Query 039138
Match_columns 177
No_of_seqs 29 out of 31
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 06:39:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039138.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039138hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06708 DUF1195: Protein of u 100.0 1.5E-93 3.2E-98 574.1 14.6 151 1-152 1-157 (157)
2 TIGR02574 stabl_TIGR02574 puta 83.1 3.5 7.6E-05 28.1 4.8 44 79-122 3-47 (63)
3 PF09720 Unstab_antitox: Putat 71.8 12 0.00026 24.4 4.7 43 79-122 2-44 (54)
4 PF13286 HD_assoc: Phosphohydr 67.4 6.4 0.00014 27.1 2.8 55 77-137 27-82 (92)
5 KOG0742 AAA+-type ATPase [Post 60.9 10 0.00022 37.0 3.7 68 65-135 495-571 (630)
6 PF10363 DUF2435: Protein of u 58.7 13 0.00027 27.3 3.1 33 108-140 2-34 (92)
7 PF12765 Cohesin_HEAT: HEAT re 50.4 23 0.0005 22.6 3.0 19 113-131 22-40 (42)
8 PRK05590 hypothetical protein; 48.3 14 0.00031 30.9 2.2 33 104-136 21-56 (166)
9 PF11972 HTH_13: HTH DNA bindi 47.9 6.7 0.00014 27.5 0.2 13 24-36 41-53 (54)
10 PF10039 DUF2275: Predicted in 47.2 12 0.00025 32.1 1.6 30 23-53 27-56 (218)
11 PF04082 Fungal_trans: Fungal 46.2 12 0.00027 27.0 1.4 64 27-90 83-152 (260)
12 PF02985 HEAT: HEAT repeat; I 45.6 28 0.0006 20.2 2.6 22 116-137 7-28 (31)
13 TIGR03715 KxYKxGKxW KxYKxGKxW 41.9 24 0.00052 21.1 2.0 14 32-45 11-24 (29)
14 PTZ00008 (NAP-S) nucleosome as 38.5 26 0.00057 28.8 2.3 13 102-114 35-47 (185)
15 PF13646 HEAT_2: HEAT repeats; 38.3 54 0.0012 21.2 3.4 29 109-137 31-59 (88)
16 COG3197 FixS Uncharacterized p 37.7 24 0.00052 25.4 1.7 38 35-85 13-55 (58)
17 PF00615 RGS: Regulator of G p 37.6 1.2E+02 0.0026 20.0 5.6 55 80-135 42-99 (118)
18 PF12273 RCR: Chitin synthesis 33.1 20 0.00044 26.9 0.8 9 34-42 2-10 (130)
19 cd04756 Commd8 COMM_Domain con 32.4 70 0.0015 25.9 3.8 41 102-145 75-115 (176)
20 PF12321 DUF3634: Protein of u 32.0 18 0.00038 28.4 0.3 66 35-103 4-74 (108)
21 PRK12651 putative monovalent c 31.7 29 0.00062 27.3 1.5 20 35-54 5-24 (158)
22 PF04226 Transgly_assoc: Trans 31.5 45 0.00098 22.0 2.2 18 33-50 31-48 (48)
23 PTZ00200 cysteine proteinase; 31.5 30 0.00065 32.0 1.8 49 50-98 62-110 (448)
24 PF13513 HEAT_EZ: HEAT-like re 31.1 90 0.002 19.3 3.4 30 106-135 25-54 (55)
25 PF03967 PRCH: Photosynthetic 29.4 39 0.00084 27.7 1.9 17 36-52 12-28 (136)
26 PF00879 Defensin_propep: Defe 28.7 41 0.00089 23.6 1.7 13 33-45 4-16 (52)
27 PRK08965 putative monovalent c 27.8 43 0.00094 26.4 1.9 20 35-54 9-28 (162)
28 PF05918 API5: Apoptosis inhib 27.3 69 0.0015 31.0 3.5 37 103-139 46-89 (556)
29 PF06985 HET: Heterokaryon inc 27.3 39 0.00084 23.6 1.4 19 82-100 58-76 (139)
30 TIGR03354 VI_FHA type VI secre 27.0 39 0.00085 30.5 1.7 29 89-117 358-393 (396)
31 PF14024 DUF4240: Protein of u 26.5 50 0.0011 25.1 2.0 40 105-145 5-44 (128)
32 PF12607 DUF3772: Protein of u 26.0 52 0.0011 22.5 1.8 24 95-118 30-53 (64)
33 COG5208 HAP5 CCAAT-binding fac 25.7 38 0.00082 30.5 1.3 18 101-118 84-101 (286)
34 KOG2140 Uncharacterized conser 24.8 82 0.0018 31.7 3.5 51 99-150 512-562 (739)
35 PF06942 GlpM: GlpM protein; 24.0 70 0.0015 25.3 2.4 17 32-48 90-106 (107)
36 COG0587 DnaE DNA polymerase II 24.0 61 0.0013 33.8 2.6 61 75-137 402-462 (1139)
37 PF06480 FtsH_ext: FtsH Extrac 24.0 28 0.0006 23.3 0.1 25 33-57 3-33 (110)
38 KOG2085 Serine/threonine prote 23.7 92 0.002 29.9 3.5 47 107-153 82-132 (457)
39 PF14851 FAM176: FAM176 family 23.0 54 0.0012 26.9 1.6 12 81-92 125-136 (153)
40 PF15168 TRIQK: Triple QxxK/R 22.9 82 0.0018 24.0 2.5 20 30-49 49-70 (79)
41 COG4103 Uncharacterized protei 22.0 59 0.0013 27.1 1.7 17 79-95 96-112 (148)
42 PRK12652 putative monovalent c 21.6 73 0.0016 28.6 2.3 28 26-54 162-189 (357)
43 COG3206 GumC Uncharacterized p 21.6 2.6E+02 0.0057 24.8 5.7 69 29-97 22-108 (458)
44 PF14719 PID_2: Phosphotyrosin 21.4 56 0.0012 27.2 1.5 50 105-154 113-173 (182)
45 PF14832 Tautomerase_3: Putati 20.5 76 0.0017 25.0 2.0 28 77-107 11-38 (136)
46 PF05225 HTH_psq: helix-turn-h 20.4 1.2E+02 0.0026 19.5 2.6 22 108-129 2-23 (45)
47 PTZ00007 (NAP-L) nucleosome as 20.4 31 0.00066 31.2 -0.3 43 72-114 49-110 (337)
No 1
>PF06708 DUF1195: Protein of unknown function (DUF1195); InterPro: IPR010608 This family consists of several plant specific hypothetical proteins of around 160 residues in length. The function of this family is unknown.
Probab=100.00 E-value=1.5e-93 Score=574.14 Aligned_cols=151 Identities=81% Similarity=1.275 Sum_probs=148.1
Q ss_pred CCCCCCCCccccc------ccccccCCCccccCCchhHHHHHHHHHHHHHHhhhhceEEEEeccCCcccccCCCCCCCCC
Q 039138 1 MKDDESLPTTTTL------NVTKKESSDSSAFGKGRYKFWALAAILLLAFWSMFTGTVTLRWSAGNLNRLSDDLGSPIHD 74 (177)
Q Consensus 1 Mkddd~lp~st~t------~~~kkes~~~~l~GkgrYKfWaLaAIlLLAfWSMftgsVtLrwSag~Ln~~s~dld~p~~d 74 (177)
|||+|++|++|++ .++|+++++++|||||||||||||||+|||||||||||||||||+||||++++|+|+|++|
T Consensus 1 mk~~~~~~~~t~~~at~~~~~~~~~~~~~~l~gKgrYK~WaLaAIlLLAfWSM~tgsvtLrwS~g~l~~~~~dl~~~~~d 80 (157)
T PF06708_consen 1 MKDDDSLPTSTPTPATTTTASSKKESSESALFGKGRYKFWALAAILLLAFWSMFTGSVTLRWSAGNLNSVSDDLDFPIHD 80 (157)
T ss_pred CCccccCCcCCCCCcccceeeecccccccccccCchhHHHHHHHHHHHHHHHHhheeeEEEeccCcccccccccCCcccc
Confidence 9999999988885 4889999999999999999999999999999999999999999999999999999999999
Q ss_pred CCchhhHHHHHHHHhHhhhhhcCCCCcCcchHHHHHHHHHHHHhhcchhhhHHHHHHHHHhhhhhccccCCCCCCCcc
Q 039138 75 DLDVLEMEEREKVVKHMWDVYTNSRRIRLPRFWQEAFEAAYEELSSDVAEVRDAAITEIAKMSVRSLVNIDSPPFHST 152 (177)
Q Consensus 75 DlDvLEmEeREKvVr~MWDvYt~s~~vrLprFWqEAFeAAYeeL~sD~~~vrdaAisEIAkmS~r~li~~dp~p~~S~ 152 (177)
|||||||||||||||||||||||++++|||||||||||||||+|+||+|+|||||||||||||+|+ |++||||.||+
T Consensus 81 DlDvLEmEeREKvVr~MWDvYt~s~~vrLPrFWqEAFeAAYe~L~sD~~~VrdaAisEIAkmS~r~-~~~~~~~~~st 157 (157)
T PF06708_consen 81 DLDVLEMEEREKVVRHMWDVYTRSRRVRLPRFWQEAFEAAYEELASDVPQVRDAAISEIAKMSVRS-IELDPPPNQST 157 (157)
T ss_pred cccHHHHHHHHHHHHHHHHHhcCCCCccCchHHHHHHHHHHHHHhccCcchhHHHHHHHHHHhhcc-ccCCCCCCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999 99999999986
No 2
>TIGR02574 stabl_TIGR02574 putative addiction module component, TIGR02574 family. Members of this family are bacterial proteins, typically are about 75 amino acids long, always found as part of a pair (at least) of two small genes. The other in the pair always belongs to a subfamily of the larger family pfam05016 (although not necessarily scoring above the designated cutoff), which contains plasmid stabilization proteins. It is likely that this protein and its pfam05016 member partner comprise some form of addiction module, although these gene pairs usually are found on the bacterial main chromosome.
Probab=83.07 E-value=3.5 Score=28.11 Aligned_cols=44 Identities=18% Similarity=0.414 Sum_probs=37.8
Q ss_pred hhHHHHHHHHhHhhhhhcC-CCCcCcchHHHHHHHHHHHHhhcch
Q 039138 79 LEMEEREKVVKHMWDVYTN-SRRIRLPRFWQEAFEAAYEELSSDV 122 (177)
Q Consensus 79 LEmEeREKvVr~MWDvYt~-s~~vrLprFWqEAFeAAYeeL~sD~ 122 (177)
|..+||-.||.+.||=-.+ ...+.+|.-|++-.+.-++++.++-
T Consensus 3 L~~~ERl~Lve~LwdSL~~~~~~~~~~~~~~~el~~R~~~~~~g~ 47 (63)
T TIGR02574 3 LSPDERIQLVEDIWDSIAAEAKHLILTEAQKAELDRRLADYKADP 47 (63)
T ss_pred CCHHHHHHHHHHHHHHhccCcccCCCCHHHHHHHHHHHHHHHcCC
Confidence 5678999999999999985 5789999999999998888776653
No 3
>PF09720 Unstab_antitox: Putative addiction module component; InterPro: IPR013406 This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilisation proteins (IPR007712 from INTERPRO). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death [] - although these gene pairs are usually found on the bacterial main chromosome.
Probab=71.84 E-value=12 Score=24.39 Aligned_cols=43 Identities=26% Similarity=0.569 Sum_probs=35.7
Q ss_pred hhHHHHHHHHhHhhhhhcCCCCcCcchHHHHHHHHHHHHhhcch
Q 039138 79 LEMEEREKVVKHMWDVYTNSRRIRLPRFWQEAFEAAYEELSSDV 122 (177)
Q Consensus 79 LEmEeREKvVr~MWDvYt~s~~vrLprFWqEAFeAAYeeL~sD~ 122 (177)
|-.+||-.++.+.|+=-.++.. -+|..|.+-.+.-++++.+.-
T Consensus 2 L~~~er~~L~e~L~~sl~~~~~-~~~~~w~~el~rR~~~~~~G~ 44 (54)
T PF09720_consen 2 LPPEERAELAEELWDSLDDPDS-EVEAWWKEELERRLAEYESGK 44 (54)
T ss_pred cCHHHHHHHHHHHHHHhccccc-cCcHHHHHHHHHHHHHHHcCC
Confidence 4578999999999997666634 899999999999888887653
No 4
>PF13286 HD_assoc: Phosphohydrolase-associated domain; PDB: 2DQB_D.
Probab=67.41 E-value=6.4 Score=27.13 Aligned_cols=55 Identities=24% Similarity=0.453 Sum_probs=33.6
Q ss_pred chhhHHHH-HHHHhHhhhhhcCCCCcCcchHHHHHHHHHHHHhhcchhhhHHHHHHHHHhhh
Q 039138 77 DVLEMEER-EKVVKHMWDVYTNSRRIRLPRFWQEAFEAAYEELSSDVAEVRDAAITEIAKMS 137 (177)
Q Consensus 77 DvLEmEeR-EKvVr~MWDvYt~s~~vrLprFWqEAFeAAYeeL~sD~~~vrdaAisEIAkmS 137 (177)
.|.+.|.+ .++++.+||.|.+...-.||..|++.++.+-+. +-....+-=||-|.
T Consensus 27 ~v~~~~~~~~~ii~~Lfd~~~~~~~~~l~~~~~~~~~~~~~~------~~~r~v~DyIaGMT 82 (92)
T PF13286_consen 27 RVVEEEEKGRRIIRELFDYFMENPERLLPEDYRERYEQAEDD------SRARVVCDYIAGMT 82 (92)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH-GG-GS-HHHHTTHHHH----------HHHHHHHHHHTS-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHhcCChhhhhHHhhhhhh------HHHHHHHHHhhcCc
Confidence 34455544 579999999999876668999999998766544 33334445566664
No 5
>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=60.89 E-value=10 Score=37.00 Aligned_cols=68 Identities=24% Similarity=0.307 Sum_probs=46.0
Q ss_pred cCCCCCCCCCCCch------hhHHHHHHHHhHhhhhhcCC-CCcCcchHHHHHHHHHHHHh--hcchhhhHHHHHHHHHh
Q 039138 65 SDDLGSPIHDDLDV------LEMEEREKVVKHMWDVYTNS-RRIRLPRFWQEAFEAAYEEL--SSDVAEVRDAAITEIAK 135 (177)
Q Consensus 65 s~dld~p~~dDlDv------LEmEeREKvVr~MWDvYt~s-~~vrLprFWqEAFeAAYeeL--~sD~~~vrdaAisEIAk 135 (177)
++|||..+.|-+|- =-+|||+|+++.-.+-|.-. ..-+=|--|+.-|..--+.+ .+| +-+.-++|.||
T Consensus 495 pgdlDsAV~DRide~veFpLPGeEERfkll~lYlnkyi~~~~~~~~~~~~~~lfkk~sQ~i~l~~~---~t~~~~~EaAk 571 (630)
T KOG0742|consen 495 PGDLDSAVNDRIDEVVEFPLPGEEERFKLLNLYLNKYILKPATSGKPGKWSHLFKKESQRIKLAGF---DTGRKCSEAAK 571 (630)
T ss_pred ccchhHHHHhhhhheeecCCCChHHHHHHHHHHHHHHhcCcCCCCCCchhhHHHhhhhheeeeccc---hHHHHHHHHHH
Confidence 57888888776662 24899999999999999632 22222889999998744332 333 44556666665
No 6
>PF10363 DUF2435: Protein of unknown function (DUF2435)
Probab=58.66 E-value=13 Score=27.31 Aligned_cols=33 Identities=18% Similarity=0.334 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhhcchhhhHHHHHHHHHhhhhhc
Q 039138 108 QEAFEAAYEELSSDVAEVRDAAITEIAKMSVRS 140 (177)
Q Consensus 108 qEAFeAAYeeL~sD~~~vrdaAisEIAkmS~r~ 140 (177)
++.|+.|.++|.+..+.||-.|+.++.++--++
T Consensus 2 ~~~~~~al~~L~dp~~PvRa~gL~~L~~Li~~~ 34 (92)
T PF10363_consen 2 RETLQEALSDLNDPLPPVRAHGLVLLRKLIESK 34 (92)
T ss_pred hHHHHHHHHHccCCCcchHHHHHHHHHHHHHcC
Confidence 578999999999999999999999999886555
No 7
>PF12765 Cohesin_HEAT: HEAT repeat associated with sister chromatid cohesion
Probab=50.35 E-value=23 Score=22.56 Aligned_cols=19 Identities=37% Similarity=0.476 Sum_probs=14.5
Q ss_pred HHHHHhhcchhhhHHHHHH
Q 039138 113 AAYEELSSDVAEVRDAAIT 131 (177)
Q Consensus 113 AAYeeL~sD~~~vrdaAis 131 (177)
+-.+.|....|.||+||+.
T Consensus 22 ~i~~rl~D~s~~VR~aav~ 40 (42)
T PF12765_consen 22 AIIRRLSDSSPSVREAAVD 40 (42)
T ss_pred HHHHHhcCCChHHHHHHHH
Confidence 3344577888999999985
No 8
>PRK05590 hypothetical protein; Provisional
Probab=48.30 E-value=14 Score=30.90 Aligned_cols=33 Identities=24% Similarity=0.499 Sum_probs=30.5
Q ss_pred chHHHHHHH---HHHHHhhcchhhhHHHHHHHHHhh
Q 039138 104 PRFWQEAFE---AAYEELSSDVAEVRDAAITEIAKM 136 (177)
Q Consensus 104 prFWqEAFe---AAYeeL~sD~~~vrdaAisEIAkm 136 (177)
-+||++-|. ..|+.|-++...|.+-.|.|+|+-
T Consensus 21 ~~fw~~y~~~ek~iy~~iL~~~~~~~~gtv~ela~k 56 (166)
T PRK05590 21 AAFWKEYGSVEKNIYTQILANHKEVVEGTVKELAEK 56 (166)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCceeeeeHHHHHHH
Confidence 799999995 689999999999999999999984
No 9
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=47.87 E-value=6.7 Score=27.52 Aligned_cols=13 Identities=38% Similarity=1.114 Sum_probs=10.5
Q ss_pred cccCCchhHHHHH
Q 039138 24 SAFGKGRYKFWAL 36 (177)
Q Consensus 24 ~l~GkgrYKfWaL 36 (177)
-+=|+|||+.|..
T Consensus 41 EiTGr~R~RaWgi 53 (54)
T PF11972_consen 41 EITGRGRYRAWGI 53 (54)
T ss_pred eecCCcccchhhc
Confidence 3579999999963
No 10
>PF10039 DUF2275: Predicted integral membrane protein (DUF2275); InterPro: IPR018734 This domain, found in various hypothetical bacterial proteins and in the RNA polymerase sigma factor, has no known function.
Probab=47.16 E-value=12 Score=32.15 Aligned_cols=30 Identities=23% Similarity=0.178 Sum_probs=23.9
Q ss_pred ccccCCchhHHHHHHHHHHHHHHhhhhceEE
Q 039138 23 SSAFGKGRYKFWALAAILLLAFWSMFTGTVT 53 (177)
Q Consensus 23 ~~l~GkgrYKfWaLaAIlLLAfWSMftgsVt 53 (177)
+.+| +.|||.|||+|++|+++=|++-+.|.
T Consensus 27 ~~~~-~k~~r~~Al~alil~i~as~~f~~v~ 56 (218)
T PF10039_consen 27 FRMW-RKYKRAIALAALILFILASLGFPPVR 56 (218)
T ss_pred HHHH-HHHHHHHHHHHHHHHHHHHHhhHHHH
Confidence 3445 56999999999999999999855543
No 11
>PF04082 Fungal_trans: Fungal specific transcription factor domain ; InterPro: IPR007219 This domain is found in a number of fungal transcription factors including transcriptional activator xlnR, yeast regulatory protein GAL4, and other transcription proteins regulating a variety of cellular and metabolic processes.; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=46.24 E-value=12 Score=26.97 Aligned_cols=64 Identities=27% Similarity=0.353 Sum_probs=41.0
Q ss_pred CCchhHHHHHHHHHHHHHHhhhhceEEEEecc-CCcccccCCCCCCCCC---C--CchhhHHHHHHHHhH
Q 039138 27 GKGRYKFWALAAILLLAFWSMFTGTVTLRWSA-GNLNRLSDDLGSPIHD---D--LDVLEMEEREKVVKH 90 (177)
Q Consensus 27 GkgrYKfWaLaAIlLLAfWSMftgsVtLrwSa-g~Ln~~s~dld~p~~d---D--lDvLEmEeREKvVr~ 90 (177)
+..+-.+..+-|++|+++|....|..+.-|.. |..-++..+++-.... + ++..|.|+|.++...
T Consensus 83 ~~~~~~l~~lqal~ll~~~~~~~~~~~~~~~~~~~a~~~a~~lgLh~~~~~~~~~~~~~~~e~rrRl~w~ 152 (260)
T PF04082_consen 83 SSESPSLESLQALLLLSIYLFSSGNPSAAWMLIGMAIRLAQSLGLHREPSYSNDRLDAEEQELRRRLWWC 152 (260)
T ss_pred ccccccccchhhhhhhhccccccccchhhccchhhhhccccccccccccccccccchhhhhhchhhHHHH
Confidence 44444578888999999999999987777765 3333444555433222 1 566566666665543
No 12
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=45.59 E-value=28 Score=20.15 Aligned_cols=22 Identities=27% Similarity=0.348 Sum_probs=16.3
Q ss_pred HHhhcchhhhHHHHHHHHHhhh
Q 039138 116 EELSSDVAEVRDAAITEIAKMS 137 (177)
Q Consensus 116 eeL~sD~~~vrdaAisEIAkmS 137 (177)
+-|..+.+.||.+|+.=+.++.
T Consensus 7 ~~l~D~~~~VR~~a~~~l~~i~ 28 (31)
T PF02985_consen 7 QLLNDPSPEVRQAAAECLGAIA 28 (31)
T ss_dssp HHHT-SSHHHHHHHHHHHHHHH
T ss_pred HHcCCCCHHHHHHHHHHHHHHH
Confidence 4566789999999988776653
No 13
>TIGR03715 KxYKxGKxW KxYKxGKxW signal peptide. This model describes a novel form of signal peptide that occurs as an N-terminal domain with a recognizable motif, reminiscent of the YSIRK and PEP-CTERM forms of signal peptide. This domain tends to occur on long, low-complexity (usually Serine-rich and heavily glycosylated) proteins of the Firmicutes, and (as with YSIRK) the majority of these proteins have the LPXTG cell wall-anchoring motif at the C-terminus.
Probab=41.86 E-value=24 Score=21.10 Aligned_cols=14 Identities=50% Similarity=0.665 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHH
Q 039138 32 KFWALAAILLLAFW 45 (177)
Q Consensus 32 KfWaLaAIlLLAfW 45 (177)
|.|+.|+|..+++=
T Consensus 11 K~Wv~a~~~~~~l~ 24 (29)
T TIGR03715 11 KQWVFAAITTLALA 24 (29)
T ss_pred cHHHHHHHHHHHHH
Confidence 57999999877653
No 14
>PTZ00008 (NAP-S) nucleosome assembly protein-S; Provisional
Probab=38.52 E-value=26 Score=28.76 Aligned_cols=13 Identities=23% Similarity=0.958 Sum_probs=11.3
Q ss_pred CcchHHHHHHHHH
Q 039138 102 RLPRFWQEAFEAA 114 (177)
Q Consensus 102 rLprFWqEAFeAA 114 (177)
++|.||--||...
T Consensus 35 gIP~FW~~vl~n~ 47 (185)
T PTZ00008 35 KIPGFWADTLRRH 47 (185)
T ss_pred cCccHHHHHHHcC
Confidence 5999999999873
No 15
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=38.25 E-value=54 Score=21.21 Aligned_cols=29 Identities=31% Similarity=0.358 Sum_probs=24.6
Q ss_pred HHHHHHHHHhhcchhhhHHHHHHHHHhhh
Q 039138 109 EAFEAAYEELSSDVAEVRDAAITEIAKMS 137 (177)
Q Consensus 109 EAFeAAYeeL~sD~~~vrdaAisEIAkmS 137 (177)
++...-.+-|.++.+.||.+|+.=++++.
T Consensus 31 ~~~~~L~~~l~d~~~~vr~~a~~aL~~i~ 59 (88)
T PF13646_consen 31 EAIPALIELLKDEDPMVRRAAARALGRIG 59 (88)
T ss_dssp HHHHHHHHHHTSSSHHHHHHHHHHHHCCH
T ss_pred hHHHHHHHHHcCCCHHHHHHHHHHHHHhC
Confidence 66777777888899999999999988874
No 16
>COG3197 FixS Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]
Probab=37.73 E-value=24 Score=25.36 Aligned_cols=38 Identities=37% Similarity=0.505 Sum_probs=20.9
Q ss_pred HHHHHHHHHHH-hhhhceEEEEeccCCcccccCCCCCC----CCCCCchhhHHHHH
Q 039138 35 ALAAILLLAFW-SMFTGTVTLRWSAGNLNRLSDDLGSP----IHDDLDVLEMEERE 85 (177)
Q Consensus 35 aLaAIlLLAfW-SMftgsVtLrwSag~Ln~~s~dld~p----~~dDlDvLEmEeRE 85 (177)
++.+|+|.||| ++=+ |. .||++-| +.||.+.++.+++.
T Consensus 13 ~l~~v~l~~flWavks---------gQ----yDDl~g~ae~IL~D~~~~~~k~~~d 55 (58)
T COG3197 13 LLGAVGLGAFLWAVKS---------GQ----YDDLDGPAERILYDDEEPLDKEPLD 55 (58)
T ss_pred HHHHHHHHHHHHhccc---------CC----cccccccHHHHhhcccccccccccc
Confidence 35566666654 4432 22 5677666 55666655555443
No 17
>PF00615 RGS: Regulator of G protein signaling domain; InterPro: IPR000342 RGS (Regulator of G Protein Signalling) proteins are multi-functional, GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways []. Upon activation by GPCRs, heterotrimeric G proteins exchange GDP for GTP, are released from the receptor, and dissociate into free, active GTP-bound alpha subunit and beta-gamma dimer, both of which activate downstream effectors. The response is terminated upon GTP hydrolysis by the alpha subunit (IPR001019 from INTERPRO), which can then bind the beta-gamma dimer (IPR001632 from INTERPRO, IPR001770 from INTERPRO) and the receptor. RGS proteins markedly reduce the lifespan of GTP-bound alpha subunits by stabilising the G protein transition state. All RGS proteins contain an 'RGS-box' (or RGS domain), which is required for activity. Some small RGS proteins such as RGS1 and RGS4 are comprised of little more than an RGS domain, while others also contain additional domains that confer further functionality []. RGS domains can be found in conjunction with a variety of domains, including: DEP for membrane targeting (IPR000591 from INTERPRO), PDZ for binding to GPCRs (IPR001478 from INTERPRO), PTB for phosphotyrosine-binding (IPR006020 from INTERPRO), RBD for Ras-binding (IPR003116 from INTERPRO), GoLoco for guanine nucleotide inhibitor activity (IPR003109 from INTERPRO), PX for phosphatidylinositol-binding (IPR001683 from INTERPRO), PXA that is associated with PX (IPR003114 from INTERPRO), PH for stimulating guanine nucleotide exchange (IPR001849 from INTERPRO), and GGL (G protein gamma subunit-like) for binding G protein beta subunits (IPR001770 from INTERPRO) []. Those RGS proteins that contain GGL domains can interact with G protein beta subunits to form novel dimers that prevent G protein gamma subunit binding and G protein alpha subunit association, thereby preventing heterotrimer formation.; GO: 0004871 signal transducer activity; PDB: 2BCJ_A 3PSC_A 3PVU_A 1YM7_B 3PVW_A 1OMW_A 2EBZ_A 2BV1_B 2GTP_D 1CMZ_A ....
Probab=37.61 E-value=1.2e+02 Score=19.99 Aligned_cols=55 Identities=16% Similarity=0.365 Sum_probs=40.1
Q ss_pred hHHHHHHHHhHhhhhhcC---CCCcCcchHHHHHHHHHHHHhhcchhhhHHHHHHHHHh
Q 039138 80 EMEEREKVVKHMWDVYTN---SRRIRLPRFWQEAFEAAYEELSSDVAEVRDAAITEIAK 135 (177)
Q Consensus 80 EmEeREKvVr~MWDvYt~---s~~vrLprFWqEAFeAAYeeL~sD~~~vrdaAisEIAk 135 (177)
..+++.+.++++++-|.. ...+.||.=..+.++...+.. .-.+.+=+.|..+|-+
T Consensus 42 ~~~~~~~~a~~I~~~fi~~~s~~~l~i~~~~~~~~~~~~~~~-~~~~~~f~~a~~~v~~ 99 (118)
T PF00615_consen 42 SEEQRKKLAQQIYNKFISPGSPNELNIPSKIRKEVQDALENA-PPSPDLFDEAQEEVYE 99 (118)
T ss_dssp SHHHHHHHHHHHHHHHTSTTSTTCCSSTHHHHHHHHHHHTST-STTTTTTHHHHHHHHH
T ss_pred chhhHHHHHHHHHHHHhcccccccccccHHHHHHHHHHHHHh-cccHHHHHHHHHHHHH
Confidence 567788889999999974 388999999998888888765 3344455555555543
No 18
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=33.08 E-value=20 Score=26.94 Aligned_cols=9 Identities=44% Similarity=1.102 Sum_probs=4.1
Q ss_pred HHHHHHHHH
Q 039138 34 WALAAILLL 42 (177)
Q Consensus 34 WaLaAIlLL 42 (177)
|+|.||+++
T Consensus 2 W~l~~iii~ 10 (130)
T PF12273_consen 2 WVLFAIIIV 10 (130)
T ss_pred eeeHHHHHH
Confidence 555444333
No 19
>cd04756 Commd8 COMM_Domain containing protein 8. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=32.36 E-value=70 Score=25.85 Aligned_cols=41 Identities=24% Similarity=0.308 Sum_probs=28.8
Q ss_pred CcchHHHHHHHHHHHHhhcchhhhHHHHHHHHHhhhhhccccCC
Q 039138 102 RLPRFWQEAFEAAYEELSSDVAEVRDAAITEIAKMSVRSLVNID 145 (177)
Q Consensus 102 rLprFWqEAFeAAYeeL~sD~~~vrdaAisEIAkmS~r~li~~d 145 (177)
.||+-|++||..+|+.-. ++++.+.+.++.-.|.-.|.++|
T Consensus 75 ~L~~~~~~a~~~~~~~~~---~ei~~~L~~~~~~is~~~L~d~d 115 (176)
T cd04756 75 DLSSSHQEALLKCVKSRK---EEIRQALVNKTNSISSAQLQDFD 115 (176)
T ss_pred cCCHHHHHHHHHHHHHhh---HHHHHHHHHHHhccCchhhcccc
Confidence 599999999999998655 45666776665545555544443
No 20
>PF12321 DUF3634: Protein of unknown function (DUF3634); InterPro: IPR022090 This family of proteins is found in bacteria. Proteins in this family are typically between 103 and 114 amino acids in length.
Probab=32.00 E-value=18 Score=28.37 Aligned_cols=66 Identities=17% Similarity=0.357 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHhhhhce-----EEEEeccCCcccccCCCCCCCCCCCchhhHHHHHHHHhHhhhhhcCCCCcCc
Q 039138 35 ALAAILLLAFWSMFTGT-----VTLRWSAGNLNRLSDDLGSPIHDDLDVLEMEEREKVVKHMWDVYTNSRRIRL 103 (177)
Q Consensus 35 aLaAIlLLAfWSMftgs-----VtLrwSag~Ln~~s~dld~p~~dDlDvLEmEeREKvVr~MWDvYt~s~~vrL 103 (177)
+|+..++|.||-||.+- ..++...|.+...-+++..-+..+ .-|+-+++++ +-==.+|-+..++||
T Consensus 4 ~ilia~~li~~Lv~~~r~~~~vf~i~f~dG~l~~~KG~iP~~F~~~--c~dIa~~~~~-~G~ik~~r~~~g~rL 74 (108)
T PF12321_consen 4 VILIAAALIFWLVFVDRRGLPVFEIHFKDGRLRVHKGHIPPGFLHN--CRDIARRYPF-RGTIKVYRQRGGVRL 74 (108)
T ss_pred HHHHHHHHHHHHHHccccCceEEEEEEECCcEEEEcCCCChHHHHH--HHHHHHhCCC-cEEEEEEEeCCceEE
Confidence 34444558999999987 456788899999888887776654 4567777777 444466766666665
No 21
>PRK12651 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=31.72 E-value=29 Score=27.27 Aligned_cols=20 Identities=35% Similarity=0.748 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHhhhhceEEE
Q 039138 35 ALAAILLLAFWSMFTGTVTL 54 (177)
Q Consensus 35 aLaAIlLLAfWSMftgsVtL 54 (177)
.+..++|.++|.+++|++++
T Consensus 5 ~~~~l~L~~~W~lL~g~~~~ 24 (158)
T PRK12651 5 LLLNIILAVLWLFLTGSFSL 24 (158)
T ss_pred HHHHHHHHHHHHHHhCCcCH
Confidence 45668889999999999764
No 22
>PF04226 Transgly_assoc: Transglycosylase associated protein; InterPro: IPR007341 This bacterial protein is predicted to be an integral membrane protein. Some family members have been annotated as transglycosylase-associated proteins, but no experimental evidence is provided. This family was annotated based on the information in P76011 from SWISSPROT.; GO: 0016021 integral to membrane
Probab=31.54 E-value=45 Score=22.02 Aligned_cols=18 Identities=22% Similarity=0.414 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHhhhhc
Q 039138 33 FWALAAILLLAFWSMFTG 50 (177)
Q Consensus 33 fWaLaAIlLLAfWSMftg 50 (177)
+=++.|++||+.|.++++
T Consensus 31 ~aviGAiill~i~~~i~r 48 (48)
T PF04226_consen 31 VAVIGAIILLFIYRLIRR 48 (48)
T ss_pred HHHHHHHHHHHHHHHHhC
Confidence 345789999999999874
No 23
>PTZ00200 cysteine proteinase; Provisional
Probab=31.49 E-value=30 Score=31.97 Aligned_cols=49 Identities=16% Similarity=0.278 Sum_probs=40.0
Q ss_pred ceEEEEeccCCcccccCCCCCCCCCCCchhhHHHHHHHHhHhhhhhcCC
Q 039138 50 GTVTLRWSAGNLNRLSDDLGSPIHDDLDVLEMEEREKVVKHMWDVYTNS 98 (177)
Q Consensus 50 gsVtLrwSag~Ln~~s~dld~p~~dDlDvLEmEeREKvVr~MWDvYt~s 98 (177)
++..|--.+-.|+.+..||+..+.-|+-.+|.+.|++.|..+=.+|...
T Consensus 62 ~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 110 (448)
T PTZ00200 62 VSYVLVSKSKMVKSFKSDLEEHIDKDFPRLDKSKRDSYVDELTRLFKDG 110 (448)
T ss_pred EEEEEEEehHhHHhHHHHHHHHHhccCCCcChhHHHHHHHHHHHHhhCC
Confidence 4444444445788999999999999999999999999999988888653
No 24
>PF13513 HEAT_EZ: HEAT-like repeat; PDB: 2Z5J_A 2OT8_B 2Z5O_A 2H4M_A 2QMR_A 1QBK_B 2Z5M_A 2Z5K_A 2Z5N_A 1GCJ_B ....
Probab=31.15 E-value=90 Score=19.27 Aligned_cols=30 Identities=27% Similarity=0.269 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHhhcchhhhHHHHHHHHHh
Q 039138 106 FWQEAFEAAYEELSSDVAEVRDAAITEIAK 135 (177)
Q Consensus 106 FWqEAFeAAYeeL~sD~~~vrdaAisEIAk 135 (177)
|=++.+..-..-|.+|.+.||.+|..=+..
T Consensus 25 ~~~~~~~~L~~~L~d~~~~VR~~A~~aLg~ 54 (55)
T PF13513_consen 25 YLPELLPALIPLLQDDDDSVRAAAAWALGN 54 (55)
T ss_dssp HHHHHHHHHHHHTTSSSHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHhc
Confidence 444555555666777888999999876554
No 25
>PF03967 PRCH: Photosynthetic reaction centre, H-chain N-terminal region; InterPro: IPR015810 The photosynthetic apparatus in non-oxygenic bacteria consists of light-harvesting (LH) protein-pigment complexes LH1 and LH2, which use carotenoid and bacteriochlorophyll as primary donors []. LH1 acts as the energy collection hub, temporarily storing it before its transfer to the photosynthetic reaction centre (RC) []. Electrons are transferred from the primary donor via an intermediate acceptor (bacteriopheophytin) to the primary acceptor (quinine Qa), and finally to the secondary acceptor (quinone Qb), resulting in the formation of ubiquinol QbH2. RC uses the excitation energy to shuffle electrons across the membrane, transferring them via ubiquinol to the cytochrome bc1 complex in order to establish a proton gradient across the membrane, which is used by ATP synthetase to form ATP [, , ]. The core complex is anchored in the cell membrane, consisting of one unit of RC surrounded by LH1; in some species there may be additional subunits []. RC consists of three subunits: L (light), M (medium), and H (heavy). Subunits L and M provide the scaffolding for the chromophore, while subunit H contains a cytoplasmic domain []. In Rhodopseudomonas viridis, there is also a non-membranous tetrahaem cytochrome (4Hcyt) subunit on the periplasmic surface. This entry represents the N-terminal domain of the photosynthetic reaction centre H subunit, which includes the transmembrane domain and part of the cytoplasmic domain [].; GO: 0045156 electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity, 0019684 photosynthesis, light reaction, 0030077 plasma membrane light-harvesting complex; PDB: 1RZZ_H 1PST_H 2J8D_H 3DUQ_H 1FNP_H 1KBY_H 1E14_H 2HG3_H 1UMX_H 1YST_H ....
Probab=29.39 E-value=39 Score=27.68 Aligned_cols=17 Identities=41% Similarity=1.019 Sum_probs=14.1
Q ss_pred HHHHHHHHHHhhhhceE
Q 039138 36 LAAILLLAFWSMFTGTV 52 (177)
Q Consensus 36 LaAIlLLAfWSMftgsV 52 (177)
+|-+.|-|||..|+|-|
T Consensus 12 vAql~lyaFwiFFagLi 28 (136)
T PF03967_consen 12 VAQLVLYAFWIFFAGLI 28 (136)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 57788899999998865
No 26
>PF00879 Defensin_propep: Defensin propeptide The pattern for this Prosite entry doesn't match the propeptide.; InterPro: IPR002366 Defensins are 2-6 kDa, cationic, microbicidal peptides active against many Gram-negative and Gram-positive bacteria, fungi, and enveloped viruses [], containing three pairs of intramolecular disulphide bonds []. On the basis of their size and pattern of disulphide bonding, mammalian defensins are classified into alpha, beta and theta categories. Alpha-defensins, which have been identified in humans, monkeys and several rodent species, are particularly abundant in neutrophils, certain macrophage populations and Paneth cells of the small intestine. Every mammalian species explored thus far has beta-defensins. In cows, as many as 13 beta-defensins exist in neutrophils. However, in other species, beta-defensins are more often produced by epithelial cells lining various organs (e.g. the epidermis, bronchial tree and genitourinary tract). Theta-defensins are cyclic and have so far only been identified in primate phagocytes. Defensins are produced constitutively and/or in response to microbial products or proinflammatory cytokines. Some defensins are also called corticostatins (CS) because they inhibit corticotropin-stimulated corticosteroid production. The mechanism(s) by which microorganisms are killed and/or inactivated by defensins is not understood completely. However, it is generally believed that killing is a consequence of disruption of the microbial membrane. The polar topology of defensins, with spatially separated charged and hydrophobic regions, allows them to insert themselves into the phospholipid membranes so that their hydrophobic regions are buried within the lipid membrane interior and their charged (mostly cationic) regions interact with anionic phospholipid head groups and water. Subsequently, some defensins can aggregate to form `channel-like' pores; others might bind to and cover the microbial membrane in a `carpet-like' manner. The net outcome is the disruption of membrane integrity and function, which ultimately leads to the lysis of microorganisms. Some defensins are synthesized as propeptides which may be relevant to this process - in neutrophils only the mature peptides have been identified but in Paneth cells, the propeptide is stored in vesicles [] and appears to be cleaved by trypsin on activation. ; GO: 0006952 defense response
Probab=28.72 E-value=41 Score=23.56 Aligned_cols=13 Identities=54% Similarity=0.577 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHH
Q 039138 33 FWALAAILLLAFW 45 (177)
Q Consensus 33 fWaLaAIlLLAfW 45 (177)
+=.|+|++||||=
T Consensus 4 L~LLaAlLLlAlq 16 (52)
T PF00879_consen 4 LALLAALLLLALQ 16 (52)
T ss_pred HHHHHHHHHHHHH
Confidence 3468999999984
No 27
>PRK08965 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=27.77 E-value=43 Score=26.43 Aligned_cols=20 Identities=25% Similarity=0.652 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHhhhhceEEE
Q 039138 35 ALAAILLLAFWSMFTGTVTL 54 (177)
Q Consensus 35 aLaAIlLLAfWSMftgsVtL 54 (177)
.+.+++|.++|-+++|+.+.
T Consensus 9 ~~~~~~l~~~W~lL~g~~~~ 28 (162)
T PRK08965 9 PLLSLWLALVWLLLNGSFSL 28 (162)
T ss_pred HHHHHHHHHHHHHHhCCCCH
Confidence 34567789999999998654
No 28
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=27.32 E-value=69 Score=30.95 Aligned_cols=37 Identities=22% Similarity=0.501 Sum_probs=29.0
Q ss_pred cchHH-------HHHHHHHHHHhhcchhhhHHHHHHHHHhhhhh
Q 039138 103 LPRFW-------QEAFEAAYEELSSDVAEVRDAAITEIAKMSVR 139 (177)
Q Consensus 103 LprFW-------qEAFeAAYeeL~sD~~~vrdaAisEIAkmS~r 139 (177)
+|||| .+||.|-+.-...|+.+||-.||.+|-...-.
T Consensus 46 I~kffk~FP~l~~~Ai~a~~DLcEDed~~iR~~aik~lp~~ck~ 89 (556)
T PF05918_consen 46 IPKFFKHFPDLQEEAINAQLDLCEDEDVQIRKQAIKGLPQLCKD 89 (556)
T ss_dssp HHHHHCC-GGGHHHHHHHHHHHHT-SSHHHHHHHHHHGGGG--T
T ss_pred HHHHHhhChhhHHHHHHHHHHHHhcccHHHHHHHHHhHHHHHHh
Confidence 57777 58999999988999999999999988665543
No 29
>PF06985 HET: Heterokaryon incompatibility protein (HET); InterPro: IPR010730 This entry represents a conserved region approximately 150 residues long within various heterokaryon incompatibility proteins that seem to be restricted to ascomycete fungi. Genetic differences in specific het genes prevent a viable heterokaryotic fungal cell from being formed by the fusion of filaments from two different wild-type strains []. Many proteins of this entry also contain the WD domain, G-beta IPR001680 from INTERPRO repeat and the NACHT IPR007111 from INTERPRO domain.
Probab=27.26 E-value=39 Score=23.62 Aligned_cols=19 Identities=32% Similarity=0.562 Sum_probs=16.5
Q ss_pred HHHHHHHhHhhhhhcCCCC
Q 039138 82 EEREKVVKHMWDVYTNSRR 100 (177)
Q Consensus 82 EeREKvVr~MWDvYt~s~~ 100 (177)
+||.+-|.+|=+||.|+..
T Consensus 58 ~ek~~qi~~M~~IY~~A~~ 76 (139)
T PF06985_consen 58 EEKSRQIALMGDIYSNASL 76 (139)
T ss_pred hhhHHHHhhhhHhhcCCCE
Confidence 4899999999999999743
No 30
>TIGR03354 VI_FHA type VI secretion system FHA domain protein. Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc.
Probab=26.96 E-value=39 Score=30.51 Aligned_cols=29 Identities=38% Similarity=0.736 Sum_probs=18.0
Q ss_pred hHhhhhhcCC-------CCcCcchHHHHHHHHHHHH
Q 039138 89 KHMWDVYTNS-------RRIRLPRFWQEAFEAAYEE 117 (177)
Q Consensus 89 r~MWDvYt~s-------~~vrLprFWqEAFeAAYee 117 (177)
.+.||.|++- +.-..=++-.|+|..|||+
T Consensus 358 a~~W~~Y~~~y~~l~~~~e~~f~~lf~e~Fa~aYe~ 393 (396)
T TIGR03354 358 AWAWDMYLRYYRELRSDREQGFERLFGEDFAQAYEE 393 (396)
T ss_pred HHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 3568888542 2334555666778888875
No 31
>PF14024 DUF4240: Protein of unknown function (DUF4240)
Probab=26.47 E-value=50 Score=25.14 Aligned_cols=40 Identities=30% Similarity=0.518 Sum_probs=32.3
Q ss_pred hHHHHHHHHHHHHhhcchhhhHHHHHHHHHhhhhhccccCC
Q 039138 105 RFWQEAFEAAYEELSSDVAEVRDAAITEIAKMSVRSLVNID 145 (177)
Q Consensus 105 rFWqEAFeAAYeeL~sD~~~vrdaAisEIAkmS~r~li~~d 145 (177)
+||+ -.+.+.+.-..|...+.+..+..+++++...++.++
T Consensus 5 ~FW~-lI~~~~~~~~~d~~~~~~~L~~~L~~l~~~ei~~F~ 44 (128)
T PF14024_consen 5 EFWE-LIERAREASGGDPDEVAEPLVELLAKLPPEEIVAFD 44 (128)
T ss_pred HHHH-HHHHHHhhcCCCHHHHHHHHHHHHHcCCHHHHHHHH
Confidence 5775 677777777888899999999999999998865543
No 32
>PF12607 DUF3772: Protein of unknown function (DUF3772); InterPro: IPR022249 This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with PF00924 from PFAM.
Probab=25.97 E-value=52 Score=22.52 Aligned_cols=24 Identities=25% Similarity=0.371 Sum_probs=18.2
Q ss_pred hcCCCCcCcchHHHHHHHHHHHHh
Q 039138 95 YTNSRRIRLPRFWQEAFEAAYEEL 118 (177)
Q Consensus 95 Yt~s~~vrLprFWqEAFeAAYeeL 118 (177)
..++...==|.||..++...-+++
T Consensus 30 ~~r~~SpL~P~~W~~~~~~~~~d~ 53 (64)
T PF12607_consen 30 LERSPSPLNPAFWSPAAAELPDDL 53 (64)
T ss_pred HHcCCCCCCHHHHHHHHHHhHHHH
Confidence 456677778999999998766544
No 33
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=25.74 E-value=38 Score=30.49 Aligned_cols=18 Identities=44% Similarity=0.805 Sum_probs=15.1
Q ss_pred cCcchHHHHHHHHHHHHh
Q 039138 101 IRLPRFWQEAFEAAYEEL 118 (177)
Q Consensus 101 vrLprFWqEAFeAAYeeL 118 (177)
-++.||||+-|.+|-++-
T Consensus 84 e~i~ryWq~ti~~~e~~~ 101 (286)
T COG5208 84 ERISRYWQQTIKAAEEER 101 (286)
T ss_pred HHHHHHHHHHHHHHHHhH
Confidence 368999999999987754
No 34
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=24.78 E-value=82 Score=31.67 Aligned_cols=51 Identities=27% Similarity=0.462 Sum_probs=40.0
Q ss_pred CCcCcchHHHHHHHHHHHHhhcchhhhHHHHHHHHHhhhhhccccCCCCCCC
Q 039138 99 RRIRLPRFWQEAFEAAYEELSSDVAEVRDAAITEIAKMSVRSLVNIDSPPFH 150 (177)
Q Consensus 99 ~~vrLprFWqEAFeAAYeeL~sD~~~vrdaAisEIAkmS~r~li~~dp~p~~ 150 (177)
|-.+|-|=||++||..+++--+-.-..--.-+.-+||+..|- |--|.+|-+
T Consensus 512 Rfc~l~r~~q~~fe~~f~q~YstIhr~EtnkLRnlakffahL-lstd~lpw~ 562 (739)
T KOG2140|consen 512 RFCMLHREWQEAFEKCFKQQYSTIHRYETNKLRNLAKFFAHL-LSTDALPWD 562 (739)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH-hcccccchH
Confidence 556788999999999988776665555556677799999998 788887753
No 35
>PF06942 GlpM: GlpM protein; InterPro: IPR009707 This family consists of several bacterial GlpM membrane proteins. GlpM is a hydrophobic protein containing 109 amino acids. It is thought that GlpM may play a role in alginate biosynthesis in Pseudomonas aeruginosa [].
Probab=24.03 E-value=70 Score=25.31 Aligned_cols=17 Identities=35% Similarity=0.872 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHHhhh
Q 039138 32 KFWALAAILLLAFWSMF 48 (177)
Q Consensus 32 KfWaLaAIlLLAfWSMf 48 (177)
-.|.++|.+|+.+|+.+
T Consensus 90 ~~W~iaA~~Li~~w~~~ 106 (107)
T PF06942_consen 90 LVWLIAAWVLILLWSRW 106 (107)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 36999999999999864
No 36
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=24.02 E-value=61 Score=33.82 Aligned_cols=61 Identities=23% Similarity=0.354 Sum_probs=45.3
Q ss_pred CCchhhHHHHHHHHhHhhhhhcCCCCcCcchHHHHHHHHHHHHhhcchhhhHHHHHHHHHhhh
Q 039138 75 DLDVLEMEEREKVVKHMWDVYTNSRRIRLPRFWQEAFEAAYEELSSDVAEVRDAAITEIAKMS 137 (177)
Q Consensus 75 DlDvLEmEeREKvVr~MWDvYt~s~~vrLprFWqEAFeAAYeeL~sD~~~vrdaAisEIAkmS 137 (177)
|+|. ++|.||+|++++-+-|++.+---.--|=.-+=.+|..+. +=+-++....+..||||=
T Consensus 402 DIDf-~~~rReeVI~YV~ekYG~d~VAqIiTFgt~~aKaaiRDV-gRvlg~~~~~~d~lsK~I 462 (1139)
T COG0587 402 DIDF-CDERREEVIQYVYEKYGRDRVAQIITFGTLRAKAAIRDV-GRVLGLPYGEVDKLAKLI 462 (1139)
T ss_pred CcCC-ccccHHHHHHHHHHHhccccEEEEEeeehhhHHHHHHHH-HHHcCCCHHHHHHHHhcC
Confidence 6666 999999999999999999766555566556667776653 234556677788888873
No 37
>PF06480 FtsH_ext: FtsH Extracellular; InterPro: IPR011546 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain is found in the FtsH family of proteins that include FtsH a membrane-bound ATP-dependent protease universally conserved in prokaryotes []. The FtsH peptidases, which belong to MEROPS peptidase family M41 (clan MA(E)), efficiently degrade proteins that have a low thermodynamic stability - e.g. they lack robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni (Leuconostoc oenos) FtsH is involved in protection against environmental stress [], and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded. The precise function of this N-terminal region is unclear. ; GO: 0004222 metalloendopeptidase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0016021 integral to membrane; PDB: 2LNA_A.
Probab=23.99 E-value=28 Score=23.27 Aligned_cols=25 Identities=20% Similarity=0.526 Sum_probs=3.4
Q ss_pred HHHHHHHHHHHHHhhhh------ceEEEEec
Q 039138 33 FWALAAILLLAFWSMFT------GTVTLRWS 57 (177)
Q Consensus 33 fWaLaAIlLLAfWSMft------gsVtLrwS 57 (177)
+|++.+++++.++.++. ..-.+.||
T Consensus 3 ~~ili~~vi~~l~~~~~~~~~~~~~~~i~YS 33 (110)
T PF06480_consen 3 LYILIILVILLLFNFFFFNSNNSQTKEISYS 33 (110)
T ss_dssp ----------------S------SSEE--HH
T ss_pred ceehhHHHHHHHHHHHHhhcccCCCcEECHH
Confidence 57777777777666653 44555554
No 38
>KOG2085 consensus Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms]
Probab=23.66 E-value=92 Score=29.94 Aligned_cols=47 Identities=21% Similarity=0.229 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHhhcchhhh----HHHHHHHHHhhhhhccccCCCCCCCcch
Q 039138 107 WQEAFEAAYEELSSDVAEV----RDAAITEIAKMSVRSLVNIDSPPFHSTS 153 (177)
Q Consensus 107 WqEAFeAAYeeL~sD~~~v----rdaAisEIAkmS~r~li~~dp~p~~S~~ 153 (177)
..|+..++..+|..|+... .+..++|+.||..+.++.-=||+.+.+.
T Consensus 82 ~keikR~tL~eLvd~v~~~~~kite~~~~~vv~m~s~nifR~lpp~~n~~~ 132 (457)
T KOG2085|consen 82 GKEIKRQTLLELVDDVISRRGKISEEVYSEVVKMFSVNIFRTLPPSVNPTG 132 (457)
T ss_pred cchhHHHHHHHHHHHHhhccccccHHHHHHHHHHHHHHhhccCCcccCCCc
Confidence 4688899999999998865 6889999999999998888788877763
No 39
>PF14851 FAM176: FAM176 family
Probab=23.02 E-value=54 Score=26.87 Aligned_cols=12 Identities=42% Similarity=1.304 Sum_probs=11.1
Q ss_pred HHHHHHHHhHhh
Q 039138 81 MEEREKVVKHMW 92 (177)
Q Consensus 81 mEeREKvVr~MW 92 (177)
.||||.++|.+|
T Consensus 125 lEeRe~iirEIW 136 (153)
T PF14851_consen 125 LEERERIIREIW 136 (153)
T ss_pred HHHHHHHHHHHH
Confidence 589999999999
No 40
>PF15168 TRIQK: Triple QxxK/R motif-containing protein family
Probab=22.87 E-value=82 Score=23.97 Aligned_cols=20 Identities=50% Similarity=0.692 Sum_probs=13.8
Q ss_pred hhHHHHHHHHH--HHHHHhhhh
Q 039138 30 RYKFWALAAIL--LLAFWSMFT 49 (177)
Q Consensus 30 rYKfWaLaAIl--LLAfWSMft 49 (177)
+=-.|+|+||+ |+||..||-
T Consensus 49 kev~l~l~ail~lL~a~Ya~fy 70 (79)
T PF15168_consen 49 KEVALVLAAILVLLLAFYAFFY 70 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 33478999986 567777663
No 41
>COG4103 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.03 E-value=59 Score=27.05 Aligned_cols=17 Identities=29% Similarity=0.728 Sum_probs=14.3
Q ss_pred hhHHHHHHHHhHhhhhh
Q 039138 79 LEMEEREKVVKHMWDVY 95 (177)
Q Consensus 79 LEmEeREKvVr~MWDvY 95 (177)
|..|.|-.++++||+|-
T Consensus 96 Ld~e~R~eli~~mweIa 112 (148)
T COG4103 96 LDEEQRLELIGLMWEIA 112 (148)
T ss_pred cCHHHHHHHHHHHHHHH
Confidence 34699999999999973
No 42
>PRK12652 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=21.58 E-value=73 Score=28.59 Aligned_cols=28 Identities=7% Similarity=-0.011 Sum_probs=19.6
Q ss_pred cCCchhHHHHHHHHHHHHHHhhhhceEEE
Q 039138 26 FGKGRYKFWALAAILLLAFWSMFTGTVTL 54 (177)
Q Consensus 26 ~GkgrYKfWaLaAIlLLAfWSMftgsVtL 54 (177)
-..|. |-.++..++|++||-+++|+.++
T Consensus 162 ~~~~~-~~~~~l~~ll~~~Wlllsg~~s~ 189 (357)
T PRK12652 162 RAATL-DKFAALFGASFGFYLLLGDPLYW 189 (357)
T ss_pred chhhh-hHHHHHHHHHHHHHHHHcCcCCH
Confidence 34444 33466678999999999998543
No 43
>COG3206 GumC Uncharacterized protein involved in exopolysaccharide biosynthesis [Cell envelope biogenesis, outer membrane]
Probab=21.57 E-value=2.6e+02 Score=24.84 Aligned_cols=69 Identities=19% Similarity=0.130 Sum_probs=39.9
Q ss_pred chhHHHHHHHHHHHHHHhh----h-----hceEEEEec-cCCcccccCCCCCCCCCCCchhhHHHH--------HHHHhH
Q 039138 29 GRYKFWALAAILLLAFWSM----F-----TGTVTLRWS-AGNLNRLSDDLGSPIHDDLDVLEMEER--------EKVVKH 90 (177)
Q Consensus 29 grYKfWaLaAIlLLAfWSM----f-----tgsVtLrwS-ag~Ln~~s~dld~p~~dDlDvLEmEeR--------EKvVr~ 90 (177)
.||++|+++++++..+=+. + ++..+|--+ .+.-+....+...+.+.+...++.|-+ +|||..
T Consensus 22 ~r~~~~il~~~~~~~~~a~~~a~~~~p~Y~a~a~l~i~~~~~~~~~~~~~~~~~~~~~~~~~~q~~il~S~~vl~~vi~~ 101 (458)
T COG3206 22 RRRRWLILLVAALVVGLAVLYAFLAPPIYEADAQLLVDPRSSSVLVLEDGQSGLPNDSSSLETEIEILQSRSVLEKVIDK 101 (458)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCceeEEEEEEEEeccccccccccccccCCCCCchhHHHHHHHHhhHHHHHHHHHH
Confidence 4788888877665544332 2 233344444 344444455656666677777777765 566666
Q ss_pred hhhhhcC
Q 039138 91 MWDVYTN 97 (177)
Q Consensus 91 MWDvYt~ 97 (177)
|=-.+.+
T Consensus 102 l~l~~~~ 108 (458)
T COG3206 102 LKLDDDP 108 (458)
T ss_pred cCCcccc
Confidence 6544444
No 44
>PF14719 PID_2: Phosphotyrosine interaction domain (PTB/PID)
Probab=21.42 E-value=56 Score=27.24 Aligned_cols=50 Identities=30% Similarity=0.390 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHHHhhcchhhhHHHH------HHHHHhhhhhccc-----cCCCCCCCcchh
Q 039138 105 RFWQEAFEAAYEELSSDVAEVRDAA------ITEIAKMSVRSLV-----NIDSPPFHSTSA 154 (177)
Q Consensus 105 rFWqEAFeAAYeeL~sD~~~vrdaA------isEIAkmS~r~li-----~~dp~p~~S~~~ 154 (177)
+-=.++|.+||++...|--....+= +..+--|-.|.|+ ++.||--.|-++
T Consensus 113 ~~L~~af~~Af~~~kr~k~~~~~~~l~~~~s~~~~p~~p~Rk~l~~~~~~~~pp~~r~~~a 173 (182)
T PF14719_consen 113 RALYQAFRSAFQEFKRDKRSRQNARLSLGNSVYSNPTMPRRKLLSNGQCNYRPPVERSKSA 173 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhchhccccCCCCChhhhHhhcCCCCcCCccccCCCC
Confidence 3447899999999998887765542 3334445555555 455554444444
No 45
>PF14832 Tautomerase_3: Putative oxalocrotonate tautomerase enzyme; PDB: 3C6V_C 3N4D_I 3N4G_C 3N4H_A 2FLZ_C 3MF8_A 3MF7_A 2FLT_A.
Probab=20.50 E-value=76 Score=25.00 Aligned_cols=28 Identities=29% Similarity=0.602 Sum_probs=23.3
Q ss_pred chhhHHHHHHHHhHhhhhhcCCCCcCcchHH
Q 039138 77 DVLEMEEREKVVKHMWDVYTNSRRIRLPRFW 107 (177)
Q Consensus 77 DvLEmEeREKvVr~MWDvYt~s~~vrLprFW 107 (177)
+.|..|+|+.|.+..=|+|+.- .||+|.
T Consensus 11 ~~lt~~~K~~LA~~IT~~y~~~---glP~Fy 38 (136)
T PF14832_consen 11 GTLTPEQKQALAEAITDIYTSI---GLPAFY 38 (136)
T ss_dssp TSS-HHHHHHHHHHHHHHHHHT---TTTGGG
T ss_pred CCCCHHHHHHHHHHHHHHHhCC---CCCCEE
Confidence 3567899999999999999765 789996
No 46
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=20.41 E-value=1.2e+02 Score=19.49 Aligned_cols=22 Identities=27% Similarity=0.416 Sum_probs=15.8
Q ss_pred HHHHHHHHHHhhcchhhhHHHH
Q 039138 108 QEAFEAAYEELSSDVAEVRDAA 129 (177)
Q Consensus 108 qEAFeAAYeeL~sD~~~vrdaA 129 (177)
+|.+++|.+++.+.-..+|.||
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA 23 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAA 23 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHH
Confidence 4778888888887766666665
No 47
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=20.39 E-value=31 Score=31.23 Aligned_cols=43 Identities=26% Similarity=0.537 Sum_probs=27.5
Q ss_pred CCCCCchhhHHHHHHHHh-------HhhhhhcCCCCc------------CcchHHHHHHHHH
Q 039138 72 IHDDLDVLEMEEREKVVK-------HMWDVYTNSRRI------------RLPRFWQEAFEAA 114 (177)
Q Consensus 72 ~~dDlDvLEmEeREKvVr-------~MWDvYt~s~~v------------rLprFWqEAFeAA 114 (177)
++.+++-||.|-.+++.+ .+-.+|..-+.| .+|.||--||...
T Consensus 49 lQ~e~~~le~ef~~ev~~LE~kY~~~~~Ply~kR~eII~G~~~~e~~~~gIP~FWl~vL~Nh 110 (337)
T PTZ00007 49 LQKEFDDLEVEYNAELRKLRSKYEDLYNPIYDKRKEALVQNGGAEIGTPGLPQFWLTAMKNN 110 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHcCCcccccccCCcccHHHHHHHcC
Confidence 455666677664444332 556677553222 6999999999875
Done!