Query 029626
Match_columns 190
No_of_seqs 128 out of 237
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 15:55:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029626.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029626hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03791 KNOX2: KNOX2 domain ; 99.9 2.7E-27 5.9E-32 163.9 7.1 50 126-179 3-52 (52)
2 PF03790 KNOX1: KNOX1 domain ; 99.9 3.8E-24 8.3E-29 144.5 3.0 44 71-114 1-44 (45)
3 KOG0773 Transcription factor M 98.7 3.8E-09 8.2E-14 93.0 1.6 116 66-183 45-165 (342)
4 KOG0774 Transcription factor P 75.2 30 0.00066 32.0 9.6 110 69-178 27-167 (334)
5 PF13097 CENP-U: CENP-A nucleo 65.3 19 0.00041 30.9 5.8 45 130-177 102-147 (175)
6 PF11288 DUF3089: Protein of u 62.3 2.9 6.4E-05 36.1 0.4 29 70-102 110-138 (207)
7 PF03792 PBC: PBC domain; Int 55.9 41 0.00089 29.3 6.2 43 69-111 25-78 (191)
8 KOG4445 Uncharacterized conser 52.2 30 0.00066 32.5 5.2 46 132-179 134-179 (368)
9 PF07425 Pardaxin: Pardaxin; 51.0 11 0.00023 24.1 1.5 17 74-90 6-22 (33)
10 PF05190 MutS_IV: MutS family 50.1 32 0.00069 24.0 4.0 25 129-153 1-25 (92)
11 KOG4460 Nuclear pore complex, 46.3 41 0.00089 34.1 5.3 38 134-178 568-605 (741)
12 PF11348 DUF3150: Protein of u 40.2 37 0.0008 30.0 3.7 51 88-151 60-118 (257)
13 PF11826 DUF3346: Protein of u 36.0 85 0.0018 27.9 5.2 45 140-189 104-148 (225)
14 PF12057 DUF3538: Domain of un 34.4 1.2E+02 0.0026 24.5 5.5 46 133-179 14-70 (120)
15 PF06295 DUF1043: Protein of u 34.1 83 0.0018 24.8 4.5 33 140-176 36-68 (128)
16 PF09763 Sec3_C: Exocyst compl 32.9 1.5E+02 0.0032 29.3 6.9 86 81-176 511-615 (701)
17 KOG3942 MIF4G domain-containin 31.9 48 0.001 31.2 3.1 46 129-174 196-245 (348)
18 PF02290 SRP14: Signal recogni 31.4 40 0.00086 25.5 2.2 19 129-147 70-88 (93)
19 PF12362 DUF3646: DNA polymera 31.1 56 0.0012 25.9 3.0 22 69-90 87-108 (117)
20 PF12022 DUF3510: Domain of un 31.0 2.2E+02 0.0048 22.3 6.4 48 133-180 43-99 (125)
21 PF11014 DUF2852: Protein of u 30.9 44 0.00095 26.9 2.4 34 102-140 79-112 (115)
22 COG1497 Predicted transcriptio 30.7 45 0.00098 30.3 2.7 39 64-102 172-211 (260)
23 cd00669 Asp_Lys_Asn_RS_core As 29.2 47 0.001 29.2 2.5 40 62-101 195-238 (269)
24 PF03401 TctC: Tripartite tric 28.3 72 0.0016 27.6 3.5 17 96-112 212-228 (274)
25 PF12805 FUSC-like: FUSC-like 28.2 3.8E+02 0.0083 23.2 8.0 95 73-178 185-281 (284)
26 PF02601 Exonuc_VII_L: Exonucl 27.4 4.2E+02 0.0092 23.2 8.5 51 58-108 84-143 (319)
27 PF10112 Halogen_Hydrol: 5-bro 27.1 1.8E+02 0.0039 23.9 5.6 46 131-178 124-173 (199)
28 COG2916 Hns DNA-binding protei 26.2 2.9E+02 0.0063 22.6 6.4 46 133-178 8-53 (128)
29 KOG2070 Guanine nucleotide exc 26.0 71 0.0015 32.1 3.4 27 128-154 181-214 (661)
30 PF10732 DUF2524: Protein of u 26.0 2.5E+02 0.0055 21.6 5.7 47 132-178 5-54 (84)
31 COG3105 Uncharacterized protei 25.5 2.2E+02 0.0048 23.7 5.6 42 132-177 37-78 (138)
32 PF12207 DUF3600: Domain of un 25.0 65 0.0014 27.4 2.6 45 127-171 104-158 (162)
33 KOG2828 Acetyl-CoA hydrolase [ 24.3 70 0.0015 31.1 2.9 30 69-98 422-451 (454)
34 PF10782 DUF2602: Protein of u 23.1 55 0.0012 23.5 1.5 41 132-178 8-54 (58)
35 KOG3647 Predicted coiled-coil 22.5 1.7E+02 0.0037 27.4 4.9 42 140-182 165-206 (338)
36 PLN02372 violaxanthin de-epoxi 22.2 3E+02 0.0066 27.0 6.7 65 99-174 328-392 (455)
37 PRK00423 tfb transcription ini 21.0 1.7E+02 0.0037 26.2 4.5 73 89-172 172-249 (310)
38 PF01533 Tospo_nucleocap: Tosp 20.9 78 0.0017 28.6 2.4 20 67-90 112-131 (248)
No 1
>PF03791 KNOX2: KNOX2 domain ; InterPro: IPR005541 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.94 E-value=2.7e-27 Score=163.86 Aligned_cols=50 Identities=46% Similarity=0.698 Sum_probs=47.9
Q ss_pred CCCCCChhHHHHHHHHHHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHhhhc
Q 029626 126 GRVLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTG 179 (190)
Q Consensus 126 ~~~~~DPELDqFMeaYc~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~sLtg 179 (190)
+++++|||||||||+||.||+||||||+|||+ ||++|||+||+||++|||
T Consensus 3 ~~~~~dpELDqFMeaYc~~L~kykeeL~~p~~----EA~~f~~~ie~qL~~Lt~ 52 (52)
T PF03791_consen 3 SSIGADPELDQFMEAYCDMLVKYKEELQRPFQ----EAMEFCREIEQQLSSLTG 52 (52)
T ss_pred CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHhC
Confidence 46899999999999999999999999999994 999999999999999996
No 2
>PF03790 KNOX1: KNOX1 domain ; InterPro: IPR005540 The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization [].; GO: 0003677 DNA binding, 0005634 nucleus
Probab=99.89 E-value=3.8e-24 Score=144.50 Aligned_cols=44 Identities=34% Similarity=0.687 Sum_probs=41.3
Q ss_pred HHHHHHHhcCCChHHHHHHHHhchhccCCCCchhhHHHHHhhhH
Q 029626 71 VKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRSR 114 (190)
Q Consensus 71 e~iKAkI~sHPlYp~LL~AyidC~KVGAPpev~~rLda~l~~~q 114 (190)
+.|||+|++||+||+||+|||+|||||||||++++||+++++++
T Consensus 1 e~iKA~I~~HP~Y~~Ll~Ayi~C~KVGAP~e~~~~L~e~~~~~~ 44 (45)
T PF03790_consen 1 EAIKAKIASHPLYPRLLAAYIDCQKVGAPPEVVARLDEILAESQ 44 (45)
T ss_pred ChHHHHHHcCCCcHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhc
Confidence 47999999999999999999999999999999999999987654
No 3
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=98.72 E-value=3.8e-09 Score=93.01 Aligned_cols=116 Identities=19% Similarity=0.182 Sum_probs=93.9
Q ss_pred hhhhhHHHHHHHhcCCChHHHHHHHHhchhccCCCCchhhHHHHHhhhHHHHhhhhhccC-----CCCCCChhHHHHHHH
Q 029626 66 EDWETVKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRSRDVLAKYSAVAN-----GRVLDDKELDQFMTH 140 (190)
Q Consensus 66 ~~~e~e~iKAkI~sHPlYp~LL~AyidC~KVGAPpev~~rLda~l~~~q~~~~k~s~~~~-----~~~~~DPELDqFMea 140 (190)
..+....+|+.+.+||+|..++.||++|++++.|.+.+.++++.+.......+++...+. ...+.+++++.||..
T Consensus 45 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~s~~~~~~~~~~~~~~~~~k 124 (342)
T KOG0773|consen 45 IMVSLASSKYLTAAQELLDEFCSAGLDCLKGKMPYDPVPRSPASLSPPEDKGARRGNATRESATLKAWLEEHRLNPYPSK 124 (342)
T ss_pred cccccccccccccchhHHhHHhhccccccccccCcCccccccccccCccccccccccccccccccccchhhhhhccCchH
Confidence 456677899999999999999999999999999999999977765544322222221111 136789999999999
Q ss_pred HHHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHhhhcCCCC
Q 029626 141 YVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGNLFP 183 (190)
Q Consensus 141 Yc~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~sLtg~sp~ 183 (190)
|+.+|..+++.|+..+. -++|+.++++|+..+...++..+.
T Consensus 125 ~~~~ll~~~~~~~~~~~--~~~~~~a~r~~~~~~~~~~~~~~~ 165 (342)
T KOG0773|consen 125 LEKILLAVITKLTLTQV--STWFANARRRLKKELKMTWGPTPL 165 (342)
T ss_pred HHHHHHHHHHHhhhhhH--HHHHHHHHHHHHhccCCCCCCccc
Confidence 99999999999999873 389999999999999999876543
No 4
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=75.18 E-value=30 Score=32.01 Aligned_cols=110 Identities=18% Similarity=0.136 Sum_probs=64.1
Q ss_pred hhHHHHHHHhcCCChHHHHHHHHhch-h---------ccCCCC-chhhHHHHHhhhHHH-Hhhh-----hhccCCCCCCC
Q 029626 69 ETVKCKAEIVGHPLYEQLLSAHVSCL-R---------IATPVD-QLPKIDAQLSRSRDV-LAKY-----SAVANGRVLDD 131 (190)
Q Consensus 69 e~e~iKAkI~sHPlYp~LL~AyidC~-K---------VGAPpe-v~~rLda~l~~~q~~-~~k~-----s~~~~~~~~~D 131 (190)
+..+.|-.|-+||+||.|.+-..+-. | =-.||| ++-|||..+-..-.. ..|. .++|++....-
T Consensus 27 eaqa~K~~lnch~mk~AlfsVLcE~KeKt~lsir~~qdeep~dpqlmRLDnML~AEGVagPekgga~~~~Asgg~hsdYR 106 (334)
T KOG0774|consen 27 EAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRGMQDEEPPDPQLMRLDNMLLAEGVAGPEKGGARAAAASGGDHSDYR 106 (334)
T ss_pred hHHhhhhccccccchHHHHHHHHHhhhhheeeeccccccCCCChHHHHHHHHHHHhcccCccccchhhhhccCCChHHHH
Confidence 45578999999999999998765532 2 234788 899999876431100 0111 11221111122
Q ss_pred hhHHHHHHHHHHHHHHHHHH---HhhHhh-----------hcHHHHHHHHHHHHHHHHhhh
Q 029626 132 KELDQFMTHYVLLLYSFKEQ---LQQHVR-----------VHAMEAVMACWDLEQSLQSLT 178 (190)
Q Consensus 132 PELDqFMeaYc~mL~kYKEE---L~rP~~-----------~~a~EA~~F~~~IE~QL~sLt 178 (190)
..|-|.-.-|-..|.||.+. .+.+|. +.+.|.-.+...|-..++.++
T Consensus 107 ~kL~qiR~iy~~ElekyeqaCneftthV~nlL~eQsr~RPi~~ke~e~m~~~i~~kF~~iq 167 (334)
T KOG0774|consen 107 AKLLQIRQIYHNELEKYEQACNEFTTHVMNLLREQSRTRPIMPKEIERMVQIISKKFSHIQ 167 (334)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHH
Confidence 56777777788888887653 222221 245566666666666665555
No 5
>PF13097 CENP-U: CENP-A nucleosome associated complex (NAC) subunit
Probab=65.35 E-value=19 Score=30.87 Aligned_cols=45 Identities=16% Similarity=0.301 Sum_probs=36.4
Q ss_pred CChhHHHHHHHHHHHHHHHHHHHhhHhhhcHHHHH-HHHHHHHHHHHhh
Q 029626 130 DDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAV-MACWDLEQSLQSL 177 (190)
Q Consensus 130 ~DPELDqFMeaYc~mL~kYKEEL~rP~~~~a~EA~-~F~~~IE~QL~sL 177 (190)
+=-|||-...++-.++..||+.+.-.+- .+|+ .|+..+..||-.+
T Consensus 102 DItELDVvL~~FEk~~~eYkq~ieS~~c---r~AI~~F~~~~keqL~~~ 147 (175)
T PF13097_consen 102 DITELDVVLSAFEKTALEYKQSIESKIC---RKAINKFYSNFKEQLIEM 147 (175)
T ss_pred cchHHHHHHHHHHHHHHHHHHhhccHHH---HHHHHHHHHHHHHHHHHH
Confidence 3489999999999999999999998875 3443 4888888887654
No 6
>PF11288 DUF3089: Protein of unknown function (DUF3089); InterPro: IPR021440 This family of proteins has no known function.
Probab=62.31 E-value=2.9 Score=36.11 Aligned_cols=29 Identities=38% Similarity=0.512 Sum_probs=26.3
Q ss_pred hHHHHHHHhcCCChHHHHHHHHhchhccCCCCc
Q 029626 70 TVKCKAEIVGHPLYEQLLSAHVSCLRIATPVDQ 102 (190)
Q Consensus 70 ~e~iKAkI~sHPlYp~LL~AyidC~KVGAPpev 102 (190)
...||.+|..+|++.+||+||+ ||.|+-+
T Consensus 110 ~~LL~e~~~~~pl~~rLVAAYl----iG~~v~~ 138 (207)
T PF11288_consen 110 LRLLKEEIAGDPLRKRLVAAYL----IGYPVTV 138 (207)
T ss_pred HHHHHHHhcCchHHhhhheeee----cCccccH
Confidence 5689999999999999999999 9999654
No 7
>PF03792 PBC: PBC domain; InterPro: IPR005542 Pbx proteins are members of the TALE (three-amino-acid loop extension) family of atypical homeodomain proteins, whose members are characterised by a three-residue insertion in the first helix of the homeodomain involved in their interaction with Hox proteins. Examination of Pbx1 has shown that, in addition to the homeodomain, a short 16-residue C-terminal tail is essential for maximal cooperative interactions with Hox partners as well as for maximal monomeric binding of Pbx1 to DNA. The PBX domain is a bipartite acidic domain [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=55.88 E-value=41 Score=29.25 Aligned_cols=43 Identities=26% Similarity=0.291 Sum_probs=32.7
Q ss_pred hhHHHHHHHhcCCChHHHHHHHHhch-hcc---------CCCC-chhhHHHHHh
Q 029626 69 ETVKCKAEIVGHPLYEQLLSAHVSCL-RIA---------TPVD-QLPKIDAQLS 111 (190)
Q Consensus 69 e~e~iKAkI~sHPlYp~LL~AyidC~-KVG---------APpe-v~~rLda~l~ 111 (190)
+....|-.|-+||+||.|-+..++-. |++ .||| ++.|||..+.
T Consensus 25 eaqa~K~~l~~hr~k~ALfsVLcE~KEkt~LSir~~qee~p~dpQl~RLDNML~ 78 (191)
T PF03792_consen 25 EAQARKHALNCHRMKPALFSVLCEIKEKTVLSIRNIQEEDPPDPQLMRLDNMLL 78 (191)
T ss_pred HHHHhchhhcCCCCchhhHHHHHHHHhhcCccccccCCcCCCchhhhhhhcchh
Confidence 44789999999999999999887654 221 2444 7889998765
No 8
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=52.24 E-value=30 Score=32.52 Aligned_cols=46 Identities=11% Similarity=0.179 Sum_probs=35.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHhhhc
Q 029626 132 KELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTG 179 (190)
Q Consensus 132 PELDqFMeaYc~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~sLtg 179 (190)
-+-|+||-.|| |.+|-.++.+-+|.++.+|-.....+-.|.+.+|.
T Consensus 134 T~C~Hy~H~~C--laRyl~~~~~~lrqe~q~~~~~~qh~~~~~eavcp 179 (368)
T KOG4445|consen 134 TACDHYMHFAC--LARYLTECLTGLRQEIQDAQKERQHMKEQVEAVCP 179 (368)
T ss_pred ehhHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHhhhhHhhhhh
Confidence 36899999999 45666666666666667887777888888888874
No 9
>PF07425 Pardaxin: Pardaxin; InterPro: IPR009990 This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin []. Pardaxin has also been found to have a shark repellent action [].; GO: 0005576 extracellular region; PDB: 1XC0_A 2KNS_A.
Probab=50.98 E-value=11 Score=24.11 Aligned_cols=17 Identities=41% Similarity=0.690 Sum_probs=14.8
Q ss_pred HHHHhcCCChHHHHHHH
Q 029626 74 KAEIVGHPLYEQLLSAH 90 (190)
Q Consensus 74 KAkI~sHPlYp~LL~Ay 90 (190)
--||++.|||.-||+|-
T Consensus 6 ipkiissplfktllsav 22 (33)
T PF07425_consen 6 IPKIISSPLFKTLLSAV 22 (33)
T ss_dssp HHHHCCTTTCHHHHHHH
T ss_pred hhHHHccHHHHHHHHHH
Confidence 45899999999999874
No 10
>PF05190 MutS_IV: MutS family domain IV C-terminus.; InterPro: IPR007861 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the clamp domain (domain 4) found in proteins of the MutS family. The clamp domain is inserted within the core domain at the top of the lever helices. It has a beta-sheet structure [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B 1WBD_A 1WB9_A 3K0S_A 1OH6_A ....
Probab=50.07 E-value=32 Score=23.98 Aligned_cols=25 Identities=28% Similarity=0.310 Sum_probs=19.4
Q ss_pred CCChhHHHHHHHHHHHHHHHHHHHh
Q 029626 129 LDDKELDQFMTHYVLLLYSFKEQLQ 153 (190)
Q Consensus 129 ~~DPELDqFMeaYc~mL~kYKEEL~ 153 (190)
|-|+|||+..+.|..+.....+.+.
T Consensus 1 g~d~~Ld~~~~~~~~~~~~l~~~~~ 25 (92)
T PF05190_consen 1 GFDEELDELREEYEEIEEELEELLE 25 (92)
T ss_dssp TSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4689999999999888766655444
No 11
>KOG4460 consensus Nuclear pore complex, Nup88/rNup84 component [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=46.27 E-value=41 Score=34.07 Aligned_cols=38 Identities=32% Similarity=0.534 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHhhh
Q 029626 134 LDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLT 178 (190)
Q Consensus 134 LDqFMeaYc~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~sLt 178 (190)
..-|-|.|..-=.+-|+|++||+. ..|+.+++||+.|.
T Consensus 568 ~~vfrEqYi~~~dlV~~e~qrH~~-------~l~~~k~~QlQ~l~ 605 (741)
T KOG4460|consen 568 TQVFREQYILKQDLVKEEIQRHVK-------LLCDQKKKQLQDLS 605 (741)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHH
Confidence 345889998888889999999972 46899999999986
No 12
>PF11348 DUF3150: Protein of unknown function (DUF3150); InterPro: IPR021496 This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=40.24 E-value=37 Score=30.01 Aligned_cols=51 Identities=18% Similarity=0.401 Sum_probs=33.5
Q ss_pred HHHHhchhccC--------CCCchhhHHHHHhhhHHHHhhhhhccCCCCCCChhHHHHHHHHHHHHHHHHHH
Q 029626 88 SAHVSCLRIAT--------PVDQLPKIDAQLSRSRDVLAKYSAVANGRVLDDKELDQFMTHYVLLLYSFKEQ 151 (190)
Q Consensus 88 ~AyidC~KVGA--------Ppev~~rLda~l~~~q~~~~k~s~~~~~~~~~DPELDqFMeaYc~mL~kYKEE 151 (190)
+|.=-|.|||+ |.+.++.|.+.+.+.+ . ..+.+.++|+..|=..+..+..+
T Consensus 60 ~A~r~~~~~G~rFlgG~aVP~~~~~~l~~~L~~i~---~----------eF~~~k~~Fl~~Yd~~i~~w~~~ 118 (257)
T PF11348_consen 60 RAERLCLKVGVRFLGGYAVPEDKAEELAEELEDIK---T----------EFEQEKQDFLANYDQAIEEWIDR 118 (257)
T ss_pred HHHHHHHHcCCcccceeEcCHHHHHHHHHHHHHHH---H----------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566999998 5555555555544322 1 13456788888888888877776
No 13
>PF11826 DUF3346: Protein of unknown function (DUF3346); InterPro: IPR021781 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 231 to 659 amino acids in length.
Probab=36.01 E-value=85 Score=27.85 Aligned_cols=45 Identities=20% Similarity=0.229 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHhhhcCCCCCCcccc
Q 029626 140 HYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGNLFPQHICVV 189 (190)
Q Consensus 140 aYc~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~sLtg~sp~~~~c~~ 189 (190)
.+|.+|...++-|.+-+ |-..|-..++.+|+.|..+...+..++|
T Consensus 104 ~d~mlLseLnqklArni-----ewrrfs~DLirEL~kl~~~~~~e~~f~v 148 (225)
T PF11826_consen 104 SDSMLLSELNQKLARNI-----EWRRFSMDLIRELRKLSEEKTKEDAFSV 148 (225)
T ss_pred hhHHHHHHHHHHHHhhh-----hHHHhhHHHHHHHHHHhcccCcCCeeEE
Confidence 58999999999999987 8889999999999999987777776654
No 14
>PF12057 DUF3538: Domain of unknown function (DUF3538); InterPro: IPR021925 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain is found associated with PF00240 from PFAM. This domain has a conserved SDL sequence motif.
Probab=34.45 E-value=1.2e+02 Score=24.54 Aligned_cols=46 Identities=22% Similarity=0.244 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHHHH-----HH------HHHHhhHhhhcHHHHHHHHHHHHHHHHhhhc
Q 029626 133 ELDQFMTHYVLLLY-----SF------KEQLQQHVRVHAMEAVMACWDLEQSLQSLTG 179 (190)
Q Consensus 133 ELDqFMeaYc~mL~-----kY------KEEL~rP~~~~a~EA~~F~~~IE~QL~sLtg 179 (190)
.|-=||+.|+++|. .| +|+=+|-|. ..-||..++..-...|++|.-
T Consensus 14 RL~Pflery~~iL~~~~~~e~~~~~~~re~~QRi~d-~VsEalh~lsHA~hAlSDL~l 70 (120)
T PF12057_consen 14 RLQPFLERYHEILQEDPSFEYENNTQEREEDQRIFD-LVSEALHYLSHAYHALSDLML 70 (120)
T ss_pred HHhHHHHHHHHHHhcCCCCCCCCCccchhhHhHHHH-HHHHHHHHHHHHHHHHHHHhh
Confidence 45569999999987 34 566666663 567888888888888888873
No 15
>PF06295 DUF1043: Protein of unknown function (DUF1043); InterPro: IPR009386 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=34.06 E-value=83 Score=24.84 Aligned_cols=33 Identities=18% Similarity=0.199 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHh
Q 029626 140 HYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQS 176 (190)
Q Consensus 140 aYc~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~s 176 (190)
.=-.-|..||.++..|| ..+...+.+|...-+.
T Consensus 36 ~~k~el~~yk~~V~~HF----~~ta~Ll~~l~~~Y~~ 68 (128)
T PF06295_consen 36 QAKQELEQYKQEVNDHF----AQTAELLDNLTQDYQK 68 (128)
T ss_pred HHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHH
Confidence 33445777888888877 5666666666554433
No 16
>PF09763 Sec3_C: Exocyst complex component Sec3; InterPro: IPR019160 The exocyst complex is composed of 8 subunits: Exoc1, Exoc2, Exoc3, Exoc4, Exoc5, Exoc6, Exoc7 and Exoc8. This entry represents the subunit Exoc1 (Sec3). Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein.
Probab=32.92 E-value=1.5e+02 Score=29.26 Aligned_cols=86 Identities=19% Similarity=0.201 Sum_probs=48.1
Q ss_pred CChHHHHHHHHhchhccCCCCch----------hhHHH---HHhhhHHHHhhhhhccC-CC-----CCCChhHHHHHHHH
Q 029626 81 PLYEQLLSAHVSCLRIATPVDQL----------PKIDA---QLSRSRDVLAKYSAVAN-GR-----VLDDKELDQFMTHY 141 (190)
Q Consensus 81 PlYp~LL~AyidC~KVGAPpev~----------~rLda---~l~~~q~~~~k~s~~~~-~~-----~~~DPELDqFMeaY 141 (190)
.=|.+|+.|-+++++..|+.+-. .++.. ++.-...+...-+.... ++ -.+....|+-+++|
T Consensus 511 ~aY~kl~~a~~~~l~~~a~~~~~~~~~~~~~dk~~~~~~v~~leN~~~~~e~l~~~~~~~~l~~~~~~A~~~~~~~~~~Y 590 (701)
T PF09763_consen 511 KAYEKLVRAMFDSLERIAKLSPKNSGSQDPEDKEKLNYHVVLLENYHHFYEELSQLKINSVLEEFRKEAKQIYDEHLEAY 590 (701)
T ss_pred HHHHHHHHHHHHHHHHhcccCcccccccCccccccchhhHHHHHHHHHHHHHHhhccchhhHHHHHHHHHHHHHHHHHHH
Confidence 34999999999999988864321 12221 22222222222222111 10 01233444445555
Q ss_pred HHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHh
Q 029626 142 VLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQS 176 (190)
Q Consensus 142 c~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~s 176 (190)
+..+ |.+|+ ..-..|+..+|.-+.+
T Consensus 591 ~~~~------l~r~~----~kL~~F~~gve~l~~~ 615 (701)
T PF09763_consen 591 VTFL------LRRPF----GKLLDFFEGVEALLQT 615 (701)
T ss_pred HHHH------HhccH----HHHHHHHHHHHHHHhc
Confidence 5433 45666 6888999999999998
No 17
>KOG3942 consensus MIF4G domain-containing protein [Translation, ribosomal structure and biogenesis]
Probab=31.89 E-value=48 Score=31.22 Aligned_cols=46 Identities=17% Similarity=0.047 Sum_probs=37.8
Q ss_pred CCChhHH-HHHHHHHHHHHHH---HHHHhhHhhhcHHHHHHHHHHHHHHH
Q 029626 129 LDDKELD-QFMTHYVLLLYSF---KEQLQQHVRVHAMEAVMACWDLEQSL 174 (190)
Q Consensus 129 ~~DPELD-qFMeaYc~mL~kY---KEEL~rP~~~~a~EA~~F~~~IE~QL 174 (190)
+.-+--+ |||+.-..+|.+| ++.|+.+-.+.+--++.|+-+++.+|
T Consensus 196 ~~~~~~gt~f~~~Lln~lrq~f~~r~gl~s~~~~rw~~fisfltelf~nl 245 (348)
T KOG3942|consen 196 GSSWRNGTQFMDELLNLLRQGFLLRTGLSSLASCRWWRFISFLTELFDNL 245 (348)
T ss_pred hhhhhccchHHHHHHHHHHHhhccchhccchhHHHHHHHHHHHHHHHhhc
Confidence 4444444 5999999999987 67788887788889999999999998
No 18
>PF02290 SRP14: Signal recognition particle 14kD protein; InterPro: IPR003210 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the 14 kDa SRP14 component. Both SRP9 and SRP14 have the same (beta)-alpha-beta(3)-alpha fold. The heterodimer has pseudo two-fold symmetry and is saddle-like, consisting of a curved six-stranded beta-sheet that has four helices packed on the convex side and an exposed concave surface lined with positively charged residues. The SRP9/SRP14 heterodimer is essential for SRP RNA binding, mediating the pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP [].; GO: 0008312 7S RNA binding, 0030942 endoplasmic reticulum signal peptide binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0005786 signal recognition particle, endoplasmic reticulum targeting; PDB: 1914_A 1RY1_D 1E8O_B 2W9J_B.
Probab=31.38 E-value=40 Score=25.49 Aligned_cols=19 Identities=32% Similarity=0.609 Sum_probs=15.8
Q ss_pred CCChhHHHHHHHHHHHHHH
Q 029626 129 LDDKELDQFMTHYVLLLYS 147 (190)
Q Consensus 129 ~~DPELDqFMeaYc~mL~k 147 (190)
..-.+|+.|...|+.+|..
T Consensus 70 V~~~~l~~F~~~Y~~v~K~ 88 (93)
T PF02290_consen 70 VDPDDLDKFWQSYANVLKA 88 (93)
T ss_dssp EETTCHHHHHHHHHHHHHH
T ss_pred ECHHHHHHHHHHHHHHHHh
Confidence 3458999999999999863
No 19
>PF12362 DUF3646: DNA polymerase III gamma and tau subunits C terminal; InterPro: IPR022107 This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with PF00004 from PFAM. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up.
Probab=31.08 E-value=56 Score=25.88 Aligned_cols=22 Identities=27% Similarity=0.381 Sum_probs=19.2
Q ss_pred hhHHHHHHHhcCCChHHHHHHH
Q 029626 69 ETVKCKAEIVGHPLYEQLLSAH 90 (190)
Q Consensus 69 e~e~iKAkI~sHPlYp~LL~Ay 90 (190)
..+..++++.+||++-..|++|
T Consensus 87 ~~~~~~~~a~~~P~V~avL~~F 108 (117)
T PF12362_consen 87 AKEARRAAARAHPLVKAVLAAF 108 (117)
T ss_pred HHHHHHHHHHhCcHHHHHHHHC
Confidence 4567899999999999999887
No 20
>PF12022 DUF3510: Domain of unknown function (DUF3510); InterPro: IPR024603 The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function []. This uncharacterised domain is found in the C-terminal of COG complex subunit 2 proteins.
Probab=31.03 E-value=2.2e+02 Score=22.29 Aligned_cols=48 Identities=21% Similarity=0.255 Sum_probs=31.4
Q ss_pred hHHHHHHHH---------HHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHhhhcC
Q 029626 133 ELDQFMTHY---------VLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGN 180 (190)
Q Consensus 133 ELDqFMeaY---------c~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~sLtg~ 180 (190)
-|.+|.+.| -+++.+.-++++.-|...+.|...-.+++|.+|+.|=..
T Consensus 43 Pl~~F~~~~~~~~~~~~~~~~~~~v~~~v~~~y~~~~~evL~sv~KtEeSL~rlkk~ 99 (125)
T PF12022_consen 43 PLKSFLEEYSSYLSPEIIEEWLQKVITEVTERYYEIASEVLTSVRKTEESLKRLKKR 99 (125)
T ss_pred HHHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455565555 334444555555555556677778889999999988753
No 21
>PF11014 DUF2852: Protein of unknown function (DUF2852); InterPro: IPR021273 This bacterial family of proteins has no known function.
Probab=30.93 E-value=44 Score=26.90 Aligned_cols=34 Identities=29% Similarity=0.539 Sum_probs=19.6
Q ss_pred chhhHHHHHhhhHHHHhhhhhccCCCCCCChhHHHHHHH
Q 029626 102 QLPKIDAQLSRSRDVLAKYSAVANGRVLDDKELDQFMTH 140 (190)
Q Consensus 102 v~~rLda~l~~~q~~~~k~s~~~~~~~~~DPELDqFMea 140 (190)
.+.||++...+...+..+-. .-.+..|.|+||..
T Consensus 79 tL~RLEeEq~eF~~Fl~rLR-----~AKDk~EFD~FM~~ 112 (115)
T PF11014_consen 79 TLRRLEEEQREFEDFLERLR-----RAKDKEEFDQFMAE 112 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHH-----HhhhHHHHHHHHHh
Confidence 35677776665544432211 12356899999963
No 22
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=30.71 E-value=45 Score=30.29 Aligned_cols=39 Identities=10% Similarity=0.068 Sum_probs=30.9
Q ss_pred chhhhhhHHHHHHHhcCCChHHH-HHHHHhchhccCCCCc
Q 029626 64 RAEDWETVKCKAEIVGHPLYEQL-LSAHVSCLRIATPVDQ 102 (190)
Q Consensus 64 ~~~~~e~e~iKAkI~sHPlYp~L-L~AyidC~KVGAPpev 102 (190)
|.-.-..+++|+.+.+||..... ..||+.|.|+|--||+
T Consensus 172 Gsr~~dld~~~el~~s~d~iaAmG~~a~va~rklgiePdi 211 (260)
T COG1497 172 GSRKVDLDRLKELSASEDIIAAMGTEALVALRKLGIEPDI 211 (260)
T ss_pred cccccchHHHHHhhcccchhhhhhHHHHHHHHHcCCCCCe
Confidence 34456678999999999954443 5789999999999875
No 23
>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=29.19 E-value=47 Score=29.19 Aligned_cols=40 Identities=10% Similarity=0.101 Sum_probs=32.2
Q ss_pred CcchhhhhhHHHHHHHhcCCChHH----HHHHHHhchhccCCCC
Q 029626 62 NGRAEDWETVKCKAEIVGHPLYEQ----LLSAHVSCLRIATPVD 101 (190)
Q Consensus 62 ~~~~~~~e~e~iKAkI~sHPlYp~----LL~AyidC~KVGAPpe 101 (190)
+|+.-.++-+.+++++..|-.-+. ...-|++.+|-|.||-
T Consensus 195 ~G~~r~~d~~~l~~~~~~~~~~~~~~~~~~~~yl~a~~~G~pp~ 238 (269)
T cd00669 195 NGSSRLHDPDIQAEVFQEQGINKEAGMEYFEFYLKALEYGLPPH 238 (269)
T ss_pred eCchhcCCHHHHHHHHHHhCcChhhccccHHHHHHHHHcCCCCC
Confidence 334456677889999999888887 7888999999999974
No 24
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=28.27 E-value=72 Score=27.63 Aligned_cols=17 Identities=18% Similarity=0.360 Sum_probs=11.3
Q ss_pred ccCCCCchhhHHHHHhh
Q 029626 96 IATPVDQLPKIDAQLSR 112 (190)
Q Consensus 96 VGAPpev~~rLda~l~~ 112 (190)
=|+|++++.+|.+.+++
T Consensus 212 ~gtp~~~~~~l~~a~~~ 228 (274)
T PF03401_consen 212 KGTPDEIVDKLADAIKK 228 (274)
T ss_dssp TTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHH
Confidence 47788888888776553
No 25
>PF12805 FUSC-like: FUSC-like inner membrane protein yccS
Probab=28.24 E-value=3.8e+02 Score=23.18 Aligned_cols=95 Identities=18% Similarity=0.195 Sum_probs=54.2
Q ss_pred HHHHHhcCCChHHHHHHHHhchhccCCCCchhhHHHHHhhhHHHHhh--hhhccCCCCCCChhHHHHHHHHHHHHHHHHH
Q 029626 73 CKAEIVGHPLYEQLLSAHVSCLRIATPVDQLPKIDAQLSRSRDVLAK--YSAVANGRVLDDKELDQFMTHYVLLLYSFKE 150 (190)
Q Consensus 73 iKAkI~sHPlYp~LL~AyidC~KVGAPpev~~rLda~l~~~q~~~~k--~s~~~~~~~~~DPELDqFMeaYc~mL~kYKE 150 (190)
.-.-+++|=.|+.|-+.+ + -++++.++...+.+......+ ............++|++-++.--.-+..|++
T Consensus 185 ~E~~~as~~~y~~l~~~f------~-~~~~l~~~~~~l~~~a~~l~~ia~ai~~~~~~~~~~~l~~~l~~l~~~l~~~~~ 257 (284)
T PF12805_consen 185 FERALASHYDYEELREQF------K-HSDVLFRFQRLLEQLAQALRQIAQAILRGRPYHHRNRLKRALEALEESLEFLRQ 257 (284)
T ss_pred HHHHHhccccHHHHHHHh------c-CChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCchHHHHHHHHHHHHHHHHHH
Confidence 333445555566655432 2 455666665544332111111 1111112344678899999998888888888
Q ss_pred HHhhHhhhcHHHHHHHHHHHHHHHHhhh
Q 029626 151 QLQQHVRVHAMEAVMACWDLEQSLQSLT 178 (190)
Q Consensus 151 EL~rP~~~~a~EA~~F~~~IE~QL~sLt 178 (190)
+ ..|. ..|+..-++.+-.-|++|.
T Consensus 258 ~-~~~~---~~~~~~~l~~l~~~l~~i~ 281 (284)
T PF12805_consen 258 Q-DQPE---NREALLALRNLLDNLRNID 281 (284)
T ss_pred h-cCcc---CHHHHHHHHHHHHHHHHHH
Confidence 8 5554 3687777777777666653
No 26
>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3.1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity
Probab=27.37 E-value=4.2e+02 Score=23.16 Aligned_cols=51 Identities=16% Similarity=0.169 Sum_probs=38.3
Q ss_pred CCCCCcchhhhhhHHHHHHHhcCCCh---------HHHHHHHHhchhccCCCCchhhHHH
Q 029626 58 ASNDNGRAEDWETVKCKAEIVGHPLY---------EQLLSAHVSCLRIATPVDQLPKIDA 108 (190)
Q Consensus 58 ~~~~~~~~~~~e~e~iKAkI~sHPlY---------p~LL~AyidC~KVGAPpev~~rLda 108 (190)
|||+-.+.....++.+=..|..=|.- ...|.-+++..+..||..++..+-.
T Consensus 84 GGGs~eDL~~FN~e~varai~~~~~PvisaIGHe~D~ti~D~vAd~ra~TPtaaAe~~~~ 143 (319)
T PF02601_consen 84 GGGSIEDLWAFNDEEVARAIAASPIPVISAIGHETDFTIADFVADLRAPTPTAAAELIVP 143 (319)
T ss_pred CCCChHHhcccChHHHHHHHHhCCCCEEEecCCCCCchHHHHHHHhhCCCHHHHHHHHhh
Confidence 66666777777888888888776642 3567889999999999887665543
No 27
>PF10112 Halogen_Hydrol: 5-bromo-4-chloroindolyl phosphate hydrolysis protein; InterPro: IPR018770 This entry consists of prokaryotic proteins that mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds.
Probab=27.13 E-value=1.8e+02 Score=23.93 Aligned_cols=46 Identities=24% Similarity=0.334 Sum_probs=32.3
Q ss_pred ChhHHHHHHHHH----HHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHhhh
Q 029626 131 DKELDQFMTHYV----LLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLT 178 (190)
Q Consensus 131 DPELDqFMeaYc----~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~sLt 178 (190)
=+..+.||..|- .++.||.+==.+|++ -.|+...+.++|.-|..|+
T Consensus 124 l~~a~~Fl~~yLp~~~~l~~kY~~l~~~~~~--~~~~~~~l~e~~~~L~~l~ 173 (199)
T PF10112_consen 124 LTQARKFLYYYLPTAVKLLEKYAELESQPVK--SEEIKQSLEEIEETLDTLN 173 (199)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHhccCC--ChhHHHHHHHHHHHHHHHH
Confidence 367999999995 567788776666763 4555566677777777665
No 28
>COG2916 Hns DNA-binding protein H-NS [General function prediction only]
Probab=26.22 E-value=2.9e+02 Score=22.59 Aligned_cols=46 Identities=20% Similarity=0.130 Sum_probs=32.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHhhh
Q 029626 133 ELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLT 178 (190)
Q Consensus 133 ELDqFMeaYc~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~sLt 178 (190)
-++.-||.|.++|.++.|-+++-++-...|.......|+++...+-
T Consensus 8 l~~~~~e~~~e~lee~~ek~eq~~~~r~~e~~~~~~~i~e~~~~~~ 53 (128)
T COG2916 8 LRAMARETYLELLEEMLEKEEQVVQERQEEEAAAIAEIEERQEKYG 53 (128)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3688899999999888877776666455555555666666666554
No 29
>KOG2070 consensus Guanine nucleotide exchange factor [Nucleotide transport and metabolism]
Probab=26.02 E-value=71 Score=32.08 Aligned_cols=27 Identities=11% Similarity=0.258 Sum_probs=21.0
Q ss_pred CCCChhHHHHHHHHHH-------HHHHHHHHHhh
Q 029626 128 VLDDKELDQFMTHYVL-------LLYSFKEQLQQ 154 (190)
Q Consensus 128 ~~~DPELDqFMeaYc~-------mL~kYKEEL~r 154 (190)
...-|++....-+||. +|.||++||++
T Consensus 181 ln~ap~mkt~~~aYcanHP~AV~VL~k~~dELek 214 (661)
T KOG2070|consen 181 LNLAPQMKTLYLAYCANHPSAVNVLTKHSDELEK 214 (661)
T ss_pred HhhhHHHHHHHHHHHhcCchhhhHHHHhHHHHHH
Confidence 4567888888888884 78888888865
No 30
>PF10732 DUF2524: Protein of unknown function (DUF2524); InterPro: IPR019668 This entry represents proteins with unknown function, and appear to be restricted to the Bacillaceae.
Probab=25.97 E-value=2.5e+02 Score=21.62 Aligned_cols=47 Identities=21% Similarity=0.239 Sum_probs=30.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhHhhh---cHHHHHHHHHHHHHHHHhhh
Q 029626 132 KELDQFMTHYVLLLYSFKEQLQQHVRV---HAMEAVMACWDLEQSLQSLT 178 (190)
Q Consensus 132 PELDqFMeaYc~mL~kYKEEL~rP~~~---~a~EA~~F~~~IE~QL~sLt 178 (190)
.-+|.|++..-+++..=+|++..--++ ...|...+.-.+|.--+.|+
T Consensus 5 qs~~~~lq~~e~~i~~a~eQ~~~~~rqehynd~eYt~Aq~~LE~a~neL~ 54 (84)
T PF10732_consen 5 QSVDEFLQQCEQAIRFAQEQFEEGSRQEHYNDEEYTEAQQMLEEAYNELE 54 (84)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHH
Confidence 457899999888888888888765552 23344444455555555444
No 31
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.45 E-value=2.2e+02 Score=23.75 Aligned_cols=42 Identities=19% Similarity=0.233 Sum_probs=30.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHhh
Q 029626 132 KELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSL 177 (190)
Q Consensus 132 PELDqFMeaYc~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~sL 177 (190)
.-|-.=|+.--.-|..||+||.+|| .+....+++|-+.-+.|
T Consensus 37 ~~~q~ELe~~K~~ld~~rqel~~HF----a~sAeLlktl~~dYqkl 78 (138)
T COG3105 37 QKLQYELEKVKAQLDEYRQELVKHF----ARSAELLKTLAQDYQKL 78 (138)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHH
Confidence 3444456667778999999999998 57777888886655544
No 32
>PF12207 DUF3600: Domain of unknown function (DUF3600); InterPro: IPR022019 This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C-terminal of the putative ecf-type sigma factor negative effector. ; PDB: 3FGG_A 3FH3_A.
Probab=25.02 E-value=65 Score=27.40 Aligned_cols=45 Identities=20% Similarity=0.248 Sum_probs=25.0
Q ss_pred CCCCChhHHHHHHH---HHHHHHHHH-------HHHhhHhhhcHHHHHHHHHHHH
Q 029626 127 RVLDDKELDQFMTH---YVLLLYSFK-------EQLQQHVRVHAMEAVMACWDLE 171 (190)
Q Consensus 127 ~~~~DPELDqFMea---Yc~mL~kYK-------EEL~rP~~~~a~EA~~F~~~IE 171 (190)
.+-.+.|+|+.|+| |--+++|-+ |++-.-++-+|.+|..|+..+.
T Consensus 104 ~vlt~~E~d~y~eALm~~e~v~vk~~~~~~~~ve~vpe~~~e~f~~a~~~~~yv~ 158 (162)
T PF12207_consen 104 EVLTQEEYDQYIEALMTYETVRVKTKSSGGITVEEVPEAYKERFIKAEQFMEYVN 158 (162)
T ss_dssp HHS-HHHHHHHHHHHHHHHHHHHHCT-SS---GGGS-HHHHHHHHHHHHHHHHHH
T ss_pred hhcCHHHHHHHHHHHhhhheeeeeccCCCCCcHHhccHHHHHHHHHHHHHHHHHH
Confidence 35677888888876 333444433 3333333344577877777654
No 33
>KOG2828 consensus Acetyl-CoA hydrolase [Energy production and conversion]
Probab=24.30 E-value=70 Score=31.06 Aligned_cols=30 Identities=20% Similarity=0.180 Sum_probs=24.1
Q ss_pred hhHHHHHHHhcCCChHHHHHHHHhchhccC
Q 029626 69 ETVKCKAEIVGHPLYEQLLSAHVSCLRIAT 98 (190)
Q Consensus 69 e~e~iKAkI~sHPlYp~LL~AyidC~KVGA 98 (190)
|.+.-=-+|..||.|+.|+.+|+|-.||=.
T Consensus 422 qRayElI~i~~p~dre~L~k~afdr~kvmp 451 (454)
T KOG2828|consen 422 QRAYELIQICAPPDREALLKAAFDRAKVMP 451 (454)
T ss_pred HHHHHHHHhhCCchHHHHHHHHHHHHhccc
Confidence 444444579999999999999999988743
No 34
>PF10782 DUF2602: Protein of unknown function (DUF2602); InterPro: IPR019718 This bacterial family of proteins that has no known function.
Probab=23.13 E-value=55 Score=23.51 Aligned_cols=41 Identities=17% Similarity=0.284 Sum_probs=29.8
Q ss_pred hhHHHHHHHHHHHH---HHHHHHHhhHhhhcHHHHHHHHHH---HHHHHHhhh
Q 029626 132 KELDQFMTHYVLLL---YSFKEQLQQHVRVHAMEAVMACWD---LEQSLQSLT 178 (190)
Q Consensus 132 PELDqFMeaYc~mL---~kYKEEL~rP~~~~a~EA~~F~~~---IE~QL~sLt 178 (190)
-|+|+.|++||.== ..|+.+..+. -|..||.+ |=.||+.|-
T Consensus 8 ~~I~~L~dtyC~gC~lk~~~rk~~gk~------~ah~fCI~~CtVGkqik~lG 54 (58)
T PF10782_consen 8 IEIDDLQDTYCKGCFLKKHFRKEKGKT------YAHSFCINQCTVGKQIKQLG 54 (58)
T ss_pred HHHHHHHHHHhcCCchHHHhHHHhccc------ccchHHHHhCcHhHHHHHHH
Confidence 47899999999754 6677887776 48888874 455565553
No 35
>KOG3647 consensus Predicted coiled-coil protein [General function prediction only]
Probab=22.47 E-value=1.7e+02 Score=27.38 Aligned_cols=42 Identities=14% Similarity=-0.077 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHHHhhhcCCC
Q 029626 140 HYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSLQSLTGNLF 182 (190)
Q Consensus 140 aYc~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL~sLtg~sp 182 (190)
+|-+.-.+|.|+|++-|++-+.-+ .-+.-+++||..++.++|
T Consensus 165 ~~MdEyE~~EeeLqkly~~Y~l~f-~nl~yL~~qldd~~rse~ 206 (338)
T KOG3647|consen 165 AHMDEYEDCEEELQKLYQRYFLRF-HNLDYLKSQLDDRTRSEP 206 (338)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-hhHHHHHHHHHHHhhhhH
Confidence 344444689999999997544443 246778999999997544
No 36
>PLN02372 violaxanthin de-epoxidase
Probab=22.24 E-value=3e+02 Score=26.96 Aligned_cols=65 Identities=15% Similarity=0.173 Sum_probs=33.1
Q ss_pred CCCchhhHHHHHhhhHHHHhhhhhccCCCCCCChhHHHHHHHHHHHHHHHHHHHhhHhhhcHHHHHHHHHHHHHHH
Q 029626 99 PVDQLPKIDAQLSRSRDVLAKYSAVANGRVLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEAVMACWDLEQSL 174 (190)
Q Consensus 99 Ppev~~rLda~l~~~q~~~~k~s~~~~~~~~~DPELDqFMeaYc~mL~kYKEEL~rP~~~~a~EA~~F~~~IE~QL 174 (190)
|.+.+++|....+..-....++...-+ .-+..|+| .+-|.|=-|+.++-+ ..|+...-.+||.+.
T Consensus 328 P~~~~p~L~~Aa~kvG~df~~F~~tDN-sCgpep~l-------~~~l~~~~e~~e~~i---~~e~~~~~~e~~~~v 392 (455)
T PLN02372 328 PESIVPELEKAAKKVGRDFSDFVRTDN-TCGPEPPL-------LERLEKDVEEGEKTI---VKEARQIEEELEKEV 392 (455)
T ss_pred ChhhhHHHHHHHHHcCCCHHHheeeCC-CCCCCchH-------HHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Confidence 666678887765543222233333322 34667777 455555555555555 244433334444333
No 37
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.97 E-value=1.7e+02 Score=26.15 Aligned_cols=73 Identities=15% Similarity=0.141 Sum_probs=38.5
Q ss_pred HHHhchhccCCCCchhhHHHHHhhh-HHHHhhhh----hccCCCCCCChhHHHHHHHHHHHHHHHHHHHhhHhhhcHHHH
Q 029626 89 AHVSCLRIATPVDQLPKIDAQLSRS-RDVLAKYS----AVANGRVLDDKELDQFMTHYVLLLYSFKEQLQQHVRVHAMEA 163 (190)
Q Consensus 89 AyidC~KVGAPpev~~rLda~l~~~-q~~~~k~s----~~~~~~~~~DPELDqFMeaYc~mL~kYKEEL~rP~~~~a~EA 163 (190)
-|+.|+.-|.|-.. ..|.+...-. ..+...|. .++......+ ...||..||..|. |...++ +.|
T Consensus 172 lYiACR~~~~prtl-~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~~~--p~~~i~r~~~~L~-----L~~~v~---~~A 240 (310)
T PRK00423 172 LYAACRRCKVPRTL-DEIAEVSRVSRKEIGRCYRFLLRELNLKLPPTD--PIDYVPRFASELG-----LSGEVQ---KKA 240 (310)
T ss_pred HHHHHHHcCCCcCH-HHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCCC--HHHHHHHHHHHcC-----CCHHHH---HHH
Confidence 38999999999643 3333322111 11111111 1221111234 4589999999983 555554 556
Q ss_pred HHHHHHHHH
Q 029626 164 VMACWDLEQ 172 (190)
Q Consensus 164 ~~F~~~IE~ 172 (190)
..++++...
T Consensus 241 ~~i~~~a~~ 249 (310)
T PRK00423 241 IEILQKAKE 249 (310)
T ss_pred HHHHHHHHh
Confidence 666665543
No 38
>PF01533 Tospo_nucleocap: Tospovirus nucleocapsid protein; InterPro: IPR002517 The tospovirus genome consists of three linear ssRNA segments, denoted L, M and S complexed with the nucleocapsid protein. The S RNA encodes the nucleocapsid protein and another non-structural protein [].; GO: 0019013 viral nucleocapsid
Probab=20.87 E-value=78 Score=28.63 Aligned_cols=20 Identities=25% Similarity=0.292 Sum_probs=16.0
Q ss_pred hhhhHHHHHHHhcCCChHHHHHHH
Q 029626 67 DWETVKCKAEIVGHPLYEQLLSAH 90 (190)
Q Consensus 67 ~~e~e~iKAkI~sHPlYp~LL~Ay 90 (190)
+++...|+.+|++|| ||+||
T Consensus 112 ~e~k~~~~~k~~~~P----LV~AY 131 (248)
T PF01533_consen 112 EEAKQKMYSKIMSLP----LVQAY 131 (248)
T ss_pred HHHHHHHHHHHhcCh----HHHHh
Confidence 445678999999999 57777
Done!