Query psy4521
Match_columns 223
No_of_seqs 120 out of 182
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 19:17:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4521.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4521hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2373|consensus 100.0 1.4E-40 3.1E-45 305.0 10.1 192 8-207 63-272 (514)
2 TIGR01391 dnaG DNA primase, ca 99.7 3.2E-16 6.9E-21 147.4 11.6 145 7-156 201-365 (415)
3 TIGR00646 MG010 DNA primase-re 99.6 1.6E-15 3.5E-20 132.1 12.1 145 4-152 55-215 (218)
4 PRK07078 hypothetical protein; 99.5 1.8E-13 3.9E-18 137.4 15.5 143 7-153 134-298 (759)
5 PRK05667 dnaG DNA primase; Val 99.5 7.7E-14 1.7E-18 136.5 12.1 145 7-156 197-364 (580)
6 PF13155 Toprim_2: Toprim-like 99.3 9.7E-13 2.1E-17 98.7 3.8 83 56-139 1-96 (96)
7 cd03364 TOPRIM_DnaG_primases T 99.2 1.4E-11 3.1E-16 90.3 6.2 72 53-127 1-78 (79)
8 PF13662 Toprim_4: Toprim doma 99.2 4.8E-12 1E-16 93.2 3.4 70 53-124 1-76 (81)
9 PHA02415 DNA primase domain-co 99.2 7.1E-11 1.5E-15 118.0 9.2 148 8-162 170-361 (930)
10 COG0358 DnaG DNA primase (bact 99.1 1.8E-10 3.9E-15 112.4 9.5 145 3-152 187-352 (568)
11 cd01029 TOPRIM_primases TOPRIM 99.1 1.3E-10 2.7E-15 84.4 5.3 65 53-120 1-69 (79)
12 PF13362 Toprim_3: Toprim doma 99.0 2.3E-09 5E-14 81.0 7.8 87 54-143 1-95 (96)
13 PHA02540 61 DNA primase; Provi 98.9 1.3E-08 2.8E-13 94.1 10.2 136 6-153 171-321 (337)
14 PHA02031 putative DnaG-like pr 98.8 2.6E-08 5.7E-13 89.3 10.1 135 5-151 115-262 (266)
15 smart00493 TOPRIM topoisomeras 98.8 8E-09 1.7E-13 74.1 4.2 67 53-121 1-74 (76)
16 PRK08624 hypothetical protein; 98.7 4.3E-08 9.3E-13 91.6 7.0 98 7-108 182-301 (373)
17 PF12965 DUF3854: Domain of un 98.4 1.4E-06 3E-11 70.6 7.7 83 45-129 2-111 (130)
18 cd00188 TOPRIM Topoisomerase-p 98.2 2.2E-06 4.7E-11 59.8 5.0 67 53-119 1-72 (83)
19 cd01027 TOPRIM_RNase_M5_like T 98.0 8.4E-06 1.8E-10 60.8 4.2 66 53-120 2-71 (81)
20 TIGR02760 TraI_TIGR conjugativ 97.8 0.00036 7.9E-09 77.2 13.9 130 6-139 1720-1869(1960)
21 PRK04031 DNA primase; Provisio 97.6 0.00012 2.5E-09 69.4 6.6 97 50-155 167-266 (408)
22 TIGR00334 5S_RNA_mat_M5 ribonu 96.4 0.011 2.5E-07 50.3 6.9 111 53-168 3-126 (174)
23 PF01751 Toprim: Toprim domain 96.3 0.013 2.9E-07 44.3 6.2 73 54-126 1-98 (100)
24 COG4643 Uncharacterized protei 94.8 0.056 1.2E-06 50.5 5.6 109 7-120 160-282 (366)
25 COG1658 Small primase-like pro 91.5 0.33 7.2E-06 39.4 4.6 75 52-127 9-89 (127)
26 PRK04017 hypothetical protein; 89.3 0.48 1E-05 38.8 3.7 66 54-121 24-92 (132)
27 PF13707 RloB: RloB-like prote 84.2 19 0.00042 29.5 10.8 145 55-202 2-182 (183)
28 cd01026 TOPRIM_OLD TOPRIM_OLD: 75.2 3.5 7.6E-05 30.9 3.2 19 52-70 3-21 (97)
29 TIGR03600 phage_DnaB phage rep 65.6 7.9 0.00017 36.4 4.0 47 153-207 143-193 (421)
30 PF13154 DUF3991: Protein of u 59.3 14 0.0003 26.8 3.5 25 4-28 26-50 (77)
31 PF04122 CW_binding_2: Putativ 55.9 24 0.00052 25.9 4.4 53 51-106 24-82 (92)
32 PRK08780 DNA topoisomerase I; 55.6 30 0.00065 35.8 6.4 93 92-210 69-170 (780)
33 cd01025 TOPRIM_recR TOPRIM_rec 55.2 34 0.00074 27.1 5.3 74 54-127 2-93 (112)
34 PF11462 DUF3203: Protein of u 51.3 7.7 0.00017 28.7 1.0 21 51-71 44-64 (74)
35 TIGR00665 DnaB replicative DNA 50.6 18 0.00038 34.1 3.6 49 155-207 146-194 (434)
36 PRK06646 DNA polymerase III su 49.8 18 0.0004 30.0 3.2 39 89-127 101-141 (154)
37 PRK05728 DNA polymerase III su 49.7 20 0.00043 29.1 3.3 22 88-109 94-115 (142)
38 PRK07561 DNA topoisomerase I s 46.7 29 0.00063 36.3 4.7 66 92-167 82-152 (859)
39 PF00626 Gelsolin: Gelsolin re 45.6 22 0.00047 24.6 2.6 49 79-127 8-65 (76)
40 PRK00076 recR recombination pr 45.3 65 0.0014 28.0 5.9 77 51-127 77-170 (196)
41 PF04364 DNA_pol3_chi: DNA pol 45.1 24 0.00052 28.4 3.1 22 88-109 95-116 (137)
42 PRK05776 DNA topoisomerase I; 44.5 37 0.0008 34.6 4.9 68 92-169 92-163 (670)
43 PRK05582 DNA topoisomerase I; 44.1 33 0.00071 34.6 4.5 67 92-168 69-140 (650)
44 PF14097 SpoVAE: Stage V sporu 43.7 43 0.00093 28.8 4.5 48 99-153 1-51 (180)
45 PRK02812 ribose-phosphate pyro 42.5 47 0.001 30.9 5.0 44 87-130 9-55 (330)
46 TIGR00615 recR recombination p 40.9 94 0.002 27.0 6.3 77 51-127 77-171 (195)
47 PF08275 Toprim_N: DNA primase 39.3 43 0.00094 26.6 3.7 23 6-28 76-98 (128)
48 PRK06319 DNA topoisomerase I/S 37.4 52 0.0011 34.5 4.9 66 93-168 70-139 (860)
49 PF12142 PPO1_DWL: Polyphenol 36.1 24 0.00051 24.7 1.5 19 10-28 11-29 (54)
50 PRK08006 replicative DNA helic 36.0 47 0.001 32.3 4.1 42 158-207 177-223 (471)
51 PRK06749 replicative DNA helic 35.8 40 0.00086 32.3 3.5 41 159-207 144-185 (428)
52 TIGR01057 topA_arch DNA topois 35.6 58 0.0013 32.7 4.8 68 92-169 89-160 (618)
53 PRK13844 recombination protein 35.6 1.4E+02 0.0031 26.1 6.5 78 51-129 81-173 (200)
54 PRK07219 DNA topoisomerase I; 34.9 73 0.0016 33.2 5.5 80 92-195 93-178 (822)
55 PF04008 Adenosine_kin: Adenos 34.7 32 0.00069 28.9 2.3 34 98-131 48-84 (155)
56 PRK08840 replicative DNA helic 34.5 51 0.0011 32.0 4.0 42 158-207 170-216 (464)
57 PRK06599 DNA topoisomerase I; 34.4 62 0.0013 32.9 4.8 67 92-168 69-143 (675)
58 PRK07220 DNA topoisomerase I; 34.2 68 0.0015 33.1 5.0 80 93-196 94-180 (740)
59 TIGR01051 topA_bact DNA topois 32.5 56 0.0012 32.8 4.1 67 92-168 65-136 (610)
60 PF13467 RHH_4: Ribbon-helix-h 32.2 15 0.00034 26.6 0.0 21 201-221 8-28 (67)
61 cd01028 TOPRIM_TopoIA TOPRIM_T 30.5 78 0.0017 25.3 3.9 37 93-129 87-128 (142)
62 cd03409 Chelatase_Class_II Cla 29.9 50 0.0011 24.0 2.5 77 110-194 22-100 (101)
63 COG4924 Uncharacterized protei 29.5 72 0.0016 30.1 3.9 78 33-115 212-301 (386)
64 PF09983 DUF2220: Uncharacteri 29.0 1.6E+02 0.0035 24.7 5.7 66 50-118 41-110 (181)
65 cd03361 TOPRIM_TopoIA_RevGyr T 28.8 82 0.0018 26.3 3.9 37 92-128 114-155 (170)
66 PF13358 DDE_3: DDE superfamil 28.7 32 0.0007 25.9 1.3 47 92-139 75-126 (146)
67 PRK07004 replicative DNA helic 28.6 61 0.0013 31.3 3.5 43 157-207 164-212 (460)
68 PRK14973 DNA topoisomerase I; 28.3 67 0.0015 34.2 3.9 65 93-167 93-164 (936)
69 cd03363 TOPRIM_TopoIA_TopoI TO 27.2 92 0.002 24.6 3.7 36 93-128 69-108 (123)
70 COG4026 Uncharacterized protei 27.1 47 0.001 30.0 2.2 112 53-169 8-136 (290)
71 PRK07726 DNA topoisomerase III 26.5 1E+02 0.0022 31.2 4.8 68 92-168 88-160 (658)
72 PF13793 Pribosyltran_N: N-ter 25.9 2E+02 0.0042 22.6 5.4 23 101-123 3-25 (116)
73 smart00262 GEL Gelsolin homolo 24.8 1.5E+02 0.0033 21.2 4.3 32 97-128 34-74 (90)
74 COG3837 Uncharacterized conser 24.7 39 0.00084 28.6 1.2 60 18-84 34-99 (161)
75 PRK14719 bifunctional RNAse/5- 24.0 80 0.0017 29.7 3.3 69 54-125 25-98 (360)
76 PRK08760 replicative DNA helic 23.8 90 0.0019 30.4 3.7 41 158-206 183-227 (476)
77 COG3593 Predicted ATP-dependen 23.6 1E+02 0.0022 31.2 4.0 57 52-109 396-460 (581)
78 PF05021 NPL4: NPL4 family; I 22.8 73 0.0016 29.5 2.7 48 79-127 15-66 (306)
79 TIGR01056 topB DNA topoisomera 22.7 1.5E+02 0.0032 30.2 5.0 64 93-165 90-162 (660)
80 cd03362 TOPRIM_TopoIA_TopoIII 22.2 1.3E+02 0.0028 24.3 3.8 36 93-128 95-136 (151)
81 COG1839 Uncharacterized conser 21.8 1.8E+02 0.0039 24.5 4.5 36 98-133 55-93 (162)
82 PF08057 Ery_res_leader2: Eryt 21.1 28 0.0006 17.7 -0.2 7 194-200 8-14 (14)
83 PRK10557 hypothetical protein; 20.9 2.3E+02 0.005 24.1 5.3 57 4-63 86-154 (192)
84 PF08874 DUF1835: Domain of un 20.0 2.5E+02 0.0055 21.4 4.9 36 93-128 82-122 (124)
No 1
>KOG2373|consensus
Probab=100.00 E-value=1.4e-40 Score=305.01 Aligned_cols=192 Identities=30% Similarity=0.523 Sum_probs=170.8
Q ss_pred eEEEe---eecCCC-cEEEEEEeec---ccc-ccccCC------CC-ccccccCCCCCCCCeEEEeCChhHHHHHhhhhc
Q psy4521 8 TLYMP---LVNYAN-EVVGYKQVHK---SIE-STVPTK------QC-QGVLHCPPYKKKTDSAVLVQRLVDFLTLCNAHL 72 (223)
Q Consensus 8 ~lvfP---~~~~~g-~lvg~K~r~~---~ke-k~~p~~------~~-~glFG~~~~~~~~~~iVItEGE~Dalav~q~~~ 72 (223)
+++|| ++++.+ .+.|+|.+.. ..+ ..++.. ++ .|+||.|+......++|||.+|+|++|++|+ +
T Consensus 63 ~~~FP~~~~~tp~~~~~~GlK~l~e~~~~~~g~~ye~~~~~~~r~a~~~~fGL~l~~rrd~~vVltsne~D~lal~~~-t 141 (514)
T KOG2373|consen 63 AILFPRYRGMTPRLRIPMGLKLLREVGDRMEGENYELPDETSVRQAFNGVFGLHLATRRDRSVVLTSNERDALALYEA-T 141 (514)
T ss_pred ccccccccccCccchhhhhhHHHHHhhhccccccCCCCcccchhhhhcceeceeecccccceEEEeecchhHHHHhhh-c
Confidence 78999 666653 6889994432 111 133222 22 5999999986655599999999999999997 4
Q ss_pred CceEEEcCCCCCCCCcccccccccCceEEEEcCCChH---HHHHHHhhcCCCceEEEecCCCCCChhHHHhCCchHHHHH
Q psy4521 73 NYNVICLPHGLTCLPQEILPCLEEYNKLYLWFGKDHE---STRVFSSKLNEKRCFLIRETENQPLPTESKAKGLDLNRII 149 (223)
Q Consensus 73 g~p~VSlP~Ga~slp~~~lp~Le~F~~IiLw~D~D~~---~a~e~A~kLg~~RC~iV~~~~~~kdane~L~~g~~l~~~i 149 (223)
+.++++||+|...+|+.+|||||+|++||+|+..|.. +|+.||++|+..||.+|||.+..+.|.+||..+..++.|+
T Consensus 142 ~~~t~~LP~g~~~lP~~~LPyLE~F~~i~fWl~~d~~sw~aAk~fa~kLn~~rClLvrp~e~~p~p~~al~~rlnl~~il 221 (514)
T KOG2373|consen 142 KALTFALPHGEILLPQLVLPYLEEFDKIYFWLPVDHVSWSAAKDFASKLNTLRCLLVRPEERPPEPVRALDHRLNLNSIL 221 (514)
T ss_pred CceEEEcccccccCcHHHHHHHHhhheEEEEecccccchHHHHHHHhhcCcceEEEECCCCCCcchhhhhcccccHHHHH
Confidence 7999999999999999999999999999999999998 9999999999999999999999999999999999999999
Q ss_pred HhcCCCCCCcccchhHHHHHHHHhhhhhHHHHHhhcccCCccccCChhhHhhhcccch
Q psy4521 150 ESASPLCHPAIITYDVLQEDVLADLQNVTLLLLRTMYCRRMCWLTYKTTNRFKVSNGN 207 (223)
Q Consensus 150 ~~A~~~~~~~I~tf~dlre~V~~el~n~~~~~~~~~~~~Gv~w~~fp~Ln~~lkG~~~ 207 (223)
.+|.|++|++|+||.|+|++|.+||+|.+++. |++|+|||.||++|||+|-
T Consensus 222 ~~a~p~~hk~i~sf~~mRe~ilseL~N~e~v~-------G~~WkRFpvLNk~LkGhR~ 272 (514)
T KOG2373|consen 222 NSAVPMRHKGIRSFTDMREGILSELLNTERVV-------GFQWKRFPVLNKYLKGHRP 272 (514)
T ss_pred hhhchhhhhhhhhHHHHHHHHHHHHhhhhhhh-------ceeehhhhHHHHHhccCCC
Confidence 99999999999999999999999999999999 9999999999999999984
No 2
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=99.67 E-value=3.2e-16 Score=147.43 Aligned_cols=145 Identities=19% Similarity=0.292 Sum_probs=109.1
Q ss_pred ceEEEeeecCCCcEEEEEEeecc--ccc--cccCC---C-CccccccCCCC---CCCCeEEEeCChhHHHHHhhhhcCce
Q psy4521 7 KTLYMPLVNYANEVVGYKQVHKS--IES--TVPTK---Q-CQGVLHCPPYK---KKTDSAVLVQRLVDFLTLCNAHLNYN 75 (223)
Q Consensus 7 ~~lvfP~~~~~g~lvg~K~r~~~--kek--~~p~~---~-~~glFG~~~~~---~~~~~iVItEGE~Dalav~q~~~g~p 75 (223)
..++||++|.+|++||+.-|... .-| +-|.. + ...|||+|... ..++++|||||++||||++|+ |++
T Consensus 201 ~RiifPi~d~~G~vvgf~gR~~~~~~pKYlNspet~~f~K~~~lygl~~a~~~~~~~~~viivEG~~Daisl~~~--G~~ 278 (415)
T TIGR01391 201 NRIMFPIHDPKGRVVGFGGRALGDEKPKYLNSPETPLFKKSELLYGLHKARKEIRKEKELILVEGYMDVIALHQA--GIK 278 (415)
T ss_pred CeEEEEEECCCCCEEEEEeeecCCCCCceeCCCCCCCccCCccccCHhHHHHhhccCCcEEEEecHHHHHHHHHC--CCC
Confidence 36899999999999999999862 111 11211 1 24678887532 346799999999999999986 566
Q ss_pred -EEEcCCCCCCCCcccccccccC-ceEEEEcCCChH---HHHHHHhhcCCC--ceEEEecCCCCCChhHHHhC-C-chHH
Q psy4521 76 -VICLPHGLTCLPQEILPCLEEY-NKLYLWFGKDHE---STRVFSSKLNEK--RCFLIRETENQPLPTESKAK-G-LDLN 146 (223)
Q Consensus 76 -~VSlP~Ga~slp~~~lp~Le~F-~~IiLw~D~D~~---~a~e~A~kLg~~--RC~iV~~~~~~kdane~L~~-g-~~l~ 146 (223)
+|+++ |++ +....+..|.++ ++||||+|+|.+ +|...+++|... .|+++.+|+ .+||+|.|++ | .++.
T Consensus 279 ~aVA~~-Gta-lt~~~~~~l~r~~~~vvl~~D~D~aG~~aa~r~~~~l~~~g~~v~v~~lp~-gkDpdd~l~~~g~~~~~ 355 (415)
T TIGR01391 279 NAVASL-GTA-LTEEHIKLLKRYADEIILCFDGDKAGRKAALRAIELLLPLGINVKVIKLPG-GKDPDEYLRKEGVEALK 355 (415)
T ss_pred cEEECC-CCC-CcHHHHHHHHhhCCeEEEEeCCCHHHHHHHHHHHHHHHHcCCeEEEEECCC-CCCHHHHHHHhCHHHHH
Confidence 78776 443 566677777765 589999999999 777777777543 588888875 7999999965 6 5799
Q ss_pred HHHHhcCCCC
Q psy4521 147 RIIESASPLC 156 (223)
Q Consensus 147 ~~i~~A~~~~ 156 (223)
++|++|.++.
T Consensus 356 ~~l~~a~~~~ 365 (415)
T TIGR01391 356 KLLENSKSLI 365 (415)
T ss_pred HHHhcCCCHH
Confidence 9999987763
No 3
>TIGR00646 MG010 DNA primase-related protein. The DNA primase DnaG of E. coli and its apparent orthologs in other eubacterial species are approximately 600 residues in length. Within this set, a conspicuous outlier in percent identity, as seen in a UPGMA difference tree, is the branch containing the Mycoplasmas. This lineage is also unique in containing the small, DNA primase-related protein modelled by this alignment, which is homologous to the central third of DNA primase. Several small regions of sequence similarity specifically to Mycoplasma sequences rather than to all DnaG homologs suggests that the divergence of this protein from DnaG post-dated the separation of bacterial lineages. The function of this DNA primase-related protein is unknown.
Probab=99.64 E-value=1.6e-15 Score=132.08 Aligned_cols=145 Identities=16% Similarity=0.233 Sum_probs=107.6
Q ss_pred CCcceEEEeeecCCCcEEEEEEeecc-ccc--cccCCC----CccccccCCCCCCCCeEEEeCChhHHHHHhhhhcCc-e
Q psy4521 4 TETKTLYMPLVNYANEVVGYKQVHKS-IES--TVPTKQ----CQGVLHCPPYKKKTDSAVLVQRLVDFLTLCNAHLNY-N 75 (223)
Q Consensus 4 ~~~~~lvfP~~~~~g~lvg~K~r~~~-kek--~~p~~~----~~glFG~~~~~~~~~~iVItEGE~Dalav~q~~~g~-p 75 (223)
....-++||.+|..|++||..=|.++ ..| +-|... ..-|||.+......+++|||||-+|++|++|+ |+ .
T Consensus 55 ~~~~RimFPI~d~~G~vvgFgGR~l~~~~KYlNspet~~f~K~~~Lygl~~~~~k~~~vilvEGymDVIsl~qa--Gi~n 132 (218)
T TIGR00646 55 GEKEWLNLPLYNFDGNLIGFLNRKVGFEKEFLYLPFNKPPSKSEAFLGLKELPIEDNSIYLVEGDFDWLAFRKA--GILN 132 (218)
T ss_pred ccCCEEEEEEECCCCCEEEEeccCCCCCCCcccCCCCCCcccchhhcCcchhhcCCCEEEEEecHHHHHHHHHC--CCCe
Confidence 34567899999999999999988772 222 222211 14677887665656799999999999999996 44 4
Q ss_pred EEEcCCCCCCCCcccccccccC--ceEEEEcCCChH---HHHHHHhhcCC--CceEEEecCCCCCChhHHHhC-CchHHH
Q psy4521 76 VICLPHGLTCLPQEILPCLEEY--NKLYLWFGKDHE---STRVFSSKLNE--KRCFLIRETENQPLPTESKAK-GLDLNR 147 (223)
Q Consensus 76 ~VSlP~Ga~slp~~~lp~Le~F--~~IiLw~D~D~~---~a~e~A~kLg~--~RC~iV~~~~~~kdane~L~~-g~~l~~ 147 (223)
+| -+.|.. +-.+.+..|.+. ++|+||+|+|.| |+...++.|-. -+|+++.+|+..||+||.|+. +..-.+
T Consensus 133 aV-AslGTA-LT~~q~~lLkr~~~~~Iil~~D~D~AG~~Aa~r~~~~L~~~G~~v~vv~lP~~~KDwNEllk~~~~~w~~ 210 (218)
T TIGR00646 133 CL-PLCGLT-ISDKQMKFFKQKKIEKIFICFDNDFAGKNAAANLEEILKKAGFITKVIEIKAAAKDWNDLFLLNNKNWAA 210 (218)
T ss_pred EE-EcCchH-hHHHHHHHHhccCCCEEEEEeCCCHHHHHHHHHHHHHHHHCCCeEEEEeCCCcCCChhHHHHHhhhhHHH
Confidence 55 566665 555556667774 799999999999 77777777732 358899998889999999965 555666
Q ss_pred HHHhc
Q psy4521 148 IIESA 152 (223)
Q Consensus 148 ~i~~A 152 (223)
+|.++
T Consensus 211 ~l~~~ 215 (218)
T TIGR00646 211 ALRDH 215 (218)
T ss_pred HHHhh
Confidence 66664
No 4
>PRK07078 hypothetical protein; Validated
Probab=99.53 E-value=1.8e-13 Score=137.41 Aligned_cols=143 Identities=13% Similarity=0.145 Sum_probs=114.3
Q ss_pred ceEEEeeecCCCcEEEEEEeec---cccccccCCC---------CccccccCCCCCCCCeEEEeCChhHHHHHhhhhcCc
Q psy4521 7 KTLYMPLVNYANEVVGYKQVHK---SIESTVPTKQ---------CQGVLHCPPYKKKTDSAVLVQRLVDFLTLCNAHLNY 74 (223)
Q Consensus 7 ~~lvfP~~~~~g~lvg~K~r~~---~kek~~p~~~---------~~glFG~~~~~~~~~~iVItEGE~Dalav~q~~~g~ 74 (223)
.+...||+|.+|+++++-+|.. +++...|..+ ...|||++.+. .++.|+|||||.||+|+.+. |+
T Consensus 134 ~~~~~~Y~D~~G~~~~~v~R~~~~~~~K~fr~~~g~~~~~~~~~~~pLy~lp~l~-~a~~V~lvEGEk~adal~~~--g~ 210 (759)
T PRK07078 134 ATAKWDYLDAAGKLIAVVYRYDPPGRRKEFRPWDAKRRKMAPPEPRPLYNQPGLL-SAEQVVLVEGEKCAQALIDA--GV 210 (759)
T ss_pred ceeEEEEECCCCCEEEEEEeecCCCCCceeecccCCcceecCCCCcCCcCchhhh-cCCeEEEEeChHHHHHHHhc--CC
Confidence 4567899999999999888865 2222444333 13689998774 36799999999999999874 79
Q ss_pred eEEEcCCCCCCCC-cccccccccCceEEEEcCCChH---HHHHHHhhc---CCCceEEEecCC---CCCChhHHHhCCch
Q psy4521 75 NVICLPHGLTCLP-QEILPCLEEYNKLYLWFGKDHE---STRVFSSKL---NEKRCFLIRETE---NQPLPTESKAKGLD 144 (223)
Q Consensus 75 p~VSlP~Ga~slp-~~~lp~Le~F~~IiLw~D~D~~---~a~e~A~kL---g~~RC~iV~~~~---~~kdane~L~~g~~ 144 (223)
+|+|.|.||++.+ ...+.-|.. .+|+||.|+|++ .|+++|+.| |...|.++.|++ ...|++|++..|.+
T Consensus 211 ~att~~~Ga~~~~~~~d~~~L~g-~~VvI~pD~D~~G~~~a~~va~~l~~~g~~~~~v~~p~~~~~~~~D~aD~~~~G~~ 289 (759)
T PRK07078 211 VATTAMHGANAPVDKTDWSPLAG-KAVLIWPDRDKPGWEYADRAAQAILSAGASSCAVLLPPEDLPEGWDAADAIAEGFD 289 (759)
T ss_pred eEEecCCCCCCCcccccccccCC-CEEEEEcCCChHHHHHHHHHHHHHHhcCCeEEEEEecCcccCcCCCHHHHHHcCCC
Confidence 9999999998763 344444888 599999999999 999999998 888999997752 45799999999988
Q ss_pred HHHHHHhcC
Q psy4521 145 LNRIIESAS 153 (223)
Q Consensus 145 l~~~i~~A~ 153 (223)
+.++|....
T Consensus 290 ~~~~~~~~~ 298 (759)
T PRK07078 290 VAGFLAHGE 298 (759)
T ss_pred HHHHHhhcc
Confidence 888887755
No 5
>PRK05667 dnaG DNA primase; Validated
Probab=99.52 E-value=7.7e-14 Score=136.48 Aligned_cols=145 Identities=17% Similarity=0.266 Sum_probs=107.7
Q ss_pred ceEEEeeecCCCcEEEEEEeecc--ccc--cccCC---C-CccccccCCCC---CCCCeEEEeCChhHHHHHhhhhcCce
Q psy4521 7 KTLYMPLVNYANEVVGYKQVHKS--IES--TVPTK---Q-CQGVLHCPPYK---KKTDSAVLVQRLVDFLTLCNAHLNYN 75 (223)
Q Consensus 7 ~~lvfP~~~~~g~lvg~K~r~~~--kek--~~p~~---~-~~glFG~~~~~---~~~~~iVItEGE~Dalav~q~~~g~p 75 (223)
..++||.+|..|++||+.-|..+ .-| +-|.. . ...|||+|... ...+++|||||++|+||++|+ |++
T Consensus 197 ~RimfPI~d~~G~vigF~GR~l~~~~pKYlNSpet~iF~K~~~LYgl~~a~~~i~~~~~viivEG~~Dvisl~q~--Gi~ 274 (580)
T PRK05667 197 NRIMFPIRDLRGRVIGFGGRVLGDDKPKYLNSPETPLFHKGRVLYGLDEARKAIAKKKQVIVVEGYMDVIALHQA--GIT 274 (580)
T ss_pred CeEEEEEECCCCcEEEEEeeecCCCCCeeeCCCCCCCccCCccccCccHHHHhcccCCeEEEEeeHHHHHHHHHc--CCC
Confidence 46899999999999999999762 111 11211 1 24678887543 235699999999999999997 454
Q ss_pred -EEEcCCCCCCCCcccccccccC-ceEEEEcCCChH---HHHHHHhh---cCC--CceEEEecCCCCCChhHHHhC-C-c
Q psy4521 76 -VICLPHGLTCLPQEILPCLEEY-NKLYLWFGKDHE---STRVFSSK---LNE--KRCFLIRETENQPLPTESKAK-G-L 143 (223)
Q Consensus 76 -~VSlP~Ga~slp~~~lp~Le~F-~~IiLw~D~D~~---~a~e~A~k---Lg~--~RC~iV~~~~~~kdane~L~~-g-~ 143 (223)
||+.. |+ ++..+.+..|.++ .+||||||+|.+ +|...++. |-. ..|++|.+|+ .+||+|.+++ | .
T Consensus 275 naVA~l-Gt-alt~~~~~~L~r~~~~vil~~D~D~AG~~aa~r~~~~~~~l~~~g~~v~vv~lp~-gkDpdd~l~~~G~~ 351 (580)
T PRK05667 275 NAVASL-GT-ALTEEHLKLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLPD-GKDPDDLVRKEGPE 351 (580)
T ss_pred cEEEeC-CC-CCCHHHHHHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHHHHhCCceEEEEECCC-CCChHHHHHHhCHH
Confidence 77665 54 3667777777775 589999999999 77666666 422 2678999875 6999999975 6 5
Q ss_pred hHHHHHHhcCCCC
Q psy4521 144 DLNRIIESASPLC 156 (223)
Q Consensus 144 ~l~~~i~~A~~~~ 156 (223)
.+.++|.+|.|+.
T Consensus 352 ~~~~~i~~a~~~~ 364 (580)
T PRK05667 352 AFRALLEQAIPLS 364 (580)
T ss_pred HHHHHHHcCCCHH
Confidence 6999999988764
No 6
>PF13155 Toprim_2: Toprim-like
Probab=99.33 E-value=9.7e-13 Score=98.73 Aligned_cols=83 Identities=17% Similarity=0.223 Sum_probs=64.6
Q ss_pred EEeCChhHHHHHhhhhcCc-e--EEEcCCCCCCCCccccccc--ccCceEEEEcCCChH---HHHHHHhhcCCC-----c
Q psy4521 56 VLVQRLVDFLTLCNAHLNY-N--VICLPHGLTCLPQEILPCL--EEYNKLYLWFGKDHE---STRVFSSKLNEK-----R 122 (223)
Q Consensus 56 VItEGE~Dalav~q~~~g~-p--~VSlP~Ga~slp~~~lp~L--e~F~~IiLw~D~D~~---~a~e~A~kLg~~-----R 122 (223)
|||||++||||++|..... . .+||+.|.....+....+| .+.++|+|+||||.+ +++++++.|... +
T Consensus 1 ~v~Eg~iDaLS~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~~~i~l~~DnD~aG~~~~~~~~~~l~~~~~~~~~ 80 (96)
T PF13155_consen 1 VVFEGPIDALSYYQLGKENIKDNSLSLAGGGTLSEKQQIKFLKENPYKKIVLAFDNDEAGRKAAEKLQKELKEEGFPNIK 80 (96)
T ss_pred cEEeCHHHHHHHHHhCchhcCCceEEEECCchHHHHHHHHHHHhCCCCcEEEEeCCCHHHHHHHHHHHHHHHhhCCCcce
Confidence 6999999999999974211 1 2789888886667778888 445789999999999 899999888754 4
Q ss_pred eEEEecCCCCCChhHHH
Q psy4521 123 CFLIRETENQPLPTESK 139 (223)
Q Consensus 123 C~iV~~~~~~kdane~L 139 (223)
..+..++.. ||.||+|
T Consensus 81 ~~~~~~~~~-KD~Nd~L 96 (96)
T PF13155_consen 81 VRIEDPPDG-KDWNDYL 96 (96)
T ss_pred eeecCCCCC-cCchhhC
Confidence 555556554 9999986
No 7
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=99.25 E-value=1.4e-11 Score=90.28 Aligned_cols=72 Identities=18% Similarity=0.165 Sum_probs=56.8
Q ss_pred CeEEEeCChhHHHHHhhhhcCceEEEcCCCCCCCCcccccccccC-ceEEEEcCCChH---HHHHHHhhcCCC--ceEEE
Q psy4521 53 DSAVLVQRLVDFLTLCNAHLNYNVICLPHGLTCLPQEILPCLEEY-NKLYLWFGKDHE---STRVFSSKLNEK--RCFLI 126 (223)
Q Consensus 53 ~~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~slp~~~lp~Le~F-~~IiLw~D~D~~---~a~e~A~kLg~~--RC~iV 126 (223)
++++||||++||||++|.. ..++|+++.+..+ ...+++|.++ ++|++|+|+|.+ ++++++++|... +++++
T Consensus 1 ~~v~i~EG~~D~ls~~~~g-~~~~va~~G~~~~--~~~~~~L~~~~~~vii~~D~D~aG~~a~~~~~~~l~~~g~~~~~~ 77 (79)
T cd03364 1 KKVILVEGYMDVIALHQAG-IKNVVASLGTALT--EEQAELLKRLAKEVILAFDGDEAGQKAALRALELLLKLGLNVRVL 77 (79)
T ss_pred CeEEEEeCHHHHHHHHHcC-CCCEEECCCccCc--HHHHHHHHhcCCeEEEEECCCHHHHHHHHHHHHHHHHCCCeEEEE
Confidence 4799999999999999963 3568888866443 3567888887 999999999999 888999988643 45554
Q ss_pred e
Q psy4521 127 R 127 (223)
Q Consensus 127 ~ 127 (223)
.
T Consensus 78 ~ 78 (79)
T cd03364 78 T 78 (79)
T ss_pred e
Confidence 3
No 8
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=99.24 E-value=4.8e-12 Score=93.22 Aligned_cols=70 Identities=23% Similarity=0.278 Sum_probs=48.7
Q ss_pred CeEEEeCChhHHHHHhhhhcCc-eEEEcCCCCC-CCCccccccccc-CceEEEEcCCChH---HHHHHHhhcCCCceE
Q psy4521 53 DSAVLVQRLVDFLTLCNAHLNY-NVICLPHGLT-CLPQEILPCLEE-YNKLYLWFGKDHE---STRVFSSKLNEKRCF 124 (223)
Q Consensus 53 ~~iVItEGE~Dalav~q~~~g~-p~VSlP~Ga~-slp~~~lp~Le~-F~~IiLw~D~D~~---~a~e~A~kLg~~RC~ 124 (223)
+++||||||+|+|+++|+ |+ .++++..|+. +.++...+.+.. +++||||+|+|.+ ++++++++|....+.
T Consensus 1 k~viIvEG~~D~~~l~~~--g~~~~v~~~g~~~~~~~~~~~~~~~~~~~~Vii~~D~D~~G~~~a~~i~~~l~~~gi~ 76 (81)
T PF13662_consen 1 KEVIIVEGEFDAIALEQA--GYKNVVAVLGGNLSPLDQILREKLEKKVKEVIIAFDNDKAGEKAAQKIAKKLLPLGIR 76 (81)
T ss_dssp --EEEESSHHHHHHHHHT--T-TTEEEESSSS---HHHHHHHHHH---SEEEEEEESSHHHHHHHHHHHHHHG-----
T ss_pred CEEEEECCHHHHHHHHHh--CCCeEEEECCCCCChHHHhChHhhhccCceEEEEeCcCHHHHHHHHHHHHHHHhhccc
Confidence 579999999999999997 45 5788877766 344444455655 8999999999999 999999988655443
No 9
>PHA02415 DNA primase domain-containing protein
Probab=99.18 E-value=7.1e-11 Score=118.04 Aligned_cols=148 Identities=11% Similarity=0.100 Sum_probs=110.8
Q ss_pred eEEEeeecCCCcEEEEEEeec-----cccc-cccCCCCccccccCCCCCC---CCeEEEeCChhHHHHHhhhhcCceEEE
Q psy4521 8 TLYMPLVNYANEVVGYKQVHK-----SIES-TVPTKQCQGVLHCPPYKKK---TDSAVLVQRLVDFLTLCNAHLNYNVIC 78 (223)
Q Consensus 8 ~lvfP~~~~~g~lvg~K~r~~-----~kek-~~p~~~~~glFG~~~~~~~---~~~iVItEGE~Dalav~q~~~g~p~VS 78 (223)
++||| |+.+|+++..|.|.. +..| .++ |++..|||+....+ +++|.||||+|||||++|. |+++++
T Consensus 170 AFIVp-f~rdGtvv~v~~Rg~d~afkG~vKanf~--Gs~~G~gW~~p~~~L~~a~eVwIvEGiIDAISL~q~--Gi~avA 244 (930)
T PHA02415 170 AFIVR-EPADGRVVAVDMRYVDPALNGGVKTQTQ--GDKAGYGWTADARRLDKAKRVFIVESAINALSIDTC--AMPGAA 244 (930)
T ss_pred EEEec-ccCCceEEEeeeccccccccCCccccCC--CCCCCCccCCCccccCCCCEEEEEechHhHHHHHHc--CchhHH
Confidence 46899 677999999999875 2232 233 46788999986532 5799999999999999986 677655
Q ss_pred c--CCCCCCCCcccccccccCceEEEEcCCChH---------------HHHHHHhhc---CCCceEEEecCC--------
Q psy4521 79 L--PHGLTCLPQEILPCLEEYNKLYLWFGKDHE---------------STRVFSSKL---NEKRCFLIRETE-------- 130 (223)
Q Consensus 79 l--P~Ga~slp~~~lp~Le~F~~IiLw~D~D~~---------------~a~e~A~kL---g~~RC~iV~~~~-------- 130 (223)
. =.|..+.+...+|.| .-++|+|++|||+| +|.++.++| |+. |++|...+
T Consensus 245 aVAL~GLan~~~iD~~~l-~~KrVvlcLDNDea~~~~~~~~g~rpG~eAA~~l~e~lta~~i~-~~lvd~~~w~~~~~~~ 322 (930)
T PHA02415 245 ALALRGLANVDAIDFSSL-RGKQVVICLDNDEPFEDGHPRAGHRPGPEAAWALYERLASLNIS-AVLVDQAGWLADLADG 322 (930)
T ss_pred HHHHcCcCCCchhhchhh-cCceEEEEecCCccccccCcccccCccHHHHHHHHHHHhhcCCc-eEEeehhhhhhhcccc
Confidence 5 578888776666766 67799999999996 566666666 443 67776432
Q ss_pred -----CCCChhHHHhC-C-chHHHHHHhcCCCCCCcccc
Q psy4521 131 -----NQPLPTESKAK-G-LDLNRIIESASPLCHPAIIT 162 (223)
Q Consensus 131 -----~~kdane~L~~-g-~~l~~~i~~A~~~~~~~I~t 162 (223)
.-.|-||.|++ | .++...++.=+|+-..|+-.
T Consensus 323 ~~~~~~~~d~nd~l~~~g~~~~~~~l~~~~~wli~g~~g 361 (930)
T PHA02415 323 ETKQQPINDVNDYLQLRGPEELARALEQLEPWLIAGLAG 361 (930)
T ss_pred cccccccccHHHHHHHhCHHHHHHHHHhccccccCCCCC
Confidence 11378999975 7 57999999999988777643
No 10
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=99.13 E-value=1.8e-10 Score=112.36 Aligned_cols=145 Identities=20% Similarity=0.317 Sum_probs=103.5
Q ss_pred CCCcceEEEeeecCCCcEEEEEEeecccc----ccccCCC----CccccccCCCCCC---CCeEEEeCChhHHHHHhhhh
Q psy4521 3 NTETKTLYMPLVNYANEVVGYKQVHKSIE----STVPTKQ----CQGVLHCPPYKKK---TDSAVLVQRLVDFLTLCNAH 71 (223)
Q Consensus 3 ~~~~~~lvfP~~~~~g~lvg~K~r~~~ke----k~~p~~~----~~glFG~~~~~~~---~~~iVItEGE~Dalav~q~~ 71 (223)
|.-+.-++||-++..|.++|.-=|....+ .+-|..- ..-|||.+..... +++||||||.+|++|++|+
T Consensus 187 drFr~RImfPI~d~~g~vigFggR~l~~~~~KYlNspet~if~Kg~~Lyg~~~a~~~~~~~~~iivVEGymDViaL~~a- 265 (568)
T COG0358 187 DRFRNRIMFPIRDLRGDVIGFGGRVLGDDKPKYLNSPETELFKKGEELYGLDPARKKIAKADQIIVVEGYMDVIALHKA- 265 (568)
T ss_pred ehhcCeeEEeccCCCCCEEeeeccccCCCCCcccCCCCCcCccCcHHhhCHHHHHHhhccCCeEEEEechHHHHHHHHc-
Confidence 44456789999999999999988876211 1222211 1356777754444 6799999999999999997
Q ss_pred cCc-eEEEcCCCCCCCCcccccccccCce-EEEEcCCChH---H---HHHHHhhcCCCceEEEecCCCCCChhHHHhC-C
Q psy4521 72 LNY-NVICLPHGLTCLPQEILPCLEEYNK-LYLWFGKDHE---S---TRVFSSKLNEKRCFLIRETENQPLPTESKAK-G 142 (223)
Q Consensus 72 ~g~-p~VSlP~Ga~slp~~~lp~Le~F~~-IiLw~D~D~~---~---a~e~A~kLg~~RC~iV~~~~~~kdane~L~~-g 142 (223)
|+ +||+ +-|++ +-++.+..|-++.+ ||||||+|.+ + |-+.+..++..-.+++..|++ +||.|.+++ |
T Consensus 266 -Gi~naVA-~lGTa-lt~ehi~~L~r~~~~vil~fDgD~AG~~Aa~ral~~~~~~~~~~v~v~~~P~G-kDpDel~~k~g 341 (568)
T COG0358 266 -GIKNAVA-SLGTA-LTEEHIKLLSRGKKKVILCFDGDRAGRKAAKRALQLVLPLDFVGVFVILLPDG-KDPDELIRKEG 341 (568)
T ss_pred -CCcceee-ccccc-CCHHHHHHHHhcCCCEEEEeCChHHHHHHHHHHHHHhhhhccCCeEEEECCCC-CChHHHHHHhC
Confidence 55 4544 56666 66777777777766 9999999999 6 444444444333899998876 999999965 7
Q ss_pred c-hHHHHHHhc
Q psy4521 143 L-DLNRIIESA 152 (223)
Q Consensus 143 ~-~l~~~i~~A 152 (223)
. .+...+.++
T Consensus 342 ~~al~~~l~~~ 352 (568)
T COG0358 342 AEALRKKLPNE 352 (568)
T ss_pred hHHHHHHHHhC
Confidence 5 468888775
No 11
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Probab=99.10 E-value=1.3e-10 Score=84.42 Aligned_cols=65 Identities=25% Similarity=0.298 Sum_probs=49.3
Q ss_pred CeEEEeCChhHHHHHhhhhcCceEEEcCCCCCCCCcccccccccC-ceEEEEcCCChH---HHHHHHhhcCC
Q psy4521 53 DSAVLVQRLVDFLTLCNAHLNYNVICLPHGLTCLPQEILPCLEEY-NKLYLWFGKDHE---STRVFSSKLNE 120 (223)
Q Consensus 53 ~~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~slp~~~lp~Le~F-~~IiLw~D~D~~---~a~e~A~kLg~ 120 (223)
++++||||++|+||++|.. ..+++++. |++..+ ..++.|.++ ++|++|+|||.+ +++...++|-.
T Consensus 1 ~~v~i~EG~~Dals~~~~~-~~~~~~~~-g~~~~~-~~~~~l~~~~~~vii~~D~D~~G~~~~~~~~~~~~~ 69 (79)
T cd01029 1 DEVIIVEGYMDVLALHQAG-IKNVVAAL-GTANTE-EQLRLLKRFARTVILAFDNDEAGKKAAARALELLLA 69 (79)
T ss_pred CEEEEEeCHHHHHHHHHcC-CCCEEECC-CccCcH-HHHHHHHhcCCEEEEEECCCHHHHHHHHHHHHHHHH
Confidence 4789999999999999863 34655555 555444 566677776 999999999999 66677666654
No 12
>PF13362 Toprim_3: Toprim domain
Probab=98.97 E-value=2.3e-09 Score=80.96 Aligned_cols=87 Identities=9% Similarity=0.116 Sum_probs=67.0
Q ss_pred eEEEeCChhHHHHHhhhhcCceEEEcCCCCCCCCcccccccccCceEEEEcCCChH-----HHHHHHhhcCCC--ceEEE
Q psy4521 54 SAVLVQRLVDFLTLCNAHLNYNVICLPHGLTCLPQEILPCLEEYNKLYLWFGKDHE-----STRVFSSKLNEK--RCFLI 126 (223)
Q Consensus 54 ~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~slp~~~lp~Le~F~~IiLw~D~D~~-----~a~e~A~kLg~~--RC~iV 126 (223)
.++|+||..|+||+.++..+.|++++.+. +++.....+ +.+++||||.|+|.+ ++++++++|-.. .+.++
T Consensus 1 tl~i~EG~etals~~~~~~~~~~~a~~~~-~nl~~~~~~--~~~~~vii~~D~D~~~~G~~~a~~~~~~~~~~g~~~~~~ 77 (96)
T PF13362_consen 1 TLIIAEGIETALSIAQQATGVPVVAALGA-GNLKNVAIP--EPGRRVIIAADNDKANEGQKAAEKAAERLEAAGIAVSIV 77 (96)
T ss_pred CEEEEEhHHHHHHHHHhcCCCeEEEEECh-hhhhhhcCC--CCCCeEEEEECCCCchhhHHHHHHHHHHHHhCCCeEEEE
Confidence 37999999999999444457899988765 445544444 699999999999998 888888888853 46777
Q ss_pred ecCCCCCChhHHHhC-Cc
Q psy4521 127 RETENQPLPTESKAK-GL 143 (223)
Q Consensus 127 ~~~~~~kdane~L~~-g~ 143 (223)
.|+...+|.||+|+. |.
T Consensus 78 ~p~~~g~D~ND~l~~~G~ 95 (96)
T PF13362_consen 78 EPGPEGKDWNDLLQARGK 95 (96)
T ss_pred CCCCCCchHHHHHHhhCC
Confidence 774456799999964 54
No 13
>PHA02540 61 DNA primase; Provisional
Probab=98.87 E-value=1.3e-08 Score=94.14 Aligned_cols=136 Identities=16% Similarity=0.140 Sum_probs=90.7
Q ss_pred cceEEEeeecCCCcEEEEEEeeccc---cc--cccCCC-CccccccCCCCCCCCeEEEeCChhHHHHHhhhhcCceEEEc
Q psy4521 6 TKTLYMPLVNYANEVVGYKQVHKSI---ES--TVPTKQ-CQGVLHCPPYKKKTDSAVLVQRLVDFLTLCNAHLNYNVICL 79 (223)
Q Consensus 6 ~~~lvfP~~~~~g~lvg~K~r~~~k---ek--~~p~~~-~~glFG~~~~~~~~~~iVItEGE~Dalav~q~~~g~p~VSl 79 (223)
+.-++||.+|.+|+++|.-=|.+.. -| +-|... ..-|||.+.+. ..+.+|||||=+|++++- ++|+
T Consensus 171 ~~RImFPI~d~~G~vigFgGR~l~~~~~pKYlNSp~f~K~~~LYGl~~a~-~~~~vilvEGYmDvi~i~------naVA- 242 (337)
T PHA02540 171 EPRLVIPIFNKDGKIESFQGRALRKDAPQKYITIKADEEATKIYGLDRID-PGKTVYVVEGPIDSLFLP------NSIA- 242 (337)
T ss_pred CCeeEEEEECCCCCEEEEEeEECCCCCCCCeeeCCcccccccccChhHhc-cCCEEEEEeCCcceeeec------ccee-
Confidence 4678999999999999999887722 12 223222 25789998764 467999999999998731 3333
Q ss_pred CCCCCCCCcccccccccCceEEEEcCCChH--HHHHHHhhcCCCceEEEecCC---CCCChhHHHhC-C---chHHHHHH
Q psy4521 80 PHGLTCLPQEILPCLEEYNKLYLWFGKDHE--STRVFSSKLNEKRCFLIRETE---NQPLPTESKAK-G---LDLNRIIE 150 (223)
Q Consensus 80 P~Ga~slp~~~lp~Le~F~~IiLw~D~D~~--~a~e~A~kLg~~RC~iV~~~~---~~kdane~L~~-g---~~l~~~i~ 150 (223)
.-|.. |-.+..+| =++++|++|+|.. ++-.-.++|-..-|.++.++. ..|||+|.+++ | .++.+.|+
T Consensus 243 tlGTa-LT~~~~~~---~~~vvl~~D~Da~~~at~r~~~~l~~~g~~v~v~~~~~~~~kDpde~i~~~G~~~~~~~~~i~ 318 (337)
T PHA02540 243 ITGGD-LDLNEVPF---KDTRVWVLDNEPRHPDTIKRISKLIDAGEKVVIWDKCPWPSKDINDMIMKGGATPEDIMEYIK 318 (337)
T ss_pred eCccc-cCHhHhCc---cceEEEEECCchhHHHHHHHHHHHHHCCCeEEEecCCCCCCcCHHHHHHhcCCCHHHHHHHHH
Confidence 23333 23333333 2589999999955 555556666433355555543 35999999965 5 46888877
Q ss_pred hcC
Q psy4521 151 SAS 153 (223)
Q Consensus 151 ~A~ 153 (223)
++.
T Consensus 319 ~n~ 321 (337)
T PHA02540 319 SNT 321 (337)
T ss_pred Hcc
Confidence 753
No 14
>PHA02031 putative DnaG-like primase
Probab=98.82 E-value=2.6e-08 Score=89.29 Aligned_cols=135 Identities=10% Similarity=0.069 Sum_probs=89.1
Q ss_pred CcceEEEeeecC-CCcEEEEEEeeccccc--cccCCCCccccccCCCCCCCCeEEEeCChhHHHHHhhh-hcCc-eEEEc
Q psy4521 5 ETKTLYMPLVNY-ANEVVGYKQVHKSIES--TVPTKQCQGVLHCPPYKKKTDSAVLVQRLVDFLTLCNA-HLNY-NVICL 79 (223)
Q Consensus 5 ~~~~lvfP~~~~-~g~lvg~K~r~~~kek--~~p~~~~~glFG~~~~~~~~~~iVItEGE~Dalav~q~-~~g~-p~VSl 79 (223)
-+.=++||..|. .|+..+ ...-| +.|+. +..||+.+......+++|||||=+|+++++++ +.|+ ++|+
T Consensus 115 Fr~RimFPI~dgFgGR~l~-----~~~PKYLN~~SP-~~~l~~~~~~~~~~~~vIlvEGYmDVI~l~~a~~aG~~naVA- 187 (266)
T PHA02031 115 RQGRLIFRTDAGWLGRATA-----DQQPKWVGYGYP-APDYVGWPPELSMPRPVVLTEDYLSALKVRWACNKPEVFAVA- 187 (266)
T ss_pred eCCEEEEeeccccccccCC-----CCCCCcCCCCCC-cHHHhhchhhhccCCeEEEEcCcHHHHHHHHHHhcCcceEEE-
Confidence 355689997762 344432 11111 21111 35788888655556799999999999999764 2354 4554
Q ss_pred CCCCCCCCcccccccccC--ceEEEEcCCChH---HHHHHHhh---cCCCceEEEecCCCCCChhHHHhCCchHHHHHHh
Q psy4521 80 PHGLTCLPQEILPCLEEY--NKLYLWFGKDHE---STRVFSSK---LNEKRCFLIRETENQPLPTESKAKGLDLNRIIES 151 (223)
Q Consensus 80 P~Ga~slp~~~lp~Le~F--~~IiLw~D~D~~---~a~e~A~k---Lg~~RC~iV~~~~~~kdane~L~~g~~l~~~i~~ 151 (223)
+-|.. |-.+.+..|-++ ++|+||||.|.+ ++....+. +| -.++++..|+ .+||-|.++ ..++++|+.
T Consensus 188 ~LGTA-LT~~q~~~L~r~~~~~Vil~fDgD~AG~~Aa~ra~~~l~~~~-~~v~vv~lP~-g~DPDd~ir--~~i~eal~~ 262 (266)
T PHA02031 188 LLGTR-LRDRLAAILLQQTCPRVLIFLDGDPAGVDGSAGAMRRLRPLL-IEGQVIITPD-GFDPKDLER--EQIRELLIG 262 (266)
T ss_pred CCccc-CCHHHHHHHHhcCCCCEEEEeCCCHHHHHHHHHHHHHHHHcC-CceEEEECCC-CCChHHHHH--HHHHHHHhc
Confidence 56665 777777788887 999999999999 44444443 44 3578888875 699999985 334455543
No 15
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=98.76 E-value=8e-09 Score=74.09 Aligned_cols=67 Identities=24% Similarity=0.246 Sum_probs=48.8
Q ss_pred CeEEEeCChhHHHHHhhhhcC-ceEEEcCCCCCCCCcccccccccC---ceEEEEcCCChH---HHHHHHhhcCCC
Q psy4521 53 DSAVLVQRLVDFLTLCNAHLN-YNVICLPHGLTCLPQEILPCLEEY---NKLYLWFGKDHE---STRVFSSKLNEK 121 (223)
Q Consensus 53 ~~iVItEGE~Dalav~q~~~g-~p~VSlP~Ga~slp~~~lp~Le~F---~~IiLw~D~D~~---~a~e~A~kLg~~ 121 (223)
++++|+||..|++++.|.... .+++++ .|.. .+...+..|.++ ++||+|+|+|.+ ++++++++|...
T Consensus 1 ~~l~ivEg~~da~~~~~~~~~~~~~~~~-~G~~-~~~~~~~~l~~~~~~~~Iii~~D~D~~G~~~~~~i~~~l~~~ 74 (76)
T smart00493 1 KVLIIVEGPADAIALEKAGGFGGNVVAL-GGHL-LKKEIIKLLKRLAKKKEVILATDPDREGEAIAWKLAELLKPA 74 (76)
T ss_pred CEEEEEcCHHHHHHHHHhcCCCEEEEEE-eeee-cHHHHHHHHHHHhcCCEEEEEcCCChhHHHHHHHHHHHhhhh
Confidence 479999999999999997421 244444 3443 344455555554 679999999999 888999988764
No 16
>PRK08624 hypothetical protein; Provisional
Probab=98.67 E-value=4.3e-08 Score=91.60 Aligned_cols=98 Identities=13% Similarity=0.157 Sum_probs=70.6
Q ss_pred ceEEEeeecCCCcEEEEEEeecccc-----ccccCC-C--------CccccccCCCC---CCCCeEEEeCChhHHH---H
Q psy4521 7 KTLYMPLVNYANEVVGYKQVHKSIE-----STVPTK-Q--------CQGVLHCPPYK---KKTDSAVLVQRLVDFL---T 66 (223)
Q Consensus 7 ~~lvfP~~~~~g~lvg~K~r~~~ke-----k~~p~~-~--------~~glFG~~~~~---~~~~~iVItEGE~Dal---a 66 (223)
.-++||.+|..|++||+.=|....+ |-+|.. + ..-|||.|... ...+++|||||.+|++ |
T Consensus 182 ~RImFPI~d~~GrvIGFgGR~l~~~~~~~~KY~p~y~Nst~~~F~Kg~~LYGl~~Ak~~irk~~~vIivEGymDVI~~~a 261 (373)
T PRK08624 182 QRIIIPHRDESGELIGIRGRLLDKELVDKNKYFPIYVNDTGYNHPKGKILYGLWQNKKYIKEKKKVIIVESEKSVLFSDK 261 (373)
T ss_pred CeeEEEEECCCCCEEEEeCeEcCCCccccccccccCCCCcccccccchhhcCHHHHHHHhccCCeEEEEeccHHHHHHHH
Confidence 4589999999999999999987322 223431 1 14567776322 3467999999999999 6
Q ss_pred HhhhhcCceEEEcCCCCCCCCcccccccccC--ceEEEEcCCCh
Q psy4521 67 LCNAHLNYNVICLPHGLTCLPQEILPCLEEY--NKLYLWFGKDH 108 (223)
Q Consensus 67 v~q~~~g~p~VSlP~Ga~slp~~~lp~Le~F--~~IiLw~D~D~ 108 (223)
++|+ |.++|+ +-| .++-++.+..|-++ ++|+||||+|.
T Consensus 262 ~~~~--G~naVA-~lG-TalT~~q~~lL~r~~~~~Vil~~Dgd~ 301 (373)
T PRK08624 262 FYGE--GNFVVA-ICG-SNISEVQAEKLLRLGVEEVTIALDKEY 301 (373)
T ss_pred HhcC--CCcEEE-CCh-hhCCHHHHHHHHhcCCCcEEEEecCCc
Confidence 6665 445554 344 45778888888888 59999999963
No 17
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [].
Probab=98.38 E-value=1.4e-06 Score=70.61 Aligned_cols=83 Identities=17% Similarity=0.242 Sum_probs=59.8
Q ss_pred cCCCCCC-CCeEEEeCChhHHHHHhhhhcCceEEEcC---CCCCC--------CCcccccccccC----ceEEEEcCCCh
Q psy4521 45 CPPYKKK-TDSAVLVQRLVDFLTLCNAHLNYNVICLP---HGLTC--------LPQEILPCLEEY----NKLYLWFGKDH 108 (223)
Q Consensus 45 ~~~~~~~-~~~iVItEGE~Dalav~q~~~g~p~VSlP---~Ga~s--------lp~~~lp~Le~F----~~IiLw~D~D~ 108 (223)
|+-+..+ .-.|+||||+.=|.|+.++ |+++|||| +|... .+..++|.|+.| ++||++||+|.
T Consensus 2 W~~v~~~p~~pi~ItEG~kKA~al~s~--G~~aIalpGV~~~~~~~~~~~~~~~~~~L~p~L~~~~~~gr~v~iaFD~D~ 79 (130)
T PF12965_consen 2 WQWVLDDPNIPIWITEGAKKAGALLSQ--GYPAIALPGVNNGYRWPKDEGDKIGKRRLIPELAKLAKPGREVYIAFDADT 79 (130)
T ss_pred ccceecCCCccEEEEechHHHHHHHcC--CceEEEeCceeccccccccccccccchhcchhHHHhccCCceEEEEecCCC
Confidence 4444344 3489999999999999874 79999999 22211 122567888888 68999999993
Q ss_pred H---------HHHHHHhhcCCC--ceEEEecC
Q psy4521 109 E---------STRVFSSKLNEK--RCFLIRET 129 (223)
Q Consensus 109 ~---------~a~e~A~kLg~~--RC~iV~~~ 129 (223)
. +.+++++.|-.. +++++.++
T Consensus 80 ~~~Tn~~V~~a~~~l~~~L~~~G~~v~~~~w~ 111 (130)
T PF12965_consen 80 KPKTNKNVRRAIKRLGKLLKEAGCKVKIITWP 111 (130)
T ss_pred ccchhHHHHHHHHHHHHHHHHCCCEEEEEEeC
Confidence 1 778888887765 45777765
No 18
>cd00188 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=98.23 E-value=2.2e-06 Score=59.78 Aligned_cols=67 Identities=19% Similarity=0.114 Sum_probs=45.8
Q ss_pred CeEEEeCChhHHHHHhhhhcC-ceEEEcCCCCCCCCcccccccccC-ceEEEEcCCChH---HHHHHHhhcC
Q psy4521 53 DSAVLVQRLVDFLTLCNAHLN-YNVICLPHGLTCLPQEILPCLEEY-NKLYLWFGKDHE---STRVFSSKLN 119 (223)
Q Consensus 53 ~~iVItEGE~Dalav~q~~~g-~p~VSlP~Ga~slp~~~lp~Le~F-~~IiLw~D~D~~---~a~e~A~kLg 119 (223)
+.+|||||+.|++++.|.... .+++++.......+...+..+.++ .+|++|+|+|.+ .+....+++.
T Consensus 1 ~~viivEg~~d~~~l~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~v~i~~D~D~~g~~~~~~~~~~~~ 72 (83)
T cd00188 1 KKLIIVEGPSDALALAQAGGYGGAVVALGGHALNKTRELLKRLLGEAKEVIIATDADREGEAIALRLLELLK 72 (83)
T ss_pred CEEEEEecHHHHHHHHHHcCCCEEEEEEccEEcHHHHHHHHHHhcCCCEEEEEcCCChhHHHHHHHHHHHHH
Confidence 468999999999999997432 355555544443244555555554 999999999999 3444544443
No 19
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=97.98 E-value=8.4e-06 Score=60.84 Aligned_cols=66 Identities=15% Similarity=0.248 Sum_probs=51.0
Q ss_pred CeEEEeCChhHHHHHhhhhcCceEEEcCCCCCCCCccccccccc-CceEEEEcCCChH---HHHHHHhhcCC
Q psy4521 53 DSAVLVQRLVDFLTLCNAHLNYNVICLPHGLTCLPQEILPCLEE-YNKLYLWFGKDHE---STRVFSSKLNE 120 (223)
Q Consensus 53 ~~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~slp~~~lp~Le~-F~~IiLw~D~D~~---~a~e~A~kLg~ 120 (223)
+.+||+||..|+.++.|+.....+|+. +|.. ++++.+..+.+ .++|||.+|.|.+ .++.+.+.|+.
T Consensus 2 ~~vIiVEG~~D~~~l~~~g~~~~~i~t-~Gt~-~~~~~~~~l~~~~~~VIiltD~D~aG~~i~~~~~~~l~~ 71 (81)
T cd01027 2 GEVIIVEGKNDTESLKKLGIEAEIIET-NGSI-INKETIELIKKAYRGVIILTDPDRKGEKIRKKLSEYLSG 71 (81)
T ss_pred CeEEEEEchHHHHHHHHhCCCccEEEE-CCCc-CCHHHHHHHHHhCCEEEEEECCCHHHHHHHHHHHHHhcc
Confidence 579999999999999998321355555 5544 56566665655 6999999999999 88999999964
No 20
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=97.77 E-value=0.00036 Score=77.17 Aligned_cols=130 Identities=12% Similarity=0.111 Sum_probs=80.7
Q ss_pred cceEEEeeecCCCcEEEEEEeecc-----ccccc--cC---CCCc-cccccCCCCCCCCeEEEeCChhHHHHHhhhhcC-
Q psy4521 6 TKTLYMPLVNYANEVVGYKQVHKS-----IESTV--PT---KQCQ-GVLHCPPYKKKTDSAVLVQRLVDFLTLCNAHLN- 73 (223)
Q Consensus 6 ~~~lvfP~~~~~g~lvg~K~r~~~-----kek~~--p~---~~~~-glFG~~~~~~~~~~iVItEGE~Dalav~q~~~g- 73 (223)
.-+++||.+|.+|+++|+-.+-+. +.+.+ |. +... +++..+. ...++.++|+||-.|++|++|+..+
T Consensus 1720 ~Paliapv~D~~G~i~gv~rt~L~p~~g~~~k~l~~~kr~~G~k~g~~v~l~~-~~~~~~liiaEGiEtaLS~~~a~~~~ 1798 (1960)
T TIGR02760 1720 HPALIAAARNEKGEITGIQITYLDKDDANKDKDMDNNKRVKGSISGQFVVINK-GMQGDRSYIAEGIETGLSIALANPKA 1798 (1960)
T ss_pred CCeEEEEEECCCCCEEEEEEEEccCCCCCCCccCCCcccccccccCcEEEecC-CCCCCeEEEEcCHHHHHHHHHhCCCC
Confidence 347899999999999999977652 22211 11 1112 2233222 2345689999999999999998542
Q ss_pred ceEEEcCCCCCCCCcccccccccCceEEEEcCCCh-----H-HHHHHHhhcCCC--ceEEEecCCCCCChhHHH
Q psy4521 74 YNVICLPHGLTCLPQEILPCLEEYNKLYLWFGKDH-----E-STRVFSSKLNEK--RCFLIRETENQPLPTESK 139 (223)
Q Consensus 74 ~p~VSlP~Ga~slp~~~lp~Le~F~~IiLw~D~D~-----~-~a~e~A~kLg~~--RC~iV~~~~~~kdane~L 139 (223)
.|++++- |+.++.....|.. -++||||.|+|. . ++.+++++|... .|.++.|+|...+..+.+
T Consensus 1799 ~~vvA~l-g~~~l~~i~~~~~--~~~viI~~D~D~~~a~G~~Aa~k~~~~l~~~G~~v~i~~P~Dfnd~g~~~~ 1869 (1960)
T TIGR02760 1799 TVVIAVG-GKNNLSPIIPKFI--PKNVVIVLDNDGEEAKSQRAIEKIINKFKQDNISARIVFPDDWNDIGEEEL 1869 (1960)
T ss_pred ccEEEEC-CccccccccCCCC--CceEEEEeCCCCcccchHHHHHHHHHHHHhCCCeeEEeCCchhhhhhHHHH
Confidence 4566554 3333333333322 379999999993 2 677888887432 478887754333344443
No 21
>PRK04031 DNA primase; Provisional
Probab=97.63 E-value=0.00012 Score=69.40 Aligned_cols=97 Identities=14% Similarity=0.246 Sum_probs=67.4
Q ss_pred CCCCeEEEeCChhHHHHHhhhhcCceEEEcCCCCCCCCcccccccccCceEEEEcCCChH---HHHHHHhhcCCCceEEE
Q psy4521 50 KKTDSAVLVQRLVDFLTLCNAHLNYNVICLPHGLTCLPQEILPCLEEYNKLYLWFGKDHE---STRVFSSKLNEKRCFLI 126 (223)
Q Consensus 50 ~~~~~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~slp~~~lp~Le~F~~IiLw~D~D~~---~a~e~A~kLg~~RC~iV 126 (223)
...+++||+||-+|.++++|+. -.++|++ .|. ++|......+. -++|++++|.|.+ ..+++.+ . ..-.|+.
T Consensus 167 ~k~~~iIVVEG~~DVi~L~~aG-i~nvVAt-~GT-~l~~~i~~l~k-~~~Vil~~DgD~aGe~I~k~l~~-v-~~~d~Va 240 (408)
T PRK04031 167 DDSDAIIVVEGRADVLNLLRYG-IKNAIAV-EGT-NVPETIIELSK-KKTVTAFLDGDRGGELILKELLQ-V-ADIDYVA 240 (408)
T ss_pred ccCCeEEEEeCHHHHHHHHhcc-cceEEEe-CCc-ccHHHHHHHhc-CCCEEEEECCCHHHHHHHHHHHh-h-cceeEEe
Confidence 3467999999999999999973 2456654 555 46776554444 8899999999999 5555554 2 3455788
Q ss_pred ecCCCCCChhHHHhCCchHHHHHHhcCCC
Q psy4521 127 RETENQPLPTESKAKGLDLNRIIESASPL 155 (223)
Q Consensus 127 ~~~~~~kdane~L~~g~~l~~~i~~A~~~ 155 (223)
+.|++ +++-++- ..++.++|.+|.|+
T Consensus 241 raP~G-~dVE~ls--~eeI~kAL~~~~p~ 266 (408)
T PRK04031 241 RAPPG-KEVEELT--KKEIAKALRNKVPV 266 (408)
T ss_pred cCCCC-CChhhCC--HHHHHHHHHhcCCH
Confidence 87754 5654442 35677777766655
No 22
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=96.41 E-value=0.011 Score=50.30 Aligned_cols=111 Identities=15% Similarity=0.223 Sum_probs=73.4
Q ss_pred CeEEEeCChhHHHHHhhhhcCceEEEcCCCCCCCCccccccc---ccCceEEEEcCCChH---HHHHHHhhcC-CCceEE
Q psy4521 53 DSAVLVQRLVDFLTLCNAHLNYNVICLPHGLTCLPQEILPCL---EEYNKLYLWFGKDHE---STRVFSSKLN-EKRCFL 125 (223)
Q Consensus 53 ~~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~slp~~~lp~L---e~F~~IiLw~D~D~~---~a~e~A~kLg-~~RC~i 125 (223)
++||||||--|...+-++- ...+|+ -+|.. ++.+.+..+ .+-+-||+..|.|.+ -.+.+.+.++ ...||+
T Consensus 3 kevIVVEGK~D~~~lk~~~-d~~~I~-T~Gs~-i~~~~i~~i~~~~~~rgVIIfTDpD~~GekIRk~i~~~vp~~khafi 79 (174)
T TIGR00334 3 KEIIVVEGKDDQARIKQAF-DVDVIE-TNGSA-LKDETINLIKKAQKKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFI 79 (174)
T ss_pred CeEEEEecchHHHHHHHhc-CceEEE-ECCCc-cCHHHHHHHHHHhhcCCEEEEeCCCCchHHHHHHHHHHCCCCeEEee
Confidence 6899999999999998762 223343 34543 677666554 566779999999999 7888888898 566777
Q ss_pred EecCCCCCChhHHH---hC-CchHHHHHHhcCCCCCC--cccchhHHHH
Q psy4521 126 IRETENQPLPTESK---AK-GLDLNRIIESASPLCHP--AIITYDVLQE 168 (223)
Q Consensus 126 V~~~~~~kdane~L---~~-g~~l~~~i~~A~~~~~~--~I~tf~dlre 168 (223)
-+-- ..+.... + .+ -.+++++|+++.....+ .-+|.+||.+
T Consensus 80 ~~~~-a~~~~~~-iGVE~As~e~I~~AL~~~~~~~~~~~~~it~~dl~~ 126 (174)
T TIGR00334 80 PKHL-AKPNKKK-IGVEEASVEAIIAALENVHEETKAQQSDISWEDLLE 126 (174)
T ss_pred eHHh-cCcCCCC-cccCCCCHHHHHHHHHHhcccccCcccccCHHHHHH
Confidence 6531 1110000 2 12 25699999998875333 3366666655
No 23
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=96.29 E-value=0.013 Score=44.31 Aligned_cols=73 Identities=18% Similarity=0.208 Sum_probs=45.4
Q ss_pred eEEEeCChhHHHHHhhhhcCceEEEcC-CCCC-CCCc--------------ccccccccCceEEEEcCCChH---HHHHH
Q psy4521 54 SAVLVQRLVDFLTLCNAHLNYNVICLP-HGLT-CLPQ--------------EILPCLEEYNKLYLWFGKDHE---STRVF 114 (223)
Q Consensus 54 ~iVItEGE~Dalav~q~~~g~p~VSlP-~Ga~-slp~--------------~~lp~Le~F~~IiLw~D~D~~---~a~e~ 114 (223)
++||+||--|+-++.++.++.....+| .|-- +++. .+...+.+.++||+|.|.|.. .+.++
T Consensus 1 ~liIvE~ps~a~~i~~~l~~~~~~v~~~~Ghl~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia~~i 80 (100)
T PF01751_consen 1 ELIIVEKPSDAKAIAKALGGEEYIVIATSGHLLELAKPEDYDPKDKKKQIKNLKKLLKKADEIIIATDPDREGELIAWEI 80 (100)
T ss_dssp EEEEESSHHHHHHHHHHSSTTTEEEEEESSSSEESTTSSHHHCHTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHHHHH
T ss_pred CEEEEeCHHHHHHHHHHcCCCCEEEEEeCCcccccccccccccccccccchhhHHHhhhccEeeecCCCChHHHHHHHHH
Confidence 589999999999999985423233333 3322 2221 123455778999999999998 44444
Q ss_pred Hhhc---C---CCceEEE
Q psy4521 115 SSKL---N---EKRCFLI 126 (223)
Q Consensus 115 A~kL---g---~~RC~iV 126 (223)
.+.+ + .+|+++-
T Consensus 81 ~~~~~~~~~~~~~R~~~~ 98 (100)
T PF01751_consen 81 IELLGKNNPKLIKRVWFS 98 (100)
T ss_dssp HHHHHHHSHHHTTEEEEE
T ss_pred HHHHhHhCCCcCCEEEEe
Confidence 4433 3 3666653
No 24
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=94.81 E-value=0.056 Score=50.49 Aligned_cols=109 Identities=12% Similarity=0.143 Sum_probs=70.6
Q ss_pred ceEEEeeecCCCcEEEEEEeeccccc-cccCCCCcccc---ccCCCCCCCCeEEEeCChhHHHHHhhhhcCceEEEcCCC
Q psy4521 7 KTLYMPLVNYANEVVGYKQVHKSIES-TVPTKQCQGVL---HCPPYKKKTDSAVLVQRLVDFLTLCNAHLNYNVICLPHG 82 (223)
Q Consensus 7 ~~lvfP~~~~~g~lvg~K~r~~~kek-~~p~~~~~glF---G~~~~~~~~~~iVItEGE~Dalav~q~~~g~p~VSlP~G 82 (223)
.++| |..|.+|++++.-++.....| ..+.+...|.| |.+. ..+..+||+||=.-+++++|+. +++++.-=+-
T Consensus 160 ~sli-p~~d~~Gel~~lq~I~~dG~Krf~~Ggr~kg~f~p~~g~~--~~aa~lvi~EGyATal~i~~~~-ga~v~aAi~a 235 (366)
T COG4643 160 GSLI-PLRDADGELTGLQLIQPDGTKRFLKGGRVKGCFIPLGGLA--GPAARLVIAEGYATALSISQAT-GAPVAAAIDA 235 (366)
T ss_pred cceE-EEEcCCCCEeeeEEEcCCccceeccCCcccceeeecCCCc--ccccceEEeechhHHHHHHHHh-hhhHHhhhhc
Confidence 4566 888999999999999874344 55544445555 3333 2245699999999999999985 6664332211
Q ss_pred CCCCC--cccccccccCceEEEEcCCChH--------HHHHHHhhcCC
Q psy4521 83 LTCLP--QEILPCLEEYNKLYLWFGKDHE--------STRVFSSKLNE 120 (223)
Q Consensus 83 a~slp--~~~lp~Le~F~~IiLw~D~D~~--------~a~e~A~kLg~ 120 (223)
.+=++ +..-..+-. ..||++-|+|.. .|++.|+--+-
T Consensus 236 gNll~VA~al~~~~Pd-a~iIIaAD~D~~~~nnpG~t~A~eaA~Avng 282 (366)
T COG4643 236 GNLLAVASALRKKFPD-AQIIIAADDDINTANNPGLTKAEEAAQAVNG 282 (366)
T ss_pred ccHHHHHHHHHHhCCC-cceEEEeccccccCCCcchHHHHHHHHhhCc
Confidence 11111 111112211 789999999993 88899887653
No 25
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=91.53 E-value=0.33 Score=39.44 Aligned_cols=75 Identities=17% Similarity=0.204 Sum_probs=55.7
Q ss_pred CCeEEEeCChhHHHHHhhhhcCceEEEcCCCCCC-CCc-ccccccccCceEEEEcCCChH---HHHHHHhhcCC-CceEE
Q psy4521 52 TDSAVLVQRLVDFLTLCNAHLNYNVICLPHGLTC-LPQ-EILPCLEEYNKLYLWFGKDHE---STRVFSSKLNE-KRCFL 125 (223)
Q Consensus 52 ~~~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~s-lp~-~~lp~Le~F~~IiLw~D~D~~---~a~e~A~kLg~-~RC~i 125 (223)
.+++||+||--|.-++-+.. ..+++-+-.++-+ ... +.+-...+.+.+||-+|.|.+ .++.+.+.|+. .-|++
T Consensus 9 ~~~vIVVEGK~D~~~l~~~~-~~~~i~~~g~~i~~~~~ie~i~~~~~~k~VIILTD~D~~Ge~Irk~l~~~l~~~~~~~i 87 (127)
T COG1658 9 LKEVIVVEGKDDTASLKRLG-DAGVIITNGSAINSLETIELIKKAQKYKGVIILTDPDRKGERIRKKLKEYLPGAKGAFI 87 (127)
T ss_pred cCceEEEeCCcHHHHHHHhc-CCceEEEcCCccchHHHHHHHHHhhccCCEEEEeCCCcchHHHHHHHHHHhcccccccc
Confidence 36899999999999998873 4566666544432 221 333444458889999999999 99999999998 77776
Q ss_pred Ee
Q psy4521 126 IR 127 (223)
Q Consensus 126 V~ 127 (223)
-+
T Consensus 88 d~ 89 (127)
T COG1658 88 DR 89 (127)
T ss_pred cH
Confidence 65
No 26
>PRK04017 hypothetical protein; Provisional
Probab=89.29 E-value=0.48 Score=38.77 Aligned_cols=66 Identities=12% Similarity=0.047 Sum_probs=44.1
Q ss_pred eEEEeCChhHHHHHhhhhcCceEEEcCCCCCCCCcccccccccCceEEEEcCCChH---HHHHHHhhcCCC
Q psy4521 54 SAVLVQRLVDFLTLCNAHLNYNVICLPHGLTCLPQEILPCLEEYNKLYLWFGKDHE---STRVFSSKLNEK 121 (223)
Q Consensus 54 ~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~slp~~~lp~Le~F~~IiLw~D~D~~---~a~e~A~kLg~~ 121 (223)
.+||+||--|.-++.++.....+|- -+|. ++....---..+.+.||+.+|.|.+ .++.+.+.|...
T Consensus 24 ~vIVVEGk~D~~~L~~lGv~~~iI~-t~g~-~~~~~~e~ia~~~r~VIILTD~D~~GekIr~~l~~~l~~~ 92 (132)
T PRK04017 24 APIIVEGKRDVESLRKLGVEGEIIK-VSRT-PLAEIAELIASRGKEVIILTDFDRKGEELAKKLSEYLQGY 92 (132)
T ss_pred CEEEEeCccHHHHHHHcCCCccEEE-ECCe-ecchHHHHHHhcCCeEEEEECCCcchHHHHHHHHHHHHhC
Confidence 7899999999999998722124443 3333 2333221115688999999999999 666666666543
No 27
>PF13707 RloB: RloB-like protein
Probab=84.18 E-value=19 Score=29.48 Aligned_cols=145 Identities=12% Similarity=0.060 Sum_probs=67.7
Q ss_pred EEEeCCh------hHHH-HHhhhhcCceEEEcCCCCCCCCccc----cc------ccccCceEEEEcCCC----hH-HHH
Q psy4521 55 AVLVQRL------VDFL-TLCNAHLNYNVICLPHGLTCLPQEI----LP------CLEEYNKLYLWFGKD----HE-STR 112 (223)
Q Consensus 55 iVItEGE------~Dal-av~q~~~g~p~VSlP~Ga~slp~~~----lp------~Le~F~~IiLw~D~D----~~-~a~ 112 (223)
+|+|||| ++.| .... .....+...|.+..+-|..+ .. ....|++|++.||.| .. .-+
T Consensus 2 lI~~EGe~TE~~YF~~l~~~~~-~~~~~i~~~~~~~~~~p~~lv~~a~~~~~~~~~~~~~d~v~~V~D~D~~~~~~~~~~ 80 (183)
T PF13707_consen 2 LIVCEGEKTEPNYFKSLRKKRR-RSNLDIKVIPSKGGSDPSSLVEKAKKKRKKKKNDNEYDEVWCVFDRDQNDFEHEKLE 80 (183)
T ss_pred EEEECCccHHHHHHHHHHHhcC-CCceEEEEeecCCCCCHHHHHHHHHHHHhhhccccCCCEEEEEEeCCCCcCcHHHHH
Confidence 5899999 5555 1111 11234555565541334322 23 345999999999999 22 222
Q ss_pred HHHhhcCCCceEEEecCCCC---------CChhH--HH-hCCchHHHHHHh-cCCCCCCcccchhHHHHHHHHhhhhhHH
Q psy4521 113 VFSSKLNEKRCFLIRETENQ---------PLPTE--SK-AKGLDLNRIIES-ASPLCHPAIITYDVLQEDVLADLQNVTL 179 (223)
Q Consensus 113 e~A~kLg~~RC~iV~~~~~~---------kdane--~L-~~g~~l~~~i~~-A~~~~~~~I~tf~dlre~V~~el~n~~~ 179 (223)
+..+.-......++-..+ + .+... .. .........+.. ...+.... ..+..+++.+...+.|..+
T Consensus 81 ~~~~~a~~~~i~l~~SnP-cFE~WlLlHf~~~~~~~~~~~~~~~~~~~~~~~~~~y~k~~-~~~~~~~~~~~~Ai~nA~~ 158 (183)
T PF13707_consen 81 EAIKKAKRNKINLAVSNP-CFELWLLLHFEDVTSPDNKSKDAAIKKLRLKKYLPDYKKKK-NLYKFLLEKIKEAIKNAKK 158 (183)
T ss_pred HHHHhccccCeEEEEecC-cHHHHHHHhccCccccccchhhHHHHHHHHHHhcccCCCCC-ccHHHHHHHHHHHHHHHHH
Confidence 222222223455554321 1 01110 00 000111111222 24444444 6677788888888877665
Q ss_pred HHHhhcccC-CccccCChhhHhhh
Q psy4521 180 LLLRTMYCR-RMCWLTYKTTNRFK 202 (223)
Q Consensus 180 ~~~~~~~~~-Gv~w~~fp~Ln~~l 202 (223)
......-.. .-++++.+.|-+.+
T Consensus 159 l~~~~~~~~~~np~T~v~~li~~l 182 (183)
T PF13707_consen 159 LRKQNEEDKEPNPYTNVHELIEEL 182 (183)
T ss_pred HHHHhhccCCCCCCCCHHHHHHHh
Confidence 442111111 23555555554444
No 28
>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=75.23 E-value=3.5 Score=30.87 Aligned_cols=19 Identities=21% Similarity=0.202 Sum_probs=16.2
Q ss_pred CCeEEEeCChhHHHHHhhh
Q psy4521 52 TDSAVLVQRLVDFLTLCNA 70 (223)
Q Consensus 52 ~~~iVItEGE~Dalav~q~ 70 (223)
++.+|++||.-|.+.+-..
T Consensus 3 a~~vIlVEG~tE~~~l~~~ 21 (97)
T cd01026 3 ADKVILVEGDSEEILLPAL 21 (97)
T ss_pred CCeEEEEecHHHHHHHHHH
Confidence 5789999999999987654
No 29
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=65.61 E-value=7.9 Score=36.41 Aligned_cols=47 Identities=19% Similarity=0.128 Sum_probs=35.9
Q ss_pred CCCCCCcccchhHHHHHHHHhhhhhH----HHHHhhcccCCccccCChhhHhhhcccch
Q psy4521 153 SPLCHPAIITYDVLQEDVLADLQNVT----LLLLRTMYCRRMCWLTYKTTNRFKVSNGN 207 (223)
Q Consensus 153 ~~~~~~~I~tf~dlre~V~~el~n~~----~~~~~~~~~~Gv~w~~fp~Ln~~lkG~~~ 207 (223)
.....++..++.|+.+++++.+.... ... |++|. |+.|++++.|++.
T Consensus 143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------gi~tG-~~~LD~~~~G~~~ 193 (421)
T TIGR03600 143 SDGQERGFVTFGEVLEDVVRDLDKRFNPKGELT-------GLSTG-LPKLDRLTNGLVK 193 (421)
T ss_pred hccCcCCchhHHHHHHHHHHHHHHHhcCCCCCc-------ceeCC-ChhHHHHhcCCCC
Confidence 44456688899999999988875421 234 89987 9999999999864
No 30
>PF13154 DUF3991: Protein of unknown function (DUF3991)
Probab=59.28 E-value=14 Score=26.79 Aligned_cols=25 Identities=8% Similarity=-0.040 Sum_probs=22.1
Q ss_pred CCcceEEEeeecCCCcEEEEEEeec
Q psy4521 4 TETKTLYMPLVNYANEVVGYKQVHK 28 (223)
Q Consensus 4 ~~~~~lvfP~~~~~g~lvg~K~r~~ 28 (223)
.++..++|||++.+|.++|.=+|+.
T Consensus 26 d~~~N~vF~~~d~~g~~~ga~~rGt 50 (77)
T PF13154_consen 26 DKYGNVVFVGYDENGKPVGAELRGT 50 (77)
T ss_pred cCCccEEEEEECCCCCEEEEEEECC
Confidence 3456899999999999999999987
No 31
>PF04122 CW_binding_2: Putative cell wall binding repeat 2; InterPro: IPR007253 This repeat is found in multiple tandem copies in proteins including amidase enhancers [] and adhesins [].
Probab=55.85 E-value=24 Score=25.88 Aligned_cols=53 Identities=21% Similarity=0.345 Sum_probs=35.2
Q ss_pred CCCeEEEeCC--hhHHHHHhhhh--cCceEEEcCCCCCCCCccccccccc--CceEEEEcCC
Q psy4521 51 KTDSAVLVQR--LVDFLTLCNAH--LNYNVICLPHGLTCLPQEILPCLEE--YNKLYLWFGK 106 (223)
Q Consensus 51 ~~~~iVItEG--E~Dalav~q~~--~g~p~VSlP~Ga~slp~~~lp~Le~--F~~IiLw~D~ 106 (223)
+.+.++|+.| ..|||+..... .+.|++=++ .++|.....+|.+ .+++|+..+.
T Consensus 24 ~~~~v~ia~g~~~~Dalsa~~~a~~~~~PIll~~---~~l~~~~~~~l~~~~~~~v~iiGg~ 82 (92)
T PF04122_consen 24 KSDKVYIASGDNFADALSASPLAAKNNAPILLVN---NSLPSSVKAFLKSLNIKKVYIIGGE 82 (92)
T ss_pred CCCEEEEEeCcchhhhhhhHHHHHhcCCeEEEEC---CCCCHHHHHHHHHcCCCEEEEECCC
Confidence 4679999998 56999987653 357887777 4455555555554 4666666444
No 32
>PRK08780 DNA topoisomerase I; Provisional
Probab=55.59 E-value=30 Score=35.82 Aligned_cols=93 Identities=16% Similarity=0.100 Sum_probs=57.8
Q ss_pred cccccCceEEEEcCCChH---HHHHHHhhcCC------CceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccc
Q psy4521 92 PCLEEYNKLYLWFGKDHE---STRVFSSKLNE------KRCFLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIIT 162 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~---~a~e~A~kLg~------~RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~t 162 (223)
..+.+-++||||.|.|-. -+.++++.|+. ..++.+...+ .--.+|++++++.+++.. .++.
T Consensus 69 ~~~k~ad~vilAtD~DREGE~Ia~~i~~~l~~~~~~~~~~v~Ri~f~e---------iT~~aI~~A~~n~r~~d~-~l~~ 138 (780)
T PRK08780 69 KAAKSADDLYLATDPDREGEAISWHLAEILKERGLLKDKPMQRVVFTE---------ITPRAIKEAMAKPRDIAS-DLVD 138 (780)
T ss_pred HHHHhCCEEEECCCCCcccHHHHHHHHHHhcccccCCCCceEEEEEcc---------CCHHHHHHHHhCCCcCcH-hHHH
Confidence 345678899999999998 78889998863 3455555432 012568888888887764 5555
Q ss_pred hhHHHHHHHHhhhhhHHHHHhhcccCCccccCChhhHhhhcccchhhh
Q psy4521 163 YDVLQEDVLADLQNVTLLLLRTMYCRRMCWLTYKTTNRFKVSNGNAFR 210 (223)
Q Consensus 163 f~dlre~V~~el~n~~~~~~~~~~~~Gv~w~~fp~Ln~~lkG~~~~~~ 210 (223)
+.+-|.. . |... |+..++ .|.+.+++...+.|
T Consensus 139 A~~aRr~-l------D~lv-------G~~lSr--~l~~~~~~~lSaGR 170 (780)
T PRK08780 139 AQQARRA-L------DYLV-------GFNLSP--LLWRKIQRGLSAGR 170 (780)
T ss_pred HHHHHHH-H------HHhc-------CeeecH--HHHHhhCCCCcccc
Confidence 5444333 2 3445 776653 35555554444443
No 33
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=55.18 E-value=34 Score=27.11 Aligned_cols=74 Identities=18% Similarity=0.203 Sum_probs=44.8
Q ss_pred eEEEeCChhHHHHHhhhh---cCceEE----EcCCCCCC--CC-cccccccc--cCceEEEEcCCChH---HHHHHHhhc
Q psy4521 54 SAVLVQRLVDFLTLCNAH---LNYNVI----CLPHGLTC--LP-QEILPCLE--EYNKLYLWFGKDHE---STRVFSSKL 118 (223)
Q Consensus 54 ~iVItEGE~Dalav~q~~---~g~p~V----SlP~Ga~s--lp-~~~lp~Le--~F~~IiLw~D~D~~---~a~e~A~kL 118 (223)
.+.|+|.=.|.+++-+.+ |.|-|+ |-=+|.+. +. ..+...++ ++++|||+++.+.. -|.-+++.|
T Consensus 2 ~lcVVE~~~Dv~~iE~~~~y~G~Y~VL~G~ispl~gi~p~~l~i~~L~~ri~~~~i~EVIlA~~pt~EGe~Ta~yi~~~l 81 (112)
T cd01025 2 KLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDGIGPDDLNIDKLLERIAKGQVKEVILATNPTVEGEATALYIAKLL 81 (112)
T ss_pred EEEEECCHHHHHHHHhhCccceEEEEeCCCcCCCCCCCccccCHHHHHHHHhcCCCcEEEEecCCCchHHHHHHHHHHHH
Confidence 578999999999988743 225555 33333331 01 12335555 45999999999998 444444444
Q ss_pred CC---CceEEEe
Q psy4521 119 NE---KRCFLIR 127 (223)
Q Consensus 119 g~---~RC~iV~ 127 (223)
.. +-.+++.
T Consensus 82 ~~~~~kvsRlA~ 93 (112)
T cd01025 82 KDFGVKVTRLAQ 93 (112)
T ss_pred hHcCCCeEEEEE
Confidence 44 4444444
No 34
>PF11462 DUF3203: Protein of unknown function (DUF3203); InterPro: IPR021564 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. ; PDB: 1YWY_A.
Probab=51.35 E-value=7.7 Score=28.73 Aligned_cols=21 Identities=19% Similarity=0.211 Sum_probs=13.9
Q ss_pred CCCeEEEeCChhHHHHHhhhh
Q psy4521 51 KTDSAVLVQRLVDFLTLCNAH 71 (223)
Q Consensus 51 ~~~~iVItEGE~Dalav~q~~ 71 (223)
++++|-|||-|.|||+|+-+.
T Consensus 44 ~g~Ri~ItEaEAdaLtVAGA~ 64 (74)
T PF11462_consen 44 DGERIYITEAEADALTVAGAV 64 (74)
T ss_dssp TT--EE--HHHHHHHHHTT-B
T ss_pred cCcEEecCHHHhhheeecccc
Confidence 478999999999999998653
No 35
>TIGR00665 DnaB replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.
Probab=50.65 E-value=18 Score=34.12 Aligned_cols=49 Identities=2% Similarity=-0.079 Sum_probs=33.3
Q ss_pred CCCCcccchhHHHHHHHHhhhhhHHHHHhhcccCCccccCChhhHhhhcccch
Q psy4521 155 LCHPAIITYDVLQEDVLADLQNVTLLLLRTMYCRRMCWLTYKTTNRFKVSNGN 207 (223)
Q Consensus 155 ~~~~~I~tf~dlre~V~~el~n~~~~~~~~~~~~Gv~w~~fp~Ln~~lkG~~~ 207 (223)
...++..++.++.+++++++.....-. -...|+++. |+.|+++++|+.-
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~gi~tG-~~~LD~~~~G~~~ 194 (434)
T TIGR00665 146 RTSGGFKSIKEILKDTVEEIEELYERG---GGITGVPTG-FTDLDKLTSGLQP 194 (434)
T ss_pred cCCCCcccHHHHHHHHHHHHHHHHhCC---CCCCcccCC-chhhHhhcCCCCC
Confidence 346688889999888888765321100 012388875 9999999988753
No 36
>PRK06646 DNA polymerase III subunit chi; Provisional
Probab=49.76 E-value=18 Score=30.03 Aligned_cols=39 Identities=5% Similarity=0.049 Sum_probs=25.2
Q ss_pred ccccccccCceEEEEcCCChH--HHHHHHhhcCCCceEEEe
Q psy4521 89 EILPCLEEYNKLYLWFGKDHE--STRVFSSKLNEKRCFLIR 127 (223)
Q Consensus 89 ~~lp~Le~F~~IiLw~D~D~~--~a~e~A~kLg~~RC~iV~ 127 (223)
++-+++++|++|+..+|+|++ .|+.-=+.+-..-|-+..
T Consensus 101 ~~p~~f~~F~RVi~vv~d~e~~~~ar~~w~~~k~~~~~~~y 141 (154)
T PRK06646 101 QAKEYIRVFKRIIIITDLPEDLKELTVKINKFTGQENKIDC 141 (154)
T ss_pred cCchhhhccCEEEEEeCChHHHHHHHHHHHHHHhCCCcceE
Confidence 455689999999999997766 555444444433333333
No 37
>PRK05728 DNA polymerase III subunit chi; Validated
Probab=49.74 E-value=20 Score=29.13 Aligned_cols=22 Identities=9% Similarity=0.256 Sum_probs=18.2
Q ss_pred cccccccccCceEEEEcCCChH
Q psy4521 88 QEILPCLEEYNKLYLWFGKDHE 109 (223)
Q Consensus 88 ~~~lp~Le~F~~IiLw~D~D~~ 109 (223)
.++-+++.+|++|+-.+++|+.
T Consensus 94 ~~~p~~~~~F~Rvieiv~~d~~ 115 (142)
T PRK05728 94 GAVPAFAAAFERVVDFVGYDEA 115 (142)
T ss_pred CCCcchhhcccEEEEEeCCCHH
Confidence 3455789999999999988887
No 38
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=46.65 E-value=29 Score=36.29 Aligned_cols=66 Identities=14% Similarity=0.098 Sum_probs=44.5
Q ss_pred cccccCceEEEEcCCChH---HHHHHHhhcC-C-CceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccchhHH
Q psy4521 92 PCLEEYNKLYLWFGKDHE---STRVFSSKLN-E-KRCFLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIITYDVL 166 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~---~a~e~A~kLg-~-~RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~tf~dl 166 (223)
..+.+-++||||.|.|-. -+.++.+.|+ . ..++.++..+- --.+|++++++.+++. ..++.+.+-
T Consensus 82 ~~~k~ad~iilAtD~DREGE~I~~~i~~~l~~~~~~v~Ri~f~~i---------T~~aI~~A~~n~~~~~-~~l~~A~~a 151 (859)
T PRK07561 82 KAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFNEI---------TKNAIQEAFENPRELD-INLVNAQQA 151 (859)
T ss_pred HHHhcCCEEEECCCCCccchHHHHHHHHHhCCCCCCeEEEEEccC---------CHHHHHHHHhCcccCC-HHHHHHHHH
Confidence 355678899999999998 7888899988 3 34555554321 1246888888877765 445444443
Q ss_pred H
Q psy4521 167 Q 167 (223)
Q Consensus 167 r 167 (223)
|
T Consensus 152 R 152 (859)
T PRK07561 152 R 152 (859)
T ss_pred H
Confidence 3
No 39
>PF00626 Gelsolin: Gelsolin repeat; InterPro: IPR007123 Gelsolin is a cytoplasmic, calcium-regulated, actin-modulating protein that binds to the barbed ends of actin filaments, preventing monomer exchange (end-blocking or capping) []. It can promote nucleation (the assembly of monomers into filaments), as well as sever existing filaments. In addition, this protein binds with high affinity to fibronectin. Plasma gelsolin and cytoplasmic gelsolin are derived from a single gene by alternate initiation sites and differential splicing. Sequence comparisons indicate an evolutionary relationship between gelsolin, villin, fragmin and severin []. Six large repeating segments occur in gelsolin and villin, and 3 similar segments in severin and fragmin. While the multiple repeats have yet to be related to any known function of the actin-severing proteins, the superfamily appears to have evolved from an ancestral sequence of 120 to 130 amino acid residues [].; PDB: 3FG6_F 1RGI_G 2FGH_A 1D0N_B 3EGD_B 2NUP_B 2NUT_B 3EGX_B 1JHW_A 1J72_A ....
Probab=45.58 E-value=22 Score=24.62 Aligned_cols=49 Identities=18% Similarity=0.271 Sum_probs=30.5
Q ss_pred cCCCCCCCCcccccccccCceEEEEcCCChH-----HHHHHHhhcC----CCceEEEe
Q psy4521 79 LPHGLTCLPQEILPCLEEYNKLYLWFGKDHE-----STRVFSSKLN----EKRCFLIR 127 (223)
Q Consensus 79 lP~Ga~slp~~~lp~Le~F~~IiLw~D~D~~-----~a~e~A~kLg----~~RC~iV~ 127 (223)
+|-..++|...-.=.|+...+||+|.+.+.. .+..+|..+. ..+|.+++
T Consensus 8 ~~~s~~~L~s~~~yIld~~~~i~vW~G~~~~~~e~~~a~~~a~~~~~~~~~~~~~~~~ 65 (76)
T PF00626_consen 8 VPLSQSSLNSDDCYILDCGYEIFVWVGKKSSPEEKAFAAQLAQELLSEERPPLPEVIR 65 (76)
T ss_dssp ESSSGGGEETTSEEEEEESSEEEEEEHTTSHHHHHHHHHHHHHHHHHHHTTTTSEEEE
T ss_pred CCCCHHHcCCCCEEEEEeCCCcEEEEeccCCHHHHHHHHHHHHHhhhhcCCCCCEEEE
Confidence 3434444433222256777799999999965 6666666666 44666665
No 40
>PRK00076 recR recombination protein RecR; Reviewed
Probab=45.25 E-value=65 Score=28.03 Aligned_cols=77 Identities=21% Similarity=0.220 Sum_probs=48.3
Q ss_pred CCCeEEEeCChhHHHHHhhhhc--C-ceEE----EcCCCCCC--CC-ccccccc-ccCceEEEEcCCChH---HHHHHHh
Q psy4521 51 KTDSAVLVQRLVDFLTLCNAHL--N-YNVI----CLPHGLTC--LP-QEILPCL-EEYNKLYLWFGKDHE---STRVFSS 116 (223)
Q Consensus 51 ~~~~iVItEGE~Dalav~q~~~--g-~p~V----SlP~Ga~s--lp-~~~lp~L-e~F~~IiLw~D~D~~---~a~e~A~ 116 (223)
+.+.+.|||.=.|.+++-+.+. | |.|+ |-=+|.+. +. ..++..+ +..++|||+++.+.. -|.-+++
T Consensus 77 d~~~icVVE~~~Dv~aiE~s~~y~G~YhVL~G~ispl~gi~p~~l~i~~L~~ri~~~v~EVIlA~~pt~EGe~Ta~yi~~ 156 (196)
T PRK00076 77 DQSLICVVESPADVLAIERTGEYRGLYHVLGGLLSPLDGIGPEDLNIDELLERLDGEVKEVILATNPTVEGEATAHYIAR 156 (196)
T ss_pred CCCEEEEECCHHHHHHHHhhCcCceEEEEecCCcCCCCCCCccccCHHHHHHHHhCCCCEEEEeCCCCchHHHHHHHHHH
Confidence 3446999999999999887532 2 4554 44455441 11 1334566 569999999999988 3444444
Q ss_pred hc---CCCceEEEe
Q psy4521 117 KL---NEKRCFLIR 127 (223)
Q Consensus 117 kL---g~~RC~iV~ 127 (223)
.| +.+-.+|++
T Consensus 157 ~lk~~~ikvtRiA~ 170 (196)
T PRK00076 157 LLKPLGVKVTRLAH 170 (196)
T ss_pred HHHHcCCCeeeeee
Confidence 44 444445554
No 41
>PF04364 DNA_pol3_chi: DNA polymerase III chi subunit, HolC; InterPro: IPR007459 The DNA polymerase III holoenzyme (2.7.7.7 from EC) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either the tau or gamma product of gene dnax, complexed to delta.delta and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3SXU_A 1EM8_C.
Probab=45.11 E-value=24 Score=28.43 Aligned_cols=22 Identities=18% Similarity=0.431 Sum_probs=16.1
Q ss_pred cccccccccCceEEEEcCCChH
Q psy4521 88 QEILPCLEEYNKLYLWFGKDHE 109 (223)
Q Consensus 88 ~~~lp~Le~F~~IiLw~D~D~~ 109 (223)
...-+.+.+|++|+-.+|.|++
T Consensus 95 ~~~p~~~~~f~rvieiv~~~~~ 116 (137)
T PF04364_consen 95 GEVPPFFSRFERVIEIVDQDDE 116 (137)
T ss_dssp SS--GGGGG-SEEEEEE-SSHH
T ss_pred CCCcchhhcccEEEEEecCCHH
Confidence 3456899999999999999988
No 42
>PRK05776 DNA topoisomerase I; Provisional
Probab=44.48 E-value=37 Score=34.58 Aligned_cols=68 Identities=12% Similarity=0.088 Sum_probs=46.8
Q ss_pred cccccCceEEEEcCCChH---HHHHHHhhcCC-CceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccchhHHH
Q psy4521 92 PCLEEYNKLYLWFGKDHE---STRVFSSKLNE-KRCFLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIITYDVLQ 167 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~---~a~e~A~kLg~-~RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~tf~dlr 167 (223)
..+.+-++||||.|.|-. -+.++.+.++. ++++.++..+ .--.+|++++++.+++. .++..+.+-|
T Consensus 92 ~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~~~~~v~R~~fs~---------iT~~~I~~A~~n~~~~d-~~l~~A~~aR 161 (670)
T PRK05776 92 SLSKYADEFINACDYDIEGSVIGYLIIKYLGDPKKAKRMKFSA---------LTKSDIRRAFRNLETLD-YEMINAGIAR 161 (670)
T ss_pred HHHhcCCEEEECCCCChhHHHHHHHHHHHhCCCCCeeEEEEcc---------CCHHHHHHHHhCccccc-hhHHHHHHHH
Confidence 355678899999999998 77888888873 3556666532 11257889999988873 4555555544
Q ss_pred HH
Q psy4521 168 ED 169 (223)
Q Consensus 168 e~ 169 (223)
+.
T Consensus 162 ~~ 163 (670)
T PRK05776 162 HE 163 (670)
T ss_pred HH
Confidence 43
No 43
>PRK05582 DNA topoisomerase I; Validated
Probab=44.14 E-value=33 Score=34.62 Aligned_cols=67 Identities=12% Similarity=0.062 Sum_probs=44.8
Q ss_pred cccccCceEEEEcCCChH---HHHHHHhhcCCC--ceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccchhHH
Q psy4521 92 PCLEEYNKLYLWFGKDHE---STRVFSSKLNEK--RCFLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIITYDVL 166 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~---~a~e~A~kLg~~--RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~tf~dl 166 (223)
..+.+.++||+|.|.|-. -+.++.+.+|.+ .++.++..+ ..-.+|++++.+..+.. .++..+.+.
T Consensus 69 ~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~~~~~~~R~~~s~---------lt~~~I~~a~~nl~~~~-~~l~~a~~a 138 (650)
T PRK05582 69 KAAKKAKKVYLATDPDREGEAIAWHLAHILGLDEKEKNRIVFNE---------ITKDAIKNAFKNPRKID-MNLVDAQQA 138 (650)
T ss_pred HHHhcCCEEEECCCCCcchHHHHHHHHHHhCCCCCCceEEEEcc---------cCHHHHHHHHhCccccc-HHHHHHHHH
Confidence 456788999999999998 788888899853 344555432 01256788888877765 445444443
Q ss_pred HH
Q psy4521 167 QE 168 (223)
Q Consensus 167 re 168 (223)
|+
T Consensus 139 R~ 140 (650)
T PRK05582 139 RR 140 (650)
T ss_pred HH
Confidence 33
No 44
>PF14097 SpoVAE: Stage V sporulation protein AE1
Probab=43.71 E-value=43 Score=28.84 Aligned_cols=48 Identities=21% Similarity=0.347 Sum_probs=35.3
Q ss_pred eEEEEcCCChH---HHHHHHhhcCCCceEEEecCCCCCChhHHHhCCchHHHHHHhcC
Q psy4521 99 KLYLWFGKDHE---STRVFSSKLNEKRCFLIRETENQPLPTESKAKGLDLNRIIESAS 153 (223)
Q Consensus 99 ~IiLw~D~D~~---~a~e~A~kLg~~RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~ 153 (223)
++||..|.|.. +.+..|+.+| .||.=..- +.|. -..|.++-+.|++|.
T Consensus 1 kVIlvTDGD~~A~ravE~aa~~iG-gRCIS~S~--GNPT----~lsG~elV~lIk~a~ 51 (180)
T PF14097_consen 1 KVILVTDGDEYAKRAVEIAAKNIG-GRCISQSA--GNPT----PLSGEELVELIKQAP 51 (180)
T ss_pred CEEEEECChHHHHHHHHHHHHHhC-cEEEeccC--CCCC----cCCHHHHHHHHHhCC
Confidence 58999999998 8888999998 46654432 2333 235788888898875
No 45
>PRK02812 ribose-phosphate pyrophosphokinase; Provisional
Probab=42.54 E-value=47 Score=30.89 Aligned_cols=44 Identities=23% Similarity=0.278 Sum_probs=34.4
Q ss_pred CcccccccccCceEEEEcCCChH-HHHHHHhhcCCC--ceEEEecCC
Q psy4521 87 PQEILPCLEEYNKLYLWFGKDHE-STRVFSSKLNEK--RCFLIRETE 130 (223)
Q Consensus 87 p~~~lp~Le~F~~IiLw~D~D~~-~a~e~A~kLg~~--RC~iV~~~~ 130 (223)
-.+.||.|+.-+++.|...+..+ .|+++|++||.. ++.+-+.++
T Consensus 9 ~~~~~~~~~~~~~~~i~~g~~~~~la~~ia~~lg~~l~~~~~~~FpD 55 (330)
T PRK02812 9 RAEQLPLLSDNNRLRLFSGSSNPALAQEVARYLGMDLGPMIRKRFAD 55 (330)
T ss_pred cCCCCccccCCCCEEEEECCCCHHHHHHHHHHhCCCceeeEEEECCC
Confidence 34678999999998888888887 999999999954 444444554
No 46
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.91 E-value=94 Score=27.05 Aligned_cols=77 Identities=16% Similarity=0.177 Sum_probs=48.4
Q ss_pred CCCeEEEeCChhHHHHHhhhhc--C-ceEE----EcCCCCCC--CC-cccccccc--cCceEEEEcCCChH---HHHHHH
Q psy4521 51 KTDSAVLVQRLVDFLTLCNAHL--N-YNVI----CLPHGLTC--LP-QEILPCLE--EYNKLYLWFGKDHE---STRVFS 115 (223)
Q Consensus 51 ~~~~iVItEGE~Dalav~q~~~--g-~p~V----SlP~Ga~s--lp-~~~lp~Le--~F~~IiLw~D~D~~---~a~e~A 115 (223)
+...+-|||.=.|.+++-+.+. | |.|+ |-=+|.+. +. ..++..++ +.++|||+++.+.. -|.-++
T Consensus 77 d~~~iCVVE~~~Dv~aiE~~~~y~G~YhVL~G~iSPldgigp~~l~i~~L~~Ri~~~~v~EVIlAt~~tvEGe~Ta~yi~ 156 (195)
T TIGR00615 77 DNSVICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGIGPEDLTIAALLKRLQEESVKEVILATNPTVEGEATALYIA 156 (195)
T ss_pred CCCEEEEECCHHHHHHHHhhCccceEEEEccCccCccCCCChhhcCHHHHHHHHhcCCCcEEEEeCCCCchHHHHHHHHH
Confidence 3447889999999999887632 2 4443 55556541 11 13445665 59999999999987 333344
Q ss_pred hh---cCCCceEEEe
Q psy4521 116 SK---LNEKRCFLIR 127 (223)
Q Consensus 116 ~k---Lg~~RC~iV~ 127 (223)
+. ++.+-.++++
T Consensus 157 ~~lk~~~ikvtRlA~ 171 (195)
T TIGR00615 157 RLLQPFGVKVTRIAS 171 (195)
T ss_pred HHhhhcCCcEEeeee
Confidence 44 4444445554
No 47
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases. DNA primase (2.7.7 from EC) is a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division []. ; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A 2AU3_A.
Probab=39.30 E-value=43 Score=26.59 Aligned_cols=23 Identities=17% Similarity=0.338 Sum_probs=19.0
Q ss_pred cceEEEeeecCCCcEEEEEEeec
Q psy4521 6 TKTLYMPLVNYANEVVGYKQVHK 28 (223)
Q Consensus 6 ~~~lvfP~~~~~g~lvg~K~r~~ 28 (223)
+..+|||.+|..|++||.-=|.+
T Consensus 76 ~~RiifPI~d~~G~vvgF~gR~l 98 (128)
T PF08275_consen 76 RGRIIFPIRDERGRVVGFGGRRL 98 (128)
T ss_dssp TTEEEEEEE-TTS-EEEEEEEES
T ss_pred CCeEEEEEEcCCCCEEEEecccC
Confidence 46799999999999999999987
No 48
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=37.44 E-value=52 Score=34.50 Aligned_cols=66 Identities=11% Similarity=0.090 Sum_probs=45.0
Q ss_pred ccccCceEEEEcCCChH---HHHHHHhhcCCC-ceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccchhHHHH
Q psy4521 93 CLEEYNKLYLWFGKDHE---STRVFSSKLNEK-RCFLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIITYDVLQE 168 (223)
Q Consensus 93 ~Le~F~~IiLw~D~D~~---~a~e~A~kLg~~-RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~tf~dlre 168 (223)
.+.+-++||||.|.|-. -+.++++.|+.+ +++.+...+- --.+|++++.+.+++. ..++.+.+-|.
T Consensus 70 ~~k~ad~iilAtDpDREGE~I~~~i~~~l~~~~~v~Rv~f~~i---------T~~aI~~A~~~~~~~d-~~l~~A~~aR~ 139 (860)
T PRK06319 70 LAKKCDVVYLSPDPDREGEAIAWHIANQLPKNTKIQRISFNAI---------TKGAVTEALKHPREID-MALVNAQQARR 139 (860)
T ss_pred HHHhCCEEEECCCCCcchHHHHHHHHHHcCCCCCeeEEEEccC---------CHHHHHHHHhCccccC-HHHHHHHHHHH
Confidence 45678899999999998 788899999853 4555654320 1246888888877775 44555444333
No 49
>PF12142 PPO1_DWL: Polyphenol oxidase middle domain; InterPro: IPR022739 This domain is found in bacteria and eukaryotes and is approximately 50 amino acids in length. It is found in association with PF00264 from PFAM and PF12143 from PFAM. Most members are annotated as being polyphenol oxidases, and many are from plants or plastids. There is a conserved DWL sequence motif. ; GO: 0004097 catechol oxidase activity, 0055114 oxidation-reduction process; PDB: 1BT3_A 1BUG_B 1BT1_B 1BT2_B 2P3X_A.
Probab=36.06 E-value=24 Score=24.67 Aligned_cols=19 Identities=11% Similarity=0.022 Sum_probs=14.8
Q ss_pred EEeeecCCCcEEEEEEeec
Q psy4521 10 YMPLVNYANEVVGYKQVHK 28 (223)
Q Consensus 10 vfP~~~~~g~lvg~K~r~~ 28 (223)
-|-+||.++++|.+|+++.
T Consensus 11 ~F~FYDen~~lVrv~vrD~ 29 (54)
T PF12142_consen 11 SFLFYDENGQLVRVKVRDV 29 (54)
T ss_dssp EEEEE-TTS-EEEEEGGGH
T ss_pred eeEEECCCCCEEEEEhhhc
Confidence 4778999999999999975
No 50
>PRK08006 replicative DNA helicase; Provisional
Probab=35.97 E-value=47 Score=32.26 Aligned_cols=42 Identities=7% Similarity=-0.003 Sum_probs=30.6
Q ss_pred CcccchhHHHHHHHHhhhhh-----HHHHHhhcccCCccccCChhhHhhhcccch
Q psy4521 158 PAIITYDVLQEDVLADLQNV-----TLLLLRTMYCRRMCWLTYKTTNRFKVSNGN 207 (223)
Q Consensus 158 ~~I~tf~dlre~V~~el~n~-----~~~~~~~~~~~Gv~w~~fp~Ln~~lkG~~~ 207 (223)
++..++.++.+++++.+... .... |+++. |+.|+++++|+..
T Consensus 177 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~-------Gi~TG-~~~LD~~~~Gl~~ 223 (471)
T PRK08006 177 EGPKNIADILDATVARIEQLFQQPHDGVT-------GVNTG-YDDLNKKTAGLQP 223 (471)
T ss_pred CCceeHHHHHHHHHHHHHHHHhcCCCCCC-------cccCC-CHHHHHhhcCCCC
Confidence 36777888888887765431 1234 88886 9999999999864
No 51
>PRK06749 replicative DNA helicase; Provisional
Probab=35.82 E-value=40 Score=32.32 Aligned_cols=41 Identities=10% Similarity=0.058 Sum_probs=29.3
Q ss_pred cccchhHHHHHHHHhhhhh-HHHHHhhcccCCccccCChhhHhhhcccch
Q psy4521 159 AIITYDVLQEDVLADLQNV-TLLLLRTMYCRRMCWLTYKTTNRFKVSNGN 207 (223)
Q Consensus 159 ~I~tf~dlre~V~~el~n~-~~~~~~~~~~~Gv~w~~fp~Ln~~lkG~~~ 207 (223)
+..++.++.++.++.+.+. .+.. |+++. |+.|+++++|++.
T Consensus 144 ~~~~~~~~~~~~~~~~~~~~~~~~-------Gi~TG-~~~LD~~t~Gl~~ 185 (428)
T PRK06749 144 CEFDLKDALVDLYEELHQDAKEIT-------GIETG-YTSLNKMTCGLQE 185 (428)
T ss_pred CCccHHHHHHHHHHHHHhcCCCCC-------CccCC-cHHHHHHhCCCCC
Confidence 4457777777777665432 2345 89987 9999999999864
No 52
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=35.63 E-value=58 Score=32.65 Aligned_cols=68 Identities=7% Similarity=-0.051 Sum_probs=45.0
Q ss_pred cccccCceEEEEcCCChH---HHHHHHhhcC-CCceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccchhHHH
Q psy4521 92 PCLEEYNKLYLWFGKDHE---STRVFSSKLN-EKRCFLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIITYDVLQ 167 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~---~a~e~A~kLg-~~RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~tf~dlr 167 (223)
..+.+-++||+|.|.|-. -+.++.+.++ .+.++.++..+ .--.+|++++.+.+... .++......|
T Consensus 89 ~l~~~~d~ii~AtD~DREGE~I~~~i~~~~~~~~~v~Rl~~~~---------lt~~~I~~a~~nl~~~~-~~l~~a~~aR 158 (618)
T TIGR01057 89 KLAKGADEYINACDYDIEGEVIGFKALKYFCGVERAKRMKFST---------LTKQDIRRAYANPEEID-YGMVDAGMAR 158 (618)
T ss_pred HHHhcCCEEEECCCCCccHHHHHHHHHHHhccCCCceEEEEcc---------CCHHHHHHHHhCcccCC-HhHHHHHHHH
Confidence 466788999999999998 7778888884 34566666532 01256888888877432 3555554444
Q ss_pred HH
Q psy4521 168 ED 169 (223)
Q Consensus 168 e~ 169 (223)
+.
T Consensus 159 ~~ 160 (618)
T TIGR01057 159 HI 160 (618)
T ss_pred HH
Confidence 43
No 53
>PRK13844 recombination protein RecR; Provisional
Probab=35.56 E-value=1.4e+02 Score=26.07 Aligned_cols=78 Identities=13% Similarity=0.240 Sum_probs=49.6
Q ss_pred CCCeEEEeCChhHHHHHhhhhc--C-ceEE----EcCCCCCC--CC-cccccccc--cCceEEEEcCCChH---HHHHHH
Q psy4521 51 KTDSAVLVQRLVDFLTLCNAHL--N-YNVI----CLPHGLTC--LP-QEILPCLE--EYNKLYLWFGKDHE---STRVFS 115 (223)
Q Consensus 51 ~~~~iVItEGE~Dalav~q~~~--g-~p~V----SlP~Ga~s--lp-~~~lp~Le--~F~~IiLw~D~D~~---~a~e~A 115 (223)
+.+.+-|||.=.|.+++-..+. | |.|+ |--+|.+- +. ..++.+++ ++++|||+++.+.. -|.-++
T Consensus 81 d~~~iCVVE~~~Dv~aiE~t~~y~G~YhVL~G~ispl~gi~p~~l~i~~L~~Ri~~~~v~EVIlAt~~t~EGe~Ta~yi~ 160 (200)
T PRK13844 81 DDTKLCIIESMLDMIAIEEAGIYRGKYFVLNGRISPLDGIGPSELKLDILQQIIADRKIDEVILAISPTVEGETTAHFIS 160 (200)
T ss_pred CCCEEEEECCHHHHHHHHhhCccceEEEEccCccCccCCCChhhcCHHHHHHHHhcCCCcEEEEeCCCCccHHHHHHHHH
Confidence 3457889999999999887632 2 3443 55555541 11 13345554 59999999999987 455555
Q ss_pred hhcCCCceEEEecC
Q psy4521 116 SKLNEKRCFLIRET 129 (223)
Q Consensus 116 ~kLg~~RC~iV~~~ 129 (223)
+.|.. -..+-|..
T Consensus 161 ~~lk~-~vkvtRlA 173 (200)
T PRK13844 161 QMIAK-DIKISRIG 173 (200)
T ss_pred HHhcC-CCcEEeee
Confidence 55554 45555543
No 54
>PRK07219 DNA topoisomerase I; Validated
Probab=34.90 E-value=73 Score=33.16 Aligned_cols=80 Identities=6% Similarity=0.021 Sum_probs=51.5
Q ss_pred cccccCceEEEEcCCChH---HH---HHHHhhcCCCceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccchhH
Q psy4521 92 PCLEEYNKLYLWFGKDHE---ST---RVFSSKLNEKRCFLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIITYDV 165 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~---~a---~e~A~kLg~~RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~tf~d 165 (223)
..+.+-++||||.|.|-. -+ .++.+.+....++.++..+ + --.+|++++++..++. .++.....
T Consensus 93 ~l~~~ad~iiiAtD~DREGE~I~~ei~~i~~~~~~~~v~R~~fs~--------i-T~~~I~~A~~n~~~~d-~~l~~a~~ 162 (822)
T PRK07219 93 KLAKDADEIIIATDYDREGELIGKEAYHILREVCQVPVKRARFSS--------L-TKKEIRKAFENPDEID-FNLADAGE 162 (822)
T ss_pred HHHhcCCEEEEcCCCChhHHHHHHHHHHHHHhcCCCceeEEEEcc--------C-CHHHHHHHHhCcccCC-HHHHHHHH
Confidence 345688899999999998 34 6677766445666676542 1 1256888888887775 45555444
Q ss_pred HHHHHHHhhhhhHHHHHhhcccCCccccCC
Q psy4521 166 LQEDVLADLQNVTLLLLRTMYCRRMCWLTY 195 (223)
Q Consensus 166 lre~V~~el~n~~~~~~~~~~~~Gv~w~~f 195 (223)
-|+. .|... |+..+|+
T Consensus 163 aR~~-------~D~lv-------G~nlSr~ 178 (822)
T PRK07219 163 ARQI-------IDLYW-------GAALTRF 178 (822)
T ss_pred HHHH-------HHHHh-------hhhhCHH
Confidence 4433 24455 7766655
No 55
>PF04008 Adenosine_kin: Adenosine specific kinase; InterPro: IPR007153 The structure of a member of this family from the hyperthermophilic archaeon Pyrobaculum aerophilum contains a modified histidine residue which is interpreted as stable phosphorylation. In vitro binding studies confirmed that adenosine and AMP but not ADP or ATP bind to the protein [].; PDB: 1VGG_A 1RLH_A 1WVQ_A 2GL0_F 2JB7_B 2EKM_C 2D16_D.
Probab=34.73 E-value=32 Score=28.92 Aligned_cols=34 Identities=18% Similarity=0.210 Sum_probs=27.8
Q ss_pred ceEEEEcCCChH---HHHHHHhhcCCCceEEEecCCC
Q psy4521 98 NKLYLWFGKDHE---STRVFSSKLNEKRCFLIRETEN 131 (223)
Q Consensus 98 ~~IiLw~D~D~~---~a~e~A~kLg~~RC~iV~~~~~ 131 (223)
++.+-|-+||+. .|.+-|.++|.+.++++-..+.
T Consensus 48 ~~LvR~~GnD~eL~~~A~~na~~IgAGH~Fii~l~~a 84 (155)
T PF04008_consen 48 PRLVRYSGNDEELIELAVKNALAIGAGHSFIIFLRNA 84 (155)
T ss_dssp TTEEEEEESSHHHHHHHHHHHHHH--TTEEEEEEESS
T ss_pred ceEEEecCCcHHHHHHHHHHHHHhcCCcEEEEEecCc
Confidence 457788899999 9999999999999999997654
No 56
>PRK08840 replicative DNA helicase; Provisional
Probab=34.53 E-value=51 Score=31.99 Aligned_cols=42 Identities=10% Similarity=-0.008 Sum_probs=30.3
Q ss_pred CcccchhHHHHHHHHhhhhhH-----HHHHhhcccCCccccCChhhHhhhcccch
Q psy4521 158 PAIITYDVLQEDVLADLQNVT-----LLLLRTMYCRRMCWLTYKTTNRFKVSNGN 207 (223)
Q Consensus 158 ~~I~tf~dlre~V~~el~n~~-----~~~~~~~~~~Gv~w~~fp~Ln~~lkG~~~ 207 (223)
.+..++.++.+++++.+.... ... |+++. |+.||++++|++.
T Consensus 170 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~~-------gi~TG-~~~LD~~~~G~~~ 216 (464)
T PRK08840 170 EGPQNVDSILEKTLERIELLYKTPQDGVT-------GVDTG-FTDLNKKTAGLQG 216 (464)
T ss_pred CCceeHHHHHHHHHHHHHHHHhcCCCCCC-------CcCCC-cHHHHHhhcCCCC
Confidence 467777888888777665321 233 88876 9999999999763
No 57
>PRK06599 DNA topoisomerase I; Validated
Probab=34.41 E-value=62 Score=32.86 Aligned_cols=67 Identities=13% Similarity=0.125 Sum_probs=43.5
Q ss_pred cccccCceEEEEcCCChH---HHHHHHhhcC-----CCceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccch
Q psy4521 92 PCLEEYNKLYLWFGKDHE---STRVFSSKLN-----EKRCFLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIITY 163 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~---~a~e~A~kLg-----~~RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~tf 163 (223)
..+.+.++||+|.|.|-. -+.++.+.|+ ..+++.++..+ + .-.+|++++.+..+.. .++...
T Consensus 69 ~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~~~~~~~v~Rl~~s~--------l-t~~~I~~a~~n~~~~~-~~l~~a 138 (675)
T PRK06599 69 KAAKKADAVYLATDPDREGEAIAWHIAEVLKEAKLKDKNVKRVVFNE--------I-TKKAVQEAIENPRDID-MDLVDA 138 (675)
T ss_pred HHHhhCCEEEECCCCCcchHHHHHHHHHHHHhhcCCCCCeeEEEEcc--------C-CHHHHHHHHhCcccCC-HHHHHH
Confidence 456788999999999998 6677777773 23566666532 0 1246778888877766 444444
Q ss_pred hHHHH
Q psy4521 164 DVLQE 168 (223)
Q Consensus 164 ~dlre 168 (223)
..-|+
T Consensus 139 ~~aR~ 143 (675)
T PRK06599 139 QQARR 143 (675)
T ss_pred HHHHH
Confidence 44443
No 58
>PRK07220 DNA topoisomerase I; Validated
Probab=34.17 E-value=68 Score=33.05 Aligned_cols=80 Identities=9% Similarity=0.025 Sum_probs=50.1
Q ss_pred ccccCceEEEEcCCChH---HHHHHHhhcC---CC-ceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccchhH
Q psy4521 93 CLEEYNKLYLWFGKDHE---STRVFSSKLN---EK-RCFLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIITYDV 165 (223)
Q Consensus 93 ~Le~F~~IiLw~D~D~~---~a~e~A~kLg---~~-RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~tf~d 165 (223)
.+.+-++||||.|.|-. -+.++.+.|+ .+ +++.++..+ + --.+|++++++.+++. .++..+.+
T Consensus 94 l~k~ad~viiAtD~DREGE~I~~~i~~~l~~~~~~~~~~R~~fs~--------i-T~~~I~~A~~n~~~~d-~~l~~A~~ 163 (740)
T PRK07220 94 LGKEADRVTIATDYDREGELIGVEALNIIKKVNPDIKFDRVRYSA--------I-TKKEIERAFSNPVEVD-FNLADAGH 163 (740)
T ss_pred HHhcCCEEEECCCCCccHHHHHHHHHHHHHhcCCCCceEEEEEcc--------C-CHHHHHHHHhCCCCCC-hhHHHHHH
Confidence 45678899999999998 5555555554 22 566666532 1 1256889999988875 44444444
Q ss_pred HHHHHHHhhhhhHHHHHhhcccCCccccCCh
Q psy4521 166 LQEDVLADLQNVTLLLLRTMYCRRMCWLTYK 196 (223)
Q Consensus 166 lre~V~~el~n~~~~~~~~~~~~Gv~w~~fp 196 (223)
-|+. .|... |+..+|+=
T Consensus 164 aR~~-------~D~lv-------G~nlSr~~ 180 (740)
T PRK07220 164 SRQV-------IDLVW-------GAALTRYI 180 (740)
T ss_pred HHHH-------HHHHh-------chhcCHHH
Confidence 4333 24555 77666543
No 59
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=32.49 E-value=56 Score=32.76 Aligned_cols=67 Identities=12% Similarity=0.104 Sum_probs=43.8
Q ss_pred cccccCceEEEEcCCChH---HHHHHHhhcCCC-ce-EEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccchhHH
Q psy4521 92 PCLEEYNKLYLWFGKDHE---STRVFSSKLNEK-RC-FLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIITYDVL 166 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~---~a~e~A~kLg~~-RC-~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~tf~dl 166 (223)
..+.+.++||+|.|.|.. -+.++.+.++.. .. +.++..+ ..-.+|++++.+.++.. .++.....-
T Consensus 65 ~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~~~~~~~Rl~~s~---------lt~~~I~~a~~~l~~~~-~~l~~aa~a 134 (610)
T TIGR01051 65 TLAKKADEVYLATDPDREGEAIAWHLAEVLKPKDPVYKRIVFNE---------ITKKAIRAALKNPREID-MNLVNAQQA 134 (610)
T ss_pred HHHhcCCEEEECCCCCcchhHHHHHHHHHhCCCCCCceEEEEcc---------CCHHHHHHHHhCccccc-hhHHHHHHH
Confidence 456788999999999998 777787888742 22 4444422 01256888888887775 445444443
Q ss_pred HH
Q psy4521 167 QE 168 (223)
Q Consensus 167 re 168 (223)
|+
T Consensus 135 R~ 136 (610)
T TIGR01051 135 RR 136 (610)
T ss_pred HH
Confidence 43
No 60
>PF13467 RHH_4: Ribbon-helix-helix domain; PDB: 3KK4_C.
Probab=32.16 E-value=15 Score=26.56 Aligned_cols=21 Identities=33% Similarity=0.719 Sum_probs=18.3
Q ss_pred hhcccchhhhcChhhHhhhhh
Q psy4521 201 FKVSNGNAFRLCPEFWEVIEE 221 (223)
Q Consensus 201 ~lkG~~~~~~~~~~~~~~~~~ 221 (223)
.+.|++.-.+|=|+||.+++|
T Consensus 8 ~i~GhrTSi~LE~~FW~~L~e 28 (67)
T PF13467_consen 8 RIAGHRTSIRLEPAFWDALEE 28 (67)
T ss_dssp EETTEEEEEEEEHHHHHHHHH
T ss_pred EECCEEeeeeehHHHHHHHHH
Confidence 367899999999999999986
No 61
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b
Probab=30.53 E-value=78 Score=25.27 Aligned_cols=37 Identities=14% Similarity=-0.036 Sum_probs=27.3
Q ss_pred ccccCceEEEEcCCChH---HHHHHHhhcCC--CceEEEecC
Q psy4521 93 CLEEYNKLYLWFGKDHE---STRVFSSKLNE--KRCFLIRET 129 (223)
Q Consensus 93 ~Le~F~~IiLw~D~D~~---~a~e~A~kLg~--~RC~iV~~~ 129 (223)
.+.+-++||+|.|.|-. -+.++.+.++. .+.+.++..
T Consensus 87 l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~~~~v~R~~fs 128 (142)
T cd01028 87 LAKKADEIVLATDPDREGELIAWEILEVLKCDNKPVKRAWFS 128 (142)
T ss_pred HHhcCCEEEEcCCCCcchHHHHHHHHHHhCCCCCCeEEEEEc
Confidence 44566899999999998 77778887775 455666653
No 62
>cd03409 Chelatase_Class_II Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. Excluded from this family are the ATP-dependent heterotrimeric chelatases (class I) and the multifunctional homodimeric enzymes with dehydrogenase and chelatase activities (class III).
Probab=29.93 E-value=50 Score=24.00 Aligned_cols=77 Identities=8% Similarity=-0.025 Sum_probs=37.2
Q ss_pred HHHHHHhhcCCCceEEEecCCCCCChhHHHhC--CchHHHHHHhcCCCCCCcccchhHHHHHHHHhhhhhHHHHHhhccc
Q psy4521 110 STRVFSSKLNEKRCFLIRETENQPLPTESKAK--GLDLNRIIESASPLCHPAIITYDVLQEDVLADLQNVTLLLLRTMYC 187 (223)
Q Consensus 110 ~a~e~A~kLg~~RC~iV~~~~~~kdane~L~~--g~~l~~~i~~A~~~~~~~I~tf~dlre~V~~el~n~~~~~~~~~~~ 187 (223)
.++.++++++...+++.......|+..+++.+ ...+.+++= -..+...+..+..|+.+++.+...+..+..
T Consensus 22 ~~~~l~~~~~~~~v~~a~~~~~~P~i~~~l~~l~~~g~~~vvv-vPl~~~~g~h~~~di~~~~~~~~~~~~~~~------ 94 (101)
T cd03409 22 QAHNLAESLPDFPYYVGFQSGLGPDTEEAIRELAEEGYQRVVI-VPLAPVSGDEVFYDIDSEIGLVRKQVGEPL------ 94 (101)
T ss_pred HHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHcCCCeEEE-EeCccccChhhHHHHHHHHHHHHHhccccc------
Confidence 56667777765666665542225665555521 011111110 111223455556677666655543322333
Q ss_pred CCccccC
Q psy4521 188 RRMCWLT 194 (223)
Q Consensus 188 ~Gv~w~~ 194 (223)
|++|++
T Consensus 95 -g~~~~~ 100 (101)
T cd03409 95 -GEKLTR 100 (101)
T ss_pred -cccccC
Confidence 888864
No 63
>COG4924 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.53 E-value=72 Score=30.07 Aligned_cols=78 Identities=17% Similarity=0.310 Sum_probs=47.9
Q ss_pred cccCCCCccccccCCCCCC----------CCeEEEeCChhHHHHHhhhhcCceEEEcCCCCCCCCccc--ccccccCceE
Q psy4521 33 TVPTKQCQGVLHCPPYKKK----------TDSAVLVQRLVDFLTLCNAHLNYNVICLPHGLTCLPQEI--LPCLEEYNKL 100 (223)
Q Consensus 33 ~~p~~~~~glFG~~~~~~~----------~~~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~slp~~~--lp~Le~F~~I 100 (223)
..|..+.+|+.|..++.-. ...|.|+|+|.-.+++=| +|=+-+--|++-=-+.+ =|||.. .+|
T Consensus 212 ~~~tPlaPGiagl~di~v~~s~l~~l~lP~srilivENe~sfl~lP~----~pg~i~i~GaGy~~~~lvr~~~l~~-~~l 286 (386)
T COG4924 212 DAPTPLAPGIAGLTDIEVPLSNLCELQLPQSRILIVENEDSFLALPT----WPGVIIIWGAGYRAVDLVRGPYLSN-GRL 286 (386)
T ss_pred ccCCCCCCcccCCcccccchhhhhhccCCceeEEEEechhhhhhcCC----CCCeEEEecCCccHHHhhccccccc-cee
Confidence 4455667888888765322 347899999998888765 45233334444111111 156644 568
Q ss_pred EEEcCCChHHHHHHH
Q psy4521 101 YLWFGKDHESTRVFS 115 (223)
Q Consensus 101 iLw~D~D~~~a~e~A 115 (223)
--|.|+|.-+-.-++
T Consensus 287 ~YWGDmDt~Gf~iL~ 301 (386)
T COG4924 287 LYWGDMDTDGFKILD 301 (386)
T ss_pred eeeccccchHHHHHH
Confidence 889999998444443
No 64
>PF09983 DUF2220: Uncharacterized protein conserved in bacteria C-term(DUF2220); InterPro: IPR024534 This is a domain of unknown function that is found predominantly in hypothetical bacterial proteins.
Probab=28.96 E-value=1.6e+02 Score=24.66 Aligned_cols=66 Identities=21% Similarity=0.281 Sum_probs=43.3
Q ss_pred CCCCeEEEeCChhHHHHHhhhhcCceEEEcCCCCCCC-CcccccccccCceEEEEcCCChH---HHHHHHhhc
Q psy4521 50 KKTDSAVLVQRLVDFLTLCNAHLNYNVICLPHGLTCL-PQEILPCLEEYNKLYLWFGKDHE---STRVFSSKL 118 (223)
Q Consensus 50 ~~~~~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~sl-p~~~lp~Le~F~~IiLw~D~D~~---~a~e~A~kL 118 (223)
...+.|+|+|+.-=.+++.+.. +.-+|- -.|..+. ....++++..- .|+=|.|-|.. -...+.+++
T Consensus 41 ~~~~~vliVEN~~tf~~~~~~~-~~~~Iy-g~G~~~~~~~~~~~~~~~~-~~~ywGDiD~~G~~I~~~lr~~~ 110 (181)
T PF09983_consen 41 LPPRRVLIVENLTTFYSLPELP-NGLVIY-GGGFAISSSRRFLKWLQPK-PVYYWGDIDPGGLRILERLRRKF 110 (181)
T ss_pred CCCCEEEEEeCHHHHHHHHhcC-CeEEEE-CCCcCcHHHHHHHhhcCCC-ceEEeccCCHhHHHHHHHHHHhC
Confidence 3467999999999888877532 122222 2333322 22337788887 99999999999 455555555
No 65
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=28.81 E-value=82 Score=26.26 Aligned_cols=37 Identities=14% Similarity=-0.064 Sum_probs=28.2
Q ss_pred cccccCceEEEEcCCChH---HHHHHHhhcCC--CceEEEec
Q psy4521 92 PCLEEYNKLYLWFGKDHE---STRVFSSKLNE--KRCFLIRE 128 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~---~a~e~A~kLg~--~RC~iV~~ 128 (223)
..+.+.++||||.|.|-. -+.++.+.++. .++..++.
T Consensus 114 ~l~~~~~~iiiatD~drEGe~I~~~i~~~~~~~~~~v~R~~f 155 (170)
T cd03361 114 ELALEVDEVLIATDPDTEGEKIAWDVYLALRPYNKNIKRAEF 155 (170)
T ss_pred HHHhhCCEEEEecCCCccHHHHHHHHHHHhccCCCCeEEEEE
Confidence 456889999999999988 77788888874 45555554
No 66
>PF13358 DDE_3: DDE superfamily endonuclease
Probab=28.67 E-value=32 Score=25.89 Aligned_cols=47 Identities=17% Similarity=0.184 Sum_probs=32.4
Q ss_pred cccccCceEEEEcCCChH-HHHHHHhhcCC--CceEEEecCCCCCC--hhHHH
Q psy4521 92 PCLEEYNKLYLWFGKDHE-STRVFSSKLNE--KRCFLIRETENQPL--PTESK 139 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~-~a~e~A~kLg~--~RC~iV~~~~~~kd--ane~L 139 (223)
++.+.. +++|.+||... .++.....|-. .+..++.+|...+| |.|.+
T Consensus 75 ~~~~~~-~~~li~DNa~~H~~~~~~~~l~~~~~~~~~~~~P~~sPdLNpiE~~ 126 (146)
T PF13358_consen 75 PYPRKG-RIVLIMDNASIHKSKKVQEWLEEHERGIELLFLPPYSPDLNPIENV 126 (146)
T ss_pred ccccce-EEEEecccccccccccccceeeccccccccccccCcCCccCHHHHH
Confidence 344444 89999999999 66667777777 77777776654554 44543
No 67
>PRK07004 replicative DNA helicase; Provisional
Probab=28.57 E-value=61 Score=31.29 Aligned_cols=43 Identities=7% Similarity=0.062 Sum_probs=30.3
Q ss_pred CCcccchhHHHHHHHHhhhhh------HHHHHhhcccCCccccCChhhHhhhcccch
Q psy4521 157 HPAIITYDVLQEDVLADLQNV------TLLLLRTMYCRRMCWLTYKTTNRFKVSNGN 207 (223)
Q Consensus 157 ~~~I~tf~dlre~V~~el~n~------~~~~~~~~~~~Gv~w~~fp~Ln~~lkG~~~ 207 (223)
..+..++.++.+++.+.+... .... |+++. |+.|+++++|+..
T Consensus 164 ~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~-------gi~TG-~~~LD~~t~G~~~ 212 (460)
T PRK07004 164 TQGFLEIGPLLTQVVERIDTLYHTANPSDVT-------GTPTG-FVDLDRMTSGMHG 212 (460)
T ss_pred cCcchhHHHHHHHHHHHHHHHHhccccCCCC-------CccCC-cHHhcccccCCCC
Confidence 356777788888877766431 1234 88865 9999999998753
No 68
>PRK14973 DNA topoisomerase I; Provisional
Probab=28.32 E-value=67 Score=34.15 Aligned_cols=65 Identities=8% Similarity=-0.069 Sum_probs=42.0
Q ss_pred ccccCceEEEEcCCChH---HHHHHHhhcCC----CceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCCCcccchhH
Q psy4521 93 CLEEYNKLYLWFGKDHE---STRVFSSKLNE----KRCFLIRETENQPLPTESKAKGLDLNRIIESASPLCHPAIITYDV 165 (223)
Q Consensus 93 ~Le~F~~IiLw~D~D~~---~a~e~A~kLg~----~RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~~~I~tf~d 165 (223)
.+.+-+.||||.|.|-. -+.++.+.++. .+++.+...+ + --.+|++++.+.++.. ..+....+
T Consensus 93 l~k~ad~IiiAtD~DREGE~I~~~i~e~~~~~~~~~~v~R~~fs~--------i-T~~~I~~A~~nl~~~d-~~l~~A~~ 162 (936)
T PRK14973 93 LAKKADRVTIATDFDTEGELIGKEAYELVRAVNPKVPIDRARFSA--------I-TKEEIVTAFAEPTDLD-FALAAAGE 162 (936)
T ss_pred HHHhCCEEEECCCCCcchHHHHHHHHHHhhhccCCCceEEEEEcc--------C-CHHHHHHHHhCCCCCc-HHHHHHHH
Confidence 45677899999999998 56666666653 2445555432 0 1256889999988875 34444444
Q ss_pred HH
Q psy4521 166 LQ 167 (223)
Q Consensus 166 lr 167 (223)
-|
T Consensus 163 aR 164 (936)
T PRK14973 163 AR 164 (936)
T ss_pred HH
Confidence 33
No 69
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=27.21 E-value=92 Score=24.56 Aligned_cols=36 Identities=17% Similarity=0.114 Sum_probs=25.1
Q ss_pred ccccCceEEEEcCCChH---HHHHHHhhcCC-CceEEEec
Q psy4521 93 CLEEYNKLYLWFGKDHE---STRVFSSKLNE-KRCFLIRE 128 (223)
Q Consensus 93 ~Le~F~~IiLw~D~D~~---~a~e~A~kLg~-~RC~iV~~ 128 (223)
.+.+.++||||.|.|.. -+.++.+.++. .+++.+..
T Consensus 69 l~~~~~eiiiAtD~drEGe~i~~~i~~~~~~~~~v~Rl~~ 108 (123)
T cd03363 69 LAKKADEIYLATDPDREGEAIAWHLAEVLKLKKNVKRVVF 108 (123)
T ss_pred HHhcCCEEEEcCCCCcchHHHHHHHHHHcCCCCCeEEEEE
Confidence 45677889999999987 66777777775 34444443
No 70
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=27.14 E-value=47 Score=29.96 Aligned_cols=112 Identities=17% Similarity=0.150 Sum_probs=60.5
Q ss_pred CeEEEeCChhHHHHHhhhh------cCce-EEE-c-CCCCCCCCcccccccccCceEEEEcCCChH---HHHHHHhhcCC
Q psy4521 53 DSAVLVQRLVDFLTLCNAH------LNYN-VIC-L-PHGLTCLPQEILPCLEEYNKLYLWFGKDHE---STRVFSSKLNE 120 (223)
Q Consensus 53 ~~iVItEGE~Dalav~q~~------~g~p-~VS-l-P~Ga~slp~~~lp~Le~F~~IiLw~D~D~~---~a~e~A~kLg~ 120 (223)
|-=||+||--|+=+++-+- +.|+ +|| + |.-.-. -...--+.-+-++++.|.|.+ .|++|-.-|--
T Consensus 8 DVRIiVEGAsDvE~iSkalQr~aLG~eYnITisSIiPTT~~e---IA~raaeGADlvlIATDaD~~GReLA~kf~eeLrg 84 (290)
T COG4026 8 DVRIIVEGASDVEVISKALQRLALGSEYNITISSIIPTTNVE---IAKRAAEGADLVLIATDADRVGRELAEKFFEELRG 84 (290)
T ss_pred eEEEEeeccchHHHHHHHHHHhhhcccceeEEEeeccCchHH---HHHHhhccCCEEEEeecCcchhHHHHHHHHHHHHH
Confidence 4568999999998877541 1132 222 2 221100 001234566778999999999 67776666653
Q ss_pred CceEE--EecCCCCCChhHHHh---CCchHHHHHHhcCCCCCCcccchhHHHHH
Q psy4521 121 KRCFL--IRETENQPLPTESKA---KGLDLNRIIESASPLCHPAIITYDVLQED 169 (223)
Q Consensus 121 ~RC~i--V~~~~~~kdane~L~---~g~~l~~~i~~A~~~~~~~I~tf~dlre~ 169 (223)
.--+| ++.|-++ -.|++. -..+++++|=.|---+..+|-+..|++++
T Consensus 85 ~VGhiERmK~PiGH--DvEhiD~elvrkEl~nAlvRAGLktL~~v~~~~d~ke~ 136 (290)
T COG4026 85 MVGHIERMKIPIGH--DVEHIDVELVRKELKNALVRAGLKTLQRVPEYMDLKED 136 (290)
T ss_pred hhhhhheeccCCCC--CccccCHHHHHHHHHHHHHHHHHHHHhccchhhHHHHH
Confidence 32233 3333221 122221 02456666555555555666666676654
No 71
>PRK07726 DNA topoisomerase III; Provisional
Probab=26.54 E-value=1e+02 Score=31.22 Aligned_cols=68 Identities=10% Similarity=0.037 Sum_probs=46.3
Q ss_pred cccccCceEEEEcCCChH---HHHHHHhhcCC-CceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCC-CcccchhHH
Q psy4521 92 PCLEEYNKLYLWFGKDHE---STRVFSSKLNE-KRCFLIRETENQPLPTESKAKGLDLNRIIESASPLCH-PAIITYDVL 166 (223)
Q Consensus 92 p~Le~F~~IiLw~D~D~~---~a~e~A~kLg~-~RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~-~~I~tf~dl 166 (223)
..+.+.++||+|.|.|-. -+.++...+|. .+++.++..+ ..-.+|++++.+.++... .++.....-
T Consensus 88 ~l~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~v~Rl~~ss---------lt~~~I~~A~~nl~~~~~~~~l~~aa~a 158 (658)
T PRK07726 88 KLLKQATEIVIATDADREGELIAREILDYCGVRKPIKRLWISS---------LTDKAIKRAFANLKPGKETIPLYYSALA 158 (658)
T ss_pred HHHhhCCeEEEcCCCCccccHHHHHHHHHhCCCCCeEEEEEcc---------CCHHHHHHHHHhcCCchhhHHHHHHHHH
Confidence 355788999999999998 77888888885 3566666532 112568888998887642 344444443
Q ss_pred HH
Q psy4521 167 QE 168 (223)
Q Consensus 167 re 168 (223)
|+
T Consensus 159 R~ 160 (658)
T PRK07726 159 RS 160 (658)
T ss_pred HH
Confidence 33
No 72
>PF13793 Pribosyltran_N: N-terminal domain of ribose phosphate pyrophosphokinase; PDB: 2JI4_A 1DKU_B 1IBS_B 1DKR_B 3MBI_C 3LRT_B 3LPN_B 3NAG_B 2H07_B 2H06_B ....
Probab=25.86 E-value=2e+02 Score=22.57 Aligned_cols=23 Identities=4% Similarity=-0.093 Sum_probs=14.9
Q ss_pred EEEcCCChHHHHHHHhhcCCCce
Q psy4521 101 YLWFGKDHESTRVFSSKLNEKRC 123 (223)
Q Consensus 101 iLw~D~D~~~a~e~A~kLg~~RC 123 (223)
++........|+++|+.||.+-+
T Consensus 3 I~~g~~~~~La~~ia~~L~~~~~ 25 (116)
T PF13793_consen 3 IFSGSSSQDLAERIAEALGIPLG 25 (116)
T ss_dssp EEESSSGHHHHHHHHHHTTS-EE
T ss_pred EEECCCCHHHHHHHHHHhCCcee
Confidence 34444444499999999997643
No 73
>smart00262 GEL Gelsolin homology domain. Gelsolin/severin/villin homology domain. Calcium-binding and actin-binding. Both intra- and extracellular domains.
Probab=24.84 E-value=1.5e+02 Score=21.21 Aligned_cols=32 Identities=16% Similarity=0.329 Sum_probs=20.7
Q ss_pred CceEEEEcCCChH-----HHHHHHhhc----CCCceEEEec
Q psy4521 97 YNKLYLWFGKDHE-----STRVFSSKL----NEKRCFLIRE 128 (223)
Q Consensus 97 F~~IiLw~D~D~~-----~a~e~A~kL----g~~RC~iV~~ 128 (223)
-.+||+|.+.+.. .|.++|..+ ....|.+...
T Consensus 34 ~~~iyvW~G~~as~~ek~~A~~~a~~~~~~~~~~~~~i~~v 74 (90)
T smart00262 34 GSEIYVWVGKKSSQDEKKKAAELAVELDDTLGPGPVQVRVV 74 (90)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHhcCCCCceEEEE
Confidence 3699999999985 555555554 3344555443
No 74
>COG3837 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=24.74 E-value=39 Score=28.65 Aligned_cols=60 Identities=13% Similarity=0.154 Sum_probs=39.7
Q ss_pred CcEEEEEEeeccccccccCCCCccccccCCCCCCCC-eEEEeCChhHHHH-----HhhhhcCceEEEcCCCCC
Q psy4521 18 NEVVGYKQVHKSIESTVPTKQCQGVLHCPPYKKKTD-SAVLVQRLVDFLT-----LCNAHLNYNVICLPHGLT 84 (223)
Q Consensus 18 g~lvg~K~r~~~kek~~p~~~~~glFG~~~~~~~~~-~iVItEGE~Dala-----v~q~~~g~p~VSlP~Ga~ 84 (223)
|...|+|-.....+ .++.++.+.++.||.. .+ =+.|.|||.+.-. ..+. -.+++-|.|.+
T Consensus 34 G~~~Gl~~fGvn~~-~v~PG~~Ss~~H~Hs~---edEfv~ILeGE~~l~~d~~e~~lrp---GD~~gFpAG~~ 99 (161)
T COG3837 34 GDALGLKRFGVNLE-IVEPGGESSLRHWHSA---EDEFVYILEGEGTLREDGGETRLRP---GDSAGFPAGVG 99 (161)
T ss_pred hhhcChhhcccceE-EeCCCCcccccccccc---CceEEEEEcCceEEEECCeeEEecC---CceeeccCCCc
Confidence 46677777766323 5666777889999953 45 5789999986522 2211 14888899864
No 75
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=23.97 E-value=80 Score=29.73 Aligned_cols=69 Identities=20% Similarity=0.262 Sum_probs=43.2
Q ss_pred eEEEeCChhHHHHHhhhhcCceEEEcCCCCCCCCccccccc--ccCceEEEEcCCChH---HHHHHHhhcCCCceEE
Q psy4521 54 SAVLVQRLVDFLTLCNAHLNYNVICLPHGLTCLPQEILPCL--EEYNKLYLWFGKDHE---STRVFSSKLNEKRCFL 125 (223)
Q Consensus 54 ~iVItEGE~Dalav~q~~~g~p~VSlP~Ga~slp~~~lp~L--e~F~~IiLw~D~D~~---~a~e~A~kLg~~RC~i 125 (223)
.+||+||--|..|+-......++|-|-.. +.. .+-+-| ..++++++.+|-|.. .++++.++|-..-+.+
T Consensus 25 ~~ilveg~~d~~~l~~lgi~g~~i~~s~~-p~~--~cad~ii~~gi~rVVi~~D~d~~G~~~~~~~~~~L~~aGi~V 98 (360)
T PRK14719 25 IPILVEGPNDILSLKNLKINANFITVSNT-PVF--QIADDLIAENISEVILLTDFDRAGRVYAKNIMEEFQSRGIKV 98 (360)
T ss_pred CEEEEEcchHHHHHHHcCCCCcEEEEeCC-chH--HHHHHHHHcCCCEEEEEECCCCCCCccchHHHHHHHHCCCEE
Confidence 79999999999999875321234433111 100 122333 367888888888876 6666677776665555
No 76
>PRK08760 replicative DNA helicase; Provisional
Probab=23.85 E-value=90 Score=30.35 Aligned_cols=41 Identities=10% Similarity=0.083 Sum_probs=29.2
Q ss_pred CcccchhHHHHHHHHhhhhh----HHHHHhhcccCCccccCChhhHhhhcccc
Q psy4521 158 PAIITYDVLQEDVLADLQNV----TLLLLRTMYCRRMCWLTYKTTNRFKVSNG 206 (223)
Q Consensus 158 ~~I~tf~dlre~V~~el~n~----~~~~~~~~~~~Gv~w~~fp~Ln~~lkG~~ 206 (223)
.+..+++++.+++++.+... .... |+++. |+.|+++++|+.
T Consensus 183 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------Gi~TG-~~~LD~~t~G~~ 227 (476)
T PRK08760 183 TDFVAMPGALKDAFEELRNRFENGGNIT-------GLPTG-YNDFDAMTAGLQ 227 (476)
T ss_pred CCceeHHHHHHHHHHHHHHHHhCCCCCC-------cccCC-cHHHHHHhcCCC
Confidence 45667788877777765421 1234 88876 999999999975
No 77
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]
Probab=23.62 E-value=1e+02 Score=31.19 Aligned_cols=57 Identities=14% Similarity=0.191 Sum_probs=41.8
Q ss_pred CCeEEEeCChhHHHHHh----hhhcCce---EEEcCCCCCCCCcccccccccCc-eEEEEcCCChH
Q psy4521 52 TDSAVLVQRLVDFLTLC----NAHLNYN---VICLPHGLTCLPQEILPCLEEYN-KLYLWFGKDHE 109 (223)
Q Consensus 52 ~~~iVItEGE~Dalav~----q~~~g~p---~VSlP~Ga~slp~~~lp~Le~F~-~IiLw~D~D~~ 109 (223)
++-+|+|||+-+.+-+- |+....+ +.-+|.|.+++++..- +-+++- +..+-.|.|++
T Consensus 396 Ar~vIlVEG~aE~ill~~la~~~~~~L~~~gi~VI~~~gs~~k~f~k-f~~~~gI~~~vitD~D~~ 460 (581)
T COG3593 396 ARGVILVEGEAEVILLPELARQCGIDLEKEGIIVIEFAGSGLKPFIK-FAEAMGIRVHVITDGDEA 460 (581)
T ss_pred hceeEEEeccchhhhHHHHHHHhccccccCcEEEEeecccCcHHHHH-HhhccCceEEEEecCCcc
Confidence 57899999999998766 2221222 3444777777887665 777777 88999999998
No 78
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=22.79 E-value=73 Score=29.48 Aligned_cols=48 Identities=21% Similarity=0.398 Sum_probs=30.9
Q ss_pred cCCCCCCCCcccc--cccccCceEEEEcCCChH-HHHHHHhhcCCCce-EEEe
Q psy4521 79 LPHGLTCLPQEIL--PCLEEYNKLYLWFGKDHE-STRVFSSKLNEKRC-FLIR 127 (223)
Q Consensus 79 lP~Ga~slp~~~l--p~Le~F~~IiLw~D~D~~-~a~e~A~kLg~~RC-~iV~ 127 (223)
+|.|....-.+.+ |.=..-+.|.| .+.+.. .+.++|++||..|+ +|-+
T Consensus 15 vplGika~VeaIYEPpQ~~~~d~~~l-~~d~~~~~vd~iA~~lGL~rVG~IfT 66 (306)
T PF05021_consen 15 VPLGIKAVVEAIYEPPQEGEPDGFTL-LPDENEERVDAIASALGLERVGWIFT 66 (306)
T ss_pred CCCceEEEEEEEECCCcCCCCCCEEE-cCCccHHHHHHHHHHCCCEEEEEEEe
Confidence 5666663222222 23346677888 444554 99999999999999 4444
No 79
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=22.66 E-value=1.5e+02 Score=30.24 Aligned_cols=64 Identities=11% Similarity=0.103 Sum_probs=42.8
Q ss_pred ccc--cCceEEEEcCCChH---HHHHHHhhcCCC---ceEEEecCCCCCChhHHHhCCchHHHHHHhcCCCCC-Ccccch
Q psy4521 93 CLE--EYNKLYLWFGKDHE---STRVFSSKLNEK---RCFLIRETENQPLPTESKAKGLDLNRIIESASPLCH-PAIITY 163 (223)
Q Consensus 93 ~Le--~F~~IiLw~D~D~~---~a~e~A~kLg~~---RC~iV~~~~~~kdane~L~~g~~l~~~i~~A~~~~~-~~I~tf 163 (223)
.+. +-++||+|.|.|-. -+.++.+.|+.. .++.+...+- --.+|++++++.++... .+++..
T Consensus 90 l~k~~~ad~Ii~AtDpDREGE~I~~~i~~~l~~~~~~~v~Ri~f~~i---------T~~~I~~A~~n~~~~~~~~~l~~a 160 (660)
T TIGR01056 90 ILKENKVDEVVIATDPDREGELIAREILDYLKVTDKVTIKRLWISSL---------VDSSIRKAFKNLRPKSETEGLYKS 160 (660)
T ss_pred HhhhcCCCEEEECCCCCcchHHHHHHHHHHhCCCCCCceEEEEeccC---------CHHHHHHHHHcCCCchhhhhHHHH
Confidence 445 77899999999998 778888888853 5666665320 12467888888776532 244444
Q ss_pred hH
Q psy4521 164 DV 165 (223)
Q Consensus 164 ~d 165 (223)
..
T Consensus 161 ~~ 162 (660)
T TIGR01056 161 GV 162 (660)
T ss_pred HH
Confidence 33
No 80
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=22.21 E-value=1.3e+02 Score=24.31 Aligned_cols=36 Identities=11% Similarity=-0.077 Sum_probs=25.8
Q ss_pred ccccCceEEEEcCCChH---HHHHHHhhcCC---CceEEEec
Q psy4521 93 CLEEYNKLYLWFGKDHE---STRVFSSKLNE---KRCFLIRE 128 (223)
Q Consensus 93 ~Le~F~~IiLw~D~D~~---~a~e~A~kLg~---~RC~iV~~ 128 (223)
.+.+-+.||+|.|.|-. -+.++.+.++. .+.+.++.
T Consensus 95 l~~~ad~ii~atD~DrEGE~I~~~i~~~~~~~~~~~v~R~~f 136 (151)
T cd03362 95 LAKRADEIVIATDADREGELIGREILEYAKCVKRKPVKRAWF 136 (151)
T ss_pred HHhCCCeEEEccCCCccccHHHHHHHHHhCCCCCCcEEEEEE
Confidence 44566889999999988 77778888876 34455554
No 81
>COG1839 Uncharacterized conserved protein [Function unknown]
Probab=21.81 E-value=1.8e+02 Score=24.50 Aligned_cols=36 Identities=22% Similarity=0.285 Sum_probs=30.4
Q ss_pred ceEEEEcCCChH---HHHHHHhhcCCCceEEEecCCCCC
Q psy4521 98 NKLYLWFGKDHE---STRVFSSKLNEKRCFLIRETENQP 133 (223)
Q Consensus 98 ~~IiLw~D~D~~---~a~e~A~kLg~~RC~iV~~~~~~k 133 (223)
++.+=+-+||+. .|-+-|.|.|.+.++++...+++|
T Consensus 55 ~rLvR~~GND~eL~~lA~ena~~I~AGHvFVI~lrna~P 93 (162)
T COG1839 55 PRLVRYTGNDEELVKLAIENALKIGAGHVFVILLRNAYP 93 (162)
T ss_pred CeeEEecCCcHHHHHHHHHHHHHhcCCcEEEEEecCccc
Confidence 456677899998 999999999999999999876553
No 82
>PF08057 Ery_res_leader2: Erythromycin resistance leader peptide; InterPro: IPR012559 This family consists of erythromycin resistance gene leader peptides. These leader peptides are involved in the transcriptional attenuation control of the synthesis of the macrolide-lincosamide -streptogramin B resistance protein. It acts as a transcriptional attenuator, in contrast to other inducible erm genes. The mRNA leader sequence can fold in either of two mutually exclusive conformations, one of which is postulated to form in the absence of induction, and to contain two rho factor-independent terminators [].; GO: 0046677 response to antibiotic
Probab=21.11 E-value=28 Score=17.71 Aligned_cols=7 Identities=29% Similarity=0.515 Sum_probs=4.9
Q ss_pred CChhhHh
Q psy4521 194 TYKTTNR 200 (223)
Q Consensus 194 ~fp~Ln~ 200 (223)
|||.||+
T Consensus 8 rfptlnq 14 (14)
T PF08057_consen 8 RFPTLNQ 14 (14)
T ss_pred eccccCC
Confidence 5888774
No 83
>PRK10557 hypothetical protein; Provisional
Probab=20.88 E-value=2.3e+02 Score=24.12 Aligned_cols=57 Identities=18% Similarity=0.299 Sum_probs=35.3
Q ss_pred CCcceEEEeeecCC------------CcEEEEEEeeccccccccCCCCccccccCCCCCCCCeEEEeCChhH
Q psy4521 4 TETKTLYMPLVNYA------------NEVVGYKQVHKSIESTVPTKQCQGVLHCPPYKKKTDSAVLVQRLVD 63 (223)
Q Consensus 4 ~~~~~lvfP~~~~~------------g~lvg~K~r~~~kek~~p~~~~~glFG~~~~~~~~~~iVItEGE~D 63 (223)
+..+|++|=| |.+ .+..|++++....|-.....+|.|= ||..+ .+.++|.||.=++.
T Consensus 86 ~~~sCi~~~Y-D~n~nG~~~~~~~~~~e~~gyrl~~~~Le~~~~~~~C~~~-gW~~L-~D~~~i~Vt~f~~~ 154 (192)
T PRK10557 86 AQGSCLIVAW-DLNSNGRWEGAPHKESEQFGYRLRNGVLETLRGATSCQGK-GWEKL-TDPDEITITTFSVE 154 (192)
T ss_pred CCCCeEEEEE-cCCCCCcccCCCCCccceEEEEecCCcEEEEeeecccCCC-Cchhc-cCCCeEEEEEEEEE
Confidence 4688999986 743 2688999887622322223334321 78876 45678888764443
No 84
>PF08874 DUF1835: Domain of unknown function (DUF1835); InterPro: IPR014973 This group of proteins are functionally uncharacterised.
Probab=20.03 E-value=2.5e+02 Score=21.43 Aligned_cols=36 Identities=22% Similarity=0.485 Sum_probs=22.4
Q ss_pred ccccCceEEEEcCCChH---HHHHHHhhcCCCc--eEEEec
Q psy4521 93 CLEEYNKLYLWFGKDHE---STRVFSSKLNEKR--CFLIRE 128 (223)
Q Consensus 93 ~Le~F~~IiLw~D~D~~---~a~e~A~kLg~~R--C~iV~~ 128 (223)
-+.+-.+|+||+..|.. +-.-+...|.-.. .++|..
T Consensus 82 ~l~~~~~I~iW~~~~~~dq~gl~~~l~~L~~~~~~I~~v~~ 122 (124)
T PF08874_consen 82 ELPEDDPIVIWYGDNAYDQLGLRYLLSLLKDKPNRIYVVNV 122 (124)
T ss_pred hCCCCCEEEEEeCCCHHHHHHHHHHHHHhcCCCCeEEEEeC
Confidence 33345578888888777 5555666666443 555554
Done!