Query 013616
Match_columns 439
No_of_seqs 188 out of 405
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 05:39:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013616.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013616hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2851 Eukaryotic-type DNA pr 100.0 3E-130 6E-135 971.6 32.0 391 14-421 10-409 (412)
2 cd04860 AE_Prim_S AE_Prim_S: p 100.0 6.3E-77 1.4E-81 574.0 19.0 230 30-368 1-232 (232)
3 TIGR00335 primase_sml DNA prim 100.0 2.8E-75 6E-80 580.8 19.7 293 20-381 2-296 (297)
4 PRK00419 DNA primase small sub 100.0 1.7E-67 3.6E-72 537.3 22.8 308 15-375 3-327 (376)
5 COG1467 PRI1 Eukaryotic-type D 100.0 7.7E-58 1.7E-62 461.6 10.9 323 12-378 4-331 (341)
6 PF01896 DNA_primase_S: Eukary 100.0 1.6E-30 3.4E-35 231.1 10.1 145 125-360 1-145 (145)
7 cd00525 AE_Prim_S_like AE_Prim 99.3 1.2E-11 2.6E-16 108.8 12.0 100 58-188 2-106 (136)
8 TIGR00335 primase_sml DNA prim 98.3 9.2E-07 2E-11 89.2 5.3 145 49-208 21-171 (297)
9 cd04861 LigD_Pol_like LigD_Pol 95.1 0.031 6.8E-07 54.8 5.1 66 121-204 99-164 (227)
10 cd04865 LigD_Pol_like_2 LigD_P 95.0 0.037 8.1E-07 54.3 5.1 66 121-204 100-165 (228)
11 cd04863 MtLigD_Pol_like MtLigD 94.7 0.14 3E-06 50.4 8.3 69 121-207 103-171 (231)
12 cd04862 PaeLigD_Pol_like PaeLi 94.5 0.055 1.2E-06 53.1 5.1 66 121-204 99-164 (227)
13 TIGR02778 ligD_pol DNA polymer 94.2 0.22 4.8E-06 49.4 8.6 69 121-207 115-183 (245)
14 cd04866 LigD_Pol_like_3 LigD_P 94.2 0.074 1.6E-06 52.1 5.1 51 121-187 94-144 (223)
15 cd04864 LigD_Pol_like_1 LigD_P 94.0 0.27 5.7E-06 48.4 8.5 68 121-207 101-168 (228)
16 TIGR02776 NHEJ_ligase_prk DNA 92.7 0.22 4.9E-06 54.7 6.4 51 121-187 392-442 (552)
17 PRK09633 ligD ATP-dependent DN 92.1 0.29 6.3E-06 54.4 6.5 51 121-187 433-483 (610)
18 COG3285 Predicted eukaryotic-t 92.0 0.35 7.6E-06 49.0 6.3 46 336-381 226-275 (299)
19 PRK05972 ligD ATP-dependent DN 89.3 0.75 1.6E-05 53.1 6.5 66 121-204 685-750 (860)
20 COG1467 PRI1 Eukaryotic-type D 89.0 0.48 1E-05 49.2 4.4 58 326-383 238-297 (341)
21 PRK09632 ATP-dependent DNA lig 88.8 1 2.2E-05 51.4 7.2 69 121-207 136-208 (764)
22 PF05190 MutS_IV: MutS family 75.6 8.6 0.00019 31.0 5.8 53 149-208 13-65 (92)
23 PF09641 DUF2026: Protein of u 52.9 6.2 0.00013 38.2 0.9 46 142-192 21-92 (204)
24 PF01116 F_bP_aldolase: Fructo 40.9 5.5 0.00012 40.4 -1.5 27 327-353 189-216 (287)
25 cd00947 TBP_aldolase_IIB Tagat 40.6 7.1 0.00015 39.5 -0.8 27 327-353 181-207 (276)
26 KOG4080 Mitochondrial ribosoma 40.1 41 0.00088 31.9 4.1 48 134-181 92-151 (176)
27 TIGR03826 YvyF flagellar opero 39.7 28 0.0006 31.8 3.0 26 141-166 17-42 (137)
28 PRK07998 gatY putative fructos 37.9 9.4 0.0002 38.8 -0.4 27 327-353 184-210 (283)
29 PRK12737 gatY tagatose-bisphos 37.1 8.5 0.00018 39.0 -0.9 26 327-352 187-212 (284)
30 COG3516 Predicted component of 34.3 24 0.00052 33.3 1.7 44 326-379 75-122 (169)
31 PRK12857 fructose-1,6-bisphosp 34.2 10 0.00022 38.5 -0.8 27 327-353 187-213 (284)
32 TIGR00167 cbbA ketose-bisphosp 32.9 11 0.00024 38.2 -0.8 27 327-353 190-217 (288)
33 TIGR01858 tag_bisphos_ald clas 32.6 11 0.00024 38.2 -0.8 27 327-353 185-211 (282)
34 PRK12738 kbaY tagatose-bisphos 32.1 12 0.00025 38.2 -0.8 26 327-352 187-212 (286)
35 PRK09195 gatY tagatose-bisphos 28.9 14 0.0003 37.5 -0.9 26 327-352 187-212 (284)
36 PRK08610 fructose-bisphosphate 28.1 15 0.00032 37.4 -0.9 27 327-353 188-214 (286)
37 cd04859 Prim_Pol Prim_Pol: Pri 27.2 1.3E+02 0.0029 26.7 5.3 23 172-194 79-101 (152)
38 PF09250 Prim-Pol: Bifunctiona 27.1 34 0.00075 30.4 1.4 18 172-189 85-102 (163)
39 COG5175 MOT2 Transcriptional r 23.8 38 0.00082 35.6 1.1 78 126-205 23-100 (480)
40 KOG0874 Sphingolipid hydroxyla 23.8 28 0.00061 34.5 0.2 38 172-211 24-66 (287)
41 PRK09462 fur ferric uptake reg 23.5 65 0.0014 28.9 2.5 87 74-178 33-131 (148)
42 COG0191 Fba Fructose/tagatose 23.3 21 0.00046 36.4 -0.8 26 327-352 189-214 (286)
43 COG2874 FlaH Predicted ATPases 22.7 45 0.00098 33.1 1.4 18 343-360 217-234 (235)
44 PF05591 DUF770: Protein of un 22.0 62 0.0013 30.2 2.1 47 325-381 68-118 (157)
45 PF13442 Cytochrome_CBB3: Cyto 21.3 70 0.0015 24.4 2.0 14 193-206 54-67 (67)
46 PF03090 Replicase: Replicase 21.3 1.4E+02 0.0031 27.1 4.3 24 149-172 84-107 (137)
47 cd00453 FTBP_aldolase_II Fruct 20.5 25 0.00054 36.8 -0.9 27 327-353 218-253 (340)
48 PF09098 Dehyd-heme_bind: Quin 20.5 63 0.0014 30.6 1.8 19 193-211 50-68 (167)
No 1
>KOG2851 consensus Eukaryotic-type DNA primase, catalytic (small) subunit [Replication, recombination and repair]
Probab=100.00 E-value=2.7e-130 Score=971.62 Aligned_cols=391 Identities=49% Similarity=0.939 Sum_probs=365.4
Q ss_pred CCCChHHHHHHhhhcCChhhhhhhhccCCCCCCCCCCCCCCCCceeEEEeCCCeeecccccCCHHHHHHHHHHhCCCcee
Q 013616 14 DGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFNSESELENSIKEKCPSKID 93 (439)
Q Consensus 14 ~~~~~~~l~~YY~~lfP~~~~~~WL~y~~~~~~~~~~~~~~~~REfaf~~~~~~y~R~~sF~~~~el~~~l~~~~P~~i~ 93 (439)
.++++++|+.||++|||++++++||+||+.+ ..||.+||||||+.+++|+||+||+|+++|++.|.+++|.+||
T Consensus 10 ~~~~~~~l~~YYr~lFP~~~~~~wL~yg~~~------~~~f~~REfsFtL~ddvYiRY~sFn~~~~~~k~i~s~nP~KiD 83 (412)
T KOG2851|consen 10 PGVDSQDLPIYYRNLFPVKPFFRWLNYGPVP------GDYFNRREFSFTLADDVYIRYLSFNNASEFEKEISSTNPDKID 83 (412)
T ss_pred CCCChhHHHHHHHhhCChHHHHHHHhCCCCc------chhhhhceEEEEecCCcEEEEeccCCHHHHHHHHhhcCCccee
Confidence 4578899999999999999999999999755 7899999999999999999999999999999999999999999
Q ss_pred eccccccCccchhhhccCCCCCcCcccceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeE
Q 013616 94 IGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHIL 173 (439)
Q Consensus 94 igavY~~~P~~~~~~~~~~~~~f~p~~~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~ 173 (439)
|||||+++|.++++..+ ++|+|++|||||||||||||+||+||+||+||+|||+||++|++|||.+|+|||||||++
T Consensus 84 IGaVY~~~P~~~~t~~~---s~~~~vekELVFDIDmTDYD~VR~CCS~a~VC~KCW~fm~lAvkIld~aLrEdFGFKh~l 160 (412)
T KOG2851|consen 84 IGAVYSHRPRNHKTLRK---SDFQAVEKELVFDIDMTDYDDVRTCCSGADVCPKCWKFMTLAVKILDTALREDFGFKHIL 160 (412)
T ss_pred ecccccCCccccccccc---cccceeeeeeEEecccccChHHhhhcccccchHHHHHHHHHHHHHHHHHHHHhcCCceEE
Confidence 99999999999999887 789999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeCCCceEEEeechhhccCChHHHHHHHhHhhhccCCCcccceeeCCCCCCcchhhHHHHHHHHHHHHHHhhhcCCCC
Q 013616 174 WVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFS 253 (439)
Q Consensus 174 ~VFSGrRG~H~wV~D~~ar~L~~e~R~aIvdYl~vv~G~~~~~k~v~l~~~~hP~i~r~~~~il~~~f~~~il~~q~~l~ 253 (439)
||||||||+||||||++||.|++.+|++||+||++++|+++..+++.+..+.||++.|++ .+|+++|++++|++|++|+
T Consensus 161 WVfSGRRGvHCWVcD~~Ar~L~~~qR~aIa~Ylnvvk~n~~~~~~~~lk~~~hP~l~Rs~-~~lK~~f~e~~l~~Q~~w~ 239 (412)
T KOG2851|consen 161 WVFSGRRGVHCWVCDKKARMLSDRQRSAIAEYLNVVKGNGQCGKRLGLKRKKHPHLARSL-NILKPFFEEIMLEDQNPWE 239 (412)
T ss_pred EEEecCCceeeeeccHHHhhccchHHHHHHHHHHHhhcCcccccccccCCCCCcHHHHHH-HHHHHHHHHHHhhhcCccc
Confidence 999999999999999999999999999999999999999999999888789999999999 8999999999999999999
Q ss_pred CHHHHHHHHccCCChhHHHHHHhhhhhccCCCCCcccchHHhHHHHHHHHhccchhh-----hhHHHHHHHHHHHhhccc
Q 013616 254 TEERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKV-----QGLRRCVEEIVFAFTYPR 328 (439)
Q Consensus 254 ~~~~~~~lL~~lpd~~~~~~l~~~~~~~~~~~~~~~~~s~~~W~~l~~~~~~~~~~~-----~~~~~~~~eivl~~~ypR 328 (439)
++++++++|+++||+.+++.|++.|+.+| .+++.++|++|++++.+...++ ..+.++.++|+|+++|||
T Consensus 240 ~ke~~~k~l~~l~d~~~~d~Lr~~w~~~~------~~s~~erW~~i~~~~~s~~~~~~s~~~~k~~~~~~eivl~~~YPR 313 (412)
T KOG2851|consen 240 DKEGFEKLLKLLPDKDLIDDLRKYWESNP------RRSSKERWEDIDKVADSDYRKTLSPSDIKLKNCKSEIVLQYLYPR 313 (412)
T ss_pred ChHHHHHHHhhcchhhhHHHHHHhhhcCc------ccchHHHHHHHHHHHhhhccccCChhhhhHHhhHHHHHHHHhccc
Confidence 99999999999999999999999999888 4689999999999998743322 346679999999999999
Q ss_pred cccccccccccccccCccccCCCccEEEEcCCCCCCCCCCCCCCcHHHHHHhhhcCCCCC---Ccccchh-ccchhHHHH
Q 013616 329 LDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTTVPTLSELLRELNTGDSRM---DVDNEWE-KTSLGKSIR 404 (439)
Q Consensus 329 LD~~VTkd~nHLLKsPfcvHpkTG~vcVPid~~~l~~FDP~~VPtl~~l~~e~~~~~~~~---~~~~~~~-~tsL~~yv~ 404 (439)
||+|||+++|||||||||||||||+||||||++++++|||++||||++|++|+++..+.. +...++. +.+|.|||.
T Consensus 314 LDveVtk~~nHLLKsPFcVHP~Tg~VcVPidv~~~d~Fdp~~vPti~~l~eEl~~~nd~~~~~e~~~d~~~~~aL~pyv~ 393 (412)
T KOG2851|consen 314 LDVEVTKGTNHLLKSPFCVHPKTGRVCVPIDVSKVDEFDPEKVPTISDLLEELESLNDEKEYTENRKDLARHGALSPYVE 393 (412)
T ss_pred hhhhhhhcchhhhcCCccccCCCCceEeecchhhccccCcccCCcHHHHHHHHhhcccccccccchhhhhhccccchHHH
Confidence 999999999999999999999999999999999999999999999999999999874321 1122322 449999999
Q ss_pred HHHHHhHHHHHHHhHHh
Q 013616 405 FFRSSFLQPLLKSCKEE 421 (439)
Q Consensus 405 ~F~~~f~~~l~~~~~~~ 421 (439)
+| +.|+..|.++.++.
T Consensus 394 ~F-e~F~s~l~~~~~g~ 409 (412)
T KOG2851|consen 394 VF-EAFVSALIKSEKGS 409 (412)
T ss_pred HH-HHHHHHHHHhhhcc
Confidence 99 99999999998876
No 2
>cd04860 AE_Prim_S AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In addition to its catalytic role in replication, DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. The function of the larger primase subunit is unclear. Included in this group are Pfu41 and Pfu46, these two proteins comprise the primase complex of the archaea Pyrococcus furiosus; Pfu41 and Pfu46 have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulat
Probab=100.00 E-value=6.3e-77 Score=574.05 Aligned_cols=230 Identities=44% Similarity=0.851 Sum_probs=203.6
Q ss_pred ChhhhhhhhccCCCCCCCCCCCCCCCCceeEEEeCCCeeecccccCCHHHHHHHHHHhCCCceeeccccccCccchhhhc
Q 013616 30 PHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYLRFQSFNSESELENSIKEKCPSKIDIGPVYSVDPAKRHAYA 109 (439)
Q Consensus 30 P~~~~~~WL~y~~~~~~~~~~~~~~~~REfaf~~~~~~y~R~~sF~~~~el~~~l~~~~P~~i~igavY~~~P~~~~~~~ 109 (439)
|+..++.||+|+..+ |.++++|||||++.+++|+||+||+|.+||+++|++++|.|+|.+++||.+|....
T Consensus 1 ~~~~~~~w~~~~~~~------~~~~~~REfaf~~~~~~~~R~~sF~~~~el~~~l~~~~P~~vY~s~~~~~~~~~~~--- 71 (232)
T cd04860 1 PSLFRYYYLNYGLEI------PDYLENREFGFTLFDGVYIRHLSFSSAEELRKYLLRNVPRAVYSSSAYYRKPSAKG--- 71 (232)
T ss_pred CccHHHHHHhCCCCC------CCCccceeEEEEeCCCeeecccCcCCHHHHHHHHHhcCChhhcccchhhhCCCccc---
Confidence 566778899987433 88999999999999999999999999999999999999999999999998887642
Q ss_pred cCCCCCcCcccceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeech
Q 013616 110 QGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDG 189 (439)
Q Consensus 110 ~~~~~~f~p~~~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~ 189 (439)
.+.|+||||||||||||||++|+||+++.||.+||++|++|+++|+.+|++||||++++|||||||||||||||+
T Consensus 72 -----~~~~~~rElVFDID~~d~d~~r~cc~~~~ic~kCw~~~~~a~~~l~~~L~~dFGf~~i~~vfSG~RG~HvwV~d~ 146 (232)
T cd04860 72 -----EKGWLGRELVFDIDADDYDDVRTCCSGATICEKCWKFAKEAVKILDDILREDFGFKHILWVFSGRRGYHVWVCDE 146 (232)
T ss_pred -----cCCccccceEEEccCCcCCCcccccccccHHHHHHHHHHHHHHHHHHHHHHHcCCceEEEEEECCCeEEEEEech
Confidence 245699999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCChHHHHHHHhHhhhccCCCcccce--eeCCCCCCcchhhHHHHHHHHHHHHHHhhhcCCCCCHHHHHHHHccCCC
Q 013616 190 KARRLTNEQRGAIADYFRVYKGNENSNKK--VSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFSTEERYEKILSMIPD 267 (439)
Q Consensus 190 ~ar~L~~e~R~aIvdYl~vv~G~~~~~k~--v~l~~~~hP~i~r~~~~il~~~f~~~il~~q~~l~~~~~~~~lL~~lpd 267 (439)
+||+|++++|+|||+||++++|+....++ +++..++||++.|++
T Consensus 147 ~~r~L~~~~R~~Iv~Yl~~~~~~~~~~~~~~~~~~~~~~~~~~R~~---------------------------------- 192 (232)
T cd04860 147 KARKLDSDERREIVDYLNGIGLNEDKIKKVKVNLGRPLHPGIRRAL---------------------------------- 192 (232)
T ss_pred hhhhCCHHHHHHHHHHHHHhccccccccccccccccCCCcchheee----------------------------------
Confidence 99999999999999999988776543321 222223333322110
Q ss_pred hhHHHHHHhhhhhccCCCCCcccchHHhHHHHHHHHhccchhhhhHHHHHHHHHHHhhccccccccccccccccccCccc
Q 013616 268 ESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKVQGLRRCVEEIVFAFTYPRLDMEVSKHRNHLLKAPFCV 347 (439)
Q Consensus 268 ~~~~~~l~~~~~~~~~~~~~~~~~s~~~W~~l~~~~~~~~~~~~~~~~~~~eivl~~~ypRLD~~VTkd~nHLLKsPfcv 347 (439)
||++||+|+|||||+||||
T Consensus 193 -------------------------------------------------------------iD~~Vt~d~~rLlr~P~Sl 211 (232)
T cd04860 193 -------------------------------------------------------------IDENVTKDINRLLRLPFSL 211 (232)
T ss_pred -------------------------------------------------------------cchhhhccccceeecCCcc
Confidence 9999999999999999999
Q ss_pred cCCCccEEEEcCCCCCCCCCC
Q 013616 348 HPKTGRVCIPIDPKDCEEFDP 368 (439)
Q Consensus 348 HpkTG~vcVPid~~~l~~FDP 368 (439)
|||||+|||||++++++.|||
T Consensus 212 H~ktg~v~vpi~~~~l~~FdP 232 (232)
T cd04860 212 HGKTGLIVVPIDPNELDKFDP 232 (232)
T ss_pred cCCCCeEEEEcCcchhccCCC
Confidence 999999999999999999998
No 3
>TIGR00335 primase_sml DNA primase, eukaryotic-type, small subunit, putative. This model is named putative because the assignment is putative for archaeal proteins. Eukaryotic proteins scoring above the trusted cutoff can be considered authentic.
Probab=100.00 E-value=2.8e-75 Score=580.79 Aligned_cols=293 Identities=26% Similarity=0.289 Sum_probs=253.9
Q ss_pred HHHHHhhhcCChhhhhhhhccCCCCCCCCCCCCCCCCceeEEEeCCCeee-cccccCCHHHHHHHHHHhCCCceeecccc
Q 013616 20 YLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDNDIYL-RFQSFNSESELENSIKEKCPSKIDIGPVY 98 (439)
Q Consensus 20 ~l~~YY~~lfP~~~~~~WL~y~~~~~~~~~~~~~~~~REfaf~~~~~~y~-R~~sF~~~~el~~~l~~~~P~~i~igavY 98 (439)
+|+.||+++||+..+++||+|++.+ ..+|++|||||++.++.|+ ||+||+|.++|+++++.++|.++|||++|
T Consensus 2 ~~~~yy~~~f~~~~~~~~l~~p~~~------~r~~~~REf~~~~~~~~~~~R~~sF~~~~el~~~~~~~~Ps~~y~~~~y 75 (297)
T TIGR00335 2 ETKLYYKEKYNFYYSKNELELPRKF------NREFAFREFGLLPDFVMHRHRYESFFRERILKNVPAKIYPSSAYYSRAY 75 (297)
T ss_pred cHHHHHHHHCchhhhcccccCCCCc------ccccceeeecccCCCceEeeeeeccCCHHHHHHHHHHhCCCeEEEcCcC
Confidence 5889999999999999999987543 6789999999999999999 99999999999999999999999999999
Q ss_pred ccCccchhhhccCCCCCcCcccceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeC
Q 013616 99 SVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSG 178 (439)
Q Consensus 99 ~~~P~~~~~~~~~~~~~f~p~~~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSG 178 (439)
+.+|.++++.. ++| .++|||||||+||||++|+||+++.+ +||.++.+|++++|..|+ ||||+++.|||||
T Consensus 76 ~~~p~~k~~~~----k~~--~~~elvFDID~~d~~~~r~~c~~~~~--k~~~~k~~a~~l~D~~l~-DfGf~~~~~vfSG 146 (297)
T TIGR00335 76 EDKPEKRGWLG----KGL--IRDELAFDIDVKDQSFEKAECDGKQV--CLEEAKLLAVLRADTGLR-DFGLYDSGGVFSG 146 (297)
T ss_pred CCChhhcCCcc----ccc--ccchhccccCCCCCcCcccchhhHHH--HHHHHHHHHHHHHHhccc-ccCeEEEEEEEec
Confidence 99999987654 456 78899999999999999999998755 999999999999997777 9999999999999
Q ss_pred CCceEEEeechhhccCChHHHHHHHhHhhhccCCCcccceeeCCCCCCcchhhHHHHHHHHHHHHHHhhhcCCCCCHHHH
Q 013616 179 RRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFSTEERY 258 (439)
Q Consensus 179 rRG~H~wV~D~~ar~L~~e~R~aIvdYl~vv~G~~~~~k~v~l~~~~hP~i~r~~~~il~~~f~~~il~~q~~l~~~~~~ 258 (439)
|||+||||||+.|++|++++|++||+||+++.|+. .++.++|...++.
T Consensus 147 ~RG~H~~V~d~~~~~l~~~~R~~i~~Yl~~~~~~~---------------------~~~~~~~~~~~l~----------- 194 (297)
T TIGR00335 147 VRGYHEEVLDLGSRELREIVRYERLRYPKIVRVEK---------------------RFLNSNAVKRVLN----------- 194 (297)
T ss_pred ceEeceEECCcchhhccHHHHHHHHcceEEeccCc---------------------ccchHHHHHHHHH-----------
Confidence 99999999999999999999999999999887753 1233455555554
Q ss_pred HHHHccCCChhHHHHHHhhhhhccCCCCCcccchHHhHHHHHHH-HhccchhhhhHHHHHHHHHHHhhcccccccccccc
Q 013616 259 EKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNT-LQSGKQKVQGLRRCVEEIVFAFTYPRLDMEVSKHR 337 (439)
Q Consensus 259 ~~lL~~lpd~~~~~~l~~~~~~~~~~~~~~~~~s~~~W~~l~~~-~~~~~~~~~~~~~~~~eivl~~~ypRLD~~VTkd~ 337 (439)
+.+|+.+| ..+..|+.+|.+++ ..+|+++.+. .++.. .+..+++++++++ |||++||+|+
T Consensus 195 ~~ll~~l~--~~~~~l~~k~~~~~----------~~~w~~i~~~~~~~~~----~~~~~~~~~~~~~---~lD~~Vt~d~ 255 (297)
T TIGR00335 195 RLLLKALE--EEILTSKLKILPND----------LRKWKLIKEVIFKSEK----KDYSALEIYIDKI---VLDDKVTLDR 255 (297)
T ss_pred HHHHHHhh--hHHHHHHHhhhccc----------hhhHHHHHHHHhhhhh----hHHHHHHHHHhhh---eecceeeecc
Confidence 56777777 33667888886543 1289999887 33221 3556788998885 9999999999
Q ss_pred ccccccCccccCCCccEEEEcCCCCCCCCCCCCCCcHHHHHHhh
Q 013616 338 NHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTTVPTLSELLREL 381 (439)
Q Consensus 338 nHLLKsPfcvHpkTG~vcVPid~~~l~~FDP~~VPtl~~l~~e~ 381 (439)
|||||+|||||||||+|||||+. ++.|||+.|||+. |++|.
T Consensus 256 ~rLLr~P~slH~kTG~v~vpi~~--~~~FdP~~~~~~~-~~~e~ 296 (297)
T TIGR00335 256 IRLLRHPKSLHRVTGVICIESFN--PEKFAPLKGAEAI-FVVKV 296 (297)
T ss_pred hhhhcCCcccCCCcceEEEEccC--ccccCCccCCchh-hhhcc
Confidence 99999999999999999999955 9999999999999 88774
No 4
>PRK00419 DNA primase small subunit; Reviewed
Probab=100.00 E-value=1.7e-67 Score=537.28 Aligned_cols=308 Identities=26% Similarity=0.367 Sum_probs=225.9
Q ss_pred CCChHHHHHHhhhcCChhhhhhhhccCCCCCCCCCCCCCCCCceeEEEeCC-Ce---eecccccCCHHHHHHHHHHhCCC
Q 013616 15 GFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFTLDN-DI---YLRFQSFNSESELENSIKEKCPS 90 (439)
Q Consensus 15 ~~~~~~l~~YY~~lfP~~~~~~WL~y~~~~~~~~~~~~~~~~REfaf~~~~-~~---y~R~~sF~~~~el~~~l~~~~P~ 90 (439)
+.+.+.|+.||+++||...+. .|.++++|||||++.+ ++ |+||+||+|.+||+++|++++|.
T Consensus 3 ~~t~~~lk~~f~~yy~~~~~~--------------~p~~~~~REf~f~~~~~~~~~~m~R~~sF~~~~el~~~l~~~~P~ 68 (376)
T PRK00419 3 ERTREYLKSRFRDYYRRAELP--------------LPPDLEKREFGFIPFGEGPSDTMVRHLSFSDLGELRDYLRRTAPR 68 (376)
T ss_pred chhHHHHHHHHHHHhhhcCCC--------------CCCCcccceeEEEecCCCcccccccccccCCHHHHHHHHHHhCCC
Confidence 346778999999988754331 3788999999999886 44 59999999999999999999999
Q ss_pred ceeeccccccCccchhhhccCCCCCcCcccceEEEeccCCCCCCcccccCCCccccccHHHH-HHHHHHHHHHHhhhcCC
Q 013616 91 KIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLM-TVAIKVIDTALRDDFGF 169 (439)
Q Consensus 91 ~i~igavY~~~P~~~~~~~~~~~~~f~p~~~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~-~~a~klld~~L~~dFGf 169 (439)
|+|||+|||.+|.++.|.. ++| .++||||||||||||++| |+++.+| +||..+ .+|++||+ +|++||||
T Consensus 69 ~iy~s~ayy~~P~~~~m~~----k~w--~~~ELvFDID~dd~~~~~--~~~~~~c-~cl~~~k~~a~klld-~L~~DFGf 138 (376)
T PRK00419 69 HVYYSVARYELPSARTMEE----KGW--LGADLIFDLDADHLPGVR--CEEDSYC-ECLERAKEEALRLLD-FLEDDFGF 138 (376)
T ss_pred eEEEeeeeecCCccccccc----cCc--cccceEEEeCCCcCCCcC--CCcccHH-HHHHHHHHHHHHHHH-HHHHHcCC
Confidence 9999999999999987655 457 899999999999999877 4788899 999988 58999999 99999999
Q ss_pred ceeEEEEeCCCceEEEeechhhccCChHHHHHHHhHhhhccCCCccc-ceee---CCC-CCCcchhhHHHHHHHHHHHHH
Q 013616 170 DHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSN-KKVS---FPG-PLHPFLVRSYTEVLREFFEEK 244 (439)
Q Consensus 170 ~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~aIvdYl~vv~G~~~~~-k~v~---l~~-~~hP~i~r~~~~il~~~f~~~ 244 (439)
+||+|||||||||||||||++||+|++++|++||+||++ .+-.. ..+. ..+ ....+|.++++..+..+...+
T Consensus 139 ~~i~~vFSG~RG~Hi~V~D~~~~~L~~~~RreIv~Yl~~---~gl~~~~~~~~~~~~g~~~~~Gw~~R~~~~~~~~~~~l 215 (376)
T PRK00419 139 EDIHVVFSGGRGYHVHVRDEDVLELDSDERREIVDYVSG---AGLPFEELIREEAVRGTGRPSGWGRRFARRLGYFIDHL 215 (376)
T ss_pred CeeEEEEeCCCeEEEEEEChHhhhCCHHHHHHHHHHHhh---cCCCHHHhhccccccCCcccCcHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999999994 33111 1110 000 112389999877776544332
Q ss_pred HhhhcC----CCC-CHHHHHHHHccCCChhHHHHHHhhhhhccCCCCCcccchHHhHHHHHHHHhccchhhhhHHHHHHH
Q 013616 245 LLLSQN----LFS-TEERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKVQGLRRCVEE 319 (439)
Q Consensus 245 il~~q~----~l~-~~~~~~~lL~~lpd~~~~~~l~~~~~~~~~~~~~~~~~s~~~W~~l~~~~~~~~~~~~~~~~~~~e 319 (439)
.-.... .-+ ++..++++|+...+ ....+ ..-+|..+.. .....+..++++
T Consensus 216 ~~~~~~~l~~~~gi~~~~~~~~l~~~~~--~~~~~-----------------~~g~~~~~~~------~~~~~~~~l~~~ 270 (376)
T PRK00419 216 RELALERLEEFDGIGEGTAKKILKAARD--NTEFL-----------------RKGNLDAFHG------IGPRLAARLFAE 270 (376)
T ss_pred hhhhhhhhhhhcccchhHHHHHHHHhhh--hhhhh-----------------hccchhhccc------hhHHHHHHHHHH
Confidence 211111 001 22345555543222 00000 0011221100 011223333344
Q ss_pred HHHHhhccccccccccccccccccCccccCCCccEEEEcCCCCCCCCCCC--CCCcHH
Q 013616 320 IVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPT--TVPTLS 375 (439)
Q Consensus 320 ivl~~~ypRLD~~VTkd~nHLLKsPfcvHpkTG~vcVPid~~~l~~FDP~--~VPtl~ 375 (439)
++-. .-..+|++||.|++||||+|+|||+|||++|+||+.++++.|||+ +||.+.
T Consensus 271 ~~~~-~~~~iDe~VT~DikRLiRlPgSLHGksGL~v~~l~~~~l~~FdPl~dAVp~F~ 327 (376)
T PRK00419 271 SVRF-SKAPIDEPVTIDIKRLIRLPGSLHGKSGLIVTELDRKNLEDFDPLKDAVPPFR 327 (376)
T ss_pred hhHh-hcCcCCCCccccchhhhhCCCCccCCcceEEEEecccccccCCchhhhHhhhc
Confidence 3211 235599999999999999999999999999999999999999998 688443
No 5
>COG1467 PRI1 Eukaryotic-type DNA primase, catalytic (small) subunit [DNA replication, recombination, and repair]
Probab=100.00 E-value=7.7e-58 Score=461.61 Aligned_cols=323 Identities=29% Similarity=0.447 Sum_probs=236.2
Q ss_pred CCCCCChHHHHHHhhhcCChhhhhhhhccCCCCCCCCCCCCCCCCceeEEE-eCCCeeecccccCCHHHHHHHHHHhCCC
Q 013616 12 IPDGFNPNYLKVYYGRLFPHADIFKWMSYGNDGRHPACDKSYFGRREFSFT-LDNDIYLRFQSFNSESELENSIKEKCPS 90 (439)
Q Consensus 12 ~~~~~~~~~l~~YY~~lfP~~~~~~WL~y~~~~~~~~~~~~~~~~REfaf~-~~~~~y~R~~sF~~~~el~~~l~~~~P~ 90 (439)
...+.+++.|+.||+.+||++.++.|+. +..|||+|+ +.++.|+||+||+|..||++++..++|.
T Consensus 4 ~~~~~t~~~~k~~fr~yY~~~~i~~~~~--------------~~~RE~~~~~~~~~~~~R~~sF~~~~el~~~l~~~~P~ 69 (341)
T COG1467 4 LLEGVTSEELKTLFREYYRFKEIFLPLD--------------IDEREEFYFPLKGGVYDRHLSFRSERELRDYLRRNAPR 69 (341)
T ss_pred ccccCCHHHHHHHHHHhcccccCCCccc--------------chhhceeeeecCCCceeeeeccCCHHHHHHHHHHhCch
Confidence 3457789999999999999999999982 466888887 5566999999999999999999999999
Q ss_pred ceeeccccccCccchhhhccCCCCCcCcccceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCc
Q 013616 91 KIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFD 170 (439)
Q Consensus 91 ~i~igavY~~~P~~~~~~~~~~~~~f~p~~~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~ 170 (439)
|+|+|++||.+|.+++|+.+ +| +|+||||||||+||+..+ || ...+|++||....+|++++..+|++||||+
T Consensus 70 h~y~S~ayy~~P~~~~m~~k----~w--~g~eLVFDIDad~lp~~~-~~-~~~v~~~c~~~~~e~~~l~~~~L~~DfGf~ 141 (341)
T COG1467 70 HVYSSAAYYEKPKERKMEEK----GW--LGAELVFDIDADHLPERR-CD-KDSVCKMCLEDKKEAVRLLNDFLREDFGFK 141 (341)
T ss_pred heeecchhhcCchhhhcccc----cc--cchhheEecccccCcccc-cc-hhhHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 99999999999999999886 57 899999999999999877 77 889999999999999999988999999999
Q ss_pred eeEEEEeCCCceEEEeechhhccCChHHHHHHHhHhhhccCCCcccceeeCCCCCCcchhhHHHHHHHHHHHHHHhhhcC
Q 013616 171 HILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQN 250 (439)
Q Consensus 171 ~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~aIvdYl~vv~G~~~~~k~v~l~~~~hP~i~r~~~~il~~~f~~~il~~q~ 250 (439)
++.|||||||||||||+|++|+.|++++||+|++|++++....+...... +.++.+.+.. ...+..+....+..++
T Consensus 142 di~ivFSG~RGyHv~V~d~~~~~Lgs~eRreI~~Yv~~~~l~~~~~~~~~---~~~~~~~~~~-~~~~~~~~~~~~~~~~ 217 (341)
T COG1467 142 DIKIVFSGRRGYHVHVSDEEVLSLGSEERREILDYVSGNRLELETVFRLR---PLKRLLGRVL-GWGKGLFIKLRLREAR 217 (341)
T ss_pred CcEEEEeCCCceEEEEeChhhhhcChHHHHHhhhhhhhcccCccchhhhh---hhhccccccc-ccCccceeehhhhhhh
Confidence 99999999999999999999999999999999999996553321111111 2445444444 4444444444444444
Q ss_pred CCCC-HHHHHHHHccCCChhHHHHHHhhhhhccCCCCCcccchHHhHHHHHHHHhccchhhhhHHHHHHHH-HHHhhccc
Q 013616 251 LFST-EERYEKILSMIPDESVTSELRGKWQENRRSSNSKEDINFFRWEQLKNTLQSGKQKVQGLRRCVEEI-VFAFTYPR 328 (439)
Q Consensus 251 ~l~~-~~~~~~lL~~lpd~~~~~~l~~~~~~~~~~~~~~~~~s~~~W~~l~~~~~~~~~~~~~~~~~~~ei-vl~~~ypR 328 (439)
+... ++.++..|..++++.+.......+...+ ++..+-... .+..........+++. ++...|
T Consensus 218 ~~~~~~~~i~~~i~~~~~~~~i~~~~~v~~d~~------------r~~~~~~~~-~~~~~l~~~~~~~~~~~~~~~l~-- 282 (341)
T COG1467 218 LMKRVKEDIENALARLPDKRLIAIDEKVTNDIT------------RLIRLPGSL-DGKGFLTVARLGLDELRVFSPLY-- 282 (341)
T ss_pred HHHhHHHHHHHHHhhCCccchhccccccccccH------------HHHhccccc-CCcceeeeccccccccccccccc--
Confidence 4333 3556666666554333222222221111 111111000 0000000011112222 345555
Q ss_pred cccccccccccccccCccccCCCccEEEEcCCCCCCCCCCC--CCCcHHHHH
Q 013616 329 LDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPT--TVPTLSELL 378 (439)
Q Consensus 329 LD~~VTkd~nHLLKsPfcvHpkTG~vcVPid~~~l~~FDP~--~VPtl~~l~ 378 (439)
+|..||+|++||+|.|+|+|++||++|+++. -..|+|. +||....+.
T Consensus 283 ~d~~v~~d~~~~~~~~~~lh~~~~~~~~~~~---~~~~~p~~~~v~~y~~~~ 331 (341)
T COG1467 283 LDGEVTKDLKRLLRLPGSLHSKLGEVKIYVF---EMPFNPGKHAVPEYVAVF 331 (341)
T ss_pred cCcccccchHHhhcccccccccccccccccc---cccCCchhHhhHHHHHHH
Confidence 8999999999999999999999999999997 3457776 577666544
No 6
>PF01896 DNA_primase_S: Eukaryotic and archaeal DNA primase small subunit; InterPro: IPR002755 DNA primase [] synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large (p60) and small (p50) subunits in eukaryotes. This family represents sequences of the small subunit and the DNA primase sequences of the Archaea []. No sequence similarity can be detected between the eukaryotic p50 and p60 subunits and the primases purified from bacteriophage and bacteria, IPR006295 from INTERPRO. ; GO: 0003896 DNA primase activity, 0006269 DNA replication, synthesis of RNA primer; PDB: 1V33_A 1V34_A 2FAR_B 2FAQ_A 2FAO_B 1G71_A 2R9L_B 3PKY_B 2IRU_B 2IRY_B ....
Probab=99.97 E-value=1.6e-30 Score=231.07 Aligned_cols=145 Identities=37% Similarity=0.598 Sum_probs=109.2
Q ss_pred EeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHHHHHh
Q 013616 125 FDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIAD 204 (439)
Q Consensus 125 FDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~aIvd 204 (439)
||||++++++ .+|.+..+|.+||..+..++.++...|.++|||+++.++|||+||+||||+++.++.|+++.|++|++
T Consensus 1 FDiD~~~~~~--~~~~~~~~~~~~i~~~~~~~~~~~~~l~~~~g~~~~~~~~SG~rG~Hi~v~~~~~~~~~~~~r~~i~~ 78 (145)
T PF01896_consen 1 FDIDPDDYPD--FRENGKSVCEKCIEFVVEEAAKLLDFLLEDFGFRCIFVKFSGNRGFHIWVPFEEARHLDSERRREIVD 78 (145)
T ss_dssp EEEECCTCSS--HSSCTTE--HHHHHHHHHHHHHHHHHHHHTTT--SEEEEE-SSSSEEEEEEECCGCCHHHHHHHHHHH
T ss_pred CccCCCCCCC--hhhccccccchhhHHHHHHHHHHHHhhhhhcCCcccEEEeCCCcEEEEEEEECcccchhHHHHhhccc
Confidence 9999999986 55688999999999999888888789999999999999999999999999999999999999999999
Q ss_pred HhhhccCCCcccceeeCCCCCCcchhhHHHHHHHHHHHHHHhhhcCCCCCHHHHHHHHccCCChhHHHHHHhhhhhccCC
Q 013616 205 YFRVYKGNENSNKKVSFPGPLHPFLVRSYTEVLREFFEEKLLLSQNLFSTEERYEKILSMIPDESVTSELRGKWQENRRS 284 (439)
Q Consensus 205 Yl~vv~G~~~~~k~v~l~~~~hP~i~r~~~~il~~~f~~~il~~q~~l~~~~~~~~lL~~lpd~~~~~~l~~~~~~~~~~ 284 (439)
|+.+. .+.|.+.+.+.+..+.+.+.
T Consensus 79 ~~~~~----------------------------~~~~~~~l~~~~~~~~~~~~--------------------------- 103 (145)
T PF01896_consen 79 YLKAI----------------------------AKAFAEELEEEDPDFVTTEM--------------------------- 103 (145)
T ss_dssp HHCTS----------------------------HHHHHHHHHHHCTTCCESSS---------------------------
T ss_pred chhhh----------------------------hHHHHHHHHHHCccccchhh---------------------------
Confidence 99942 12222222222221111110
Q ss_pred CCCcccchHHhHHHHHHHHhccchhhhhHHHHHHHHHHHhhccccccccccccccccccCccccCCCccEEEEcCC
Q 013616 285 SNSKEDINFFRWEQLKNTLQSGKQKVQGLRRCVEEIVFAFTYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDP 360 (439)
Q Consensus 285 ~~~~~~~s~~~W~~l~~~~~~~~~~~~~~~~~~~eivl~~~ypRLD~~VTkd~nHLLKsPfcvHpkTG~vcVPid~ 360 (439)
|. .....+|.||.+|+.+.+||+|+|+|+|+|||++|+||++
T Consensus 104 -----------~~-----------------------~~~~~~~~iD~~v~~~~~~lir~P~s~~~k~~~~s~pi~~ 145 (145)
T PF01896_consen 104 -----------GK-----------------------AKRKGKPFIDYQVNGDGKRLIRAPYSLHPKTGLVSVPIDW 145 (145)
T ss_dssp -----------HH-----------------------HHHCCSCECEHHHHCTTT-EEETTTSEETTTTEE-EEE--
T ss_pred -----------hh-----------------------hhccCCcccCCCccCCCCCEEecccccCCCCCccccccCC
Confidence 00 2234589999999999999999999999999999999975
No 7
>cd00525 AE_Prim_S_like AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the pri
Probab=99.34 E-value=1.2e-11 Score=108.79 Aligned_cols=100 Identities=26% Similarity=0.360 Sum_probs=81.5
Q ss_pred eeEEEeC--CCeeeccccc---CCHHHHHHHHHHhCCCceeeccccccCccchhhhccCCCCCcCcccceEEEeccCCCC
Q 013616 58 EFSFTLD--NDIYLRFQSF---NSESELENSIKEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITDY 132 (439)
Q Consensus 58 Efaf~~~--~~~y~R~~sF---~~~~el~~~l~~~~P~~i~igavY~~~P~~~~~~~~~~~~~f~p~~~ELVFDID~~dy 132 (439)
++.+... ...+.|+.++ .+.+++++++.+..+..++++...+..+ + ...++|||||..|+
T Consensus 2 ~~~p~~~~~K~p~~~~~~~~~~~d~~~~~~~~~~~~~~~i~i~~~~~~~~-------------~--~~~~iv~DiD~~~~ 66 (136)
T cd00525 2 PVSPIRPPGKGPFQRHWPFGATTDDAEILAWLANLPPGNIGLSLGRYDKL-------------W--KPDLLVFDLDPDDY 66 (136)
T ss_pred CceeeeCCCCcCccccCCCCcccCcHHHHHHHHhcCCeEEEcCccccCcc-------------C--CCCEEEEECCCCCC
Confidence 4444433 4678899999 8999999999999998888777666431 2 45899999999988
Q ss_pred CCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeec
Q 013616 133 DDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCD 188 (439)
Q Consensus 133 d~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D 188 (439)
+ ||..+..++..+...|.+.| .+..+++||+||+|+|+..
T Consensus 67 ~--------------~~~~~~~~~~~l~~ll~~~~--~~~~~~~Tg~~G~H~~~~~ 106 (136)
T cd00525 67 D--------------CWEDVKEAALLLRELLDEDG--LNTLVVTSGSRGLHVYVRL 106 (136)
T ss_pred C--------------CHHHHHHHHHHHHHHHHHhC--CccceEEeCCCEEEEEEEe
Confidence 4 88888888787887887776 8899999999999999998
No 8
>TIGR00335 primase_sml DNA primase, eukaryotic-type, small subunit, putative. This model is named putative because the assignment is putative for archaeal proteins. Eukaryotic proteins scoring above the trusted cutoff can be considered authentic.
Probab=98.27 E-value=9.2e-07 Score=89.20 Aligned_cols=145 Identities=19% Similarity=0.085 Sum_probs=111.9
Q ss_pred CCCCCCCCceeEEEeCCCeee--ccc-ccCCHHHHHHHHHHhCCCceeeccccccCccchhhhccCCCCCcCcccceEEE
Q 013616 49 CDKSYFGRREFSFTLDNDIYL--RFQ-SFNSESELENSIKEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIF 125 (439)
Q Consensus 49 ~~~~~~~~REfaf~~~~~~y~--R~~-sF~~~~el~~~l~~~~P~~i~igavY~~~P~~~~~~~~~~~~~f~p~~~ELVF 125 (439)
..|... .|||++.-++-... -|+ -+.|..... .+++.|.+.+.+.+|+..|....+.. ++| .+++|+|
T Consensus 21 ~~p~~~-~r~~~~REf~~~~~~~~~~~R~~sF~~~~--el~~~~~~~~Ps~~y~~~~y~~~p~~----k~~--~~k~~~~ 91 (297)
T TIGR00335 21 ELPRKF-NREFAFREFGLLPDFVMHRHRYESFFRER--ILKNVPAKIYPSSAYYSRAYEDKPEK----RGW--LGKGLIR 91 (297)
T ss_pred cCCCCc-ccccceeeecccCCCceEeeeeeccCCHH--HHHHHHHHhCCCeEEEcCcCCCChhh----cCC--ccccccc
Confidence 335555 99999986654332 355 556665554 45789999999999999999876554 456 7899999
Q ss_pred eccCCCCCCcccccCCCccccccHHH---HHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHHHH
Q 013616 126 DIDITDYDDVRYCCSGADVCLECWPL---MTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAI 202 (439)
Q Consensus 126 DID~~dyd~ir~CC~~~~iC~kCw~~---~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~aI 202 (439)
|+|+.|.|- | +...|..|-.. +...++.+. ++.-|||++++-+.|||.||.|.++.+..+..++..+|+++
T Consensus 92 ~elvFDID~---~--d~~~~r~~c~~~~~k~~~~k~~a-~~l~D~~l~DfGf~~~~~vfSG~RG~H~~V~d~~~~~l~~~ 165 (297)
T TIGR00335 92 DELAFDIDV---K--DQSFEKAECDGKQVCLEEAKLLA-VLRADTGLRDFGLYDSGGVFSGVRGYHEEVLDLGSRELREI 165 (297)
T ss_pred chhccccCC---C--CCcCcccchhhHHHHHHHHHHHH-HHHHHhcccccCeEEEEEEEecceEeceEECCcchhhccHH
Confidence 999999972 2 34455545333 334556665 88889999999999999999999999999999999999999
Q ss_pred HhHhhh
Q 013616 203 ADYFRV 208 (439)
Q Consensus 203 vdYl~v 208 (439)
+.|..+
T Consensus 166 ~R~~i~ 171 (297)
T TIGR00335 166 VRYERL 171 (297)
T ss_pred HHHHHH
Confidence 998773
No 9
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=95.14 E-value=0.031 Score=54.78 Aligned_cols=66 Identities=26% Similarity=0.342 Sum_probs=44.4
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHH
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRG 200 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~ 200 (439)
-.||||+|-.+-.+... +..|..++...| +++|.... .--||++|+|+.|-=+ ...+-++=+
T Consensus 99 D~lvfDLDP~~~~~f~~--------------v~~~A~~vr~~L-~~lgL~~f-~KTSG~kGlHV~vPl~--~~~~~~~~r 160 (227)
T cd04861 99 DRLVFDLDPGPGVPFED--------------VVEAALLLRELL-DELGLESF-PKTSGGKGLHVYVPLA--PRYTWDEVR 160 (227)
T ss_pred CEEEEECCCCCCCCHHH--------------HHHHHHHHHHHH-HHcCCccc-eEccCCCeEEEEEEcC--CCCCHHHHH
Confidence 57999999875544443 445566676555 68899876 4789999999999432 244544444
Q ss_pred HHHh
Q 013616 201 AIAD 204 (439)
Q Consensus 201 aIvd 204 (439)
+.+.
T Consensus 161 ~fa~ 164 (227)
T cd04861 161 AFAK 164 (227)
T ss_pred HHHH
Confidence 4443
No 10
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=94.96 E-value=0.037 Score=54.28 Aligned_cols=66 Identities=26% Similarity=0.338 Sum_probs=43.7
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHH
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRG 200 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~ 200 (439)
-+||||+|-.+--+ |..+..|..++...| +++|.... .-=||++|+|+.|-=+ ...+-++=+
T Consensus 100 D~lvfDLDP~~~~~--------------f~~v~~~A~~vr~~L-~~lgL~sf-~KTSG~kGlHv~vPl~--~~~~~~~~r 161 (228)
T cd04865 100 DELVIDLDPQPGTS--------------FEDVVEVALLVREVL-DELGLRGY-PKTSGARGLHIYVPIA--PRYTFEEVR 161 (228)
T ss_pred CEEEEECCCCCCCC--------------HHHHHHHHHHHHHHH-HHcCCccc-eEccCCCeEEEEEEcC--CCCCHHHHH
Confidence 57999999874433 333445667777555 68899886 4789999999999421 245544433
Q ss_pred HHHh
Q 013616 201 AIAD 204 (439)
Q Consensus 201 aIvd 204 (439)
+.+.
T Consensus 162 ~fa~ 165 (228)
T cd04865 162 RFAE 165 (228)
T ss_pred HHHH
Confidence 3333
No 11
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=94.68 E-value=0.14 Score=50.40 Aligned_cols=69 Identities=19% Similarity=0.247 Sum_probs=46.6
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHH
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRG 200 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~ 200 (439)
-.||||+|-.+-.+ |..+..+..++...| +++|.+.. .-=||++|+|++|-= ....+-++=+
T Consensus 103 D~~vfDLDP~~~~~--------------f~~v~~~A~~~r~~L-~~lgL~s~-~KTSG~kGlHV~vPl--~~~~~~~~vr 164 (231)
T cd04863 103 DRLVFDLDPGEPAG--------------LVECARVALWLRDRL-AALGLASF-PKTSGSKGLHLYVPL--DGPVSSDQTK 164 (231)
T ss_pred CEEEEECCCCCCCC--------------HHHHHHHHHHHHHHH-HHcCCccc-eECCCCCeEEEEEEc--CCCCCHHHHH
Confidence 57899999875432 445556667777566 56999876 378999999999943 2356655544
Q ss_pred HHHhHhh
Q 013616 201 AIADYFR 207 (439)
Q Consensus 201 aIvdYl~ 207 (439)
+.+..|.
T Consensus 165 ~fa~~~A 171 (231)
T cd04863 165 EFAKALA 171 (231)
T ss_pred HHHHHHH
Confidence 4444443
No 12
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=94.54 E-value=0.055 Score=53.09 Aligned_cols=66 Identities=23% Similarity=0.297 Sum_probs=43.8
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHH
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRG 200 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~ 200 (439)
-.||||+|-.+--+.. .+..+..++...| +++|.... ..=||++|+|++|-=. ...+-++=+
T Consensus 99 D~lvfDLDP~~~~~f~--------------~v~~~A~~~r~~L-~~lgL~~~-~KTSG~kGlHV~vPl~--~~~~~~~~r 160 (227)
T cd04862 99 DRIVFDLDPGPGVPWK--------------AVVEAALLVRELL-DELGLESF-VKTSGGKGLHVVVPLA--PRAGWDEVK 160 (227)
T ss_pred CEEEEECCCCCCCCHH--------------HHHHHHHHHHHHH-HHcCCccc-eEccCCCeEEEEEEcC--CCCCHHHHH
Confidence 5699999987543333 3445666776555 68899876 4789999999999422 245544444
Q ss_pred HHHh
Q 013616 201 AIAD 204 (439)
Q Consensus 201 aIvd 204 (439)
+.+.
T Consensus 161 ~fa~ 164 (227)
T cd04862 161 AFAK 164 (227)
T ss_pred HHHH
Confidence 4444
No 13
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=94.23 E-value=0.22 Score=49.43 Aligned_cols=69 Identities=25% Similarity=0.421 Sum_probs=46.5
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHH
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRG 200 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~ 200 (439)
-.||||+|-.+--+ |..+..|...+...| +++|.+.. .-=||++|+|+.|-=.. ..+-++=+
T Consensus 115 D~lvfDLDP~~~~~--------------f~~v~~~A~~~r~~L-~~lgL~~f-~KTSG~kGlHV~vPl~~--~~~~~~~r 176 (245)
T TIGR02778 115 DRIVFDLDPGPGVA--------------WKLVVEAAQLIRELL-DELGLESF-VKTSGGKGLHVYVPLRP--TLSWDEVK 176 (245)
T ss_pred CEEEEECCCCCCCC--------------HHHHHHHHHHHHHHH-HHcCCccc-eEccCCCeEEEEEECCC--CCCHHHHH
Confidence 57999999875433 334445667777565 68899886 47899999999995322 56655545
Q ss_pred HHHhHhh
Q 013616 201 AIADYFR 207 (439)
Q Consensus 201 aIvdYl~ 207 (439)
+.+..|.
T Consensus 177 ~fa~~iA 183 (245)
T TIGR02778 177 DFAKALA 183 (245)
T ss_pred HHHHHHH
Confidence 4554443
No 14
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=94.17 E-value=0.074 Score=52.05 Aligned_cols=51 Identities=25% Similarity=0.503 Sum_probs=37.4
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEee
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVC 187 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~ 187 (439)
-.||||+|-.+--+.. .+..+..++...| +++|.... .-=||.+|+|+.|-
T Consensus 94 D~lvfDLDP~~~~~f~--------------~v~~~A~~vr~~L-~~lgL~~f-~KTSG~kGlHV~vP 144 (223)
T cd04866 94 SEIVFDLDPPSRDHFS--------------LAVEAANLLKEIL-DALGLTSF-VKTSGNKGLQVYIP 144 (223)
T ss_pred CeEEEECCCCCCCCHH--------------HHHHHHHHHHHHH-HHcCCccc-eEccCCCeEEEEEE
Confidence 4599999987443333 3445667777566 68899876 47899999999994
No 15
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=93.97 E-value=0.27 Score=48.40 Aligned_cols=68 Identities=24% Similarity=0.262 Sum_probs=46.0
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHH
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRG 200 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~ 200 (439)
-+||||+|-.+- + |..+..+..++...| +.+|.... ..=||++|+|+.|-=+. ..+-++=+
T Consensus 101 D~~vfDLDP~~~-~--------------f~~v~~~A~~~r~~L-~~~gL~~f-~KTSG~kGlHv~vPl~~--~~~~~~~r 161 (228)
T cd04864 101 DLMVFDLDPSAD-D--------------IEAVRTAALAVRELL-DELGLPSF-VKTTGSRGFHVVVPLDG--RGDFDDVR 161 (228)
T ss_pred CEEEEecCCCCC-C--------------HHHHHHHHHHHHHHH-HHcCCccc-eEccCCCeEEEEEEcCC--CCCHHHHH
Confidence 679999998633 3 334455666777565 68899876 47899999999995322 46655555
Q ss_pred HHHhHhh
Q 013616 201 AIADYFR 207 (439)
Q Consensus 201 aIvdYl~ 207 (439)
+++..|.
T Consensus 162 ~fa~~lA 168 (228)
T cd04864 162 AFAAEAA 168 (228)
T ss_pred HHHHHHH
Confidence 5555443
No 16
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=92.71 E-value=0.22 Score=54.66 Aligned_cols=51 Identities=25% Similarity=0.408 Sum_probs=38.7
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEee
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVC 187 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~ 187 (439)
-+||||+|-.+-.+ |..+..|..++...| +.+|.... .--||++|+|++|-
T Consensus 392 d~~v~DLDP~~~~~--------------f~~v~~~A~~~r~~L-~~~gl~~~-~KtSG~kGlhv~vP 442 (552)
T TIGR02776 392 DRIVFDLDPPPGVA--------------FKLAVEAAQLMKQLL-DELGLVSF-VKTSGGKGLHVVVP 442 (552)
T ss_pred CEEEEECCCCCCCC--------------HHHHHHHHHHHHHHH-HHcCCccc-eEccCCCeEEEEEE
Confidence 57999999874433 444556667777566 58899886 47899999999994
No 17
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=92.12 E-value=0.29 Score=54.40 Aligned_cols=51 Identities=27% Similarity=0.563 Sum_probs=38.4
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEee
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVC 187 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~ 187 (439)
-+||||+|-.+-.+ |..+..|..++...| +++|.... .--||++|+|++|-
T Consensus 433 d~~v~DLDP~~~~~--------------~~~v~~~A~~~r~~L-~~~gl~~~-~ktSG~kGlhv~vP 483 (610)
T PRK09633 433 TEIVFDLDPPSRDE--------------FPLAVEAALELKRLF-DQFGLTSF-VKTSGNKGLQLYIP 483 (610)
T ss_pred CEEEEECCCCCCCC--------------HHHHHHHHHHHHHHH-HHcCCccc-eEccCCCeEEEEEE
Confidence 67999999865544 334455667777565 66899886 47899999999994
No 18
>COG3285 Predicted eukaryotic-type DNA primase [DNA replication, recombination, and repair]
Probab=92.05 E-value=0.35 Score=49.05 Aligned_cols=46 Identities=26% Similarity=0.395 Sum_probs=37.1
Q ss_pred ccccccccCccccCCCc-cEEEEcCCCCCCCCC-C--CCCCcHHHHHHhh
Q 013616 336 HRNHLLKAPFCVHPKTG-RVCIPIDPKDCEEFD-P--TTVPTLSELLREL 381 (439)
Q Consensus 336 d~nHLLKsPfcvHpkTG-~vcVPid~~~l~~FD-P--~~VPtl~~l~~e~ 381 (439)
+..+=.-+|||+-+.+| .|++|+..++|+.=+ | ++..|+-+++...
T Consensus 226 ~rg~T~vapYS~Rar~g~~Vs~Pl~W~el~~~~~p~~ft~~tvp~rl~~~ 275 (299)
T COG3285 226 ARGKTAVAPYSPRARPGATVSTPLTWEELEGLLAPDQFTIRTVPERLAKS 275 (299)
T ss_pred CCCceeecccCccCCCCCcccccccHHHhcCccChhhccccchHHHHHhc
Confidence 44556679999999998 899999999988877 6 4677777777765
No 19
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=89.26 E-value=0.75 Score=53.09 Aligned_cols=66 Identities=32% Similarity=0.503 Sum_probs=44.7
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHH
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRG 200 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~ 200 (439)
-+||||+|-..-.+ |..+..|..++...| +++|..... -=||++|+||+|-=. ...+-++=+
T Consensus 685 d~lvfDLDP~~~~~--------------f~~v~~aA~~~r~~L-~~lgL~sf~-KTSG~kGlHv~vPl~--~~~~~~~~~ 746 (860)
T PRK05972 685 DRLVFDLDPGPGVP--------------WKAVVEAARLMRTRL-DELGLESFL-KTSGGKGLHVVVPLA--RRLDWDEVK 746 (860)
T ss_pred CEEEEECCCCCCCC--------------HHHHHHHHHHHHHHH-HHcCCceee-ECCCCCeEEEEEEcC--CCCCHHHHH
Confidence 57999999875433 444556667777555 689998764 789999999999432 245544444
Q ss_pred HHHh
Q 013616 201 AIAD 204 (439)
Q Consensus 201 aIvd 204 (439)
+.+.
T Consensus 747 ~fa~ 750 (860)
T PRK05972 747 AFAQ 750 (860)
T ss_pred HHHH
Confidence 4444
No 20
>COG1467 PRI1 Eukaryotic-type DNA primase, catalytic (small) subunit [DNA replication, recombination, and repair]
Probab=89.00 E-value=0.48 Score=49.18 Aligned_cols=58 Identities=17% Similarity=0.174 Sum_probs=49.3
Q ss_pred ccccccccccccccccccCccccCCCccEEEEcCCCCCCCCCCCC--CCcHHHHHHhhhc
Q 013616 326 YPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPTT--VPTLSELLRELNT 383 (439)
Q Consensus 326 ypRLD~~VTkd~nHLLKsPfcvHpkTG~vcVPid~~~l~~FDP~~--VPtl~~l~~e~~~ 383 (439)
-..+|++||.+..+|++.|.|+|++++++|.++.+.+...|+|+. ++-..++-+.+..
T Consensus 238 ~i~~~~~v~~d~~r~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~d~~v~~d~~~~~~~ 297 (341)
T COG1467 238 LIAIDEKVTNDITRLIRLPGSLDGKGFLTVARLGLDELRVFSPLYLDGEVTKDLKRLLRL 297 (341)
T ss_pred hhccccccccccHHHHhcccccCCcceeeeccccccccccccccccCcccccchHHhhcc
Confidence 356899999999999999999999999999999999999999997 4555555555544
No 21
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=88.79 E-value=1 Score=51.38 Aligned_cols=69 Identities=20% Similarity=0.334 Sum_probs=45.5
Q ss_pred ceEEEeccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHH
Q 013616 121 RELIFDIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRG 200 (439)
Q Consensus 121 ~ELVFDID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~ 200 (439)
-.||||+|-.+--+.. .+..|...+...| +++|.... ..=||.+|+|++|-= ....+-++=+
T Consensus 136 D~lv~DLDP~~~~~f~--------------~v~~~A~~~r~~L-~~lgL~~~-~KTSG~kGlHv~vPl--~~~~~~~~~~ 197 (764)
T PRK09632 136 TRLVFDLDPGEGVGLA--------------ECAEVARAVRDLL-ADIGLETF-PVTSGSKGIHLYAPL--DGPVSSEGAS 197 (764)
T ss_pred CEEEEECCCCCCCCHH--------------HHHHHHHHHHHHH-HHcCCcee-eECCCCCeEEEEEEC--CCCCCHHHHH
Confidence 4699999986543333 3445667777565 68899876 488999999999942 2245544433
Q ss_pred ----HHHhHhh
Q 013616 201 ----AIADYFR 207 (439)
Q Consensus 201 ----aIvdYl~ 207 (439)
+|+.+|.
T Consensus 198 ~fa~~~A~~l~ 208 (764)
T PRK09632 198 VVAKEVARALE 208 (764)
T ss_pred HHHHHHHHHHH
Confidence 4455544
No 22
>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=75.58 E-value=8.6 Score=31.00 Aligned_cols=53 Identities=19% Similarity=0.357 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHHHHHhHhhh
Q 013616 149 WPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADYFRV 208 (439)
Q Consensus 149 w~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~aIvdYl~v 208 (439)
+.-+...+.-+-.-+++.+|...+.++|++.+||++-|....+-++.+ +|+.+
T Consensus 13 ~~~~~~~l~~~~~~~~~~~~~~~lk~~~~~~~gy~i~v~~~~~~~~p~-------~~~~~ 65 (92)
T PF05190_consen 13 YEEIEEELEELLEEIRKKLGIPSLKLVYIPKRGYLIEVPKSDEKKLPK-------DFIIV 65 (92)
T ss_dssp HHHHHHHHHHHHHHHHHHCT-TTBEEEEETTTEEEEEEETCCGGGSTT-------TEEEE
T ss_pred HHHHHHHHHHHHHHHHHHcCCCcEEEEEcCceEEEEEEEccccccCCC-------ceEEE
Confidence 334444444444578899999999999999999999998777777744 77764
No 23
>PF09641 DUF2026: Protein of unknown function (DUF2026); InterPro: IPR018599 This protein of approx. 100 residues is found in bacteria. It contains up to five alpha helices and up to seven beta strands and is probably monomeric. Its function is unknown. ; PDB: 2HLY_A.
Probab=52.88 E-value=6.2 Score=38.15 Aligned_cols=46 Identities=26% Similarity=0.454 Sum_probs=23.8
Q ss_pred CccccccHHHHHHHHHHHHHHHhhhcCCc-------------------------eeEEEEeCCCceEEEe-echhhc
Q 013616 142 ADVCLECWPLMTVAIKVIDTALRDDFGFD-------------------------HILWVYSGRRGVHCWV-CDGKAR 192 (439)
Q Consensus 142 ~~iC~kCw~~~~~a~klld~~L~~dFGf~-------------------------~i~~VFSGrRG~H~wV-~D~~ar 192 (439)
++.-.-||-|....+-||. +.++.+ +=.|+.+|- |||||| ||.-|.
T Consensus 21 Ad~~~Ac~fFs~~Ga~IL~----~hYk~~A~~~~G~aay~l~e~~~vl~Fg~~edg~v~~~~d-~FH~WVeaDg~~I 92 (204)
T PF09641_consen 21 ADTAKACMFFSTFGAFILR----DHYKIEAKPKAGAAAYNLGEEETVLFFGRIEDGQVQSAED-AFHCWVEADGWAI 92 (204)
T ss_dssp --HHHHHHHHHHHHHHHHH----HHH---EEEEEEEEEEEET--TEEEEES------B--SST-T-EEEEEETTEEE
T ss_pred CChhHHHHHHHHHHHHHHH----HHhcccceechhHHHHhcccccceeEEEeeeCCeEeccCc-ceEEEEEeCCEee
Confidence 3444568888877766654 333332 112444444 999999 787765
No 24
>PF01116 F_bP_aldolase: Fructose-bisphosphate aldolase class-II; InterPro: IPR000771 Fructose-bisphosphate aldolase [, ] is a glycolytic enzyme that catalyses the reversible aldol cleavage or condensation of fructose-1,6-bisphosphate into dihydroxyacetone-phosphate and glyceraldehyde 3-phosphate. There are two classes of fructose-bisphosphate aldolases with different catalytic mechanisms. Class-II aldolases [], mainly found in prokaryotes and fungi, are homodimeric enzymes, which require a divalent metal ion, generally zinc, for their activity. This family also includes the Escherichia coli galactitol operon protein, gatY, which catalyses the transformation of tagatose 1,6-bisphosphate into glycerone phosphate and D-glyceraldehyde 3-phosphate; and E. coli N-acetyl galactosamine operon protein, agaY, which catalyses the same reaction. There are two histidine residues in the first half of the sequence of these enzymes that have been shown to be involved in binding a zinc ion [].; GO: 0008270 zinc ion binding, 0016832 aldehyde-lyase activity, 0005975 carbohydrate metabolic process; PDB: 3Q94_A 1RVG_B 1RV8_C 3C4U_A 3C56_B 3C52_A 2FJK_A 3N9R_P 3N9S_A 1GVF_B ....
Probab=40.93 E-value=5.5 Score=40.41 Aligned_cols=27 Identities=26% Similarity=0.519 Sum_probs=22.8
Q ss_pred ccccccccccccccc-ccCccccCCCcc
Q 013616 327 PRLDMEVSKHRNHLL-KAPFCVHPKTGR 353 (439)
Q Consensus 327 pRLD~~VTkd~nHLL-KsPfcvHpkTG~ 353 (439)
|.||..+-+.++..+ ..|..+||+||.
T Consensus 189 p~Ld~~~L~~I~~~~~~iPLVlHGgSG~ 216 (287)
T PF01116_consen 189 PKLDFDRLKEIREAVPDIPLVLHGGSGL 216 (287)
T ss_dssp TC--HHHHHHHHHHHHTSEEEESSCTTS
T ss_pred cccCHHHHHHHHHhcCCCCEEEECCCCC
Confidence 778888899999999 999999999994
No 25
>cd00947 TBP_aldolase_IIB Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. The type A and type B Class II FBPA's differ in the presence and absence of distinct indels in the sequence that result in differing loop lengths in the structures.
Probab=40.56 E-value=7.1 Score=39.48 Aligned_cols=27 Identities=26% Similarity=0.512 Sum_probs=24.8
Q ss_pred cccccccccccccccccCccccCCCcc
Q 013616 327 PRLDMEVSKHRNHLLKAPFCVHPKTGR 353 (439)
Q Consensus 327 pRLD~~VTkd~nHLLKsPfcvHpkTG~ 353 (439)
|.||.++-+.++.-+..|..+||+||.
T Consensus 181 p~L~~~~L~~i~~~~~vPLVlHGgSG~ 207 (276)
T cd00947 181 PKLDFDRLKEIAERVNVPLVLHGGSGI 207 (276)
T ss_pred CccCHHHHHHHHHHhCCCEEEeCCCCC
Confidence 889999999999999999999999973
No 26
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=40.09 E-value=41 Score=31.90 Aligned_cols=48 Identities=15% Similarity=0.466 Sum_probs=30.7
Q ss_pred Ccccc--cC----CCccccccHHHHHHHHHHHHH--HHhhhcCC----ceeEEEEeCCCc
Q 013616 134 DVRYC--CS----GADVCLECWPLMTVAIKVIDT--ALRDDFGF----DHILWVYSGRRG 181 (439)
Q Consensus 134 ~ir~C--C~----~~~iC~kCw~~~~~a~klld~--~L~~dFGf----~~i~~VFSGrRG 181 (439)
.+++| |+ ...+|.-|+.-+..-...+.. ...+-.++ +...+.|-|++-
T Consensus 92 nl~~CP~CGh~k~a~~LC~~Cy~kV~ket~ei~~k~~iq~~~~~e~~d~e~~Vly~Ge~d 151 (176)
T KOG4080|consen 92 NLNTCPACGHIKPAHTLCDYCYAKVHKETSEIKKKMMIQEPYVGEKQDKEVYVLYRGEPD 151 (176)
T ss_pred ccccCcccCccccccccHHHHHHHHHHHHHHHHHHHhccCCCCCCcCcceEEEEecCCCC
Confidence 45677 54 345899999887643333332 33455555 578889999963
No 27
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=39.71 E-value=28 Score=31.84 Aligned_cols=26 Identities=27% Similarity=0.512 Sum_probs=21.6
Q ss_pred CCccccccHHHHHHHHHHHHHHHhhh
Q 013616 141 GADVCLECWPLMTVAIKVIDTALRDD 166 (439)
Q Consensus 141 ~~~iC~kCw~~~~~a~klld~~L~~d 166 (439)
+..+|+.|+.........+..+|++.
T Consensus 17 ~~~iCp~C~~~~e~~f~kV~~yLr~~ 42 (137)
T TIGR03826 17 GRDVCPSCYEEEEREFEKVYKFLRKH 42 (137)
T ss_pred CCccCHHHhHHHHHHHHHHHHHHHHC
Confidence 67899999999888877777788854
No 28
>PRK07998 gatY putative fructose-1,6-bisphosphate aldolase; Reviewed
Probab=37.91 E-value=9.4 Score=38.79 Aligned_cols=27 Identities=26% Similarity=0.543 Sum_probs=25.1
Q ss_pred cccccccccccccccccCccccCCCcc
Q 013616 327 PRLDMEVSKHRNHLLKAPFCVHPKTGR 353 (439)
Q Consensus 327 pRLD~~VTkd~nHLLKsPfcvHpkTG~ 353 (439)
|.||.++.+.++..+..|..+||+||.
T Consensus 184 p~l~~~~l~~I~~~~~vPLVlHGgSG~ 210 (283)
T PRK07998 184 PRIDIPLLKRIAEVSPVPLVIHGGSGI 210 (283)
T ss_pred CCcCHHHHHHHHhhCCCCEEEeCCCCC
Confidence 999999999999999999999999973
No 29
>PRK12737 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=37.13 E-value=8.5 Score=39.05 Aligned_cols=26 Identities=27% Similarity=0.525 Sum_probs=24.6
Q ss_pred cccccccccccccccccCccccCCCc
Q 013616 327 PRLDMEVSKHRNHLLKAPFCVHPKTG 352 (439)
Q Consensus 327 pRLD~~VTkd~nHLLKsPfcvHpkTG 352 (439)
|+||..+-+.++..+..|-.+||+||
T Consensus 187 p~Ld~~~L~~I~~~~~iPLVlHGgSG 212 (284)
T PRK12737 187 PKLDFERLAEIREKVSIPLVLHGASG 212 (284)
T ss_pred CcCCHHHHHHHHHHhCCCEEEeCCCC
Confidence 88999999999999999999999999
No 30
>COG3516 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.33 E-value=24 Score=33.34 Aligned_cols=44 Identities=27% Similarity=0.541 Sum_probs=37.5
Q ss_pred ccccccccccccccccccCccccCCCccEEEEcCCCCCCCCCCC----CCCcHHHHHH
Q 013616 326 YPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPT----TVPTLSELLR 379 (439)
Q Consensus 326 ypRLD~~VTkd~nHLLKsPfcvHpkTG~vcVPid~~~l~~FDP~----~VPtl~~l~~ 379 (439)
-||+=-.| |-.+-+..|...|-|+.+.+++|.|. .||-+.+|++
T Consensus 75 ~prl~~~V----------~NtL~gdg~~l~V~L~f~smdDFsP~~Va~qVp~L~kLLe 122 (169)
T COG3516 75 EPRLKFAV----------PNTLTGDGTELAVDLTFESMDDFSPDAVARQVPELKKLLE 122 (169)
T ss_pred CCCcEEEC----------CccccCCCceeeeeeeecccccCCHHHHHHhhHHHHHHHH
Confidence 48877666 66777888899999999999999998 5899999886
No 31
>PRK12857 fructose-1,6-bisphosphate aldolase; Reviewed
Probab=34.19 E-value=10 Score=38.51 Aligned_cols=27 Identities=26% Similarity=0.556 Sum_probs=23.4
Q ss_pred cccccccccccccccccCccccCCCcc
Q 013616 327 PRLDMEVSKHRNHLLKAPFCVHPKTGR 353 (439)
Q Consensus 327 pRLD~~VTkd~nHLLKsPfcvHpkTG~ 353 (439)
|+||..+-+.++-.+..|..+||+||.
T Consensus 187 p~Ld~~~L~~i~~~~~vPLVlHGgSG~ 213 (284)
T PRK12857 187 PKLDFDRLAKIKELVNIPIVLHGSSGV 213 (284)
T ss_pred CcCCHHHHHHHHHHhCCCEEEeCCCCC
Confidence 778888888888888899999999984
No 32
>TIGR00167 cbbA ketose-bisphosphate aldolases. fructose-bisphosphate and tagatose-bisphosphate aldolase.
Probab=32.95 E-value=11 Score=38.23 Aligned_cols=27 Identities=26% Similarity=0.524 Sum_probs=24.4
Q ss_pred cc-cccccccccccccccCccccCCCcc
Q 013616 327 PR-LDMEVSKHRNHLLKAPFCVHPKTGR 353 (439)
Q Consensus 327 pR-LD~~VTkd~nHLLKsPfcvHpkTG~ 353 (439)
|. ||..+-+.++..+..|..+||+||.
T Consensus 190 p~~Ld~~~L~~I~~~v~vPLVlHGgSG~ 217 (288)
T TIGR00167 190 PKGLDFERLEEIQKYVNLPLVLHGGSGI 217 (288)
T ss_pred CCccCHHHHHHHHHHhCCCEEEeCCCCC
Confidence 77 8999999999999999999999973
No 33
>TIGR01858 tag_bisphos_ald class II aldolase, tagatose bisphosphate family. This model describes tagatose-1,6-bisphosphate aldolases, and perhaps other closely related class II aldolases. This tetrameric, Zn2+-dependent enzyme is related to the class II fructose bisphosphate aldolase; fructose 1,6-bisphosphate and tagatose 1,6 bisphosphate differ only in chirality at C4.
Probab=32.65 E-value=11 Score=38.18 Aligned_cols=27 Identities=19% Similarity=0.454 Sum_probs=24.7
Q ss_pred cccccccccccccccccCccccCCCcc
Q 013616 327 PRLDMEVSKHRNHLLKAPFCVHPKTGR 353 (439)
Q Consensus 327 pRLD~~VTkd~nHLLKsPfcvHpkTG~ 353 (439)
|.||.++-+.++..+..|..+||+||.
T Consensus 185 p~Ldf~~L~~I~~~~~iPLVlHGgSG~ 211 (282)
T TIGR01858 185 PKLDFDRLAEIREVVDVPLVLHGASDV 211 (282)
T ss_pred CccCHHHHHHHHHHhCCCeEEecCCCC
Confidence 888888888888888999999999997
No 34
>PRK12738 kbaY tagatose-bisphosphate aldolase; Reviewed
Probab=32.13 E-value=12 Score=38.15 Aligned_cols=26 Identities=15% Similarity=0.469 Sum_probs=24.1
Q ss_pred cccccccccccccccccCccccCCCc
Q 013616 327 PRLDMEVSKHRNHLLKAPFCVHPKTG 352 (439)
Q Consensus 327 pRLD~~VTkd~nHLLKsPfcvHpkTG 352 (439)
|+||-..-+.++..+..|-.+||+||
T Consensus 187 p~Ldfd~l~~I~~~~~vPLVLHGgSG 212 (286)
T PRK12738 187 PKIDFQRLAEIREVVDVPLVLHGASD 212 (286)
T ss_pred CcCCHHHHHHHHHHhCCCEEEeCCCC
Confidence 88898888888888999999999999
No 35
>PRK09195 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=28.95 E-value=14 Score=37.53 Aligned_cols=26 Identities=23% Similarity=0.581 Sum_probs=24.1
Q ss_pred cccccccccccccccccCccccCCCc
Q 013616 327 PRLDMEVSKHRNHLLKAPFCVHPKTG 352 (439)
Q Consensus 327 pRLD~~VTkd~nHLLKsPfcvHpkTG 352 (439)
|.||.++.+.++..+..|-.+||+||
T Consensus 187 p~Ld~~~L~~I~~~~~vPLVLHGgSG 212 (284)
T PRK09195 187 PKLDFDRLENIRQWVNIPLVLHGASG 212 (284)
T ss_pred CcCCHHHHHHHHHHhCCCeEEecCCC
Confidence 88999999999999999999999997
No 36
>PRK08610 fructose-bisphosphate aldolase; Reviewed
Probab=28.08 E-value=15 Score=37.41 Aligned_cols=27 Identities=22% Similarity=0.338 Sum_probs=23.7
Q ss_pred cccccccccccccccccCccccCCCcc
Q 013616 327 PRLDMEVSKHRNHLLKAPFCVHPKTGR 353 (439)
Q Consensus 327 pRLD~~VTkd~nHLLKsPfcvHpkTG~ 353 (439)
|.||..+-+.++..+..|..+||+||.
T Consensus 188 p~Ld~~~L~~I~~~~~vPLVLHGgSG~ 214 (286)
T PRK08610 188 PKLGFKEMEEIGLSTGLPLVLHGGTGI 214 (286)
T ss_pred CCCCHHHHHHHHHHHCCCEEEeCCCCC
Confidence 788888888888888899999999984
No 37
>cd04859 Prim_Pol Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.
Probab=27.18 E-value=1.3e+02 Score=26.65 Aligned_cols=23 Identities=22% Similarity=0.218 Sum_probs=16.9
Q ss_pred eEEEEeCCCceEEEeechhhccC
Q 013616 172 ILWVYSGRRGVHCWVCDGKARRL 194 (439)
Q Consensus 172 i~~VFSGrRG~H~wV~D~~ar~L 194 (439)
-.+|-||+.|+|++..-+.-...
T Consensus 79 t~~~~t~~~G~h~~f~~p~~~~~ 101 (152)
T cd04859 79 TLTVRTGSGGRHLYFRVPDGVPV 101 (152)
T ss_pred CeEEECCCCceEEEEeCCCCccc
Confidence 56789999999999875544433
No 38
>PF09250 Prim-Pol: Bifunctional DNA primase/polymerase, N-terminal; InterPro: IPR015330 Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities []. ; PDB: 1RO0_A 1RNI_A 1RO2_A 3M1M_A.
Probab=27.14 E-value=34 Score=30.44 Aligned_cols=18 Identities=17% Similarity=0.041 Sum_probs=11.7
Q ss_pred eEEEEeCCCceEEEeech
Q 013616 172 ILWVYSGRRGVHCWVCDG 189 (439)
Q Consensus 172 i~~VFSGrRG~H~wV~D~ 189 (439)
-.+|=|++.|+|++..-+
T Consensus 85 t~~~~T~~gG~h~~f~~~ 102 (163)
T PF09250_consen 85 TPVVRTPSGGRHFYFRVP 102 (163)
T ss_dssp S-EEE-TTS-EEEEEE-S
T ss_pred cEEEECCCCCEEEEEEcC
Confidence 567899999999999633
No 39
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=23.80 E-value=38 Score=35.58 Aligned_cols=78 Identities=18% Similarity=0.314 Sum_probs=43.5
Q ss_pred eccCCCCCCcccccCCCccccccHHHHHHHHHHHHHHHhhhcCCceeEEEEeCCCceEEEeechhhccCChHHHHHHHhH
Q 013616 126 DIDITDYDDVRYCCSGADVCLECWPLMTVAIKVIDTALRDDFGFDHILWVYSGRRGVHCWVCDGKARRLTNEQRGAIADY 205 (439)
Q Consensus 126 DID~~dyd~ir~CC~~~~iC~kCw~~~~~a~klld~~L~~dFGf~~i~~VFSGrRG~H~wV~D~~ar~L~~e~R~aIvdY 205 (439)
-||++|-. .--|.-|..||.=||.-|++-+.=---+.|.-+.-+++.||=-----.-.-+.-++-|++-..+|.+ ++|
T Consensus 23 ~mditdkn-f~pc~cgy~ic~fc~~~irq~lngrcpacrr~y~denv~~~~~s~ee~kmel~rk~erk~rekerke-~e~ 100 (480)
T COG5175 23 PMDITDKN-FFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDENVRYVTLSPEELKMELARKEERKMREKERKE-AEG 100 (480)
T ss_pred ccccccCC-cccCCcccHHHHHHHHHHHhhccCCChHhhhhccccceeEEecCHHHHHHHHHhhhhhhccHHHHhh-hhc
Confidence 47888774 4568779999999999988642221234445545567777632221111112223344555555553 444
No 40
>KOG0874 consensus Sphingolipid hydroxylase [Lipid transport and metabolism]
Probab=23.78 E-value=28 Score=34.54 Aligned_cols=38 Identities=29% Similarity=0.496 Sum_probs=23.3
Q ss_pred eEEEEeCCCceEEEeechh---hccCC--hHHHHHHHhHhhhccC
Q 013616 172 ILWVYSGRRGVHCWVCDGK---ARRLT--NEQRGAIADYFRVYKG 211 (439)
Q Consensus 172 i~~VFSGrRG~H~wV~D~~---ar~L~--~e~R~aIvdYl~vv~G 211 (439)
+-||+|| |+|+.++=.. .|-=+ .++||..|.=..||+|
T Consensus 24 vYWv~Sg--~f~~yi~l~~~ekYRiHp~ee~a~rN~vskmaVvk~ 66 (287)
T KOG0874|consen 24 VYWVYSG--IFHVYITLHSLEKYRIHPKEEEAERNLVSKMAVVKG 66 (287)
T ss_pred HHhhhcC--CceEEEEechhhhhcCCChHHHHHhccchHHHHHHH
Confidence 4699999 9999997433 33222 2345555555555443
No 41
>PRK09462 fur ferric uptake regulator; Provisional
Probab=23.55 E-value=65 Score=28.93 Aligned_cols=87 Identities=15% Similarity=0.292 Sum_probs=49.6
Q ss_pred cCCHHHHHHHHHHhCCCceeeccccccCccchhhhccCCCCCcCcccceEEEeccCCC----CCCcccc-cC--CCcccc
Q 013616 74 FNSESELENSIKEKCPSKIDIGPVYSVDPAKRHAYAQGGDNVFAPVERELIFDIDITD----YDDVRYC-CS--GADVCL 146 (439)
Q Consensus 74 F~~~~el~~~l~~~~P~~i~igavY~~~P~~~~~~~~~~~~~f~p~~~ELVFDID~~d----yd~ir~C-C~--~~~iC~ 146 (439)
.-|++|+.+.|.+..| .+..+.||..-- . | .+.-||-=++..+ |+ .| +. ..-||.
T Consensus 33 h~sa~eI~~~l~~~~~-~i~~aTVYR~L~----~--------L--~e~Gli~~~~~~~~~~~y~---~~~~~~H~H~iC~ 94 (148)
T PRK09462 33 HVSAEDLYKRLIDMGE-EIGLATVYRVLN----Q--------F--DDAGIVTRHNFEGGKSVFE---LTQQHHHDHLICL 94 (148)
T ss_pred CCCHHHHHHHHHhhCC-CCCHHHHHHHHH----H--------H--HHCCCEEEEEcCCCcEEEE---eCCCCCCCceEEC
Confidence 4599999999998886 577899998421 1 2 3333343333222 21 11 11 124788
Q ss_pred ccHHHHH---HHHHHHHHHHhhhcCC--ceeEEEEeC
Q 013616 147 ECWPLMT---VAIKVIDTALRDDFGF--DHILWVYSG 178 (439)
Q Consensus 147 kCw~~~~---~a~klld~~L~~dFGf--~~i~~VFSG 178 (439)
+|-..+. ..+..+...+.+.-|| ....++|.|
T Consensus 95 ~Cg~i~~i~~~~~~~~~~~~~~~~gf~i~~~~l~i~G 131 (148)
T PRK09462 95 DCGKVIEFSDDSIEARQREIAAKHGIKLTNHSLYLYG 131 (148)
T ss_pred CCCCEEEeCCcHHHHHHHHHHHHcCCEEeeeEEEEEE
Confidence 8876543 2333333355566688 556677777
No 42
>COG0191 Fba Fructose/tagatose bisphosphate aldolase [Carbohydrate transport and metabolism]
Probab=23.35 E-value=21 Score=36.44 Aligned_cols=26 Identities=27% Similarity=0.562 Sum_probs=23.0
Q ss_pred cccccccccccccccccCccccCCCc
Q 013616 327 PRLDMEVSKHRNHLLKAPFCVHPKTG 352 (439)
Q Consensus 327 pRLD~~VTkd~nHLLKsPfcvHpkTG 352 (439)
|.||...-+.++.+...|+.+||+||
T Consensus 189 p~L~~~~L~~i~~~~~~PlVlHGgSG 214 (286)
T COG0191 189 PKLDFDRLKEIQEAVSLPLVLHGGSG 214 (286)
T ss_pred CCCCHHHHHHHHHHhCCCEEEeCCCC
Confidence 67888888888888889999999995
No 43
>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=22.75 E-value=45 Score=33.12 Aligned_cols=18 Identities=28% Similarity=0.335 Sum_probs=16.0
Q ss_pred cCccccCCCccEEEEcCC
Q 013616 343 APFCVHPKTGRVCIPIDP 360 (439)
Q Consensus 343 sPfcvHpkTG~vcVPid~ 360 (439)
.||.|+||+|.+++|++.
T Consensus 217 I~F~V~P~~Glkvep~Sv 234 (235)
T COG2874 217 ISFRVEPGFGLKVEPASV 234 (235)
T ss_pred eeEEecCCCceEEEEeec
Confidence 389999999999999864
No 44
>PF05591 DUF770: Protein of unknown function (DUF770); InterPro: IPR008312 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, these proteins are encoded in type VI secretion loci (including the SCI genomic island in Salmonella enterica and the imp locus in Rhizobium leguminosarum) implicated in pathogenicity and protein secretion [, , [].
Probab=22.04 E-value=62 Score=30.24 Aligned_cols=47 Identities=26% Similarity=0.516 Sum_probs=36.2
Q ss_pred hccccccccccccccccccCccccCCCccEEEEcCCCCCCCCCCC----CCCcHHHHHHhh
Q 013616 325 TYPRLDMEVSKHRNHLLKAPFCVHPKTGRVCIPIDPKDCEEFDPT----TVPTLSELLREL 381 (439)
Q Consensus 325 ~ypRLD~~VTkd~nHLLKsPfcvHpkTG~vcVPid~~~l~~FDP~----~VPtl~~l~~e~ 381 (439)
+-|+++..|-.. +-...|.+.|.+..+.+++|.|. .||-+..|++--
T Consensus 68 ~~p~l~~~V~n~----------L~~~~~~l~V~L~f~sm~DF~Pd~v~~qVp~L~~LlelR 118 (157)
T PF05591_consen 68 MAPRLSFSVPNR----------LSDDGGELSVDLKFESMDDFHPDAVAEQVPELRKLLELR 118 (157)
T ss_pred CCCceEEEeCCc----------cccCCCcceeEEeeCccccCCHHHHHHhhHHHHHHHHHH
Confidence 458888888332 33446889999999999999998 589888887643
No 45
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=21.35 E-value=70 Score=24.36 Aligned_cols=14 Identities=36% Similarity=0.653 Sum_probs=13.4
Q ss_pred cCChHHHHHHHhHh
Q 013616 193 RLTNEQRGAIADYF 206 (439)
Q Consensus 193 ~L~~e~R~aIvdYl 206 (439)
.|+++++.+|+.||
T Consensus 54 ~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 54 QLSDEEIEALAAYI 67 (67)
T ss_dssp TSTHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHC
Confidence 89999999999997
No 46
>PF03090 Replicase: Replicase family; InterPro: IPR004322 This is a family of bacterial plasmid DNA replication initiator proteins. These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or may be mediated by Hsp70 chaperones. A similar RepA family of proteins found mainly in Escherichia coli is involved in plasmid replication (see IPR000525 from INTERPRO).
Probab=21.33 E-value=1.4e+02 Score=27.11 Aligned_cols=24 Identities=13% Similarity=0.300 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHHHhhhcCCcee
Q 013616 149 WPLMTVAIKVIDTALRDDFGFDHI 172 (439)
Q Consensus 149 w~~~~~a~klld~~L~~dFGf~~i 172 (439)
..+++...+-|...|..|-||.++
T Consensus 84 l~ylaav~~~L~~~L~aD~~ysg~ 107 (137)
T PF03090_consen 84 LRYLAAVERALTRKLGADPGYSGL 107 (137)
T ss_pred HHHHHHHHHHHHHHhCCCcccCCc
Confidence 355555566666788888887443
No 47
>cd00453 FTBP_aldolase_II Fructose/tagarose-bisphosphate aldolase class II. This family includes fructose-1,6-bisphosphate (FBP) and tagarose 1,6-bisphosphate (TBP) aldolases. FBP-aldolase is homodimeric and used in gluconeogenesis and glycolysis; the enzyme controls the condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to yield fructose-1,6-bisphosphate. TBP-aldolase is tetrameric and produces tagarose-1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. Although structurally similar, the class I aldolases use a different mechanism and are believed to have an independent evolutionary origin.
Probab=20.50 E-value=25 Score=36.75 Aligned_cols=27 Identities=15% Similarity=0.258 Sum_probs=21.3
Q ss_pred ccccccccccccccc---------ccCccccCCCcc
Q 013616 327 PRLDMEVSKHRNHLL---------KAPFCVHPKTGR 353 (439)
Q Consensus 327 pRLD~~VTkd~nHLL---------KsPfcvHpkTG~ 353 (439)
|+||..+-+.++..+ ..|+.+||+||.
T Consensus 218 p~L~~~~L~~i~~~~~~~~gl~~~~~pLVlHGgSG~ 253 (340)
T cd00453 218 VVLTPTILRDSQEYVSKKHNLPHNSLNFVFHGGSGS 253 (340)
T ss_pred CccCHHHHHHHHHHHHhhcccCCCCCceEEeCCCCC
Confidence 667777777776666 689999999995
No 48
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=20.50 E-value=63 Score=30.61 Aligned_cols=19 Identities=26% Similarity=0.529 Sum_probs=13.2
Q ss_pred cCChHHHHHHHhHhhhccC
Q 013616 193 RLTNEQRGAIADYFRVYKG 211 (439)
Q Consensus 193 ~L~~e~R~aIvdYl~vv~G 211 (439)
.+++++|++||+||.=-.|
T Consensus 50 ~Is~eer~avVkYLAd~~G 68 (167)
T PF09098_consen 50 PISPEERRAVVKYLADTQG 68 (167)
T ss_dssp ---HHHHHHHHHHHHHHT-
T ss_pred CCCHHHHHHHHHHHHHccC
Confidence 6899999999999985444
Done!