% Similarity=0.357 Sum_probs=40.7
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCCh-------hHHHHHHhHHhhccCCCCcH
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPANN-------TIFIKSISETLAKNEPHLTL 64 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d~-------t~Fi~~IS~~LA~~~P~LTl 64 (98)
++-++++..|++++|..+ +.--++|+ +||-.+ ..|...|.+.|++..|+++.
T Consensus 122 ~~A~~~r~~L~~lgL~s~~KTSG~kGlHV~vPl~~~~~~~~vr~fa~~~A~~l~~~~P~~~t 183 (231)
T cd04863 122 RVALWLRDRLAALGLASFPKTSGSKGLHLYVPLDGPVSSDQTKEFAKALARELEREHPDLVV 183 (231)
T ss_pred HHHHHHHHHHHHcCCccceECCCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhh
Confidence 567889999999999976 44455554 677654 56899999999999999764
No 6
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=78.20 E-value=4.2 Score=31.58 Aligned_cols=51 Identities=29% Similarity=0.458 Sum_probs=40.2
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCCh-------hHHHHHHhHHhhccCCCCc
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPANN-------TIFIKSISETLAKNEPHLT 63 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d~-------t~Fi~~IS~~LA~~~P~LT 63 (98)
++-++++..|++++|..+ +.--++|+ +||-.+ ..|...|.+.|++..|+++
T Consensus 119 ~~A~~~r~~L~~~gL~~f~KTSG~kGlHv~vPl~~~~~~~~~r~fa~~lA~~l~~~~P~~~ 179 (228)
T cd04864 119 TAALAVRELLDELGLPSFVKTTGSRGFHVVVPLDGRGDFDDVRAFAAEAADALAKRDPDLL 179 (228)
T ss_pred HHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhh
Confidence 677889999999999966 44455555 566554 5689999999999999874
No 7
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=77.74 E-value=4.4 Score=31.79 Aligned_cols=55 Identities=33% Similarity=0.449 Sum_probs=41.5
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCCh-------hHHHHHHhHHhhccCCCC-cHHHH
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPANN-------TIFIKSISETLAKNEPHL-TLEFL 67 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d~-------t~Fi~~IS~~LA~~~P~L-Tl~Fl 67 (98)
++-.+++..|++.+|..+ +.--++|+ ++|-.+ ..|...|.+.+++..|++ |.+..
T Consensus 134 ~~A~~~r~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l~~~~Pd~~t~~~~ 199 (245)
T TIGR02778 134 EAAQLIRELLDELGLESFVKTSGGKGLHVYVPLRPTLSWDEVKDFAKALAQALAQQMPDRFTAEMS 199 (245)
T ss_pred HHHHHHHHHHHHcCCccceEccCCCeEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhh
Confidence 567789999999999976 44455554 577654 568999999999999976 34433
No 8
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=73.39 E-value=6.7 Score=30.44 Aligned_cols=56 Identities=36% Similarity=0.476 Sum_probs=42.2
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCCh-------hHHHHHHhHHhhccCCCC-cHHHHH
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPANN-------TIFIKSISETLAKNEPHL-TLEFLE 68 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d~-------t~Fi~~IS~~LA~~~P~L-Tl~Fl~ 68 (98)
++-.+++..|++++|..+ +.--++|+ ++|-.+ ..|...|.+.|++..|++ |.+..+
T Consensus 118 ~~A~~vr~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l~~~~P~~~t~~~~k 184 (227)
T cd04861 118 EAALLLRELLDELGLESFPKTSGGKGLHVYVPLAPRYTWDEVRAFAKALARELARRLPDLFTAEMAK 184 (227)
T ss_pred HHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhhHhhH
Confidence 677889999999999976 45555555 677554 578999999999999975 444433
No 9
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=73.36 E-value=6.8 Score=30.43 Aligned_cols=56 Identities=29% Similarity=0.405 Sum_probs=42.4
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCCh-------hHHHHHHhHHhhccCCCC-cHHHHH
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPANN-------TIFIKSISETLAKNEPHL-TLEFLE 68 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d~-------t~Fi~~IS~~LA~~~P~L-Tl~Fl~ 68 (98)
++-.+++..+++.+|..+ +.--++|+ ++|-.+ ..|...|.+.|++..|++ |.+..+
T Consensus 118 ~~A~~~r~~L~~lgL~~~~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~lA~~l~~~~P~~~t~~~~k 184 (227)
T cd04862 118 EAALLVRELLDELGLESFVKTSGGKGLHVVVPLAPRAGWDEVKAFAKALAQHLARTNPDRFVATMGK 184 (227)
T ss_pred HHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhhhHHhhH
Confidence 677889999999999966 44555555 677654 568999999999999995 445444
No 10
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=73.27 E-value=6 Score=34.10 Aligned_cols=51 Identities=33% Similarity=0.473 Sum_probs=40.6
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCCh--------hHHHHHHhHHhhccCCCCc
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPANN--------TIFIKSISETLAKNEPHLT 63 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d~--------t~Fi~~IS~~LA~~~P~LT 63 (98)
++-.+++..|++++|..+ +.--++|+ +||-.+ ..|...|.+.|++..|++.
T Consensus 411 ~~A~~~r~~L~~~gl~~~~KtSG~kGlhv~vPl~~~~~~~~~~~~fa~~~a~~~~~~~P~~~ 472 (552)
T TIGR02776 411 EAAQLMKQLLDELGLVSFVKTSGGKGLHVVVPLRPNTFTWDETKLFAKAIAEYLARQFPERF 472 (552)
T ss_pred HHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHCccee
Confidence 567789999999999976 44445554 677776 5689999999999999763
No 11
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=70.89 E-value=8.2 Score=29.92 Aligned_cols=56 Identities=34% Similarity=0.418 Sum_probs=42.3
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCC--------hhHHHHHHhHHhhccCCCC-cHHHHH
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPAN--------NTIFIKSISETLAKNEPHL-TLEFLE 68 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d--------~t~Fi~~IS~~LA~~~P~L-Tl~Fl~ 68 (98)
++-++++..|++.||..+ +.--++|+ ++|-. ...|...|.+.+++..|++ |.+..+
T Consensus 113 ~~A~~vr~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~~r~fa~~iA~~l~~~~P~~~t~~~~k 180 (223)
T cd04866 113 EAANLLKEILDALGLTSFVKTSGNKGLQVYIPLPDNKFTYDETRLFTEFIAEYLCQQFPELFTTERLK 180 (223)
T ss_pred HHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHCchhhhHHhhH
Confidence 677899999999999966 44455554 67766 2468999999999999974 444443
No 12
>COG3285 Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]
Probab=61.79 E-value=13 Score=30.21 Aligned_cols=50 Identities=36% Similarity=0.460 Sum_probs=39.2
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCC-------hhHHHHHHhHHhhccCCCC
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPAN-------NTIFIKSISETLAKNEPHL 62 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d-------~t~Fi~~IS~~LA~~~P~L 62 (98)
||-+.++..||++||..+ ..--|||+ ++|-. ...|-..|+++||+..|++
T Consensus 145 eaA~~lr~~Ld~lGL~~f~KTSGGKG~Hv~~PL~~~~~w~e~k~fa~~va~~la~~~Pd~ 204 (299)
T COG3285 145 EAALELRDLLDELGLVSFPKTSGGKGLHVYVPLAPKATWEEVKQFAKAVAQQLARAAPDL 204 (299)
T ss_pred HHHHHHHHHHHHcCCccceeccCCCeeEEEEecCCcCCcHHHHHHHHHHHHHHHHhChHH
Confidence 556699999999999966 45555665 56654 3578999999999999985
No 13
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=60.93 E-value=15 Score=32.15 Aligned_cols=55 Identities=35% Similarity=0.416 Sum_probs=41.7
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCCh--------hHHHHHHhHHhhccCCCC-cHHHH
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPANN--------TIFIKSISETLAKNEPHL-TLEFL 67 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d~--------t~Fi~~IS~~LA~~~P~L-Tl~Fl 67 (98)
++-.+++..|++.+|..+ ..--++|+ +||-.+ ..|...|.+.|++..|++ |.+..
T Consensus 452 ~~A~~~r~~L~~~gl~~~~ktSG~kGlhv~vPl~~~~~~~~~~~~fa~~~a~~~~~~~P~~~t~~~~ 518 (610)
T PRK09633 452 EAALELKRLFDQFGLTSFVKTSGNKGLQLYIPLSKNAFTYEETRLFTEFIAEYLCSQFPELFTTERL 518 (610)
T ss_pred HHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHHHHCcceehhhhh
Confidence 677889999999999976 44445554 677655 468999999999999995 44433
No 14
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=53.97 E-value=22 Score=32.12 Aligned_cols=52 Identities=21% Similarity=0.376 Sum_probs=40.5
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCCh-------hHHHHHHhHHhhccCCCCcH
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPANN-------TIFIKSISETLAKNEPHLTL 64 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d~-------t~Fi~~IS~~LA~~~P~LTl 64 (98)
++-.+++..|++.+|..+ ..--++|+ ++|-.+ ..|...|.+.|++..|++..
T Consensus 155 ~~A~~~r~~L~~lgL~~~~KTSG~kGlHv~vPl~~~~~~~~~~~fa~~~A~~l~~~~P~~~t 216 (764)
T PRK09632 155 EVARAVRDLLADIGLETFPVTSGSKGIHLYAPLDGPVSSEGASVVAKEVARALEQDHPDLVT 216 (764)
T ss_pred HHHHHHHHHHHHcCCceeeECCCCCeEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCcceeh
Confidence 677889999999999966 44444554 677654 56999999999999999753
No 15
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=51.93 E-value=24 Score=32.31 Aligned_cols=55 Identities=27% Similarity=0.446 Sum_probs=41.7
Q ss_pred HHHHHHHHhhhhccCCCc-eeeeccce--eecCCh-------hHHHHHHhHHhhccCCCC-cHHHH
Q psy14865 13 EAQRVLRLSLDEFALPKF-YLLFGVSL--CIPANN-------TIFIKSISETLAKNEPHL-TLEFL 67 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~-~Ll~s~~l--~vP~d~-------t~Fi~~IS~~LA~~~P~L-Tl~Fl 67 (98)
++-++++..|++++|..+ ..--++|+ +||-.+ -.|...|.+.|++..|++ |.+..
T Consensus 704 ~aA~~~r~~L~~lgL~sf~KTSG~kGlHv~vPl~~~~~~~~~~~fa~~ia~~l~~~~P~~~t~~~~ 769 (860)
T PRK05972 704 EAARLMRTRLDELGLESFLKTSGGKGLHVVVPLARRLDWDEVKAFAQAVCQHMARDLPERFLAKMG 769 (860)
T ss_pred HHHHHHHHHHHHcCCceeeECCCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHHHHCchhehhhhh
Confidence 677889999999999966 44555555 677654 468999999999999985 44433
No 16
>cd01785 PDZ_GEF_RA Ubiquitin-like domain of PDZ_GEF_RA. PDZ_GEF_RA PDZ-GEF is a guanine nucleotide exchange factor (GEF) characterised by the presence of a PSD-95/DlgA/ZO-1 (PDZ) domain, a Ras-association (RA) domain and a region related to a cyclic nucleotide binding domain (RCBD). RA-GEF exchanges nucleotides of both Rap1 and Rap2, but is also thought to mediate cAMP-induced Ras activation. The RA domain interacts with Rap1 and also contributes to the membrane localization of RA-GEF. This domain may function in a positive feedback loop.
Probab=42.59 E-value=11 Score=25.36 Aligned_cols=22 Identities=32% Similarity=0.617 Sum_probs=19.3
Q ss_pred cccchHHHHHHHHhhhhccCCC
Q psy14865 8 CYRHEEAQRVLRLSLDEFALPK 29 (98)
Q Consensus 8 ~~~~~~ay~lL~~~~~~F~L~k 29 (98)
.++.-.|+.+..++++|||++.
T Consensus 19 i~K~Tta~evv~lal~eFgi~~ 40 (85)
T cd01785 19 IYKETTAHEVVMLALQEFGITA 40 (85)
T ss_pred EeccccHHHHHHHHHHHhCCCC
Confidence 4667789999999999999993
No 17
>PLN03220 uncharacterized protein; Provisional
Probab=42.30 E-value=48 Score=23.08 Aligned_cols=39 Identities=23% Similarity=0.362 Sum_probs=30.2
Q ss_pred HHHHHHHHhhhhccCCCceeeeccceeecCChhHHHHHHhHHh
Q psy14865 13 EAQRVLRLSLDEFALPKFYLLFGVSLCIPANNTIFIKSISETL 55 (98)
Q Consensus 13 ~ay~lL~~~~~~F~L~k~~Ll~s~~l~vP~d~t~Fi~~IS~~L 55 (98)
-=..||..+.+|||++.. .-.+.||=|...|..-++.+|
T Consensus 66 ~F~~LL~~AeEEfGf~~~----~G~L~IPCd~~~F~~ll~s~~ 104 (105)
T PLN03220 66 SFKEFLSRAEEEFGFNHP----MGGLTIPCREEVFLDLIASRL 104 (105)
T ss_pred HHHHHHHHHHHHhCCCCC----CCCEEeeCCHHHHHHHHHhhc
Confidence 346799999999999731 124789999999988887765
No 18
>cd00015 ALBUMIN Albumin domain, contains five or six internal disulphide bonds; albuminoid superfamily includes alpha-fetoprotein which binds various cations, fatty acids and bilirubin; vitamin D-binding protein which binds to vitamin D, its metabolites, and fatty acids; alpha-albumin which binds water, cations (such as Ca2+, Na+ and K+), fatty acids, hormones, bilirubin and drugs; and afamin of which little is known; these belong to a multigene family with highly conserved intron/exon organization and encoded protein structures; evolutionary comparisons strongly support vitamin D-binding protein as the original gene in this group with subsequent local duplications generating the remaining genes in the cluster
Probab=37.18 E-value=48 Score=24.22 Aligned_cols=47 Identities=11% Similarity=0.198 Sum_probs=36.5
Q ss_pred eeeeccceee--cCChhHHHHHHhHHhhccCCCCcHHHHHHHHhccccC
Q psy14865 31 YLLFGVSLCI--PANNTIFIKSISETLAKNEPHLTLEFLEECISGFKQS 77 (98)
Q Consensus 31 ~Ll~s~~l~v--P~d~t~Fi~~IS~~LA~~~P~LTl~Fl~e~~~g~~~~ 77 (98)
...+...++- -.+...|..+.-=.+++.+|+++-++|..+..+|++.
T Consensus 116 ~~~~~~~~C~~~~e~~~~~~~~fl~e~srrhP~~~~~~ll~~a~~y~~~ 164 (185)
T cd00015 116 VFPEDEEVCQAFEEDPQKFLGRFLYEYSRRHPELSVPELLRLAKEYEEL 164 (185)
T ss_pred ccCCcHHHhcCchhhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHH
Confidence 3344444442 3467778888888899999999999999999999876
No 19
>cd08816 CARD_RIG-I_1 Caspase activation and recruitment domain found in RIG-I, first repeat. Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), first repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, RIG-I recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction doma
Probab=37.02 E-value=10 Score=25.69 Aligned_cols=27 Identities=26% Similarity=0.368 Sum_probs=16.1
Q ss_pred HHHHHhccccCchhhhhHHHhhhcccCCC
Q psy14865 67 LEECISGFKQSTIVLKHLCLEYMTPWLPN 95 (98)
Q Consensus 67 l~e~~~g~~~~~~~~k~~~L~Ym~PWl~N 95 (98)
|..|-+-..+.=+|. ..+.||+||+++
T Consensus 8 L~af~~yi~ktl~P~--yIl~~m~~~~~~ 34 (89)
T cd08816 8 LQRFRDYIKKILRPS--YILGFMTTWLED 34 (89)
T ss_pred HHHHHHHHHHhhchH--HHHHHHHHhcCH
Confidence 334444444443443 457899999985
No 20
>PLN03219 uncharacterized protein; Provisional
Probab=33.20 E-value=76 Score=22.18 Aligned_cols=36 Identities=19% Similarity=0.273 Sum_probs=28.6
Q ss_pred HHHHHHhhhhccCCCceeeeccceeecCChhHHHHHHhHH
Q psy14865 15 QRVLRLSLDEFALPKFYLLFGVSLCIPANNTIFIKSISET 54 (98)
Q Consensus 15 y~lL~~~~~~F~L~k~~Ll~s~~l~vP~d~t~Fi~~IS~~ 54 (98)
+.||..+.+|||++.. .-++.||=+...|..-+|.+
T Consensus 70 ~~LL~~AeEEfGf~~~----~G~L~IPCd~~~F~~ll~~~ 105 (108)
T PLN03219 70 REFLNRAEEECGFHHS----MGGLTIPCREESFLHLITSH 105 (108)
T ss_pred HHHHHHHHHHhCCCCC----CCCEEEeCCHHHHHHHHHhh
Confidence 5799999999999731 13488999999998887764
No 21
>smart00103 ALBUMIN serum albumin.
Probab=31.81 E-value=55 Score=23.99 Aligned_cols=51 Identities=16% Similarity=0.276 Sum_probs=39.0
Q ss_pred CCCceeeeccceeec--CChhHHHHHHhHHhhccCCCCcHHHHHHHHhccccC
Q psy14865 27 LPKFYLLFGVSLCIP--ANNTIFIKSISETLAKNEPHLTLEFLEECISGFKQS 77 (98)
Q Consensus 27 L~k~~Ll~s~~l~vP--~d~t~Fi~~IS~~LA~~~P~LTl~Fl~e~~~g~~~~ 77 (98)
||...+.+..+++-. .+...|..+.-=.+++.+|+++-++|..+..+|.+.
T Consensus 119 l~~~~~~~~~~~C~~~~e~~~~~~~~fl~e~~rrhP~~~~~~ll~~~~~y~~~ 171 (187)
T smart00103 119 LPPDKFPEDKDVCQAYEEDKDVFLGKFLYELSRRHPELSEPQLLRVAKEYEAL 171 (187)
T ss_pred CChhccCCCHHHHcCcHhhHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence 343445555555533 566778888888899999999999999999999876
No 22
>PF00273 Serum_albumin: Serum albumin family; InterPro: IPR014760 A number of serum transport proteins are known to be evolutionarily related, including albumin, alpha-fetoprotein, vitamin D-binding protein and afamin [, , ]. Albumin is the main protein of plasma; it binds water, cations (such as Ca2+, Na+ and K+), fatty acids, hormones, bilirubin and drugs - its main function is to regulate the colloidal osmotic pressure of blood. Alphafeto- protein (alpha-fetoglobulin) is a foetal plasma protein that binds various cations, fatty acids and bilirubin. Vitamin D-binding protein binds to vitamin D and its metabolites, as well as to fatty acids. The biological role of afamin (alpha-albumin) has not yet been characterised. The 3D structure of human serum albumin has been determined by X-ray crystallography to a resolution of 2.8A []. It comprises three homologous domains that assemble to form a heart-shaped molecule []. Each domain is a product of two subdomains that possess common structural motifs []. The principal regions of ligand binding to human serum albumin are located in hydrophobic cavities in subdomains IIA and IIIA, which exhibit similar chemistry. Structurally, the serum albumins are similar, each domain containing five or six internal disulphide bonds, as shown schematically below: +---+ +----+ +-----+ | | | | | | xxCxxxxxxxxxxxxxxxxCCxxCxxxxCxxxxxCCxxxCxxxxxxxxxCxxxxxxxxxxxxxxCCxxxxCxxxx | | | | | | +-----------------+ +-----+ +---------------+ ; GO: 0005615 extracellular space; PDB: 3V09_A 3V03_B 3MRK_P 1MA9_A 1KW2_A 1KXP_D 1J7E_A 1J78_A 1LOT_A 2BXL_A ....
Probab=28.89 E-value=67 Score=23.24 Aligned_cols=35 Identities=17% Similarity=0.326 Sum_probs=27.5
Q ss_pred ChhHHHHHHhHHhhccCCCCcHHHHHHHHhccccC
Q psy14865 43 NNTIFIKSISETLAKNEPHLTLEFLEECISGFKQS 77 (98)
Q Consensus 43 d~t~Fi~~IS~~LA~~~P~LTl~Fl~e~~~g~~~~ 77 (98)
+.-.|..+.-=.+|+.+|+++.+.|..+..+|++.
T Consensus 130 ~~~~~~~~~lye~~RrhP~~~~~~l~~~~~~y~~~ 164 (178)
T PF00273_consen 130 DPQKFLQRFLYELSRRHPELSDPQLLRIAKGYEKM 164 (178)
T ss_dssp CHHHHHHHHHHHHHHHSTTS-HHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 45555666666788999999999999999999876
No 23
>TIGR03342 dsrC_tusE_dsvC sulfur relay protein, TusE/DsrC/DsvC family. Members of this protein family may be described as TusE, a partner to TusBCD in a sulfur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Other members are DsrC, a functionally similar protein in species where the sulfur relay system exists primarily for sulfur metabolism rather than tRNA base modification. Some members of this family are known explicitly as the gamma subunit of sulfite reductases.
Probab=25.83 E-value=1.5e+02 Score=20.47 Aligned_cols=47 Identities=19% Similarity=0.150 Sum_probs=36.2
Q ss_pred eeeccceeecCChhHHHHHHhHHhhccCC-CCcH------HHHHHHHhccccCc
Q psy14865 32 LLFGVSLCIPANNTIFIKSISETLAKNEP-HLTL------EFLEECISGFKQST 78 (98)
Q Consensus 32 Ll~s~~l~vP~d~t~Fi~~IS~~LA~~~P-~LTl------~Fl~e~~~g~~~~~ 78 (98)
-+...+-.+..|..++...|.+.||+.+- +||- +|+.+|+.-+..++
T Consensus 7 ~i~~D~~GfL~~~~dW~e~vA~~lA~~egieLT~~Hw~vI~~lR~~y~e~~~~P 60 (108)
T TIGR03342 7 EIELDEDGYLLDLDDWSEDVAEALAEEEGIELTEAHWEVINFLRDFYAEYNISP 60 (108)
T ss_pred eeeeCCCCCcCChHHCCHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHCCCC
Confidence 34455566888999999999999999865 6874 57788887776554
No 24
>PF11732 Thoc2: Transcription- and export-related complex subunit; InterPro: IPR021726 The THO/TREX complex is the transcription- and export-related complex associated with spliceosomes that preferentially deal with spliced mRNAs as opposed to unspliced mRNAs. Thoc2 plays a role in RNA polymerase II (RNA pol II)-dependent transcription and is required for the stability of DNA repeats []. In humans, the TRE complex is comprised of the exon-junction-associated proteins Aly/REF and UAP56 together with the THO proteins THOC1 (hHpr1/p84), Thoc2 (hRlr1), THOC3 (hTex1), THOC5 (fSAP79), THOC6 (fSAP35), and THOC7 (fSAP24). Although much evidence indicates that the function of the TREX complex as an adaptor between the mRNA and components of the export machinery is conserved among eukaryotes, in Drosophila the majority of mRNAs can be exported from the nucleus independently of the THO complex []. This entry represents a conserved domain found towards the N terminus of these proteins.
Probab=25.61 E-value=15 Score=24.01 Aligned_cols=42 Identities=21% Similarity=0.314 Sum_probs=23.8
Q ss_pred hccCCCCcHHHHHHHHh-ccccCc-hhhhhHHHhhhcccCCCCCC
Q psy14865 56 AKNEPHLTLEFLEECIS-GFKQST-IVLKHLCLEYMTPWLPNLVK 98 (98)
Q Consensus 56 A~~~P~LTl~Fl~e~~~-g~~~~~-~~~k~~~L~Ym~PWl~NL~~ 98 (98)
++-...|.+|-|..++. .+.... ...|.-- .-+++|+++|++
T Consensus 34 ~ky~t~l~~DvL~~~ll~~L~~~~r~~~k~dg-~~~s~Wlq~Las 77 (77)
T PF11732_consen 34 LKYFTDLGYDVLTFCLLERLSNPGRSRLKDDG-TNISQWLQSLAS 77 (77)
T ss_pred HhhcchhhHHHHHHHHHHHHhcccchhcCcCC-CCHHHHHHHHhC
Confidence 36678899999888873 222111 1111111 335669999874
No 25
>KOG0953|consensus
Probab=24.62 E-value=1.5e+02 Score=26.72 Aligned_cols=60 Identities=18% Similarity=0.230 Sum_probs=39.6
Q ss_pred HHHHHHhhhhccCC-Ccee--eecccee-ecCChhHHHHHHhHHhhccCCCCcHHHHHHHHhccccC
Q psy14865 15 QRVLRLSLDEFALP-KFYL--LFGVSLC-IPANNTIFIKSISETLAKNEPHLTLEFLEECISGFKQS 77 (98)
Q Consensus 15 y~lL~~~~~~F~L~-k~~L--l~s~~l~-vP~d~t~Fi~~IS~~LA~~~P~LTl~Fl~e~~~g~~~~ 77 (98)
..-++.+++.-.|| +-++ ..+.-+- .|.. ..+...+.++.|+++| +|+++++ +..||.+.
T Consensus 541 ~k~va~liehi~L~l~dr~~fc~aPvnk~~p~v-~~~f~kfa~~~s~~~~-l~~~~l~-~~~~~p~~ 604 (700)
T KOG0953|consen 541 FKFVAELIEHIELPLKDRYKFCTAPVNKKMPRV-CSAFLKFARQYSQNEP-LTFLWLK-FNLGWPNK 604 (700)
T ss_pred HHHHHHHHHhCCcchhhhheeecCcccccCchH-HHHHHHHHHHHhcCCc-ccHHHHH-HhhcCCCC
Confidence 34456667777788 4333 3332212 3433 4455678888898887 8999999 88888887
No 26
>PF11903 DUF3423: Protein of unknown function (DUF3423); InterPro: IPR021831 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 73 to 118 amino acids in length.
Probab=23.91 E-value=72 Score=20.51 Aligned_cols=29 Identities=24% Similarity=0.457 Sum_probs=21.2
Q ss_pred HHHHhHHhhccCCCCcHHHHHHHHhccccC
Q psy14865 48 IKSISETLAKNEPHLTLEFLEECISGFKQS 77 (98)
Q Consensus 48 i~~IS~~LA~~~P~LTl~Fl~e~~~g~~~~ 77 (98)
-.+|+. ++...|.|++.|+.+-..+-+..
T Consensus 32 WariGr-~~E~np~l~~~~I~~~l~~~~~~ 60 (72)
T PF11903_consen 32 WARIGR-AAEDNPDLSYSFIEEMLLAAEEE 60 (72)
T ss_pred HHHHHH-HHHHCCCCCHHHHHHHHHHhhhc
Confidence 344443 56789999999999988776543
No 27
>KOG0460|consensus
Probab=22.09 E-value=94 Score=26.50 Aligned_cols=60 Identities=23% Similarity=0.437 Sum_probs=46.5
Q ss_pred HHHhhhhccCC--CceeeeccceeecCChhHHHHHHhHHhhccCCCCcHHHHHHHHhcccc-CchhhhhHHHhhhcc
Q psy14865 18 LRLSLDEFALP--KFYLLFGVSLCIPANNTIFIKSISETLAKNEPHLTLEFLEECISGFKQ-STIVLKHLCLEYMTP 91 (98)
Q Consensus 18 L~~~~~~F~L~--k~~Ll~s~~l~vP~d~t~Fi~~IS~~LA~~~P~LTl~Fl~e~~~g~~~-~~~~~k~~~L~Ym~P 91 (98)
+|.+|.+|++| ..+++.+..+| .|--..|++-.+-+...++..+. .+.++|-+-.-++-|
T Consensus 196 ~RElLse~gf~Gd~~PvI~GSAL~--------------ALeg~~peig~~aI~kLldavDsyip~P~R~~~~pFl~p 258 (449)
T KOG0460|consen 196 IRELLSEFGFDGDNTPVIRGSALC--------------ALEGRQPEIGLEAIEKLLDAVDSYIPTPERDLDKPFLLP 258 (449)
T ss_pred HHHHHHHcCCCCCCCCeeecchhh--------------hhcCCCccccHHHHHHHHHHHhccCCCcccccCCCceee
Confidence 57889999999 55888888765 23346799999999999988888 688888776665554
No 28
>PRK13679 hypothetical protein; Provisional
Probab=21.09 E-value=24 Score=24.90 Aligned_cols=8 Identities=50% Similarity=0.820 Sum_probs=3.8
Q ss_pred CCCCcHHH
Q psy14865 59 EPHLTLEF 66 (98)
Q Consensus 59 ~P~LTl~F 66 (98)
.||+|+.|
T Consensus 32 ~pHITL~f 39 (168)
T PRK13679 32 PPHITLKE 39 (168)
T ss_pred CCceEEec
Confidence 34555544
No 29
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=20.85 E-value=1e+02 Score=20.10 Aligned_cols=23 Identities=26% Similarity=0.312 Sum_probs=17.2
Q ss_pred HHhhccCCCCcHHHHHHHHhccc
Q psy14865 53 ETLAKNEPHLTLEFLEECISGFK 75 (98)
Q Consensus 53 ~~LA~~~P~LTl~Fl~e~~~g~~ 75 (98)
+.++...|+||.+=+.+++.-..
T Consensus 47 eeil~dyp~Lt~~dI~aal~ya~ 69 (79)
T COG2442 47 EEILADYPDLTLEDIRAALRYAA 69 (79)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHH
Confidence 34678889999888888876443
No 30
>KOG4088|consensus
Probab=20.55 E-value=59 Score=24.20 Aligned_cols=57 Identities=26% Similarity=0.215 Sum_probs=32.7
Q ss_pred ccccccccchHHHHHHHHhhh-hccCCCceeeeccceeecCChhHHHHHHhHHhhccCCCCcHHHHHHHHhc
Q psy14865 3 SLNVRCYRHEEAQRVLRLSLD-EFALPKFYLLFGVSLCIPANNTIFIKSISETLAKNEPHLTLEFLEECISG 73 (98)
Q Consensus 3 ~~~~~~~~~~~ay~lL~~~~~-~F~L~k~~Ll~s~~l~vP~d~t~Fi~~IS~~LA~~~P~LTl~Fl~e~~~g 73 (98)
..|||.| .||.|.++|-.+. .=+.+..+=+++. +++..=+.+-|-+.-|-|..++.+
T Consensus 95 t~~vr~F-DEegya~~rKaQRdgdk~S~~kpLftv-------------sv~h~G~~~gpwissE~lAa~iv~ 152 (167)
T KOG4088|consen 95 TFNVRIF-DEEGYAQYRKAQRDGDKPSVTKPLFTV-------------SVSHGGLATGPWISSETLAAIIVV 152 (167)
T ss_pred eEEEEEe-CchhHHHHHHhhccCCCCccccccEEE-------------EecCCCcccCCcccHHHHHHHHHH
Confidence 3689999 8899999998873 2122211222222 223333455666667777666643
No 31
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=20.44 E-value=1.7e+02 Score=19.63 Aligned_cols=30 Identities=27% Similarity=0.423 Sum_probs=23.3
Q ss_pred HHHHHHhhhhccCC-CceeeeccceeecCChhHHHHH
Q psy14865 15 QRVLRLSLDEFALP-KFYLLFGVSLCIPANNTIFIKS 50 (98)
Q Consensus 15 y~lL~~~~~~F~L~-k~~Ll~s~~l~vP~d~t~Fi~~ 50 (98)
+.||..+.+|||++ ++ .+.||=+...|-.-
T Consensus 65 ~~LL~~aeeEfG~~~~G------~l~iPC~~~~Fe~~ 95 (100)
T PF02519_consen 65 QELLEQAEEEFGFDQDG------PLTIPCDVVLFEHL 95 (100)
T ss_pred HHHHHHHhhhcCcCCCC------cEEeeCCHHHHHHH
Confidence 57999999999999 33 36788888877543
No 32
>PF13876 Phage_gp49_66: Phage protein (N4 Gp49/phage Sf6 gene 66) family
Probab=20.20 E-value=76 Score=20.86 Aligned_cols=31 Identities=26% Similarity=0.462 Sum_probs=23.7
Q ss_pred ccCC-CceeeeccceeecCChhHHHHHHhHHhhcc
Q psy14865 25 FALP-KFYLLFGVSLCIPANNTIFIKSISETLAKN 58 (98)
Q Consensus 25 F~L~-k~~Ll~s~~l~vP~d~t~Fi~~IS~~LA~~ 58 (98)
..|+ |+.+. +.+.| .|+..|-..|.+++|..
T Consensus 31 l~L~NGF~V~-g~SAc--vdp~nfD~eiG~~iA~~ 62 (81)
T PF13876_consen 31 LTLKNGFTVT-GESAC--VDPENFDAEIGRKIARE 62 (81)
T ss_pred EEECCCcEEE-EeEcc--CChHHcCHHHHHHHHHH
Confidence 3467 55555 66655 78999999999999975
No 33
>PF07684 NODP: NOTCH protein; InterPro: IPR011656 NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals []. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. The role of the NOD and NODP domains remains to be elucidated.; GO: 0007219 Notch signaling pathway, 0007275 multicellular organismal development, 0030154 cell differentiation, 0016021 integral to membrane; PDB: 3ETO_A 3I08_D 3L95_X 2OO4_A.
Probab=20.16 E-value=1.4e+02 Score=18.59 Aligned_cols=37 Identities=19% Similarity=0.174 Sum_probs=21.9
Q ss_pred cccccc-hHHHHHHHHhhhhccCC-CceeeeccceeecC
Q psy14865 6 VRCYRH-EEAQRVLRLSLDEFALP-KFYLLFGVSLCIPA 42 (98)
Q Consensus 6 ~~~~~~-~~ay~lL~~~~~~F~L~-k~~Ll~s~~l~vP~ 42 (98)
-+||.+ .++-+.|++...--+|+ .+++....+..-|.
T Consensus 21 ~~CF~~a~~aA~fLaA~aa~~~L~~~~PI~~v~~~~~~~ 59 (63)
T PF07684_consen 21 SECFSSADSAADFLAAMAAKGTLNFPFPIYSVRSEPPPP 59 (63)
T ss_dssp S---SBHHHHHHHHHHHHHCT---SSSEEEEEEEES---
T ss_pred CcCcCCHHHHHHHHHHHHhhccCCCCCceEEEEeecCCC
Confidence 357866 78899999999888998 77777766654443
Done!