Query 029480
Match_columns 192
No_of_seqs 110 out of 243
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 13:35:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029480.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029480hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1106 Uncharacterized conser 100.0 5.3E-48 1.2E-52 301.5 9.9 167 7-175 10-177 (177)
2 COG5138 Uncharacterized conser 100.0 1E-43 2.3E-48 268.1 7.2 164 9-173 1-166 (168)
3 PF05916 Sld5: GINS complex pr 99.8 4.2E-20 9.1E-25 134.3 4.0 102 52-155 1-108 (108)
4 KOG4071 Uncharacterized conser 99.2 9.9E-12 2.1E-16 98.2 5.3 142 16-159 9-156 (187)
5 PTZ00362 hypothetical protein; 99.2 4.4E-11 9.5E-16 106.2 6.0 147 19-165 282-451 (479)
6 COG5093 Uncharacterized conser 98.0 6E-06 1.3E-10 64.0 3.6 138 17-156 18-162 (185)
7 COG1711 DNA replication initia 95.4 0.014 3E-07 48.0 3.2 54 115-171 61-114 (223)
8 PF09652 Cas_VVA1548: Putative 57.0 6.8 0.00015 28.1 1.5 34 44-77 30-69 (93)
9 cd04487 RecJ_OBF2_like RecJ_OB 31.2 31 0.00067 23.2 1.4 34 10-53 17-51 (73)
10 PF06825 HSBP1: Heat shock fac 31.0 1.5E+02 0.0032 19.0 4.7 44 115-162 6-49 (54)
11 PF10441 Urb2: Urb2/Npa2 famil 29.9 1.3E+02 0.0029 24.3 5.3 54 116-172 169-222 (223)
12 COG1054 Predicted sulfurtransf 26.4 47 0.001 28.9 2.0 76 38-113 67-152 (308)
13 PF02773 S-AdoMet_synt_C: S-ad 23.5 59 0.0013 25.0 1.9 66 53-135 45-113 (138)
14 COG1939 Ribonuclease III famil 22.8 1.6E+02 0.0034 22.5 4.0 22 144-165 63-84 (132)
15 PF01788 PsbJ: PsbJ; InterPro 22.1 38 0.00082 20.4 0.5 15 50-64 4-18 (40)
16 COG5140 UFD1 Ubiquitin fusion- 21.2 84 0.0018 26.8 2.5 42 23-64 64-106 (331)
17 TIGR01837 PHA_granule_1 poly(h 20.7 1.9E+02 0.004 21.3 4.1 41 119-159 74-114 (118)
No 1
>KOG1106 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5.3e-48 Score=301.52 Aligned_cols=167 Identities=37% Similarity=0.665 Sum_probs=157.8
Q ss_pred CCCcccccchhhhccceeceEEEeccCcccc-CCCCcccccccCCcccchhhhhhhhhhhhheeccCCcccchhhHHHhh
Q 029480 7 RNGKYFDIDEILIEEELVPVVFHKSANGVKV-DPSAEKDCVDEGAKVELPFWLSQELYLRQAVSINVPACFNQKTRREIQ 85 (192)
Q Consensus 7 ~~~~YydiddILa~~ekVpc~f~~~~~~lG~-d~~~~~~~l~~g~kveLPlWLA~~L~~~~~v~i~~P~~~~~~~~~~L~ 85 (192)
..+.|||||||||++++|||+|++++|++|| ++-+ .++++|++||||+|||..|+.+++|+|.+|++|++.++++++
T Consensus 10 ~e~~~~~lddIla~~~ki~ct~e~~i~~lgfl~~~~--~~~~~g~kVelP~wl~~~L~~~~~~si~lP~~fs~~~rn~i~ 87 (177)
T KOG1106|consen 10 EEENFLDLDDILASGEKIPCTFETKIPNLGFLQAPP--RELPAGRKVELPYWLAEELAINQFVSILLPDIFSEKVRNVIK 87 (177)
T ss_pred hhhccccHHHHHhcCCcccceeeecCCCCCccCCCc--ccCCCCCcccchHHHHHHHhhccceeecCchHHHHHHHHHHh
Confidence 3567889999999999999999999999998 5322 579999999999999999999999999999999999999999
Q ss_pred hccccccccccCcceeecCceecccccchhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHhhhhhhhhHHHHHHHHH
Q 029480 86 ADAANVDLRSRCPYFYEFGCKIAPIVGDRTIGKMLLSTFQMRYKDILTKAHTAAYAVASKFLAVLTKEETNLYEAAQSSM 165 (192)
Q Consensus 86 Adp~~V~L~~~~~~fY~~g~~l~~l~~d~~l~~~L~~~f~~R~~~I~~~a~~~~~~~~~~~~~~Lt~~Er~lf~~g~~s~ 165 (192)
|||+.||||+.|||||++|++|+.+..+..+..++.++|.+|+++|++.+.+....+++++..+||.+|+.||.+|+++.
T Consensus 88 Adp~~vdL~s~~phFY~fg~kl~~l~s~~~l~~~~se~l~~R~~~~l~~~~s~~~~~~s~~~~rLD~~E~~l~~~~~r~~ 167 (177)
T KOG1106|consen 88 ADPNKVDLRSLCPHFYEFGMKLLPLDSGENLGIILSETLRSRVREILDSSLSATNTQTSKFVERLDEMERKLFEAGHRSL 167 (177)
T ss_pred cCcceeeccccccHHHHHHHHHhhcccCcchhHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999997777889999999999999999999999
Q ss_pred HHhhhhhhcC
Q 029480 166 AAFKKWRIGG 175 (192)
Q Consensus 166 ~~~~~W~~~~ 175 (192)
.+|++|+.++
T Consensus 168 ~d~~~Wl~~~ 177 (177)
T KOG1106|consen 168 NDFKCWLKGT 177 (177)
T ss_pred HHHHHHHhcC
Confidence 9999999864
No 2
>COG5138 Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1e-43 Score=268.07 Aligned_cols=164 Identities=26% Similarity=0.413 Sum_probs=153.1
Q ss_pred CcccccchhhhccceeceEEEeccCccccCCCCcccccccCCcccchhhhhhhhhhhhheeccCCcccchhhHHHhhhcc
Q 029480 9 GKYFDIDEILIEEELVPVVFHKSANGVKVDPSAEKDCVDEGAKVELPFWLSQELYLRQAVSINVPACFNQKTRREIQADA 88 (192)
Q Consensus 9 ~~YydiddILa~~ekVpc~f~~~~~~lG~d~~~~~~~l~~g~kveLPlWLA~~L~~~~~v~i~~P~~~~~~~~~~L~Adp 88 (192)
|+||||||||+++++|||+|.+++||+||-+.. ...+++|+|||||+|||..|+.+.+|.+..|.+|++.++|+++|+|
T Consensus 1 M~YYdiDdiL~~~s~ipctf~~~IpglG~l~~~-gr~~p~n~kvelP~wLa~~Lainsfv~~l~p~~fs~~v~naika~P 79 (168)
T COG5138 1 MEYYDIDDILLGESRIPCTFKHKIPGLGFLGPR-GRILPENRKVELPYWLASFLAINSFVCELGPGFFSESVLNAIKAKP 79 (168)
T ss_pred CCccCHHHHhcCCCccceeeEeecCCcccCCCC-CcccCCCCeeechHHHHHHHHHhhhHHhcCcchHHHHHHHHHhcCC
Confidence 799999999999999999999999999983222 2589999999999999999999999999999999999999999999
Q ss_pred ccccccccCcceeecCceecccccchhHHHHHHHHHHHHHHHHHHhhhhhhh--hhhhhHHHhhhhhhhhHHHHHHHHHH
Q 029480 89 ANVDLRSRCPYFYEFGCKIAPIVGDRTIGKMLLSTFQMRYKDILTKAHTAAY--AVASKFLAVLTKEETNLYEAAQSSMA 166 (192)
Q Consensus 89 ~~V~L~~~~~~fY~~g~~l~~l~~d~~l~~~L~~~f~~R~~~I~~~a~~~~~--~~~~~~~~~Lt~~Er~lf~~g~~s~~ 166 (192)
.+||||+.|||||.++.+++.++++.+|.+.+.+++.+|...+.+.+.|..+ ..++.|+.+||..||.|+...|++.+
T Consensus 80 ~tvdlrsI~~hff~lA~K~~mL~se~sLv~~~~e~l~~Ra~~~~~ASLn~~g~~s~nSqfv~~Ld~~Ek~i~~~Sh~~~~ 159 (168)
T COG5138 80 STVDLRSICPHFFYLAEKYAMLLSEGSLVAGLPEFLYERAGDYSSASLNLKGTFSENSQFVWRLDMVEKSIVVGSHRRFQ 159 (168)
T ss_pred ceeehhhcchHHHHHHHHHHHHhcCchHhhhhHHHHHHHHHhhhccccCcccccccccHHHHHHHHHHHHHHHHhHHHHH
Confidence 9999999999999999999999999999999999999999999997766643 35677999999999999999999999
Q ss_pred Hhhhhhh
Q 029480 167 AFKKWRI 173 (192)
Q Consensus 167 ~~~~W~~ 173 (192)
.+.+|+.
T Consensus 160 ~~~~w~~ 166 (168)
T COG5138 160 RFCAWLV 166 (168)
T ss_pred HHHHHHh
Confidence 9999985
No 3
>PF05916 Sld5: GINS complex protein; InterPro: IPR021151 DNA replication in eukaryotes results from a highly coordinated interaction between proteins, often as part of protein complexes, and the DNA template. One of the key early steps leading to DNA replication is formation of the pre- replication complex, or pre-RC. The pre-RC is formed by the sequential binding of the origin recognition complex (ORC), Cdc6 and Cdt1 proteins, and the MCM complex. Activation of the pre-RC into the initiation complex (IC) is achieved via the action of S-phase kinases, eventually leading to the loading of the replication machinery. Recently, a novel replication complex, GINS (for Go, Ichi, Nii, and San; five, one, two, and three in Japanese), has been identified [, ]. The precise function of GINS is not known. However, genetic and two-hybrid interactions indicate that it mediates the loading of the enzymatic replication machinery at a step after the action of the S-phase kinases []. Furthermore, GINS may be a part of the replication machinery itself, since it is found associated with replicating DNA [, ]. Electron microscopy of GINS shows that it forms a ring-like structure [], reminiscent of the structure of PCNA [], the DNA polymerase delta replication clamp.This observation, coupled with the observed interactions for GINS, indicates that the complex may represent the replication clamp for DNA polymerase epsilon []. The GINS complex is essential for initiation of DNA replication in Xenopus egg extracts []. This 100 kDa stable complex includes Sld5, Psf1, Psf2, and Psf3. Homologues of these components are found also in other eukaryotes. ; PDB: 2EHO_L 2E9X_G 2Q9Q_H 3ANW_B.
Probab=99.79 E-value=4.2e-20 Score=134.33 Aligned_cols=102 Identities=34% Similarity=0.568 Sum_probs=94.4
Q ss_pred ccchhhhhhhhhhhhheeccCCcccchhhHHHhhhcccc----ccccccCcceeecCceecccccchhHHHHHHHHHHHH
Q 029480 52 VELPFWLSQELYLRQAVSINVPACFNQKTRREIQADAAN----VDLRSRCPYFYEFGCKIAPIVGDRTIGKMLLSTFQMR 127 (192)
Q Consensus 52 veLPlWLA~~L~~~~~v~i~~P~~~~~~~~~~L~Adp~~----V~L~~~~~~fY~~g~~l~~l~~d~~l~~~L~~~f~~R 127 (192)
|+||+|+|..|..+++|+|..|++|+.++++++.|++.. ++|..+++|||++|..++.++ ..+..+|.+++..|
T Consensus 1 v~lP~w~a~~L~~~~~~~i~~p~~~~~~~~~~l~~e~~~~~~~~~l~~l~~~f~~~~~~l~~~~--~~ik~~l~~~~~~R 78 (108)
T PF05916_consen 1 VELPLWLAKELKKRNLVEIQPPDWFSIEYLNALEAEEKNNSNKVDLSKLPPYFYELGEMLLELL--ERIKRLLRDYLRIR 78 (108)
T ss_dssp EEEEHHHHHHHHHTTSEEEE-TCCHCHHHHHHHHHHHCCCS-HCSCCTSSTTHHHHHHHHHHHH--HHHHHHHHHHHHHH
T ss_pred CcCCcchHHHHHHcCCeeecCcHhhhHHHHHHHHhhhccccchhhhhcCChHHHHHHHHHHHHH--HHHHHHHHHHHHHH
Confidence 689999999999999999999999999999999999988 899999999999999999999 78999999999999
Q ss_pred HHHHHHhhhhh--hhhhhhhHHHhhhhhhh
Q 029480 128 YKDILTKAHTA--AYAVASKFLAVLTKEET 155 (192)
Q Consensus 128 ~~~I~~~a~~~--~~~~~~~~~~~Lt~~Er 155 (192)
+.+|.+.+.+. .+.+.+.+..+||++||
T Consensus 79 ~~KI~~~~~~~~~~~~~~~~~~~~Ls~~Er 108 (108)
T PF05916_consen 79 LKKILSLAWHLLSGNDDPQEILENLSEEER 108 (108)
T ss_dssp HHHHHHHHCHHHHHCTTCHHHHTTS-HHHH
T ss_pred HHHHHHHHHHhccccCCcHHHHccCCHhhC
Confidence 99999999999 55567889999999997
No 4
>KOG4071 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.24 E-value=9.9e-12 Score=98.21 Aligned_cols=142 Identities=18% Similarity=0.242 Sum_probs=116.9
Q ss_pred hhhhccceeceEEEeccCccccCCCCcccccccCCcccchhhhhhhhhhhhheeccCCcccchhhHHHhhhc-ccccccc
Q 029480 16 EILIEEELVPVVFHKSANGVKVDPSAEKDCVDEGAKVELPFWLSQELYLRQAVSINVPACFNQKTRREIQAD-AANVDLR 94 (192)
Q Consensus 16 dILa~~ekVpc~f~~~~~~lG~d~~~~~~~l~~g~kveLPlWLA~~L~~~~~v~i~~P~~~~~~~~~~L~Ad-p~~V~L~ 94 (192)
+++|+++.|.+.+++....+-+..+.. .++.+|.++.+|+|+|..|.+++.|+|..|.|++...+..+... -..--++
T Consensus 9 efia~~eli~I~P~~S~~~l~li~~d~-gp~~p~~~~rVpLWlAllLKkq~kc~Iv~P~wm~~~~L~~i~d~E~e~~tfs 87 (187)
T KOG4071|consen 9 EFIAENELIEIIPNISMDQLHLISGDI-GPFNPGVPCRVPLWLALLLKKQNKCRIVPPEWMDVDELEKIRDVEKESETFS 87 (187)
T ss_pred HHHhcccceeeccCCcchhhhhhcCCC-cccCCCCcceehHHHHHHHhhccCceEeCcccccHHHHHHHHHHhhcccccc
Confidence 589999999999999999888633332 47999999999999999999999999999999998877666643 2233556
Q ss_pred ccCcceeecCceecccccc-----hhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHhhhhhhhhHHH
Q 029480 95 SRCPYFYEFGCKIAPIVGD-----RTIGKMLLSTFQMRYKDILTKAHTAAYAVASKFLAVLTKEETNLYE 159 (192)
Q Consensus 95 ~~~~~fY~~g~~l~~l~~d-----~~l~~~L~~~f~~R~~~I~~~a~~~~~~~~~~~~~~Lt~~Er~lf~ 159 (192)
.+.++|++++..|.++..| +++..++.+++..|..|+...+...... .+.-+++||-.|..--+
T Consensus 88 ~lp~~~~ela~lL~n~a~Ddi~~~eeiR~lV~DI~d~R~aKlr~s~~~f~~~-~hakldNltLmEiN~~r 156 (187)
T KOG4071|consen 88 KLPFYYFELATLLLNFARDDIPDIEEIRTLVKDIRDIRLAKLRTSLDSFNRQ-AHAKLDNLTLMEINEIR 156 (187)
T ss_pred cCChHHHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHHHHhHHHHhhH-hhcCcccceeeeeccch
Confidence 6678899999999998654 5899999999999999999998888653 45678889988876433
No 5
>PTZ00362 hypothetical protein; Provisional
Probab=99.16 E-value=4.4e-11 Score=106.21 Aligned_cols=147 Identities=18% Similarity=0.205 Sum_probs=114.3
Q ss_pred hccceeceEEEeccCcccc--CCCCcccccccCCcccchhhhhhhhhhhhheeccCCcccchhhHHHhhhcc-cc-cccc
Q 029480 19 IEEELVPVVFHKSANGVKV--DPSAEKDCVDEGAKVELPFWLSQELYLRQAVSINVPACFNQKTRREIQADA-AN-VDLR 94 (192)
Q Consensus 19 a~~ekVpc~f~~~~~~lG~--d~~~~~~~l~~g~kveLPlWLA~~L~~~~~v~i~~P~~~~~~~~~~L~Adp-~~-V~L~ 94 (192)
|-.|.|-|+-..|+|++.+ -.|-.-.++++|.++++|+|||..|.+++.|+|.+|.|++.+....++... +. -.+.
T Consensus 282 al~eLvVvKalvDip~~~L~lI~G~digpfkag~~~~VPLWLAi~LKq~~KC~IvpP~Wm~ie~Lk~I~eeE~~~~~~Ft 361 (479)
T PTZ00362 282 ALDELVVVKALVDIPYIDLSEIEGFDFKEMKSGERQWLPIYIAKELSHFGLVTVEFPFWFYIKNLKNIYEREFEDQNELT 361 (479)
T ss_pred HhcceEEEEEecCCCCCcceeeeccccCCcCCCCeeEEeeeehhhhcccCceEEeCcccccHHHHHHHHHHHhhCccccc
Confidence 4578999999999999875 233233589999999999999999999999999999999988876666443 33 2333
Q ss_pred cc-CcceeecCceeccc-------cc-c----------hhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHhhhhhhh
Q 029480 95 SR-CPYFYEFGCKIAPI-------VG-D----------RTIGKMLLSTFQMRYKDILTKAHTAAYAVASKFLAVLTKEET 155 (192)
Q Consensus 95 ~~-~~~fY~~g~~l~~l-------~~-d----------~~l~~~L~~~f~~R~~~I~~~a~~~~~~~~~~~~~~Lt~~Er 155 (192)
.+ +|||++++..+.+. .. | .+++..+.++...|..+|.....+.......--+..|+.+|.
T Consensus 362 ~LP~p~y~EIa~lLl~~~~F~~~~a~edi~~~d~~~~~~kVR~LIeDIrd~R~~KIr~~Le~~~~~ss~i~LdNLslmEi 441 (479)
T PTZ00362 362 DLPSPYFFEISSMFLENNIFKKVTPIETIGQRTVYKYISKVAGLVEDIRYKRLKKIMNHLENQDVHSSIIYIDNLQISET 441 (479)
T ss_pred cCCchhHHHHHHHHHhcccccccCChhhcccccccccHHHHHHHHHHHHHHHHHHHHHHHHhccccccEEEECCccHHHH
Confidence 33 47999999988876 21 1 479999999999999999998877643223446889999999
Q ss_pred hHHHHHHHHH
Q 029480 156 NLYEAAQSSM 165 (192)
Q Consensus 156 ~lf~~g~~s~ 165 (192)
.+-+....+.
T Consensus 442 ~~Vn~~Ls~f 451 (479)
T PTZ00362 442 YCVNQLLSVF 451 (479)
T ss_pred HHHHHHHHHH
Confidence 8887754443
No 6
>COG5093 Uncharacterized conserved protein [Function unknown]
Probab=97.99 E-value=6e-06 Score=64.02 Aligned_cols=138 Identities=14% Similarity=0.148 Sum_probs=94.1
Q ss_pred hhhccceeceEEEeccCccccCCCCcccccccCCcccchhhhhhhhhhhhheeccCCcccchhhHHH-hhhcccc-cccc
Q 029480 17 ILIEEELVPVVFHKSANGVKVDPSAEKDCVDEGAKVELPFWLSQELYLRQAVSINVPACFNQKTRRE-IQADAAN-VDLR 94 (192)
Q Consensus 17 ILa~~ekVpc~f~~~~~~lG~d~~~~~~~l~~g~kveLPlWLA~~L~~~~~v~i~~P~~~~~~~~~~-L~Adp~~-V~L~ 94 (192)
++|.+|.|...+....+.+-+-....-+++.+-.+..+|||+|.-|.+++.|+|..|.|+...-... +.-+-.. -..+
T Consensus 18 fia~nE~i~I~P~~t~~qlrL~~~~t~p~m~p~~~~rvpLw~ALlLKkqn~c~Iv~P~wl~~~~L~~~i~~e~~~~d~fS 97 (185)
T COG5093 18 FIAYNELIEIEPMTTIPQLRLLERATYPPMMPLDIARVPLWAALLLKKQNMCKIVLPSWLQLESLKMSIDVEIEKADEFS 97 (185)
T ss_pred HHhcccceeeecccccchhhhhhhhcCCCCCCchhhhhHHHHHHHHHhcccccccChhHhhHHHHHhhhhHHHhcccccc
Confidence 6899999999999999988763333345788888999999999999999999999999998664333 3333222 2234
Q ss_pred ccCcceeecCceecccccc-----hhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHhhhhhhhh
Q 029480 95 SRCPYFYEFGCKIAPIVGD-----RTIGKMLLSTFQMRYKDILTKAHTAAYAVASKFLAVLTKEETN 156 (192)
Q Consensus 95 ~~~~~fY~~g~~l~~l~~d-----~~l~~~L~~~f~~R~~~I~~~a~~~~~~~~~~~~~~Lt~~Er~ 156 (192)
.+.+||+.++..|.+.--| +++..++.++-..|..+.+.--- ..+ ..+--++.||..|..
T Consensus 98 elp~~wl~lA~~Lln~~~ddvediee~r~iv~dirEiRq~K~lkGlk-~ln-e~~L~ldNl~l~EiN 162 (185)
T COG5093 98 ELPPYWLPLATELLNENCDDVEDIEESRMIVEDIREIRQAKTLKGLK-CLN-EKALNLDNLTLFEIN 162 (185)
T ss_pred cCCchHHHHHHHHHHhccchHhHHHHHHHHHHHHHHHHHHHHHhhHh-hhh-hhhcCccccchhhhh
Confidence 4679999999988876543 45666666666666655443211 111 112235666666643
No 7
>COG1711 DNA replication initiation complex subunit, GINS family [Replication, recombination, and repair]
Probab=95.44 E-value=0.014 Score=48.04 Aligned_cols=54 Identities=28% Similarity=0.262 Sum_probs=44.5
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHhhhhhhhhHHHHHHHHHHHhhhh
Q 029480 115 TIGKMLLSTFQMRYKDILTKAHTAAYAVASKFLAVLTKEETNLYEAAQSSMAAFKKW 171 (192)
Q Consensus 115 ~l~~~L~~~f~~R~~~I~~~a~~~~~~~~~~~~~~Lt~~Er~lf~~g~~s~~~~~~W 171 (192)
.+.+.....|.+|+.+|+..|.-.+.+ +.+.+||.+|+.||...+....+...-
T Consensus 61 t~~~~~r~ifqrR~~Kiv~~A~~~~~~---~~~~~Lt~eEk~ly~~l~~~I~~e~~~ 114 (223)
T COG1711 61 TAKSDARSIFQRRYGKIVSRAIYDVPG---ETISNLTPEEKELYEDLVNFIEDERIS 114 (223)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccc---cchhcCCHHHHHHHHHHHHHHhhchhh
Confidence 566777788999999999999887653 238999999999999999887766543
No 8
>PF09652 Cas_VVA1548: Putative CRISPR-associated protein (Cas_VVA1548); InterPro: IPR013443 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPR repeats. In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas genes.
Probab=57.01 E-value=6.8 Score=28.08 Aligned_cols=34 Identities=29% Similarity=0.446 Sum_probs=27.0
Q ss_pred cccccCCcc--cchhhhhhhhhhhhh----eeccCCcccc
Q 029480 44 DCVDEGAKV--ELPFWLSQELYLRQA----VSINVPACFN 77 (192)
Q Consensus 44 ~~l~~g~kv--eLPlWLA~~L~~~~~----v~i~~P~~~~ 77 (192)
.++.+|.+| .||.+||..+..+|. +++++|....
T Consensus 30 ~~i~~GD~ViGtLPvhLaA~vc~kGa~y~~L~l~lp~e~R 69 (93)
T PF09652_consen 30 ADIQPGDVVIGTLPVHLAAEVCEKGARYYHLSLDLPAEQR 69 (93)
T ss_pred HHccCCCEEEEeCcHHHHHHHHhCCcEEEEEEccCChHHc
Confidence 468899887 699999999998877 6777665433
No 9
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=31.24 E-value=31 Score=23.23 Aligned_cols=34 Identities=18% Similarity=0.132 Sum_probs=20.8
Q ss_pred cccccchhhhccceeceEEEec-cCccccCCCCcccccccCCccc
Q 029480 10 KYFDIDEILIEEELVPVVFHKS-ANGVKVDPSAEKDCVDEGAKVE 53 (192)
Q Consensus 10 ~YydiddILa~~ekVpc~f~~~-~~~lG~d~~~~~~~l~~g~kve 53 (192)
=||+|.| +.-.|+|.+-.. ..++.+ .+++|.+|+
T Consensus 17 vyfsLkD---~~a~i~cv~f~~~~~~~~~-------~l~~Gd~V~ 51 (73)
T cd04487 17 TIFTLRD---ETGTVWAAAFEEAGVRAYP-------EVEVGDIVR 51 (73)
T ss_pred EEEEEEc---CCEEEEEEEEchhccCCcC-------CCCCCCEEE
Confidence 4999988 556799976533 234444 355555544
No 10
>PF06825 HSBP1: Heat shock factor binding protein 1; InterPro: IPR009643 Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response [].; PDB: 3CI9_A.
Probab=30.98 E-value=1.5e+02 Score=19.04 Aligned_cols=44 Identities=9% Similarity=0.153 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHhhhhhhhhHHHHHH
Q 029480 115 TIGKMLLSTFQMRYKDILTKAHTAAYAVASKFLAVLTKEETNLYEAAQ 162 (192)
Q Consensus 115 ~l~~~L~~~f~~R~~~I~~~a~~~~~~~~~~~~~~Lt~~Er~lf~~g~ 162 (192)
...+.|++-+..||..+-+...... .+.-.++|..|+.|-....
T Consensus 6 ~~v~~lL~qmq~kFq~mS~~I~~ri----DeM~~RIDdLE~si~dl~~ 49 (54)
T PF06825_consen 6 AFVQNLLQQMQDKFQTMSDQILGRI----DEMSSRIDDLEKSIADLMT 49 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHCCHHHH-----
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH----HHHHhhHHHHHHHHHHHHH
Confidence 3566777888889888877766654 3467789999988765443
No 11
>PF10441 Urb2: Urb2/Npa2 family; InterPro: IPR018849 This entry represents a conserved domain found towards the C terminus of proteins involved in ribosome biogenesis, such as the Urb2 protein from yeast [].
Probab=29.92 E-value=1.3e+02 Score=24.34 Aligned_cols=54 Identities=9% Similarity=0.184 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhhhhhHHHhhhhhhhhHHHHHHHHHHHhhhhh
Q 029480 116 IGKMLLSTFQMRYKDILTKAHTAAYAVASKFLAVLTKEETNLYEAAQSSMAAFKKWR 172 (192)
Q Consensus 116 l~~~L~~~f~~R~~~I~~~a~~~~~~~~~~~~~~Lt~~Er~lf~~g~~s~~~~~~W~ 172 (192)
+..-+++.+..=+-.|+|..... +..-+...||...|.+|+...+..+.|-+|.
T Consensus 169 l~~~vr~~L~pGiy~l~d~~s~~---e~~~l~a~Ld~~gr~~fk~Ly~dY~k~~K~~ 222 (223)
T PF10441_consen 169 LPPEVREALMPGIYALFDVCSQH---ELQQLNASLDASGRAVFKSLYKDYKKFGKWK 222 (223)
T ss_pred CCHHHHHHHHHHHHHHHHhCCHH---HHHHHHHHcChHHHHHHHHHHHHHHHhCCCC
Confidence 44444444444444555554322 3456788999999999999999999999996
No 12
>COG1054 Predicted sulfurtransferase [General function prediction only]
Probab=26.39 E-value=47 Score=28.89 Aligned_cols=76 Identities=21% Similarity=0.275 Sum_probs=57.3
Q ss_pred CCCCcccccccCCcccchhhhhhhhhhhhheeccCCc----------ccchhhHHHhhhccccccccccCcceeecCcee
Q 029480 38 DPSAEKDCVDEGAKVELPFWLSQELYLRQAVSINVPA----------CFNQKTRREIQADAANVDLRSRCPYFYEFGCKI 107 (192)
Q Consensus 38 d~~~~~~~l~~g~kveLPlWLA~~L~~~~~v~i~~P~----------~~~~~~~~~L~Adp~~V~L~~~~~~fY~~g~~l 107 (192)
+|+-.+-.++....-+-|||-.+.=.++.+|+.-+|+ +.+++..+.+..||.+|=+-..|.|=|.+|.-=
T Consensus 67 ~~~f~~l~~K~s~~~~~pF~r~kVk~kkEIV~lg~~ddv~p~~~vG~yl~p~~wn~~l~D~~~vviDtRN~YE~~iG~F~ 146 (308)
T COG1054 67 DPGFADLRFKISEADEKPFWRLKVKLKKEIVALGVEDDVDPLENVGTYLSPKDWNELLSDPDVVVIDTRNDYEVAIGHFE 146 (308)
T ss_pred CcccccceeeeccccCCCcceEEEeehhhheecCCCCCcCccccccCccCHHHHHHHhcCCCeEEEEcCcceeEeeeeec
Confidence 4554445566666677899988777777888776665 456677999999999999999999999998755
Q ss_pred cccccc
Q 029480 108 APIVGD 113 (192)
Q Consensus 108 ~~l~~d 113 (192)
....++
T Consensus 147 gAv~p~ 152 (308)
T COG1054 147 GAVEPD 152 (308)
T ss_pred CccCCC
Confidence 555444
No 13
>PF02773 S-AdoMet_synt_C: S-adenosylmethionine synthetase, C-terminal domain; InterPro: IPR022630 The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. This entry represents the C-terminal domain of S=adenosylmethionine synthetase and is found in association with PF00438 from PFAM and PF02772 from PFAM. S-adenosylmethionine synthetase (MAT, 2.5.1.6 from EC) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP []. AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis. In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family. The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex, and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance []; GO: 0004478 methionine adenosyltransferase activity; PDB: 3IML_B 1QM4_B 1O9T_B 1O93_A 1O92_B 1O90_A 1FUG_A 1RG9_D 1XRA_A 1P7L_C ....
Probab=23.47 E-value=59 Score=25.01 Aligned_cols=66 Identities=11% Similarity=0.280 Sum_probs=40.0
Q ss_pred cchhhhhhhhhhhhhe---eccCCcccchhhHHHhhhccccccccccCcceeecCceecccccchhHHHHHHHHHHHHHH
Q 029480 53 ELPFWLSQELYLRQAV---SINVPACFNQKTRREIQADAANVDLRSRCPYFYEFGCKIAPIVGDRTIGKMLLSTFQMRYK 129 (192)
Q Consensus 53 eLPlWLA~~L~~~~~v---~i~~P~~~~~~~~~~L~Adp~~V~L~~~~~~fY~~g~~l~~l~~d~~l~~~L~~~f~~R~~ 129 (192)
-+-.|+|+.+...+.+ +|++ .|. +=.+.|.+|...+ |.-+. ..|++|.+++.+.|.-|-.
T Consensus 45 Y~aR~iAKniVaagla~~c~vql--sYa-----IGv~~P~si~v~t-----fgT~~-----~~d~~i~~~I~~~Fdl~P~ 107 (138)
T PF02773_consen 45 YMARYIAKNIVAAGLAKRCEVQL--SYA-----IGVAEPVSIYVDT-----FGTGK-----ISDEEILEIIKENFDLRPA 107 (138)
T ss_dssp HHHHHHHHHHHHTTSBSEEEEEE--EE------TT-SS-SEEEEEE-----TT-BS-----S-HHHHHHHHHHHS--SHH
T ss_pred HHHHHHHHHHHHccchHHHHhhc--eee-----eccccCcccEEEe-----CCCcc-----chHHHHHHHHHHHhCCcHH
Confidence 4567888888766653 4443 233 2246677777754 22222 4688999999999999999
Q ss_pred HHHHhh
Q 029480 130 DILTKA 135 (192)
Q Consensus 130 ~I~~~a 135 (192)
.|++.-
T Consensus 108 ~II~~L 113 (138)
T PF02773_consen 108 GIIKEL 113 (138)
T ss_dssp HHHHHC
T ss_pred HHHHHh
Confidence 998754
No 14
>COG1939 Ribonuclease III family protein [Replication, recombination, and repair]
Probab=22.78 E-value=1.6e+02 Score=22.49 Aligned_cols=22 Identities=23% Similarity=0.401 Sum_probs=18.8
Q ss_pred hhHHHhhhhhhhhHHHHHHHHH
Q 029480 144 SKFLAVLTKEETNLYEAAQSSM 165 (192)
Q Consensus 144 ~~~~~~Lt~~Er~lf~~g~~s~ 165 (192)
..+...||++|..+++-|+.+.
T Consensus 63 ~~~~~~Lte~E~~I~KRgRNak 84 (132)
T COG1939 63 KALLEFLTEEEEEIVKRGRNAK 84 (132)
T ss_pred HHHHHHhhHHHHHHHHHhcccc
Confidence 4577899999999999998874
No 15
>PF01788 PsbJ: PsbJ; InterPro: IPR002682 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. This family represents the low molecular weight transmembrane protein PsbJ found in PSII. PsbJ is one of the most hydrophobic proteins in the thylakoid membrane, and is located in a gene cluster with PsbE, PsbF and PsbL (PsbEFJL). Both PsbJ and PsbL (IPR003372 from INTERPRO) are essential for proper assembly of the OEC. Mutations in PsbJ cause the light-harvesting antenna to remain detached from the PSII dimers []. In addition, both PsbJ and PsbL are involved in the unidirectional flow of electrons, where PsbJ regulates the forward electron flow from D2 (Qa) to the plastoquinone pool, and PsbL prevents the reduction of PSII by back electron flow from plastoquinol protecting PSII from photo-inactivation [].; GO: 0015979 photosynthesis, 0009523 photosystem II, 0009539 photosystem II reaction center, 0016020 membrane; PDB: 3A0H_J 3ARC_J 3A0B_J 3KZI_J 2AXT_J 3PRQ_J 4FBY_b 3BZ2_J 1S5L_j 3PRR_J ....
Probab=22.09 E-value=38 Score=20.39 Aligned_cols=15 Identities=20% Similarity=0.479 Sum_probs=8.8
Q ss_pred Ccccchhhhhhhhhh
Q 029480 50 AKVELPFWLSQELYL 64 (192)
Q Consensus 50 ~kveLPlWLA~~L~~ 64 (192)
+.=.+||||.-....
T Consensus 4 ttGRIPLWlVgtv~G 18 (40)
T PF01788_consen 4 TTGRIPLWLVGTVAG 18 (40)
T ss_dssp -TTSS-HHHHHHHHH
T ss_pred CCCcccchHHHHHHH
Confidence 334689999766543
No 16
>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]
Probab=21.19 E-value=84 Score=26.76 Aligned_cols=42 Identities=24% Similarity=0.387 Sum_probs=25.8
Q ss_pred eeceEEEeccCcccc-CCCCcccccccCCcccchhhhhhhhhh
Q 029480 23 LVPVVFHKSANGVKV-DPSAEKDCVDEGAKVELPFWLSQELYL 64 (192)
Q Consensus 23 kVpc~f~~~~~~lG~-d~~~~~~~l~~g~kveLPlWLA~~L~~ 64 (192)
.-|-.|.+....-++ -.+.--+-+.+--.|-||.||.+.|..
T Consensus 64 ~yPmlF~~s~~~~~~~THgGVLEFiaEEGrVylP~WMm~tLs~ 106 (331)
T COG5140 64 QYPMLFEISHSDGIYRTHGGVLEFIAEEGRVYLPSWMMQTLSM 106 (331)
T ss_pred CCceEEEEecccceeEecccEEEEeecCCcEeehHHHHHhccC
Confidence 445566666554443 111111346666789999999999975
No 17
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=20.71 E-value=1.9e+02 Score=21.34 Aligned_cols=41 Identities=15% Similarity=0.165 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHhhhhhhhhhhhhHHHhhhhhhhhHHH
Q 029480 119 MLLSTFQMRYKDILTKAHTAAYAVASKFLAVLTKEETNLYE 159 (192)
Q Consensus 119 ~L~~~f~~R~~~I~~~a~~~~~~~~~~~~~~Lt~~Er~lf~ 159 (192)
-+..+|..|+..++....-+...+-..+..+++..|..|=.
T Consensus 74 ~le~~~~~~v~~~L~~lg~~tk~ev~~L~~RI~~Le~~l~~ 114 (118)
T TIGR01837 74 KLEKAFDERVEQALNRLNIPSREEIEALSAKIEQLAVQVEE 114 (118)
T ss_pred HHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 44567788888887776555555677788888888887643
Done!