Query psy876
Match_columns 179
No_of_seqs 161 out of 647
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 18:32:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy876.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/876hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1133|consensus 99.8 3.1E-20 6.8E-25 176.5 7.6 112 56-178 496-612 (821)
2 KOG1132|consensus 99.7 9.8E-18 2.1E-22 162.5 6.8 85 83-178 459-544 (945)
3 TIGR00604 rad3 DNA repair heli 99.7 1.6E-17 3.5E-22 158.5 7.6 107 61-178 395-505 (705)
4 KOG1131|consensus 99.4 3.5E-14 7.6E-19 132.9 1.9 110 57-179 405-514 (755)
5 KOG1132|consensus 98.5 6.7E-08 1.4E-12 94.9 2.3 63 1-66 139-203 (945)
6 TIGR01407 dinG_rel DnaQ family 97.3 0.0004 8.7E-09 68.4 6.4 65 81-146 572-643 (850)
7 PRK11747 dinG ATP-dependent DN 97.3 0.0006 1.3E-08 66.1 7.3 67 80-146 432-505 (697)
8 COG1199 DinG Rad3-related DNA 97.2 0.00025 5.3E-09 67.2 3.7 42 84-125 384-425 (654)
9 PF06733 DEAD_2: DEAD_2; Inte 96.7 0.00047 1E-08 55.0 0.7 44 1-44 31-78 (174)
10 TIGR00604 rad3 DNA repair heli 96.7 0.0013 2.9E-08 63.5 3.8 45 1-45 99-155 (705)
11 PRK08074 bifunctional ATP-depe 96.7 0.0043 9.3E-08 62.1 7.4 65 82-146 650-721 (928)
12 PRK07246 bifunctional ATP-depe 95.7 0.022 4.8E-07 56.5 6.2 62 83-146 554-617 (820)
13 TIGR03117 cas_csf4 CRISPR-asso 93.0 0.29 6.4E-06 47.6 7.0 55 83-138 350-413 (636)
14 KOG1133|consensus 92.1 0.081 1.8E-06 52.2 1.9 30 3-32 224-255 (821)
15 smart00488 DEXDc2 DEAD-like he 91.9 0.11 2.3E-06 45.3 2.3 44 2-45 116-172 (289)
16 smart00489 DEXDc3 DEAD-like he 91.9 0.11 2.3E-06 45.3 2.3 44 2-45 116-172 (289)
17 KOG1131|consensus 82.3 0.67 1.5E-05 45.0 1.4 51 4-55 109-172 (755)
18 PHA02707 hypothetical protein; 30.8 42 0.0009 20.9 1.8 22 88-109 6-27 (37)
19 PF08785 Ku_PK_bind: Ku C term 26.3 33 0.00072 26.1 1.0 15 111-125 1-15 (120)
No 1
>KOG1133|consensus
Probab=99.81 E-value=3.1e-20 Score=176.50 Aligned_cols=112 Identities=23% Similarity=0.325 Sum_probs=102.3
Q ss_pred cCCCChhhhhhhccccccccCCCC--CCCeEEEEEecChHHHHHHHHhhcceeEEeccccCChHhHHHhhCC---CCCeE
Q psy876 56 SQGPHADEYQGESNRWYRKDRTPM--SIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGT---QFPIK 130 (179)
Q Consensus 56 ~~~~~~~~f~~~~~~~~~~~~~~~--~~~~~L~~~cLdPs~~f~~I~~~arSVILtSGTLsPi~~f~~~Lg~---~f~~~ 130 (179)
...+++.+|+..|+|...|||..- ....+|+|++|+|+..|.+++.+||+|||++|||+|+++|.+.|+. +....
T Consensus 496 s~l~~l~~FL~~LTn~~~dGri~~~k~~s~~lky~lL~pA~~f~evv~earavvLAGGTMeP~~e~~e~L~~~~~~~i~~ 575 (821)
T KOG1133|consen 496 SPLFELSSFLGALTNNNEDGRIFYSKQGSGTLKYMLLNPAKHFAEVVLEARAVVLAGGTMEPVDELREQLFPGCPERISP 575 (821)
T ss_pred chhHHHHHHHHHHhCCCCCCcEEEeccCCceEEEEecCcHHHHHHHHHHhheeeecCCccccHHHHHHHhcccchhhccc
Confidence 478899999999999999999753 2337899999999999999999999999999999999999999986 33477
Q ss_pred EEeCCccCCCCceEEEeccccceeeeeeccCCCCcceEEEeccccCCC
Q psy876 131 LEANHVIDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGD 178 (179)
Q Consensus 131 ls~~HVI~~enl~~~i~~~~~~~~~~vl~~G~~g~~L~~ty~~R~~~~ 178 (179)
++|.||||++|+++++ +.+||+|.+|.|||++|.++.
T Consensus 576 fsc~Hvip~e~il~~v-----------v~~gpsg~p~eftf~~R~s~~ 612 (821)
T KOG1133|consen 576 FSCSHVIPPENILPLV-----------VSSGPSGQPLEFTFETRESPE 612 (821)
T ss_pred eecccccChhheeeee-----------eccCCCCCceEEEeeccCChH
Confidence 9999999999999999 999999999999999999864
No 2
>KOG1132|consensus
Probab=99.71 E-value=9.8e-18 Score=162.45 Aligned_cols=85 Identities=46% Similarity=0.882 Sum_probs=81.4
Q ss_pred eEEEEEecChHHHHHHHHhh-cceeEEeccccCChHhHHHhhCCCCCeEEEeCCccCCCCceEEEeccccceeeeeeccC
Q psy876 83 YTLHFWCLNSGLVFSDIRES-ARSVILTSGTLAPVDSFQSELGTQFPIKLEANHVIDKDQVFIGVLGQGQKVFIGVLGQG 161 (179)
Q Consensus 83 ~~L~~~cLdPs~~f~~I~~~-arSVILtSGTLsPi~~f~~~Lg~~f~~~ls~~HVI~~enl~~~i~~~~~~~~~~vl~~G 161 (179)
+.++|||++|+..|.+++.+ +||||||||||+||+.|+.+||.+|+..++++|+|++.|+|+.+ +++|
T Consensus 459 ~vi~~wcf~p~~sf~d~~~k~vrsIiLtSGTLsP~~s~~~El~~~f~~~lEn~hii~~~qv~~~v-----------v~~G 527 (945)
T KOG1132|consen 459 PVINFWCFSPGYSFRDLLGKGVRSIILTSGTLSPMDSFASELGLEFKIQLENPHIINKSQVWVGV-----------VPKG 527 (945)
T ss_pred cceeeeecCcchhHHHHhcccceeEEEecccccCchhHHHHhCCccceeeecchhccccceEEEe-----------eccC
Confidence 55899999999999999965 99999999999999999999999999999999999999999999 9999
Q ss_pred CCCcceEEEeccccCCC
Q psy876 162 PQNIPLQALYKNTLVGD 178 (179)
Q Consensus 162 ~~g~~L~~ty~~R~~~~ 178 (179)
|+|..|+.+|.||++++
T Consensus 528 p~~~ql~sty~nr~~~e 544 (945)
T KOG1132|consen 528 PDGAQLDSTYGNRFTPE 544 (945)
T ss_pred CCccccccccccccCHH
Confidence 99999999999999874
No 3
>TIGR00604 rad3 DNA repair helicase (rad3). All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.70 E-value=1.6e-17 Score=158.51 Aligned_cols=107 Identities=22% Similarity=0.392 Sum_probs=92.6
Q ss_pred hhhhhhhccccccccCCC----CCCCeEEEEEecChHHHHHHHHhhcceeEEeccccCChHhHHHhhCCCCCeEEEeCCc
Q psy876 61 ADEYQGESNRWYRKDRTP----MSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHV 136 (179)
Q Consensus 61 ~~~f~~~~~~~~~~~~~~----~~~~~~L~~~cLdPs~~f~~I~~~arSVILtSGTLsPi~~f~~~Lg~~f~~~ls~~HV 136 (179)
...|+..+.+.+.+++.. ...+..|++|||||+..|+++++.+||||||||||+|+++|..+||++++..++.+|+
T Consensus 395 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~l~ps~~~~~i~~~~~svil~SgTL~p~~~~~~~Lg~~~~~~~~~~~~ 474 (705)
T TIGR00604 395 FATLVLTYTNGFLEGIEPYENKTVPNPILKFMCLDPSIALKPLFERVRSVILASGTLSPLDAFPRNLGFNPVSQDSPTHI 474 (705)
T ss_pred HHHHHHHhccccccceeEeecCCCCCceEEEEecChHHHHHHHHHhcCEEEEecccCCcHHHHHHHhCCCCccceecCcc
Confidence 345566666655555432 2356889999999999999999999999999999999999999999988888899999
Q ss_pred cCCCCceEEEeccccceeeeeeccCCCCcceEEEeccccCCC
Q psy876 137 IDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGD 178 (179)
Q Consensus 137 I~~enl~~~i~~~~~~~~~~vl~~G~~g~~L~~ty~~R~~~~ 178 (179)
|+++|+++++ ++.|++|.+|+++|++|++++
T Consensus 475 ~~~~~~~~~i-----------~~~~~~~~~l~~~~~~r~~~~ 505 (705)
T TIGR00604 475 LKRENLLTLI-----------VTRGSDQVPLSSTFEIRNDPS 505 (705)
T ss_pred cchHHeEEEE-----------EeeCCCCCeeeeehhccCCHH
Confidence 9999999999 999999999999999998753
No 4
>KOG1131|consensus
Probab=99.43 E-value=3.5e-14 Score=132.93 Aligned_cols=110 Identities=19% Similarity=0.314 Sum_probs=92.0
Q ss_pred CCCChhhhhhhccccccccCCCCCCCeEEEEEecChHHHHHHHHhhcceeEEeccccCChHhHHHhhCCCCCeEEEeCCc
Q psy876 57 QGPHADEYQGESNRWYRKDRTPMSIKYTLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGTQFPIKLEANHV 136 (179)
Q Consensus 57 ~~~~~~~f~~~~~~~~~~~~~~~~~~~~L~~~cLdPs~~f~~I~~~arSVILtSGTLsPi~~f~~~Lg~~f~~~ls~~HV 136 (179)
++....||....++. |++++...++.|+|.|+|+|++++++++.++|||+|||||+|+++|..+|........+..-.
T Consensus 405 VstY~kGF~iIiEPf--d~~~~tv~npil~~sClDaSiAikPVf~RFqsViITSGTlspldmyPk~lnf~pv~~~s~~mt 482 (755)
T KOG1131|consen 405 VSTYSKGFSIIIEPF--DDRNPTVPNPILRFSCLDASIAIKPVFERFQSVIITSGTLSPLDMYPKILNFGPVVGASFTMT 482 (755)
T ss_pred HHHHhcCcEEEEccc--ccCCCCCCCCeeEEeecccchhhhHHHHhhheEEEecCcccccccCchhhccCcccchhhhee
Confidence 345567888888886 888899999999999999999999999999999999999999999999998743333333333
Q ss_pred cCCCCceEEEeccccceeeeeeccCCCCcceEEEeccccCCCC
Q psy876 137 IDKDQVFIGVLGQGQKVFIGVLGQGPQNIPLQALYKNTLVGDV 179 (179)
Q Consensus 137 I~~enl~~~i~~~~~~~~~~vl~~G~~g~~L~~ty~~R~~~~v 179 (179)
...+-+++++ +++|.+...+...|+.|.++.|
T Consensus 483 LaR~c~~Pmi-----------itrG~Dqv~iss~fe~r~d~~V 514 (755)
T KOG1131|consen 483 LARNCLLPLI-----------ITRGNDQVAISSKFEARGDPSV 514 (755)
T ss_pred ccccccccee-----------eecCCcchhhhhhhhhccChHH
Confidence 3334467788 9999999999999999999875
No 5
>KOG1132|consensus
Probab=98.46 E-value=6.7e-08 Score=94.94 Aligned_cols=63 Identities=25% Similarity=0.319 Sum_probs=47.5
Q ss_pred CceeccCCccccChhhhc--cccCHHHHHHHhhhccCccceEeccCCCCCCCCCccccCCCChhhhhh
Q psy876 1 MTILSSRKHTCINDEVLK--AKENINDLCQELKETEGESNRWYRKDRTPMRGIEPVVSQGPHADEYQG 66 (179)
Q Consensus 1 mtil~sr~~tci~~~~~~--~~~~~~~~c~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~f~~ 66 (179)
||||+||||.||||+|.+ -+.+++.+|+++. ++.+|.||+....++-.-.-+-+ -.++..+-.
T Consensus 139 mtVLgSReq~Cinpev~k~~~~~~~~~~C~k~~--~~~~C~f~~~~~~~sl~~~l~~~-i~DIEDLVk 203 (945)
T KOG1132|consen 139 MTVLGSREQLCINPEVKKLEGNALQNHVCKKLV--KSRSCHFYKIVEEKSLQPRLHDE-IFDIEDLVK 203 (945)
T ss_pred eEEeecchhhccCHHHhhhhcchhhhhHHHhhc--ccccccccccccccccccccCCC-cccHHHHHH
Confidence 899999999999998887 3445689999987 78999999887777655443333 455555533
No 6
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=97.34 E-value=0.0004 Score=68.45 Aligned_cols=65 Identities=22% Similarity=0.215 Sum_probs=50.8
Q ss_pred CCeEEEEEecChHHHH-HHHHhhcceeEEeccccC---ChHhHHHhhCCCCC--eEEEeCCccC-CCCceEEE
Q psy876 81 IKYTLHFWCLNSGLVF-SDIRESARSVILTSGTLA---PVDSFQSELGTQFP--IKLEANHVID-KDQVFIGV 146 (179)
Q Consensus 81 ~~~~L~~~cLdPs~~f-~~I~~~arSVILtSGTLs---Pi~~f~~~Lg~~f~--~~ls~~HVI~-~enl~~~i 146 (179)
....|+..++||+..+ +.++...+++|||||||+ |+++|.+.||.+-. ..+. ++.++ ++|..+++
T Consensus 572 ~~~~l~~~pl~~~~~l~~~~~~~~~~~il~SATL~~~~~~~~~~~~lGl~~~~~~~~~-~spf~~~~~~~l~v 643 (850)
T TIGR01407 572 STIRLYIKDYEVGDVLTKRLLPKFKSLIFTSATLKFSHSFESFPQLLGLTDVHFNTIE-PTPLNYAENQRVLI 643 (850)
T ss_pred ceEEEEeeeCcHHHHHHHHHhccCCeEEEEecccccCCChHHHHHhcCCCccccceec-CCCCCHHHcCEEEe
Confidence 4567899999999777 556689999999999999 89999999998532 2333 66667 57777666
No 7
>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional
Probab=97.32 E-value=0.0006 Score=66.11 Aligned_cols=67 Identities=24% Similarity=0.149 Sum_probs=49.8
Q ss_pred CCCeEEEEEecChHHHHH-HHHhhcceeEEeccccCCh---HhHHHhhCCCC---CeEEEeCCccCCCCceEEE
Q psy876 80 SIKYTLHFWCLNSGLVFS-DIRESARSVILTSGTLAPV---DSFQSELGTQF---PIKLEANHVIDKDQVFIGV 146 (179)
Q Consensus 80 ~~~~~L~~~cLdPs~~f~-~I~~~arSVILtSGTLsPi---~~f~~~Lg~~f---~~~ls~~HVI~~enl~~~i 146 (179)
..+..|+...+||+..+. .++..++++|||||||+|. ++|...||++. ...+..+..++.+|...++
T Consensus 432 ~~~~~l~~~Pl~~~~~l~~~l~~~~~~vIltSATL~~~~~f~~~~~~lGL~~~~~~~~~~~~SpF~~~~q~~l~ 505 (697)
T PRK11747 432 QGDYLFHASPIRVGDQLERLLWSRAPGAVLTSATLRSLNSFDRFQEQSGLPEKDGDRFLALPSPFDYPNQGKLV 505 (697)
T ss_pred CceEEEEEecCCHHHHHHHHHHhhCCEEEEEeeeCCCCCchHHHHHHcCCCCCCCceEEEcCCCCCHHHccEEE
Confidence 356778999999999996 5679999999999999975 67778899853 3445556666654433343
No 8
>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]
Probab=97.24 E-value=0.00025 Score=67.22 Aligned_cols=42 Identities=38% Similarity=0.481 Sum_probs=39.6
Q ss_pred EEEEEecChHHHHHHHHhhcceeEEeccccCChHhHHHhhCC
Q psy876 84 TLHFWCLNSGLVFSDIRESARSVILTSGTLAPVDSFQSELGT 125 (179)
Q Consensus 84 ~L~~~cLdPs~~f~~I~~~arSVILtSGTLsPi~~f~~~Lg~ 125 (179)
.+..+|++|+...++++..++++|||||||+|+++|...++.
T Consensus 384 ~~~~~~~~~~~l~~~~~~~~~~~vl~SaTL~~~~~f~~~~~~ 425 (654)
T COG1199 384 LLVLPLLVPSKLLEELFSKVASVVLTSATLSPLDSFSSLLGL 425 (654)
T ss_pred eEEeecccHHHHHHHHHhhcCcEEEeeeeccCCCcHHHHHHH
Confidence 578999999999999999999999999999999999998876
No 9
>PF06733 DEAD_2: DEAD_2; InterPro: IPR010614 This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast [].; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 3CRV_A 3CRW_1 2VL7_A 4A15_A 2VSF_A.
Probab=96.75 E-value=0.00047 Score=54.98 Aligned_cols=44 Identities=36% Similarity=0.710 Sum_probs=32.8
Q ss_pred CceeccCCccccChhhhcc--ccCHHHHHHHhhhc--cCccceEeccC
Q psy876 1 MTILSSRKHTCINDEVLKA--KENINDLCQELKET--EGESNRWYRKD 44 (179)
Q Consensus 1 mtil~sr~~tci~~~~~~~--~~~~~~~c~~~~~~--~~~~c~~~~~~ 44 (179)
|++|+||++.|+|+.+... ..+.++.|.++.+. ....|.||++.
T Consensus 31 ~~~l~gR~~~C~~~~v~~~~~~~~~~~~C~~l~~~~~~~~~C~~~~~~ 78 (174)
T PF06733_consen 31 AVILKGRQNLCINSKVKRLANNEDINEFCRELRKSGKRKESCPYYNNF 78 (174)
T ss_dssp EEEE--CCCC-TTCHHHTT-SHHHHHHHHHHHHHHHHCTCCSTTTTGG
T ss_pred eeEeccccccccCchhhhhhhhhhHHHHHHHhhcccccccccchhHHH
Confidence 5799999999999998862 34678999998873 34589999876
No 10
>TIGR00604 rad3 DNA repair helicase (rad3). All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.73 E-value=0.0013 Score=63.47 Aligned_cols=45 Identities=31% Similarity=0.462 Sum_probs=35.0
Q ss_pred CceeccCCccccChhhhccc--cCHHHHHHHhhhc----------cCccceEeccCC
Q psy876 1 MTILSSRKHTCINDEVLKAK--ENINDLCQELKET----------EGESNRWYRKDR 45 (179)
Q Consensus 1 mtil~sr~~tci~~~~~~~~--~~~~~~c~~~~~~----------~~~~c~~~~~~~ 45 (179)
+++|+||++.||||.|.+.. ...|+.|+++... ++.+|.||++..
T Consensus 99 ~v~L~SR~~lCin~~v~~~~~~~~~~~~C~~l~~~~~~~~~~~~~~~~~C~yy~~~~ 155 (705)
T TIGR00604 99 GLSLASRKNLCLHPEVSKERQGKVVNGKCIKLTVSKIKEQRTEKPNVESCEFYENFD 155 (705)
T ss_pred EEEechHhhcccChHHHhhcchhhHHHHHHHHHhhhhcccccccCCCCCCCCCchhh
Confidence 35899999999999998632 2478899998652 246799998854
No 11
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.72 E-value=0.0043 Score=62.06 Aligned_cols=65 Identities=23% Similarity=0.150 Sum_probs=48.9
Q ss_pred CeEEEEEecChHHHHHHHH-hhcceeEEeccccC---ChHhHHHhhCCCC-C-eEEEeCCccCC-CCceEEE
Q psy876 82 KYTLHFWCLNSGLVFSDIR-ESARSVILTSGTLA---PVDSFQSELGTQF-P-IKLEANHVIDK-DQVFIGV 146 (179)
Q Consensus 82 ~~~L~~~cLdPs~~f~~I~-~~arSVILtSGTLs---Pi~~f~~~Lg~~f-~-~~ls~~HVI~~-enl~~~i 146 (179)
...|+..++|++..+.+.+ ..++++|||||||+ ++++|...||.+. . ..+..+..++. +|..+++
T Consensus 650 ~~~l~~~pld~~~~l~~~l~~~~~~~iltSATL~~~~~f~~~~~~lGl~~~~~~~~~~~SpF~~~~q~~l~v 721 (928)
T PRK08074 650 ATRLYAQPVEVAERLADEFFAKKKSVILTSATLTVNGSFDYIIERLGLEDFYPRTLQIPSPFSYEEQAKLMI 721 (928)
T ss_pred eEEEEEeeccHHHHHHHHHHhcCCcEEEEeeecccCCCcHHHHHhcCCCCCCccEEEeCCCCCHHHhcEEEe
Confidence 4678999999999998755 89999999999999 6777888999852 2 23444444453 5666655
No 12
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=95.70 E-value=0.022 Score=56.50 Aligned_cols=62 Identities=18% Similarity=0.077 Sum_probs=46.2
Q ss_pred eEEEEEecChHHHHHHHHhhcceeEEeccccC--ChHhHHHhhCCCCCeEEEeCCccCCCCceEEE
Q psy876 83 YTLHFWCLNSGLVFSDIRESARSVILTSGTLA--PVDSFQSELGTQFPIKLEANHVIDKDQVFIGV 146 (179)
Q Consensus 83 ~~L~~~cLdPs~~f~~I~~~arSVILtSGTLs--Pi~~f~~~Lg~~f~~~ls~~HVI~~enl~~~i 146 (179)
..|+...++.+ .++.++...+++|||||||+ |..+|.+.||.+....++.++..+ +|...++
T Consensus 554 ~~l~~~pl~v~-~~~~~~~~~~~~i~tSATL~v~~~f~~~~~lGl~~~~~~~~~~~~~-~~~~~~i 617 (820)
T PRK07246 554 TYLNSASKAFT-HFSQLLPETCKTYFVSATLQISPRVSLADLLGFEEYLFHKIEKDKK-QDQLVVV 617 (820)
T ss_pred eEEEeeeCcHH-HHHHHHhcCCeEEEEecccccCCCCcHHHHcCCCccceecCCCChH-HccEEEe
Confidence 46888889998 45889999999999999996 766799999986544555555433 4444443
No 13
>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome.
Probab=93.04 E-value=0.29 Score=47.65 Aligned_cols=55 Identities=20% Similarity=0.215 Sum_probs=44.1
Q ss_pred eEEEEEecChHHHHHHHH-hhcceeEEeccccCC--------hHhHHHhhCCCCCeEEEeCCccC
Q psy876 83 YTLHFWCLNSGLVFSDIR-ESARSVILTSGTLAP--------VDSFQSELGTQFPIKLEANHVID 138 (179)
Q Consensus 83 ~~L~~~cLdPs~~f~~I~-~~arSVILtSGTLsP--------i~~f~~~Lg~~f~~~ls~~HVI~ 138 (179)
+.|....+|.+..|+.++ +..+++||||+||+- +++|+..||++.. .+.-+..++
T Consensus 350 ~~L~~~Pl~va~~l~~~~~~~~~~~I~TSATL~v~~~~~~~~F~~f~~~lGL~~~-~l~~~SPFd 413 (636)
T TIGR03117 350 PSLIVGREDLGKVMGGLWKDVTHGAIIVSATLYLPDRFGQMSCDYLKRVLSLPLS-RLDTPSPIV 413 (636)
T ss_pred eEEEEecccHHHHHHHHHhcCCCeEEEEccccccCCcCCCcCcHHHHHhcCCCcc-ceeCCCCCC
Confidence 478888899999999887 577899999999998 7899999998543 444444445
No 14
>KOG1133|consensus
Probab=92.10 E-value=0.081 Score=52.17 Aligned_cols=30 Identities=43% Similarity=0.766 Sum_probs=25.9
Q ss_pred eeccCCccccChhhhcc--ccCHHHHHHHhhh
Q psy876 3 ILSSRKHTCINDEVLKA--KENINDLCQELKE 32 (179)
Q Consensus 3 il~sr~~tci~~~~~~~--~~~~~~~c~~~~~ 32 (179)
-|+||+.-|||+.|.++ ..-+||.|.++-.
T Consensus 224 sL~SRk~LCiNe~V~Klk~~~~iNE~Cldlq~ 255 (821)
T KOG1133|consen 224 SLGSRKNLCINEDVKKLKSVDAINERCLDLQK 255 (821)
T ss_pred eecchhhcccCHHhccccchhHHHHHHHHHHh
Confidence 48999999999999994 3469999999865
No 15
>smart00488 DEXDc2 DEAD-like helicases superfamily.
Probab=91.91 E-value=0.11 Score=45.30 Aligned_cols=44 Identities=27% Similarity=0.500 Sum_probs=31.2
Q ss_pred ceeccCCccccChhhhc--cccCHH-HHHHHhhh----------ccCccceEeccCC
Q psy876 2 TILSSRKHTCINDEVLK--AKENIN-DLCQELKE----------TEGESNRWYRKDR 45 (179)
Q Consensus 2 til~sr~~tci~~~~~~--~~~~~~-~~c~~~~~----------~~~~~c~~~~~~~ 45 (179)
++|.||+|.|||+.+.+ ...+.+ +.|.++.. .+..+|.||.+..
T Consensus 116 ~~l~sR~~lCin~~v~~~~~~~~~~~~~C~~l~~~~~~~~~~~~~~~~~c~~~~~~~ 172 (289)
T smart00488 116 LSLTSRKNLCLNPEVRTLKQNGLVVDEVCRSLTASKARKYRYENPKVERCPFYENTE 172 (289)
T ss_pred eEeechhhcCCChHHhhcccccchHHHHHHHHHhhccccccccccCCCCCCccchhh
Confidence 57999999999999974 122234 78998754 2345788887653
No 16
>smart00489 DEXDc3 DEAD-like helicases superfamily.
Probab=91.91 E-value=0.11 Score=45.30 Aligned_cols=44 Identities=27% Similarity=0.500 Sum_probs=31.2
Q ss_pred ceeccCCccccChhhhc--cccCHH-HHHHHhhh----------ccCccceEeccCC
Q psy876 2 TILSSRKHTCINDEVLK--AKENIN-DLCQELKE----------TEGESNRWYRKDR 45 (179)
Q Consensus 2 til~sr~~tci~~~~~~--~~~~~~-~~c~~~~~----------~~~~~c~~~~~~~ 45 (179)
++|.||+|.|||+.+.+ ...+.+ +.|.++.. .+..+|.||.+..
T Consensus 116 ~~l~sR~~lCin~~v~~~~~~~~~~~~~C~~l~~~~~~~~~~~~~~~~~c~~~~~~~ 172 (289)
T smart00489 116 LSLTSRKNLCLNPEVRTLKQNGLVVDEVCRSLTASKARKYRYENPKVERCPFYENTE 172 (289)
T ss_pred eEeechhhcCCChHHhhcccccchHHHHHHHHHhhccccccccccCCCCCCccchhh
Confidence 57999999999999974 122234 78998754 2345788887653
No 17
>KOG1131|consensus
Probab=82.28 E-value=0.67 Score=45.00 Aligned_cols=51 Identities=31% Similarity=0.463 Sum_probs=39.1
Q ss_pred eccCCccccChhhhccccC---HHHHHHHhhh----------ccCccceEeccCCCCCCCCCccc
Q psy876 4 LSSRKHTCINDEVLKAKEN---INDLCQELKE----------TEGESNRWYRKDRTPMRGIEPVV 55 (179)
Q Consensus 4 l~sr~~tci~~~~~~~~~~---~~~~c~~~~~----------~~~~~c~~~~~~~~~~~~~~~~~ 55 (179)
|+||.--||||.|++ ..+ .+..|..+.- .+...|.||.|=..+.+...+-+
T Consensus 109 lssRKNlCi~~~v~~-~r~g~~VD~~Cr~ltas~vr~~~~ed~~~~~C~f~en~~~~~~~lp~gv 172 (755)
T KOG1131|consen 109 LSSRKNLCIHPEVLK-ERNGNVVDAACRKLTASYVRAKLAEDPNVELCDFFENLEDKESLLPVGV 172 (755)
T ss_pred eccccccccCHHHHH-HhcCCchhHHHHHHhHHHHHHHHhcCCCcchhhHHhhhhcccccCCccc
Confidence 899999999999998 335 7789988743 46678999999888655544333
No 18
>PHA02707 hypothetical protein; Provisional
Probab=30.82 E-value=42 Score=20.87 Aligned_cols=22 Identities=23% Similarity=0.455 Sum_probs=19.7
Q ss_pred EecChHHHHHHHHhhcceeEEe
Q psy876 88 WCLNSGLVFSDIRESARSVILT 109 (179)
Q Consensus 88 ~cLdPs~~f~~I~~~arSVILt 109 (179)
.||.|-..+..++-...|+||-
T Consensus 6 lcl~pvfil~klv~rtqsiilh 27 (37)
T PHA02707 6 LCLCPVFILDKLVFRTQSIILH 27 (37)
T ss_pred eehhhHHHHHHHHHhhhheeee
Confidence 6899999999998889999985
No 19
>PF08785 Ku_PK_bind: Ku C terminal domain like; InterPro: IPR014893 The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C-terminal of Ku which binds to DNA-PKcs []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 1RW2_A 1Q2Z_A 3ISM_C.
Probab=26.31 E-value=33 Score=26.11 Aligned_cols=15 Identities=33% Similarity=0.740 Sum_probs=13.3
Q ss_pred cccCChHhHHHhhCC
Q psy876 111 GTLAPVDSFQSELGT 125 (179)
Q Consensus 111 GTLsPi~~f~~~Lg~ 125 (179)
||+.|+.+|..+|.-
T Consensus 1 Gsv~Pv~DFk~ll~~ 15 (120)
T PF08785_consen 1 GSVNPVQDFKALLAQ 15 (120)
T ss_dssp SSSSCCHHHHHHCCC
T ss_pred CCCChHHHHHHHHHc
Confidence 899999999998854
Done!