Query 038596
Match_columns 163
No_of_seqs 164 out of 271
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 12:37:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038596.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038596hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1043 Ca2+-binding transmemb 100.0 5.3E-39 1.1E-43 291.5 8.1 162 1-162 296-460 (499)
2 PF07766 LETM1: LETM1-like pro 100.0 3.9E-31 8.4E-36 224.2 10.0 94 1-94 174-268 (268)
3 KOG4263 Putative receptor CCR1 99.5 2.1E-14 4.6E-19 122.3 9.3 88 10-97 200-288 (299)
4 PF02037 SAP: SAP domain; Int 97.4 0.0003 6.4E-09 42.9 4.3 34 45-78 2-35 (35)
5 smart00513 SAP Putative DNA-bi 97.2 0.00087 1.9E-08 40.6 4.3 35 44-78 1-35 (35)
6 smart00513 SAP Putative DNA-bi 88.7 0.51 1.1E-05 28.3 2.6 28 1-28 7-34 (35)
7 PF02037 SAP: SAP domain; Int 88.4 0.66 1.4E-05 28.0 3.0 29 1-29 7-35 (35)
8 TIGR00578 ku70 ATP-dependent D 83.5 2.4 5.1E-05 40.2 5.5 37 43-79 548-584 (584)
9 smart00540 LEM in nuclear memb 74.5 3 6.5E-05 26.9 2.3 32 44-75 3-38 (44)
10 PF07498 Rho_N: Rho terminatio 62.1 18 0.0004 22.6 4.0 31 45-75 3-35 (43)
11 PF10281 Ish1: Putative stress 57.1 37 0.0008 20.5 4.6 31 45-75 2-35 (38)
12 PF03683 UPF0175: Uncharacteri 51.9 34 0.00074 23.7 4.3 31 45-75 44-74 (76)
13 PF11300 DUF3102: Protein of u 41.8 28 0.00061 27.2 2.9 20 40-59 111-130 (130)
14 TIGR00599 rad18 DNA repair pro 41.1 83 0.0018 28.9 6.2 52 1-77 272-325 (397)
15 PF12095 DUF3571: Protein of u 36.2 40 0.00087 24.6 2.8 27 65-93 24-50 (83)
16 PF05698 Trigger_C: Bacterial 35.2 1.9E+02 0.004 21.5 7.6 68 6-74 71-138 (162)
17 TIGR00444 mazG MazG family pro 31.3 1.6E+02 0.0034 25.2 6.1 51 3-56 192-244 (248)
18 PF13817 DDE_Tnp_IS66_C: IS66 31.0 45 0.00099 20.7 2.0 21 3-26 2-22 (39)
19 PF14871 GHL6: Hypothetical gl 30.8 26 0.00056 27.0 1.1 36 50-85 47-87 (132)
20 PF13427 DUF4111: Domain of un 30.4 1.3E+02 0.0027 22.2 4.7 54 70-124 17-76 (106)
21 PF06840 DUF1241: Protein of u 29.9 50 0.0011 26.6 2.6 18 106-123 98-115 (154)
22 PF13297 Telomere_Sde2_2: Telo 29.6 70 0.0015 22.1 2.9 30 44-73 12-41 (60)
23 COG3160 Rsd Regulator of sigma 27.8 86 0.0019 25.4 3.6 18 41-58 43-60 (162)
24 PF07631 PSD4: Protein of unkn 27.5 1.1E+02 0.0024 23.4 4.1 65 24-88 9-73 (128)
25 PF07766 LETM1: LETM1-like pro 27.4 56 0.0012 27.9 2.7 39 43-81 167-205 (268)
26 PF05385 Adeno_E4: Mastadenovi 26.8 35 0.00077 26.1 1.2 46 38-83 18-63 (109)
27 PF12949 HeH: HeH/LEM domain; 26.7 70 0.0015 19.6 2.3 31 45-75 2-34 (35)
28 PF08098 ATX_III: Anemonia sul 26.1 25 0.00055 20.4 0.2 15 5-19 7-21 (27)
29 PF03020 LEM: LEM domain; Int 25.0 3.9 8.4E-05 26.3 -3.7 21 44-64 3-23 (43)
30 PF09274 ParG: ParG; InterPro 23.6 89 0.0019 22.4 2.7 27 50-79 47-73 (76)
31 PF06971 Put_DNA-bind_N: Putat 23.3 1.5E+02 0.0032 19.3 3.5 41 23-74 9-49 (50)
32 PF04405 ScdA_N: Domain of Unk 22.8 1.2E+02 0.0026 20.1 3.1 32 40-75 20-53 (56)
33 PF04904 NCD1: NAB conserved r 22.2 3.2E+02 0.0069 19.9 6.0 60 20-79 10-75 (82)
34 COG4199 Uncharacterized protei 21.8 20 0.00044 30.1 -1.0 73 2-76 118-197 (201)
35 PF04437 RINT1_TIP1: RINT-1 / 20.7 57 0.0012 29.9 1.5 57 2-59 437-493 (494)
36 PF13443 HTH_26: Cro/C1-type H 20.4 47 0.001 21.2 0.7 13 2-14 42-54 (63)
37 COG1861 SpsF Spore coat polysa 20.4 96 0.0021 26.8 2.7 100 12-123 22-128 (241)
No 1
>KOG1043 consensus Ca2+-binding transmembrane protein LETM1/MRS7 [Function unknown]
Probab=100.00 E-value=5.3e-39 Score=291.53 Aligned_cols=162 Identities=48% Similarity=0.742 Sum_probs=153.3
Q ss_pred ChHHHhHHHhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhC-cCCCCHHHHHHHHHhcCCCC-CCCHHHHHHHHHHHH
Q 038596 1 PRLVNMCKYMGISPFGTDSYLRYMLRKRLQWIKNDDKLIQAEG-VESLSEAELREDCRERGMLG-LLSVEEMRQQLRDWL 78 (163)
Q Consensus 1 pqLvalck~m~l~p~Gt~~~LR~rLr~rL~~L~~DD~~I~~EG-v~sLs~~EL~~AC~~RGi~~-~~s~e~Lr~~L~~WL 78 (163)
|||++||+||+++|||||+++||+||+++++|+.||+.|.+|| |++|+..||+.||++|||++ ++++++|+.||..|+
T Consensus 296 ~qL~al~k~m~l~~~Gt~~~lr~~lr~kik~ik~dD~~I~~eg~v~~ls~~el~~aC~~rgmra~gv~~e~l~~ql~~wl 375 (499)
T KOG1043|consen 296 PQLVALCKYMDLNSFGTDKLLRYQLRKKIKEIKKDDKHIATEGAVESLSLLELQIACRERGMRALGVSEERLREQLRVWL 375 (499)
T ss_pred HHHHHHHHhhcccccCchHHHHHHHHHHHHHhcccccchhhhhhhhHhhHHHHHHHHHhhhcchhccchhhhhHHHHHHH
Confidence 7999999999999999999999999999999999999999999 99999999999999999998 589999999999999
Q ss_pred hhhcCCCCChHHHHhHhhhccCCCCCcHHHHHHHHcc-CChHHhhhhhhcccCCCcchhHHhhhHHHHHHHHHHHHHHHH
Q 038596 79 DLSLNHSVPSSLLILSRAFTVSGKLRPEEAVQATLSS-LPDEVVDTVGVTALPSEDSVSERRRKLEYLAMQEELIKEEEE 157 (163)
Q Consensus 79 ~Lsl~~~ip~sLLllsra~~~~~~~~~~~~l~~~ls~-lPd~~~~e~~~~~~~~e~~~~~~k~kle~l~~qee~I~eE~~ 157 (163)
++|++++||++||+|||+|++.+.....+++.++++. +|+.+..-...++.+.+++.++++.|++.++++|+.|.+|.+
T Consensus 376 dlsl~~~vps~lL~Lsr~~~~~~~~~~~~s~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~kl~~l~~~e~~~~~e~e 455 (499)
T KOG1043|consen 376 DLSLDKKVPSVLLLLSRTFSLGQNSKAPSSSSGKLQIAAPDDLEKLEKLKKEESELGAVDRKKKLELLREGEEIISEEEE 455 (499)
T ss_pred hhhccccCchHHHHHhhhhhhhhcccCCchhhhHhhhhccccHHHhcccccccccccccchHHHHHhhhccccccchhhh
Confidence 9999999999999999999999888788888888885 999999888888888877788899999999999999999999
Q ss_pred hhccc
Q 038596 158 KEGKE 162 (163)
Q Consensus 158 q~~~~ 162 (163)
+++++
T Consensus 456 ee~~~ 460 (499)
T KOG1043|consen 456 EEEKQ 460 (499)
T ss_pred ccccc
Confidence 88875
No 2
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=99.97 E-value=3.9e-31 Score=224.22 Aligned_cols=94 Identities=54% Similarity=0.950 Sum_probs=78.5
Q ss_pred ChHHHhHHHhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHhcCCCC-CCCHHHHHHHHHHHHh
Q 038596 1 PRLVNMCKYMGISPFGTDSYLRYMLRKRLQWIKNDDKLIQAEGVESLSEAELREDCRERGMLG-LLSVEEMRQQLRDWLD 79 (163)
Q Consensus 1 pqLvalck~m~l~p~Gt~~~LR~rLr~rL~~L~~DD~~I~~EGv~sLs~~EL~~AC~~RGi~~-~~s~e~Lr~~L~~WL~ 79 (163)
|||++|||+||++||||++++|+||++|+.+|+.||++|.+|||++||.+||+.||++|||++ ++|+++||.||++||+
T Consensus 174 ~~L~~L~r~~~l~~~~~~~~lr~rL~~~~~~l~~dD~~i~~eGv~~Ls~~EL~~Ac~~RGl~~~~~s~~~lr~~L~~WL~ 253 (268)
T PF07766_consen 174 PHLRALCRLLGLTPFGPSSLLRRRLRKRLRYLKQDDRLIKREGVDSLSEEELQDACYERGLRSTGLSEEELREWLKQWLQ 253 (268)
T ss_dssp HHHHHHHHHTT----SSHHHHHHHHHHHHHHHHHHHHHHHHH-GGGS-HHHHHHHHHHTT---TT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHhccCcCCchHHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHHHHhCCCcCCCCHHHHHHHHHHHHH
Confidence 589999999999999999999999999999999999999999999999999999999999998 6999999999999999
Q ss_pred hhcCCCCChHHHHhH
Q 038596 80 LSLNHSVPSSLLILS 94 (163)
Q Consensus 80 Lsl~~~ip~sLLlls 94 (163)
+|.+.++|+++|+||
T Consensus 254 ls~~~~~p~~lLlL~ 268 (268)
T PF07766_consen 254 LSSNKKVPSSLLLLH 268 (268)
T ss_dssp HHHTS---HHHHHHH
T ss_pred HHccCCCCchhhccC
Confidence 999999999999997
No 3
>KOG4263 consensus Putative receptor CCR1 [Signal transduction mechanisms]
Probab=99.55 E-value=2.1e-14 Score=122.35 Aligned_cols=88 Identities=25% Similarity=0.426 Sum_probs=78.9
Q ss_pred hCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHhcCCCCC-CCHHHHHHHHHHHHhhhcCCCCCh
Q 038596 10 MGISPFGTDSYLRYMLRKRLQWIKNDDKLIQAEGVESLSEAELREDCRERGMLGL-LSVEEMRQQLRDWLDLSLNHSVPS 88 (163)
Q Consensus 10 m~l~p~Gt~~~LR~rLr~rL~~L~~DD~~I~~EGv~sLs~~EL~~AC~~RGi~~~-~s~e~Lr~~L~~WL~Lsl~~~ip~ 88 (163)
|.++.|-++.++|.||..|+.-|+..|++|.++||++|+..||+.||+-||++++ +++++||+||++|+.+|..-+-|.
T Consensus 200 ~~l~~yp~p~~~rHRl~~h~~~ih~lD~al~~~gi~~lt~~~l~~~CYlRgln~~~~~~~~mr~wLr~wvkiS~Slk~~~ 279 (299)
T KOG4263|consen 200 MLLTSYPPPPLLRHRLKTHTTVIHQLDKALAKLGIGQLTAQELKSACYLRGLNSTHIGEDRMRTWLREWVKISCSLKEAE 279 (299)
T ss_pred hhhccCCCChHHHHHHHHHHHHHHHHHHHHHHhccccCCHHHHHHHhhhccCCCCccChHHHHHHHHHHHhhhhcccccc
Confidence 5677888899999999999999999999999999999999999999999999986 999999999999999999877776
Q ss_pred HHHHhHhhh
Q 038596 89 SLLILSRAF 97 (163)
Q Consensus 89 sLLllsra~ 97 (163)
-.|+|....
T Consensus 280 ~slllh~pv 288 (299)
T KOG4263|consen 280 LSLLLHNPV 288 (299)
T ss_pred hhhhhhhhH
Confidence 555554433
No 4
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=97.42 E-value=0.0003 Score=42.95 Aligned_cols=34 Identities=32% Similarity=0.494 Sum_probs=31.0
Q ss_pred CCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Q 038596 45 ESLSEAELREDCRERGMLGLLSVEEMRQQLRDWL 78 (163)
Q Consensus 45 ~sLs~~EL~~AC~~RGi~~~~s~e~Lr~~L~~WL 78 (163)
++|++.||+..|..||+.+.++.++|.+.|.+|+
T Consensus 2 ~~l~v~eLk~~l~~~gL~~~G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 2 SKLTVAELKEELKERGLSTSGKKAELIERLKEHL 35 (35)
T ss_dssp TTSHHHHHHHHHHHTTS-STSSHHHHHHHHHHHH
T ss_pred CcCcHHHHHHHHHHCCCCCCCCHHHHHHHHHHhC
Confidence 5799999999999999999999999999999986
No 5
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=97.17 E-value=0.00087 Score=40.60 Aligned_cols=35 Identities=23% Similarity=0.375 Sum_probs=31.8
Q ss_pred cCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH
Q 038596 44 VESLSEAELREDCRERGMLGLLSVEEMRQQLRDWL 78 (163)
Q Consensus 44 v~sLs~~EL~~AC~~RGi~~~~s~e~Lr~~L~~WL 78 (163)
+.+|+..||+..|.++|+.+.++.++|.+.+.+|+
T Consensus 1 ~~~l~~~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 1 LAKLKVSELKDELKKRGLSTSGTKAELVDRLLEAL 35 (35)
T ss_pred CCcCcHHHHHHHHHHcCCCCCCCHHHHHHHHHHhC
Confidence 35799999999999999999888999999999885
No 6
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=88.65 E-value=0.51 Score=28.30 Aligned_cols=28 Identities=29% Similarity=0.216 Sum_probs=24.6
Q ss_pred ChHHHhHHHhCCCCCCCcHHHHHHHHHH
Q 038596 1 PRLVNMCKYMGISPFGTDSYLRYMLRKR 28 (163)
Q Consensus 1 pqLvalck~m~l~p~Gt~~~LR~rLr~r 28 (163)
++|.+.|+-.|+++-|+..-|..||..+
T Consensus 7 ~~Lk~~l~~~gl~~~G~K~~Lv~Rl~~~ 34 (35)
T smart00513 7 SELKDELKKRGLSTSGTKAELVDRLLEA 34 (35)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHh
Confidence 3799999999999999999888888765
No 7
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=88.41 E-value=0.66 Score=28.04 Aligned_cols=29 Identities=28% Similarity=0.271 Sum_probs=24.3
Q ss_pred ChHHHhHHHhCCCCCCCcHHHHHHHHHHH
Q 038596 1 PRLVNMCKYMGISPFGTDSYLRYMLRKRL 29 (163)
Q Consensus 1 pqLvalck~m~l~p~Gt~~~LR~rLr~rL 29 (163)
++|..+|+-+|+++-|+..-|.-||..++
T Consensus 7 ~eLk~~l~~~gL~~~G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 7 AELKEELKERGLSTSGKKAELIERLKEHL 35 (35)
T ss_dssp HHHHHHHHHTTS-STSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHHHhC
Confidence 47999999999999999988888887653
No 8
>TIGR00578 ku70 ATP-dependent DNA helicase ii, 70 kDa subunit (ku70). Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast.
Probab=83.47 E-value=2.4 Score=40.19 Aligned_cols=37 Identities=19% Similarity=0.310 Sum_probs=33.9
Q ss_pred CcCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHh
Q 038596 43 GVESLSEAELREDCRERGMLGLLSVEEMRQQLRDWLD 79 (163)
Q Consensus 43 Gv~sLs~~EL~~AC~~RGi~~~~s~e~Lr~~L~~WL~ 79 (163)
++.+||+.+|+..|...|+++....++|.+.+..|++
T Consensus 548 ~l~kltv~~Lk~~l~~~g~~~~~kKadLi~~i~~~~~ 584 (584)
T TIGR00578 548 TLGKLTVSVLKDFCRAYGLRSGSKKQELLDALTKHFK 584 (584)
T ss_pred ChhhccHHHHHHHHHHcCCCccccHHHHHHHHHHHhC
Confidence 4889999999999999999977789999999999984
No 9
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=74.55 E-value=3 Score=26.91 Aligned_cols=32 Identities=31% Similarity=0.490 Sum_probs=23.8
Q ss_pred cCCCCHHHHHHHHHhcCCCCC-C---CHHHHHHHHH
Q 038596 44 VESLSEAELREDCRERGMLGL-L---SVEEMRQQLR 75 (163)
Q Consensus 44 v~sLs~~EL~~AC~~RGi~~~-~---s~e~Lr~~L~ 75 (163)
++.||..||+.-|.+-|+..+ + ++.-+...|.
T Consensus 3 ~~~LSd~eL~~~L~~~G~~~gPIt~sTR~vy~kkL~ 38 (44)
T smart00540 3 VDRLSDAELRAELKQYGLPPGPITDTTRKLYEKKLR 38 (44)
T ss_pred hhHcCHHHHHHHHHHcCCCCCCcCcchHHHHHHHHH
Confidence 578999999999999999864 4 3333444444
No 10
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=62.13 E-value=18 Score=22.61 Aligned_cols=31 Identities=29% Similarity=0.409 Sum_probs=22.6
Q ss_pred CCCCHHHHHHHHHhcCCCC--CCCHHHHHHHHH
Q 038596 45 ESLSEAELREDCRERGMLG--LLSVEEMRQQLR 75 (163)
Q Consensus 45 ~sLs~~EL~~AC~~RGi~~--~~s~e~Lr~~L~ 75 (163)
.++|..||+..|.+.||.. .+..++|...+-
T Consensus 3 ~~~~~~eL~~iAk~lgI~~~~~~~K~eLI~~Il 35 (43)
T PF07498_consen 3 KSMTLSELREIAKELGIEGYSKMRKQELIFAIL 35 (43)
T ss_dssp HCS-HHHHHHHHHCTT-TTGCCS-HHHHHHHHH
T ss_pred ccCCHHHHHHHHHHcCCCCCCcCCHHHHHHHHH
Confidence 4789999999999999975 378888876653
No 11
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=57.05 E-value=37 Score=20.50 Aligned_cols=31 Identities=13% Similarity=0.257 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHHhcCCCCC--C-CHHHHHHHHH
Q 038596 45 ESLSEAELREDCRERGMLGL--L-SVEEMRQQLR 75 (163)
Q Consensus 45 ~sLs~~EL~~AC~~RGi~~~--~-s~e~Lr~~L~ 75 (163)
++-|.++|+.-+.+.||... . +.++|....+
T Consensus 2 dtWs~~~L~~wL~~~gi~~~~~~~~rd~Ll~~~k 35 (38)
T PF10281_consen 2 DTWSDSDLKSWLKSHGIPVPKSAKTRDELLKLAK 35 (38)
T ss_pred CCCCHHHHHHHHHHcCCCCCCCCCCHHHHHHHHH
Confidence 56789999999999999863 4 7888887765
No 12
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=51.86 E-value=34 Score=23.74 Aligned_cols=31 Identities=29% Similarity=0.324 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHHHhcCCCCCCCHHHHHHHHH
Q 038596 45 ESLSEAELREDCRERGMLGLLSVEEMRQQLR 75 (163)
Q Consensus 45 ~sLs~~EL~~AC~~RGi~~~~s~e~Lr~~L~ 75 (163)
-++|..+....+..|||....+.+++.+.+.
T Consensus 44 ag~s~~eF~~~L~~~gI~~~~~~eel~~dle 74 (76)
T PF03683_consen 44 AGMSRWEFLELLKERGIPINYDEEELEEDLE 74 (76)
T ss_pred hCCCHHHHHHHHHHCCCCCCCCHHHHHHHHH
Confidence 3589999999999999995589999988775
No 13
>PF11300 DUF3102: Protein of unknown function (DUF3102); InterPro: IPR021451 This entry is represented by Streptococcus phage 7201, Orf2. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=41.80 E-value=28 Score=27.25 Aligned_cols=20 Identities=30% Similarity=0.547 Sum_probs=16.0
Q ss_pred HHhCcCCCCHHHHHHHHHhc
Q 038596 40 QAEGVESLSEAELREDCRER 59 (163)
Q Consensus 40 ~~EGv~sLs~~EL~~AC~~R 59 (163)
...-|++||.-||+.|-++|
T Consensus 111 ~~~dv~~Mt~REL~~avke~ 130 (130)
T PF11300_consen 111 EENDVERMTVRELQQAVKER 130 (130)
T ss_pred HHhhhccccHHHHHHHHhcC
Confidence 33358899999999998876
No 14
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.09 E-value=83 Score=28.90 Aligned_cols=52 Identities=17% Similarity=0.240 Sum_probs=0.0
Q ss_pred ChHHHhHHHhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHhcCCCC-C-CCHHHHHHHHHHH
Q 038596 1 PRLVNMCKYMGISPFGTDSYLRYMLRKRLQWIKNDDKLIQAEGVESLSEAELREDCRERGMLG-L-LSVEEMRQQLRDW 77 (163)
Q Consensus 1 pqLvalck~m~l~p~Gt~~~LR~rLr~rL~~L~~DD~~I~~EGv~sLs~~EL~~AC~~RGi~~-~-~s~e~Lr~~L~~W 77 (163)
++|..+.+=+||+++|+...|..|-++.+..-... ..+ . ++..+|+.+|.+|
T Consensus 272 ~~lr~kL~~lglpt~G~r~~l~~Rh~e~~~l~Nan-------------------------~Ds~~p~s~~~L~~~l~~w 325 (397)
T TIGR00599 272 SQIRKKLSELGLSTNGTRQLLQKRHNEWETLWNSN-------------------------CDSLEPVDKRELLRQLDSW 325 (397)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHhc-------------------------cccCCCCCHHHHHHHHHHH
No 15
>PF12095 DUF3571: Protein of unknown function (DUF3571); InterPro: IPR021954 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 85 to 97 amino acids in length. ; PDB: 2KRX_A.
Probab=36.19 E-value=40 Score=24.59 Aligned_cols=27 Identities=30% Similarity=0.677 Sum_probs=20.4
Q ss_pred CCHHHHHHHHHHHHhhhcCCCCChHHHHh
Q 038596 65 LSVEEMRQQLRDWLDLSLNHSVPSSLLIL 93 (163)
Q Consensus 65 ~s~e~Lr~~L~~WL~Lsl~~~ip~sLLll 93 (163)
+|++++..+|+.||.- ...+|.-|--+
T Consensus 24 lt~~Ell~~Lk~~L~~--~~~LP~dL~~~ 50 (83)
T PF12095_consen 24 LTPEELLEKLKEWLQN--QDDLPPDLAKF 50 (83)
T ss_dssp E-HHHHHHHHHHHHHH--TTTS-HHHHH-
T ss_pred CCHHHHHHHHHHHHHc--CCCCCHHHHhC
Confidence 7899999999999998 67788876543
No 16
>PF05698 Trigger_C: Bacterial trigger factor protein (TF) C-terminus; InterPro: IPR008880 In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains []. This entry represents the C-terminal domain of bacterial trigger factor proteins, which has a multi-helical structure consisting of an irregular array of long and short helices. This domain is structurally similar to the peptide-binding domain of the bacterial porin chaperone SurA.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 1T11_A 3GU0_A 3GTY_X 2NSA_A 1ZXJ_A 1W26_A.
Probab=35.20 E-value=1.9e+02 Score=21.49 Aligned_cols=68 Identities=19% Similarity=0.168 Sum_probs=46.2
Q ss_pred hHHHhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 038596 6 MCKYMGISPFGTDSYLRYMLRKRLQWIKNDDKLIQAEGVESLSEAELREDCRERGMLGLLSVEEMRQQL 74 (163)
Q Consensus 6 lck~m~l~p~Gt~~~LR~rLr~rL~~L~~DD~~I~~EGv~sLs~~EL~~AC~~RGi~~~~s~e~Lr~~L 74 (163)
+|...|.++--...-++.....+++.--.-|.+...+|+ ..|.+|+...+..---..+.+++.++..+
T Consensus 71 ~~~~~~~~~~~~~~~~~~~a~~~lk~~lil~~Ia~~e~I-~v~~eev~~~~~~~a~~~~~~~~~~~~~~ 138 (162)
T PF05698_consen 71 YLQMSGKTEEEFREEFREEAEKRLKQQLILDAIAKKEKI-EVSDEEVEEEIEKLAQQYGMNPEELKEQY 138 (162)
T ss_dssp HHHHHCTCCCSHCHHHHHHHHHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHCSTS-HHHHHHHH
T ss_pred HHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CCCHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 455666655555667788899999999999999999998 48899998887552223345777776665
No 17
>TIGR00444 mazG MazG family protein. This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli.
Probab=31.34 E-value=1.6e+02 Score=25.24 Aligned_cols=51 Identities=16% Similarity=0.199 Sum_probs=36.2
Q ss_pred HHHhHHHhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhC--cCCCCHHHHHHHH
Q 038596 3 LVNMCKYMGISPFGTDSYLRYMLRKRLQWIKNDDKLIQAEG--VESLSEAELREDC 56 (163)
Q Consensus 3 Lvalck~m~l~p~Gt~~~LR~rLr~rL~~L~~DD~~I~~EG--v~sLs~~EL~~AC 56 (163)
|+++|+++|+.|= .-||.-.++-.+.....-..+...| ++.+|.+|+....
T Consensus 192 lvnlAr~~giDpE---~ALr~a~~KF~~Rf~~~E~~~~~~g~~~~~~slee~~~lW 244 (248)
T TIGR00444 192 TVNLARHLKTDAE---IALQKANEKFERRFREVERIVAARGLELTGVDLEEMEELW 244 (248)
T ss_pred HHHHHHHcCCCHH---HHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHH
Confidence 7889999999884 4566655555555555556777777 4588888887654
No 18
>PF13817 DDE_Tnp_IS66_C: IS66 C-terminal element
Probab=30.99 E-value=45 Score=20.71 Aligned_cols=21 Identities=38% Similarity=0.937 Sum_probs=16.5
Q ss_pred HHHhHHHhCCCCCCCcHHHHHHHH
Q 038596 3 LVNMCKYMGISPFGTDSYLRYMLR 26 (163)
Q Consensus 3 Lvalck~m~l~p~Gt~~~LR~rLr 26 (163)
|+.-||.-|+.|| .+|++-|.
T Consensus 2 lieTcK~ngv~P~---~yL~~vL~ 22 (39)
T PF13817_consen 2 LIETCKLNGVNPY---AYLTDVLE 22 (39)
T ss_pred HHHHHHHcCCCHH---HHHHHHHH
Confidence 6788999999998 47666443
No 19
>PF14871 GHL6: Hypothetical glycosyl hydrolase 6
Probab=30.77 E-value=26 Score=27.02 Aligned_cols=36 Identities=22% Similarity=0.432 Sum_probs=24.2
Q ss_pred HHHHHHHHhcCCCC--CCC---HHHHHHHHHHHHhhhcCCC
Q 038596 50 AELREDCRERGMLG--LLS---VEEMRQQLRDWLDLSLNHS 85 (163)
Q Consensus 50 ~EL~~AC~~RGi~~--~~s---~e~Lr~~L~~WL~Lsl~~~ 85 (163)
.|+..||.++||++ .++ .+..-.+==+|.-....-+
T Consensus 47 ge~v~a~h~~Girv~ay~~~~~d~~~~~~HPeW~~~~~~G~ 87 (132)
T PF14871_consen 47 GEQVEACHERGIRVPAYFDFSWDEDAAERHPEWFVRDADGR 87 (132)
T ss_pred HHHHHHHHHCCCEEEEEEeeecChHHHHhCCceeeECCCCC
Confidence 58999999999995 233 3445555557877655433
No 20
>PF13427 DUF4111: Domain of unknown function (DUF4111)
Probab=30.44 E-value=1.3e+02 Score=22.24 Aligned_cols=54 Identities=24% Similarity=0.395 Sum_probs=35.9
Q ss_pred HHHHHHHHHhhhcCCCCChHHHHhHhhhccC--CC-CCcHHHHHHHHccCChH---Hhhhh
Q 038596 70 MRQQLRDWLDLSLNHSVPSSLLILSRAFTVS--GK-LRPEEAVQATLSSLPDE---VVDTV 124 (163)
Q Consensus 70 Lr~~L~~WL~Lsl~~~ip~sLLllsra~~~~--~~-~~~~~~l~~~ls~lPd~---~~~e~ 124 (163)
++..+.+|..=.. ..--.++|-|||++++- +. .|-.+|-.=+|..+|++ ++..+
T Consensus 17 i~~~l~~~~~~~~-~~~~~~vL~LcR~~~tl~tg~i~SK~~aa~Wal~~lp~~~~~~i~~A 76 (106)
T PF13427_consen 17 IRDDLPEWEADIE-GDPRYVVLNLCRILYTLRTGEIVSKDEAAEWALERLPEEWRPLIQEA 76 (106)
T ss_pred HHHHHHHHHHhhc-cChHHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHCCHHHHHHHHHH
Confidence 6667777722222 22234899999999873 33 36678889999999974 44444
No 21
>PF06840 DUF1241: Protein of unknown function (DUF1241); InterPro: IPR009652 This family consists of several programmed cell death 10 protein (PDCD10 or TFAR15) sequences. The function of this family is unknown.; PDB: 3L8I_A 3RQG_B 3RQE_B 3L8J_A 3RQF_B 3AJM_B.
Probab=29.92 E-value=50 Score=26.61 Aligned_cols=18 Identities=39% Similarity=0.661 Sum_probs=14.8
Q ss_pred HHHHHHHHccCChHHhhh
Q 038596 106 EEAVQATLSSLPDEVVDT 123 (163)
Q Consensus 106 ~~~l~~~ls~lPd~~~~e 123 (163)
..+||.+||.|||++-+-
T Consensus 98 A~~LK~iLSrIPdei~dR 115 (154)
T PF06840_consen 98 ATALKRILSRIPDEISDR 115 (154)
T ss_dssp HHHHHHHHHTHHHHTTSH
T ss_pred HHHHHHHHhcCcHhhcch
Confidence 578999999999976543
No 22
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=29.63 E-value=70 Score=22.05 Aligned_cols=30 Identities=17% Similarity=0.152 Sum_probs=22.9
Q ss_pred cCCCCHHHHHHHHHhcCCCCCCCHHHHHHH
Q 038596 44 VESLSEAELREDCRERGMLGLLSVEEMRQQ 73 (163)
Q Consensus 44 v~sLs~~EL~~AC~~RGi~~~~s~e~Lr~~ 73 (163)
+++|-.+-|..|..+||++++++..+=-..
T Consensus 12 Le~lGldrLK~~L~a~GLKcGGTl~ERA~R 41 (60)
T PF13297_consen 12 LEALGLDRLKSALMALGLKCGGTLQERAAR 41 (60)
T ss_pred HHHhCHHHHHHHHHHcCCccCCCHHHHHHH
Confidence 346778899999999999998776543333
No 23
>COG3160 Rsd Regulator of sigma D [Transcription]
Probab=27.76 E-value=86 Score=25.41 Aligned_cols=18 Identities=22% Similarity=0.381 Sum_probs=13.9
Q ss_pred HhCcCCCCHHHHHHHHHh
Q 038596 41 AEGVESLSEAELREDCRE 58 (163)
Q Consensus 41 ~EGv~sLs~~EL~~AC~~ 58 (163)
+|.+.-|+.++|...|++
T Consensus 43 ke~~~plnakaL~~FCq~ 60 (162)
T COG3160 43 KESYMPLNAKALDDFCQS 60 (162)
T ss_pred ccccCCCCHHHHHHHHHH
Confidence 344567899999999976
No 24
>PF07631 PSD4: Protein of unknown function (DUF1592); InterPro: IPR013042 A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also contain IPR011478 from INTERPRO, IPR013036 from INTERPRO, IPR013039 from INTERPRO and IPR013043 from INTERPRO.
Probab=27.47 E-value=1.1e+02 Score=23.43 Aligned_cols=65 Identities=23% Similarity=0.205 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhcCCCCCh
Q 038596 24 MLRKRLQWIKNDDKLIQAEGVESLSEAELREDCRERGMLGLLSVEEMRQQLRDWLDLSLNHSVPS 88 (163)
Q Consensus 24 rLr~rL~~L~~DD~~I~~EGv~sLs~~EL~~AC~~RGi~~~~s~e~Lr~~L~~WL~Lsl~~~ip~ 88 (163)
||.+=|-.-.-|+.++..-.-+.|+..|-..+=..|=+....+..-+..-..|||++..-..++.
T Consensus 9 rLSYfLw~s~PD~~L~~aA~~g~L~~~~~l~~q~~RML~dpr~~~~~~~F~~qWL~l~~~~~~~~ 73 (128)
T PF07631_consen 9 RLSYFLWGSPPDAELLDAAAAGELRTPEQLRAQAERMLADPRARRFVERFFRQWLDLDRLDSIVK 73 (128)
T ss_pred HHHHHHhcCCCCHHHHHHHHhCCCCCHHHHHHHHHHHHcCccHHHHHHHHHHHHhCCCcccccCC
Confidence 33333333444666665443346766666666666656555677788999999999986555543
No 25
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=27.39 E-value=56 Score=27.91 Aligned_cols=39 Identities=28% Similarity=0.412 Sum_probs=27.6
Q ss_pred CcCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhh
Q 038596 43 GVESLSEAELREDCRERGMLGLLSVEEMRQQLRDWLDLS 81 (163)
Q Consensus 43 Gv~sLs~~EL~~AC~~RGi~~~~s~e~Lr~~L~~WL~Ls 81 (163)
++++|+..-|+..|+.=|+.+..+..-+|.+|..|+..=
T Consensus 167 ~Ld~Lsr~~L~~L~r~~~l~~~~~~~~lr~rL~~~~~~l 205 (268)
T PF07766_consen 167 TLDNLSRPHLRALCRLLGLTPFGPSSLLRRRLRKRLRYL 205 (268)
T ss_dssp HHHHS-HHHHHHHHHHTT----SSHHHHHHHHHHHHHHH
T ss_pred ccccCCHHHHHHHHHHhccCcCCchHHHHHHHHHHHHHH
Confidence 467888889999999888887778888888888887643
No 26
>PF05385 Adeno_E4: Mastadenovirus early E4 13 kDa protein; InterPro: IPR008680 This family consists of Homo sapiens and simian mastadenovirus early E4 13 kDa proteins. Human adenovirus 9 (HAdV-9) is unique in eliciting exclusively estrogen-dependent mammary tumours in Rattus spp. and in not requiring viral E1 region transforming genes for tumorigenicity. E4 codes for an oncoprotein essential for tumourigenesis by Ad9 [].
Probab=26.82 E-value=35 Score=26.12 Aligned_cols=46 Identities=22% Similarity=0.318 Sum_probs=35.2
Q ss_pred HHHHhCcCCCCHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHhhhcC
Q 038596 38 LIQAEGVESLSEAELREDCRERGMLGLLSVEEMRQQLRDWLDLSLN 83 (163)
Q Consensus 38 ~I~~EGv~sLs~~EL~~AC~~RGi~~~~s~e~Lr~~L~~WL~Lsl~ 83 (163)
.|.+-|+.-=+..++--+++..|+......+++-..|++||-.+.+
T Consensus 18 Ci~WLglA~at~~Dv~r~ir~~g~~ispeAe~lL~~LrEWLy~a~~ 63 (109)
T PF05385_consen 18 CIAWLGLAYATVVDVIRAIRRDGVFISPEAERLLTGLREWLYFALM 63 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCeeECHHHHHHHHHHHHHHHHHHH
Confidence 4666666655667777788888887766777899999999988764
No 27
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=26.74 E-value=70 Score=19.58 Aligned_cols=31 Identities=23% Similarity=0.185 Sum_probs=17.7
Q ss_pred CCCCHHHHHHHHHhcCCCC--CCCHHHHHHHHH
Q 038596 45 ESLSEAELREDCRERGMLG--LLSVEEMRQQLR 75 (163)
Q Consensus 45 ~sLs~~EL~~AC~~RGi~~--~~s~e~Lr~~L~ 75 (163)
.+|++.+|+....++||.. .-..++|-.-++
T Consensus 2 ~sltV~~Lk~iL~~~~I~~ps~AkKaeLv~L~~ 34 (35)
T PF12949_consen 2 KSLTVAQLKRILDEHGIEFPSNAKKAELVALFN 34 (35)
T ss_dssp TT--SHHHHHHHHHHT---SSS--SHHHHHH--
T ss_pred CcCcHHHHHHHHHHcCCCCCCCCCHHHHHHHHc
Confidence 5799999999999999974 355666655443
No 28
>PF08098 ATX_III: Anemonia sulcata toxin III family; InterPro: IPR012509 This entry occurs within the Anemonia sulcata toxin III (ATX III) neurotoxin family. ATX III is a neurotoxin that is produced by sea anemone; it adopts a compact structure containing four reverse turns and two other chain reversals, but no regular alpha-helix or beta-sheet. A hydrophobic patch found on the surface of the peptide may constitute part of the sodium channel binding surface [].; GO: 0019871 sodium channel inhibitor activity, 0009405 pathogenesis, 0042151 nematocyst; PDB: 1ANS_A.
Probab=26.08 E-value=25 Score=20.44 Aligned_cols=15 Identities=47% Similarity=1.070 Sum_probs=7.6
Q ss_pred HhHHHhCCCCCCCcH
Q 038596 5 NMCKYMGISPFGTDS 19 (163)
Q Consensus 5 alck~m~l~p~Gt~~ 19 (163)
|||+|.|--|||-+.
T Consensus 7 amc~~~~gC~WGQ~~ 21 (27)
T PF08098_consen 7 AMCKYTGGCPWGQNC 21 (27)
T ss_dssp ----TTTT-SSS-SS
T ss_pred ccceeecCCcccccc
Confidence 799999999999653
No 29
>PF03020 LEM: LEM domain; InterPro: IPR003887 The LEM domain is found in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin []. Defects in the emerin gene are a cause of Emery-Dreifuss muscular dystrophy, an X-linked disorder characterised by early contractures, muscle wasting, weakness and cardiomyopathy.; GO: 0005635 nuclear envelope; PDB: 2ODG_C 2ODC_I 1JEI_A 1H9F_A 1GJJ_A.
Probab=25.04 E-value=3.9 Score=26.34 Aligned_cols=21 Identities=52% Similarity=0.589 Sum_probs=15.9
Q ss_pred cCCCCHHHHHHHHHhcCCCCC
Q 038596 44 VESLSEAELREDCRERGMLGL 64 (163)
Q Consensus 44 v~sLs~~EL~~AC~~RGi~~~ 64 (163)
|++||.+||+.-+.+.|+.++
T Consensus 3 v~~LSd~ELr~~L~~~G~~~G 23 (43)
T PF03020_consen 3 VDSLSDEELREELREYGEPPG 23 (43)
T ss_dssp CCCC-CCCCHHCCCCCT-S--
T ss_pred hhhcCHHHHHHHHHHcCCCCC
Confidence 678999999999999999864
No 30
>PF09274 ParG: ParG; InterPro: IPR015354 This entry represents plasmid partition proteins; it adopts a ribbon-helix-helix fold, with a core of four alpha-helices. The proteins are an essential component of the DNA partition complex of the multi drug resistance plasmid TP228 []. ; PDB: 1P94_B.
Probab=23.59 E-value=89 Score=22.44 Aligned_cols=27 Identities=19% Similarity=0.557 Sum_probs=18.9
Q ss_pred HHHHHHHHhcCCCCCCCHHHHHHHHHHHHh
Q 038596 50 AELREDCRERGMLGLLSVEEMRQQLRDWLD 79 (163)
Q Consensus 50 ~EL~~AC~~RGi~~~~s~e~Lr~~L~~WL~ 79 (163)
..+..||..+|... .+.+++-+..||+
T Consensus 47 ~r~K~~ca~~G~si---sdvv~eLid~wL~ 73 (76)
T PF09274_consen 47 RRFKAACAKQGTSI---SDVVRELIDKWLK 73 (76)
T ss_dssp HHHHHHHHHHT--H---HHHHHHHHHHHHC
T ss_pred HHHHHHHHHcCCcH---HHHHHHHHHHHHh
Confidence 36789999999843 2457778888985
No 31
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=23.25 E-value=1.5e+02 Score=19.35 Aligned_cols=41 Identities=32% Similarity=0.550 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHhcCCCCCCCHHHHHHHH
Q 038596 23 YMLRKRLQWIKNDDKLIQAEGVESLSEAELREDCRERGMLGLLSVEEMRQQL 74 (163)
Q Consensus 23 ~rLr~rL~~L~~DD~~I~~EGv~sLs~~EL~~AC~~RGi~~~~s~e~Lr~~L 74 (163)
.||-..++.|+. +..+|++..|-.||-.+| | +++.+.|..|
T Consensus 9 ~RL~~Y~r~L~~----l~~~G~~~vSS~~La~~~---g----i~~~qVRKDl 49 (50)
T PF06971_consen 9 RRLPLYLRYLEQ----LKEEGVERVSSQELAEAL---G----ITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHHHHH----HHHTT-SEE-HHHHHHHH---T----S-HHHHHHHH
T ss_pred HHHHHHHHHHHH----HHHcCCeeECHHHHHHHH---C----CCHHHhcccC
Confidence 456666666654 456899999999999998 4 4666677665
No 32
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=22.81 E-value=1.2e+02 Score=20.10 Aligned_cols=32 Identities=28% Similarity=0.504 Sum_probs=18.6
Q ss_pred HHhCcCC--CCHHHHHHHHHhcCCCCCCCHHHHHHHHH
Q 038596 40 QAEGVES--LSEAELREDCRERGMLGLLSVEEMRQQLR 75 (163)
Q Consensus 40 ~~EGv~s--Ls~~EL~~AC~~RGi~~~~s~e~Lr~~L~ 75 (163)
.+-|+|- =-..-|..||..+|++ ++.+...|+
T Consensus 20 ~~~gIDfCCgG~~~L~eA~~~~~ld----~~~vl~~L~ 53 (56)
T PF04405_consen 20 RKYGIDFCCGGNRSLEEACEEKGLD----PEEVLEELN 53 (56)
T ss_pred HHcCCcccCCCCchHHHHHHHcCCC----HHHHHHHHH
Confidence 3445551 2234578899999985 444444443
No 33
>PF04904 NCD1: NAB conserved region 1 (NCD1); InterPro: IPR006988 Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of eukaryotic (metazoa) transcription factors []. This entry represents the N-terminal NAB domain, which interacts with the EGR1 inhibitory domain (R1) []. It may also mediate multimerisation.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=22.21 E-value=3.2e+02 Score=19.94 Aligned_cols=60 Identities=25% Similarity=0.391 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhC--cC---CCCHHHHHHHHHhcCCCCC-CCHHHHHHHHHHHHh
Q 038596 20 YLRYMLRKRLQWIKNDDKLIQAEG--VE---SLSEAELREDCRERGMLGL-LSVEEMRQQLRDWLD 79 (163)
Q Consensus 20 ~LR~rLr~rL~~L~~DD~~I~~EG--v~---sLs~~EL~~AC~~RGi~~~-~s~e~Lr~~L~~WL~ 79 (163)
+=-|++=+|..-+.-=|..|...| |. ....+|..+.-.-=||-+- +-..++.+.|++|-.
T Consensus 10 lqly~vLqrAnLl~Yyd~fi~~GgDDvqQL~~~~e~eF~eim~lvGM~sKPLHVrRlqKAL~ew~~ 75 (82)
T PF04904_consen 10 LQLYRVLQRANLLQYYDTFIAQGGDDVQQLCEAGEEEFLEIMALVGMASKPLHVRRLQKALQEWST 75 (82)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHcChhHHHHHhcChHHHHHHHHHhCccCccHHHHHHHHHHHHHhc
Confidence 335778888999999999999877 33 3557889999999999874 778899999999964
No 34
>COG4199 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.76 E-value=20 Score=30.09 Aligned_cols=73 Identities=22% Similarity=0.310 Sum_probs=46.1
Q ss_pred hHHHhHHHhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHh-CcC--CCCHH----HHHHHHHhcCCCCCCCHHHHHHHH
Q 038596 2 RLVNMCKYMGISPFGTDSYLRYMLRKRLQWIKNDDKLIQAE-GVE--SLSEA----ELREDCRERGMLGLLSVEEMRQQL 74 (163)
Q Consensus 2 qLvalck~m~l~p~Gt~~~LR~rLr~rL~~L~~DD~~I~~E-Gv~--sLs~~----EL~~AC~~RGi~~~~s~e~Lr~~L 74 (163)
++..+|+|+|+++-.-+.|.+ +=--|.+.+-||-+|.-- +++ +++.+ .+++-...+-+-.+-|.++|.+||
T Consensus 118 ~~~~La~~l~~~~e~l~fM~K--VF~eL~FVtiddGlitvn~~a~KR~ideS~iYQ~kqe~v~~qe~l~yss~~El~~wl 195 (201)
T COG4199 118 KGKRLAQYLGWNKETLVFMIK--VFFELGFVTIDDGLITVNQQAEKREIDESQIYQQKQELVKTQEKLAYSSYEELKQWL 195 (201)
T ss_pred HHHHHHHHcCCCHHHHHHHHH--HHHHcceeEeeCCeEEeccCccccCCcHHHHHHHHHHHHHHHHHHhcCCHHHHHHHH
Confidence 356789999998876666644 666778888888887422 332 34444 444444444444566777777776
Q ss_pred HH
Q 038596 75 RD 76 (163)
Q Consensus 75 ~~ 76 (163)
..
T Consensus 196 ~~ 197 (201)
T COG4199 196 KS 197 (201)
T ss_pred HH
Confidence 53
No 35
>PF04437 RINT1_TIP1: RINT-1 / TIP-1 family; InterPro: IPR007528 This family includes RINT-1, a Rad50 interacting protein which participates in radiation induced checkpoint control [], that interacts with Rad50 only during late S and G2/M phases. RINT1 also functions in membrane trafficking from the endoplasmic reticulum(ER) to the Golgi complex in interphase cells [, , ]. In addition to this, the TIP-1 protein, which is involved in the retrograde transport from the Golgi to the ER []. They share a similar domain organisation with an N-terminal leucine heptad repeat rich coiled coil and an ~500-residue C-terminal RINT1/TIP20 domain, which might be a protein-protein interaction module necessary for the formation of functional complexes.; PDB: 3FHN_A.
Probab=20.75 E-value=57 Score=29.92 Aligned_cols=57 Identities=30% Similarity=0.490 Sum_probs=29.4
Q ss_pred hHHHhHHHhCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHhc
Q 038596 2 RLVNMCKYMGISPFGTDSYLRYMLRKRLQWIKNDDKLIQAEGVESLSEAELREDCRER 59 (163)
Q Consensus 2 qLvalck~m~l~p~Gt~~~LR~rLr~rL~~L~~DD~~I~~EGv~sLs~~EL~~AC~~R 59 (163)
.|..-|++|+++ .|+...++--++.-...-..-..++..-||..||..|.+.+++.|
T Consensus 437 ~l~E~~~LL~L~-~~~~~~~~~~l~~~~~~~~~~~~~l~~lgI~~Ls~~ea~~vL~rR 493 (494)
T PF04437_consen 437 RLREACKLLNLP-YGSAKLLKEFLSKSYIKNENARKLLEELGISHLSPSEARDVLYRR 493 (494)
T ss_dssp HHHHHHHHHGGG-G-CGG--TTTTSHHHHHHT--SHHHHHTT-SSS-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCC-CcchhhhHHHHhhhhccchHHHHHHHHCCCCcCCHHHHHHHHHcc
Confidence 456677788765 333332221121111112223455556699999999999998766
No 36
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=20.37 E-value=47 Score=21.18 Aligned_cols=13 Identities=31% Similarity=0.478 Sum_probs=9.0
Q ss_pred hHHHhHHHhCCCC
Q 038596 2 RLVNMCKYMGISP 14 (163)
Q Consensus 2 qLvalck~m~l~p 14 (163)
+|.++|++||++|
T Consensus 42 ~l~~ia~~l~~~~ 54 (63)
T PF13443_consen 42 TLEKIAKALNCSP 54 (63)
T ss_dssp HHHHHHHHHT--H
T ss_pred HHHHHHHHcCCCH
Confidence 4778999999875
No 37
>COG1861 SpsF Spore coat polysaccharide biosynthesis protein F, CMP-KDO synthetase homolog [Cell envelope biogenesis, outer membrane]
Probab=20.37 E-value=96 Score=26.83 Aligned_cols=100 Identities=25% Similarity=0.343 Sum_probs=60.6
Q ss_pred CCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHHHhcCCCCC-CCHHHHHHHHHHHHhhhcCCCCChHH
Q 038596 12 ISPFGTDSYLRYMLRKRLQWIKNDDKLIQAEGVESLSEAELREDCRERGMLGL-LSVEEMRQQLRDWLDLSLNHSVPSSL 90 (163)
Q Consensus 12 l~p~Gt~~~LR~rLr~rL~~L~~DD~~I~~EGv~sLs~~EL~~AC~~RGi~~~-~s~e~Lr~~L~~WL~Lsl~~~ip~sL 90 (163)
|-|.|+..|+-++| .|++..+.-|+++..-- +.=+..-|...|.++|+.+. +|+++.-+..-.=++-.. .+
T Consensus 22 LlpL~~~pmI~~~l-ervrks~~~d~ivvATS-~~~~d~~l~~~~~~~G~~vfrGs~~dVL~Rf~~a~~a~~-----~~- 93 (241)
T COG1861 22 LLPLGGEPMIEYQL-ERVRKSKDLDKIVVATS-DKEEDDALEEVCRSHGFYVFRGSEEDVLQRFIIAIKAYS-----AD- 93 (241)
T ss_pred hhhcCCCchHHHHH-HHHhccccccceEEEec-CCcchhHHHHHHHHcCeeEecCCHHHHHHHHHHHHHhcC-----CC-
Confidence 45788888888877 46666665555543211 12345679999999999985 899887666655554433 22
Q ss_pred HHhHhhhccCCCCCc------HHHHHHHHccCChHHhhh
Q 038596 91 LILSRAFTVSGKLRP------EEAVQATLSSLPDEVVDT 123 (163)
Q Consensus 91 Lllsra~~~~~~~~~------~~~l~~~ls~lPd~~~~e 123 (163)
-...+||.-++ ..++..-+++=-|-+.+.
T Consensus 94 ----~VVRvTGD~P~~dp~l~d~~v~~~l~~gaDY~s~~ 128 (241)
T COG1861 94 ----VVVRVTGDNPFLDPELVDAAVDRHLEKGADYVSNT 128 (241)
T ss_pred ----eEEEeeCCCCCCCHHHHHHHHHHHHhcCCcccccc
Confidence 22234554433 244555566555544443
Done!