Query gi|254781194|ref|YP_003065607.1| hypothetical protein CLIBASIA_05505 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 98
No_of_seqs 107 out of 430
Neff 6.2
Searched_HMMs 39220
Date Mon May 30 05:57:28 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781194.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 pfam08774 VRR_NUC VRR-NUC doma 99.7 1E-16 2.7E-21 119.9 7.4 81 6-86 1-96 (96)
2 KOG2143 consensus 98.9 4.6E-09 1.2E-13 75.1 6.2 51 34-84 794-845 (854)
3 pfam01870 Hjc Archaeal hollida 97.6 0.0014 3.5E-08 42.9 10.2 72 11-83 2-79 (93)
4 cd00523 archeal_HJR Holliday j 97.4 0.0024 6.2E-08 41.5 10.2 76 7-83 4-85 (123)
5 COG1591 Holliday junction reso 96.6 0.035 8.9E-07 34.7 9.6 76 7-83 5-86 (137)
6 PHA01753 Holliday junction res 93.4 0.36 9.2E-06 28.7 6.5 64 9-73 8-76 (121)
7 COG2810 Predicted type IV rest 92.9 0.95 2.4E-05 26.3 8.2 77 8-84 23-105 (284)
8 pfam03838 RecU Recombination p 92.5 1.1 2.8E-05 25.9 9.3 77 7-84 6-110 (167)
9 cd00221 Vsr Very Short Patch R 92.5 0.81 2.1E-05 26.7 7.3 76 7-84 16-112 (115)
10 pfam10107 Endonuc_Holl Endonuc 92.1 0.58 1.5E-05 27.5 6.2 48 36-83 97-151 (153)
11 pfam02021 UPF0102 Uncharacteri 91.3 1.5 3.9E-05 25.1 8.4 60 12-72 3-70 (94)
12 pfam08722 TnsA_N TnsA endonucl 90.4 0.74 1.9E-05 26.9 5.3 48 36-83 29-80 (81)
13 COG4741 Predicted secreted end 89.6 0.74 1.9E-05 26.9 4.8 48 36-83 113-167 (175)
14 TIGR00632 vsr DNA mismatch end 89.3 0.23 5.8E-06 29.9 1.9 84 1-85 32-142 (143)
15 PRK12497 hypothetical protein; 89.1 2.3 5.9E-05 24.0 8.8 61 10-71 11-79 (118)
16 PRK04247 hypothetical protein; 88.4 2.3 5.8E-05 24.0 6.6 90 5-94 127-225 (250)
17 PRK03298 hypothetical protein; 87.8 2.8 7.2E-05 23.5 8.2 88 6-94 103-200 (224)
18 pfam01939 DUF91 Protein of unk 86.6 3.1 8E-05 23.2 6.4 90 5-94 103-202 (228)
19 pfam03852 Vsr DNA mismatch end 83.1 2.7 6.9E-05 23.6 4.8 44 7-52 19-62 (75)
20 COG3727 Vsr DNA G:T-mismatch r 83.0 4.9 0.00012 22.1 7.0 80 2-84 15-116 (150)
21 COG1637 Predicted nuclease of 77.4 7.5 0.00019 21.0 5.9 90 5-94 128-226 (253)
22 pfam07711 RabGGT_insert Rab ge 77.2 3.8 9.7E-05 22.7 3.9 45 21-66 11-55 (102)
23 PRK02234 recU Holliday junctio 76.2 8.1 0.00021 20.8 8.8 77 6-83 31-135 (199)
24 cd01037 Restriction_endonuclea 75.1 8.7 0.00022 20.6 6.8 70 11-83 2-79 (80)
25 PRK09225 threonine synthase; V 74.9 5.1 0.00013 22.0 4.1 40 56-95 164-204 (465)
26 cd01560 Thr-synth_2 Threonine 74.6 4.6 0.00012 22.2 3.8 40 56-95 163-203 (460)
27 COG0792 Predicted endonuclease 74.2 9.2 0.00023 20.5 6.3 52 7-59 4-55 (114)
28 pfam06319 DUF1052 Protein of u 74.0 9.3 0.00024 20.5 6.7 54 8-61 21-74 (158)
29 TIGR00252 TIGR00252 conserved 73.1 3.3 8.4E-05 23.1 2.7 48 10-57 22-70 (141)
30 pfam08378 NERD Nuclease-relate 73.0 2.4 6.2E-05 23.9 2.1 88 4-95 4-97 (123)
31 pfam06250 DUF1016 Protein of u 66.3 9.7 0.00025 20.3 4.0 59 4-62 180-249 (320)
32 pfam09520 RE_MjaII MjaII restr 64.3 13 0.00034 19.6 4.3 22 37-58 144-165 (252)
33 PRK13731 conjugal transfer sur 63.0 16 0.0004 19.1 6.0 53 36-90 38-92 (243)
34 TIGR00260 thrC threonine synth 62.9 5.3 0.00013 21.9 2.1 41 56-96 114-155 (423)
35 cd02410 archeal_CPSF_KH The ar 57.2 20 0.00051 18.5 5.8 84 9-95 25-132 (145)
36 pfam03460 NIR_SIR_ferr Nitrite 55.1 22 0.00055 18.3 6.2 52 45-97 4-66 (67)
37 pfam06555 consensus 54.6 22 0.00057 18.2 4.2 12 15-26 3-14 (200)
38 pfam05818 TraT Enterobacterial 54.1 23 0.00058 18.2 4.5 52 38-91 9-63 (215)
39 PRK03379 vitamin B12-transport 53.6 23 0.00059 18.1 5.2 30 66-95 90-121 (265)
40 pfam08011 DUF1703 Protein of u 53.4 23 0.00059 18.1 8.8 70 8-78 3-74 (101)
41 COG1139 Uncharacterized conser 53.1 23 0.0006 18.1 4.6 37 60-96 62-98 (459)
42 pfam06616 BsuBI_PstI_RE BsuBI/ 53.0 24 0.0006 18.1 7.5 63 34-96 212-279 (306)
43 cd00114 LIGANc NAD+ dependent 52.8 24 0.00061 18.1 6.1 48 49-96 213-264 (307)
44 TIGR02291 rimK_rel_E_lig alpha 52.5 14 0.00037 19.3 2.9 60 4-65 108-188 (320)
45 COG0610 Type I site-specific r 50.5 25 0.00064 17.9 3.9 35 35-70 124-161 (962)
46 KOG2364 consensus 49.3 27 0.00069 17.7 5.0 59 6-66 231-290 (433)
47 pfam04313 HSDR_N Type I restri 47.6 20 0.00051 18.5 3.0 23 34-57 17-40 (90)
48 pfam05116 S6PP Sucrose-6F-phos 47.3 29 0.00074 17.5 7.0 35 14-51 26-73 (247)
49 pfam04471 Mrr_cat Restriction 46.7 30 0.00076 17.5 8.1 77 16-93 2-84 (98)
50 PRK01395 V-type ATP synthase s 45.4 27 0.00068 17.8 3.3 27 70-96 16-42 (104)
51 PRK09534 btuF corrinoid ABC tr 44.6 32 0.00082 17.3 5.1 30 66-95 131-163 (364)
52 pfam09588 YqaJ YqaJ-like viral 42.1 35 0.0009 17.1 3.6 50 10-60 56-113 (141)
53 PRK10767 chaperone protein Dna 41.7 36 0.00091 17.0 6.4 60 35-95 308-374 (376)
54 PRK00453 rpsF 30S ribosomal pr 40.6 37 0.00094 16.9 4.7 56 10-65 21-76 (95)
55 pfam09564 RE_NgoBV NgoBV restr 40.6 37 0.00095 16.9 4.7 61 10-73 46-112 (194)
56 pfam10313 DUF2415 Uncharacteri 38.1 41 0.001 16.7 4.2 30 25-56 4-34 (43)
57 PRK09566 nirA ferredoxin-nitri 36.5 43 0.0011 16.5 6.8 48 49-96 65-124 (513)
58 TIGR01213 TIGR01213 conserved 36.4 43 0.0011 16.5 3.9 62 19-83 254-317 (450)
59 PRK08058 DNA polymerase III su 35.2 35 0.00089 17.1 2.6 50 36-96 76-135 (329)
60 PRK09567 nirA ferredoxin-nitri 33.7 48 0.0012 16.3 7.9 26 49-74 113-138 (591)
61 TIGR00348 hsdR type I site-spe 33.5 48 0.0012 16.3 4.0 26 34-60 133-162 (813)
62 PRK10361 DNA recombination pro 33.3 48 0.0012 16.3 3.1 25 33-57 236-260 (475)
63 COG1258 Predicted pseudouridyl 31.1 53 0.0014 16.0 5.7 81 8-92 190-275 (398)
64 TIGR00678 holB DNA polymerase 29.0 53 0.0013 16.0 2.7 60 36-96 62-144 (216)
65 COG0498 ThrC Threonine synthas 28.6 59 0.0015 15.8 3.9 41 53-96 153-194 (411)
66 TIGR02349 DnaJ_bact chaperone 27.5 61 0.0016 15.6 4.9 40 35-75 343-385 (386)
67 COG5321 Uncharacterized protei 27.4 56 0.0014 15.9 2.6 43 13-57 26-70 (164)
68 smart00532 LIGANc Ligase N fam 25.4 67 0.0017 15.4 6.0 34 63-96 231-268 (441)
69 cd01473 vWA_CTRP CTRP for CS 24.7 69 0.0018 15.3 5.9 66 31-96 102-187 (192)
70 pfam01250 Ribosomal_S6 Ribosom 23.8 72 0.0018 15.2 4.1 59 6-64 13-74 (92)
71 TIGR00963 secA preprotein tran 23.7 72 0.0018 15.2 4.0 53 23-84 58-111 (904)
72 COG3331 PrfA Penicillin-bindin 23.4 73 0.0019 15.2 9.1 77 6-83 9-113 (177)
73 TIGR02502 type_III_YscX type I 23.2 25 0.00064 17.9 0.2 17 34-50 24-40 (126)
74 pfam06241 DUF1012 Protein of u 23.1 61 0.0016 15.6 2.1 18 34-51 111-130 (208)
75 pfam08608 Wyosine_form Wyosine 22.6 36 0.00093 17.0 0.9 26 47-72 2-33 (62)
76 TIGR02258 2_5_ligase 2'-5' RNA 22.3 77 0.002 15.0 5.3 63 13-79 55-121 (189)
77 TIGR03081 metmalonyl_epim meth 22.2 78 0.002 15.0 5.8 85 6-96 7-91 (128)
78 TIGR03675 arCOG00543 arCOG0178 22.1 78 0.002 15.0 6.1 84 8-94 41-148 (630)
79 pfam09521 RE_NgoPII NgoPII res 21.9 79 0.002 15.0 2.6 40 8-57 49-88 (263)
80 pfam04720 DUF506 Protein of un 21.8 79 0.002 15.0 2.8 73 9-95 87-184 (218)
81 cd03008 TryX_like_RdCVF Trypar 20.9 83 0.0021 14.9 4.4 39 12-50 77-126 (146)
82 pfam09491 RE_AlwI AlwI restric 20.3 85 0.0022 14.8 6.3 54 30-86 333-396 (429)
No 1
>pfam08774 VRR_NUC VRR-NUC domain.
Probab=99.68 E-value=1e-16 Score=119.92 Aligned_cols=81 Identities=32% Similarity=0.371 Sum_probs=72.5
Q ss_pred CCHHHHHHHHHHHHHHCC-CEEEEEECC-------------CCCCCCCEEEEECCCC-EEEEEEECCCCCCCHHHHHHHH
Q ss_conf 059999999999999789-889997148-------------9887662799915991-9999972789886989999999
Q gi|254781194|r 6 LSEAKLEKRLVKGSKKLD-CLVFKTQFI-------------NQRGCPDRLIITPNGA-HFWVEMKTSRGRLSNAQKRVIA 70 (98)
Q Consensus 6 m~E~~ie~~i~~~~k~~g-~~~~k~~~~-------------g~~G~PDli~~~~~g~-~~fIEvK~~~gkls~~Q~~~~~ 70 (98)
|+|..+|..+...+++.| +..++..+. +..|+|||+++.|.|+ +.|||||+|++++|++|+.|++
T Consensus 1 ~~e~~~e~~~~~~~~k~g~~~~~~~~~~~~~~~~~~~~~~g~~~G~PDli~~~~~~~~~~~iEvK~p~~~~~~~Q~~~~~ 80 (96)
T pfam08774 1 MREGRIEVALVEALKKLGYPLPRKNWGKKGAEALGKYFRYGLRKGVPDLILFLPPGKRFLLVEVKGPGDKLSPEQRAWLD 80 (96)
T ss_pred CCCCEEEHHHHHHHHHHCCCCCCCCCCCCCHHHHCCHHHCCCCCCCCCEEEEECCCCEEEEEEEECCCCCCCHHHHHHHH
T ss_conf 97640000999999982898876553543867731044157879998789981599869999987899998989999999
Q ss_pred HHHHCCCEEEEECCHH
Q ss_conf 9997898699983989
Q gi|254781194|r 71 TLLLYHQKVQVLSSTE 86 (98)
Q Consensus 71 ~l~~~G~~~~Vv~s~e 86 (98)
.|+++|+.++||+|.+
T Consensus 81 ~l~~~g~~v~V~~~~~ 96 (96)
T pfam08774 81 RLARSGFKVAVCDSVE 96 (96)
T ss_pred HHHHCCCEEEEEECCC
T ss_conf 9997799499960769
No 2
>KOG2143 consensus
Probab=98.87 E-value=4.6e-09 Score=75.06 Aligned_cols=51 Identities=29% Similarity=0.323 Sum_probs=47.9
Q ss_pred CCCCCCEEEEEC-CCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf 887662799915-991999997278988698999999999978986999839
Q gi|254781194|r 34 QRGCPDRLIITP-NGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQKVQVLSS 84 (98)
Q Consensus 34 ~~G~PDli~~~~-~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s 84 (98)
++|+|||.++.| .+++.++|||.|++|||..|+.|+..|.+.|..|.||.-
T Consensus 794 rsG~PDL~lWNp~~k~fklvEVKgpnDRLSekQr~WLalL~dsg~~VEVChV 845 (854)
T KOG2143 794 RSGFPDLTLWNPETKRFKLVEVKGPNDRLSEKQRLWLALLADSGIRVEVCHV 845 (854)
T ss_pred CCCCCCEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf 3799844323577761789983488651028999999999857887799885
No 3
>pfam01870 Hjc Archaeal holliday junction resolvase (hjc). This family of archaebacterial proteins are holliday junction resolvases (hjc gene). The Holliday junction is an essential intermediate of homologous recombination. This protein is the archaeal equivalent of RuvC but is not sequence similar.
Probab=97.56 E-value=0.0014 Score=42.94 Aligned_cols=72 Identities=17% Similarity=0.173 Sum_probs=56.1
Q ss_pred HHHHHHHHHHHCCCEEEEEECCC--CCCCCCEEEEECCCCEEEEEEECCCC---CCCHHHHHHHHHHH-HCCCEEEEEC
Q ss_conf 99999999997898899971489--88766279991599199999727898---86989999999999-7898699983
Q gi|254781194|r 11 LEKRLVKGSKKLDCLVFKTQFIN--QRGCPDRLIITPNGAHFWVEMKTSRG---RLSNAQKRVIATLL-LYHQKVQVLS 83 (98)
Q Consensus 11 ie~~i~~~~k~~g~~~~k~~~~g--~~G~PDli~~~~~g~~~fIEvK~~~g---kls~~Q~~~~~~l~-~~G~~~~Vv~ 83 (98)
.|+.++..+...|..+.....+| +.+.||++... ++.++.||||...+ .++..|..-+..+. ..|+..+++.
T Consensus 2 ~ERel~~~l~~~gFavvR~~gSG~~~~~~pDiiA~~-g~~~~~iEvKst~~~kiyl~~eqve~L~~f~~~fg~~p~iav 79 (93)
T pfam01870 2 YERELVKILEERGFAVVRAAGSGGAVKPLPDIIAGN-GGVYLVIEVKSRKKDKIYLKKEQVEKLVEFARRFGGEPFLAV 79 (93)
T ss_pred HHHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEEC-CCEEEEEEEEECCCCCEEECHHHHHHHHHHHHHCCCEEEEEE
T ss_conf 079999999868916999567899888999889856-987999999961698188789999999999997399699999
No 4
>cd00523 archeal_HJR Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain eukaryotes, however this CD includes only the archeal HJR's. The bacterial and archeal HJRs perform a similar function but differ in both sequence and structure. Structural similarity does however, exist between the archeal HJRs and type II restriction endonucleases, such as EcoRV, BglII, and Fok, and this similarity includes their active site configurations.
Probab=97.45 E-value=0.0024 Score=41.47 Aligned_cols=76 Identities=16% Similarity=0.194 Sum_probs=58.3
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCC--CCCCCCEEEEECCCCEEEEEEECCCCC---CCHHHHHHHHHHH-HCCCEEE
Q ss_conf 599999999999997898899971489--887662799915991999997278988---6989999999999-7898699
Q gi|254781194|r 7 SEAKLEKRLVKGSKKLDCLVFKTQFIN--QRGCPDRLIITPNGAHFWVEMKTSRGR---LSNAQKRVIATLL-LYHQKVQ 80 (98)
Q Consensus 7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g--~~G~PDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l~-~~G~~~~ 80 (98)
+=+..|+.|+..+...|+-+....++| ++..||++... +++++.||||...+. ++..|..-+..+. ..|+..+
T Consensus 4 kG~~~EReL~~~l~~~GfavvR~~gSG~~~~~~pDiiA~~-~~~~~~iEvKst~~~~iYi~~e~ve~L~~Fa~~fG~~p~ 82 (123)
T cd00523 4 KGSRAERELVKILEEKGFAVVRAPGSGGGPRPLPDIVAGN-GGTYLAIEVKSTKKDKIYIKKEQVEKLVEFARRFGGEPY 82 (123)
T ss_pred CCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCEEEEC-CCEEEEEEEEECCCCEEEECHHHHHHHHHHHHHCCCEEE
T ss_conf 5037999999999865934998346788878899889756-985999999962698089849999999999997499389
Q ss_pred EEC
Q ss_conf 983
Q gi|254781194|r 81 VLS 83 (98)
Q Consensus 81 Vv~ 83 (98)
|+-
T Consensus 83 iav 85 (123)
T cd00523 83 LAV 85 (123)
T ss_pred EEE
T ss_conf 999
No 5
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=96.59 E-value=0.035 Score=34.69 Aligned_cols=76 Identities=17% Similarity=0.225 Sum_probs=57.1
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCC--CCCCCCEEEEECCCCEEEEEEECCC-CC--CCHHHHHHHHHH-HHCCCEEE
Q ss_conf 599999999999997898899971489--8876627999159919999972789-88--698999999999-97898699
Q gi|254781194|r 7 SEAKLEKRLVKGSKKLDCLVFKTQFIN--QRGCPDRLIITPNGAHFWVEMKTSR-GR--LSNAQKRVIATL-LLYHQKVQ 80 (98)
Q Consensus 7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g--~~G~PDli~~~~~g~~~fIEvK~~~-gk--ls~~Q~~~~~~l-~~~G~~~~ 80 (98)
+=+..|+.|+..++..|+-+....+.| .+=+||++... +|.++.||||+.. ++ +.+.|..-+-.+ +..|+..+
T Consensus 5 kG~~~EReLv~~L~e~GfAvvR~paSG~sk~p~pDivA~~-g~~~l~iE~K~~~~~kiYl~~e~ve~L~~FA~~fGg~p~ 83 (137)
T COG1591 5 KGSRFERELVRILWERGFAVVRAPASGGSKRPLPDIVAGN-GGVYLAIEVKSRRETKIYLDKEQVEKLVEFARRFGGEPY 83 (137)
T ss_pred CCCHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEECC-CCEEEEEEEEECCCCCEEECHHHHHHHHHHHHHCCCCEE
T ss_conf 3326889999999864854998346789999998788528-978999999861588478759999999999997199568
Q ss_pred EEC
Q ss_conf 983
Q gi|254781194|r 81 VLS 83 (98)
Q Consensus 81 Vv~ 83 (98)
+.-
T Consensus 84 iav 86 (137)
T COG1591 84 IAV 86 (137)
T ss_pred EEE
T ss_conf 999
No 6
>PHA01753 Holliday junction resolvase
Probab=93.40 E-value=0.36 Score=28.73 Aligned_cols=64 Identities=11% Similarity=0.132 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHHHCCCEEEEEECCC--CCCCCCEEEEECCCCEEEEEEECCCCC---CCHHHHHHHHHHH
Q ss_conf 9999999999997898899971489--887662799915991999997278988---6989999999999
Q gi|254781194|r 9 AKLEKRLVKGSKKLDCLVFKTQFIN--QRGCPDRLIITPNGAHFWVEMKTSRGR---LSNAQKRVIATLL 73 (98)
Q Consensus 9 ~~ie~~i~~~~k~~g~~~~k~~~~g--~~G~PDli~~~~~g~~~fIEvK~~~gk---ls~~Q~~~~~~l~ 73 (98)
...|..++..++..|--+....++| .+-.||++... ++.++.||+|+...+ ....|..-+-++.
T Consensus 8 k~~Er~lv~~L~~~GF~avRiPaSgs~~~plPDIiA~k-~n~~laiEvKST~~~~I~Vd~~QI~KL~eF~ 76 (121)
T PHA01753 8 KYYEYKTLEILESNGFKALRIPVSGTGKQALPDIIATK-NNTIYPIEVKSTSKDVVTVDKFQIEKLFRFC 76 (121)
T ss_pred HHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEEEC-CCEEEEEEEEECCCCEEEECHHHHHHHHHHH
T ss_conf 36699999999867911798115789999898578736-9789999985033426997189999999999
No 7
>COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]
Probab=92.93 E-value=0.95 Score=26.25 Aligned_cols=77 Identities=13% Similarity=0.101 Sum_probs=55.4
Q ss_pred HHHHHHHHH-HHHHHCCCEEEEE--ECC---CCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEE
Q ss_conf 999999999-9999789889997--148---9887662799915991999997278988698999999999978986999
Q gi|254781194|r 8 EAKLEKRLV-KGSKKLDCLVFKT--QFI---NQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQKVQV 81 (98)
Q Consensus 8 E~~ie~~i~-~~~k~~g~~~~k~--~~~---g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~V 81 (98)
|.-+.+.|+ ..+.+.||-.... +-| +--|.||..++..++-|.|+|-|.-.-.+...|..-....-+.|..+.+
T Consensus 23 Ea~vrq~lIlp~L~slGwdi~nPkEV~PEe~t~~GraDyalikd~kvfafieak~ls~~~akd~qq~~~Yav~~Gv~~~i 102 (284)
T COG2810 23 EAAVRQHLILPFLSSLGWDIDNPKEVRPEEKTEEGRADYALIKDGKVFAFIEAKNLSVNPAKDVQQLAKYAVDKGVEVGI 102 (284)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf 88888998899999707778990205864245557654488856938998721134757268999999998852837999
Q ss_pred ECC
Q ss_conf 839
Q gi|254781194|r 82 LSS 84 (98)
Q Consensus 82 v~s 84 (98)
|.+
T Consensus 103 Vtn 105 (284)
T COG2810 103 VTN 105 (284)
T ss_pred EEC
T ss_conf 967
No 8
>pfam03838 RecU Recombination protein U.
Probab=92.51 E-value=1.1 Score=25.91 Aligned_cols=77 Identities=13% Similarity=0.016 Sum_probs=58.3
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECC---------------------CCCCCCCEEEEECCCCEEEEEEECCC-------
Q ss_conf 59999999999999789889997148---------------------98876627999159919999972789-------
Q gi|254781194|r 7 SEAKLEKRLVKGSKKLDCLVFKTQFI---------------------NQRGCPDRLIITPNGAHFWVEMKTSR------- 58 (98)
Q Consensus 7 ~E~~ie~~i~~~~k~~g~~~~k~~~~---------------------g~~G~PDli~~~~~g~~~fIEvK~~~------- 58 (98)
.|..|.....-+..+.=+...|..+| -++.-+|...++ .|+++..|.|.-.
T Consensus 6 lE~~IN~tn~~Y~~~~~A~I~KkptPi~ivkv~~~~r~~a~I~~ayf~~kSt~DY~Gvy-~G~~i~FEAKeT~nkt~Fpl 84 (167)
T pfam03838 6 LEELINETNQYYLANGIAVIHKKPTPIQIVKVDYPKRSAAVIKEAYFKQKSTTDYNGVY-KGRYIDFEAKETKNKTSFPL 84 (167)
T ss_pred HHHHHHHHHHHHHHCCEEEEEEECCCEEEEECCCCCCCCCEEEEEEECCCCCCCCCEEE-CCEEEEEECCCCCCCCCCCH
T ss_conf 99999999999987797999970788179943786555334677887357767733167-78999998224356674572
Q ss_pred CCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf 88698999999999978986999839
Q gi|254781194|r 59 GRLSNAQKRVIATLLLYHQKVQVLSS 84 (98)
Q Consensus 59 gkls~~Q~~~~~~l~~~G~~~~Vv~s 84 (98)
....++|...++++..+|+.++++=.
T Consensus 85 ~Ni~~HQi~~L~~~~~~gGiaF~ii~ 110 (167)
T pfam03838 85 KNIHEHQIEHLKQVLKQGGICFVIIR 110 (167)
T ss_pred HHCCHHHHHHHHHHHHCCCEEEEEEE
T ss_conf 45569999999999988997999999
No 9
>cd00221 Vsr Very Short Patch Repair (Vsr) Endonuclease. Endonucleases in DNA repair that recognize damaged DNA and cleave the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches.
Probab=92.48 E-value=0.81 Score=26.67 Aligned_cols=76 Identities=16% Similarity=0.072 Sum_probs=46.7
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEE----CC---CCCCCHHHHHHH----------
Q ss_conf 5999999999999978988999714898876627999159919999972----78---988698999999----------
Q gi|254781194|r 7 SEAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMK----TS---RGRLSNAQKRVI---------- 69 (98)
Q Consensus 7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK----~~---~gkls~~Q~~~~---------- 69 (98)
+.+..|..+.+.|.+.|.++. .....-+|-||+. +.+-..++||-== -| ...|..|...|.
T Consensus 16 k~TkpE~~vrk~L~~~G~Ryr-~~~k~lpG~PDiv-~~~~k~aIFvdGCFWHgh~~~~~~~pk~n~~fW~~Ki~~N~~RD 93 (115)
T cd00221 16 KDTKPERAVRSALWELGYRFR-KQDKDLPGKPDIV-VPGYRLAIFVDGCFWHGHPCHKRKPPPKNTEFWLEKIERNVERD 93 (115)
T ss_pred CCCHHHHHHHHHHHHCCCEEE-ECCCCCCCCCCEE-ECCCCEEEEECCEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 998699999999998899899-6688779999997-35762899932404338887578889853899999999999989
Q ss_pred ----HHHHHCCCEEEEECC
Q ss_conf ----999978986999839
Q gi|254781194|r 70 ----ATLLLYHQKVQVLSS 84 (98)
Q Consensus 70 ----~~l~~~G~~~~Vv~s 84 (98)
+.|.++|+.+.+++.
T Consensus 94 ~~~~~~L~~~GW~v~~vWE 112 (115)
T cd00221 94 RRVQAALERLGWRVLRVWE 112 (115)
T ss_pred HHHHHHHHHCCCEEEEEEE
T ss_conf 9999999988998999983
No 10
>pfam10107 Endonuc_Holl Endonuclease related to archaeal Holliday junction resolvase. This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases.
Probab=92.12 E-value=0.58 Score=27.52 Aligned_cols=48 Identities=23% Similarity=0.362 Sum_probs=36.3
Q ss_pred CCC-CEEEEEC-----CCCEEEEEEECC-CCCCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf 766-2799915-----991999997278-98869899999999997898699983
Q gi|254781194|r 36 GCP-DRLIITP-----NGAHFWVEMKTS-RGRLSNAQKRVIATLLLYHQKVQVLS 83 (98)
Q Consensus 36 G~P-Dli~~~~-----~g~~~fIEvK~~-~gkls~~Q~~~~~~l~~~G~~~~Vv~ 83 (98)
|-| |+++|.. ...+.|+|+|+. ..+||..|+...+.+++--..+..++
T Consensus 97 G~PIDyIvFdgl~~~~~~~IvfiEVKsGksa~Lt~~qr~IrdaIe~g~V~w~~ir 151 (153)
T pfam10107 97 GTPVDYIVFDGLSEGEIREIVFVEVKTGKSARLTEREKAVREAIEAGRVRFETIR 151 (153)
T ss_pred CCCEEEEEECCCCCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHCCEEEEEEE
T ss_conf 8980489974878787444999996458642458778999999985976899986
No 11
>pfam02021 UPF0102 Uncharacterized protein family UPF0102. The function of this family is unknown.
Probab=91.27 E-value=1.5 Score=25.08 Aligned_cols=60 Identities=15% Similarity=0.225 Sum_probs=40.2
Q ss_pred HHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCC--------CCCHHHHHHHHHH
Q ss_conf 999999999789889997148988766279991599199999727898--------8698999999999
Q gi|254781194|r 12 EKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRG--------RLSNAQKRVIATL 72 (98)
Q Consensus 12 e~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~g--------kls~~Q~~~~~~l 72 (98)
|..-..+|.+.|+....--.-.+.|==||+.. .++...|||||+-.+ .+++.|...+.+.
T Consensus 3 E~~A~~~L~~~Gy~Il~rN~r~~~GEIDiIa~-~~~~lvFVEVK~R~~~~~g~~~eav~~~K~~ri~~a 70 (94)
T pfam02021 3 EALAARWLESKGLIILERNWRSRTGEIDIIAR-DDRTIVFVEVKTRSGENYGPAAEAVTPRKQKKIIRT 70 (94)
T ss_pred HHHHHHHHHHCCCEEEEEEECCCCCCEEEEEE-ECCEEEEEEEEEEECCCCCCHHHHCCHHHHHHHHHH
T ss_conf 99999999987999987783268983769998-299999999997106997496692999999999999
No 12
>pfam08722 TnsA_N TnsA endonuclease N terminal. The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5' end of the transposon is carried out by TnsA, and breakage and joining at the 3' end is carried out by TnsB. The N terminal domain of TnsA is catalytic.
Probab=90.36 E-value=0.74 Score=26.90 Aligned_cols=48 Identities=19% Similarity=0.056 Sum_probs=32.6
Q ss_pred CCCCEEEEECCCCEEEEEEECCCC----CCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf 766279991599199999727898----869899999999997898699983
Q gi|254781194|r 36 GCPDRLIITPNGAHFWVEMKTSRG----RLSNAQKRVIATLLLYHQKVQVLS 83 (98)
Q Consensus 36 G~PDli~~~~~g~~~fIEvK~~~g----kls~~Q~~~~~~l~~~G~~~~Vv~ 83 (98)
=.||+++...+|...++|+|.... +....-..-....+..|....++.
T Consensus 29 yTpDflv~~~dg~~~~~eVK~~~~l~~~~~~~K~~~~r~~~~~~g~~~~i~T 80 (81)
T pfam08722 29 YTPDFLVTYKDGKPEAVEVKYSEDLEDERTLEKFEIERRYAEERGIPFRIVT 80 (81)
T ss_pred ECCCEEEEEECCCEEEEEEEHHHHHCCHHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf 9988999996793999997447563377789999999999998498599970
No 13
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=89.62 E-value=0.74 Score=26.89 Aligned_cols=48 Identities=25% Similarity=0.350 Sum_probs=37.1
Q ss_pred CCC-CEEEEEC--CCCE---EEEEEECC-CCCCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf 766-2799915--9919---99997278-98869899999999997898699983
Q gi|254781194|r 36 GCP-DRLIITP--NGAH---FWVEMKTS-RGRLSNAQKRVIATLLLYHQKVQVLS 83 (98)
Q Consensus 36 G~P-Dli~~~~--~g~~---~fIEvK~~-~gkls~~Q~~~~~~l~~~G~~~~Vv~ 83 (98)
|-| |+++|.. +|.. +|||+|+. ++++|..-+...+.+.+.-..+.+.+
T Consensus 113 GTPvD~iVFdGLs~G~i~~IvFvEVKtGkt~~LseREk~Vr~ai~~~rVs~ei~~ 167 (175)
T COG4741 113 GTPVDFIVFDGLSEGNIESIVFVEVKTGKTSSLSEREKAVRDAIENGRVSWEIYH 167 (175)
T ss_pred CCCCEEEEECCCCCCCEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCEEEEEEE
T ss_conf 7971289873777686107999998328767721889999999961813799885
No 14
>TIGR00632 vsr DNA mismatch endonuclease Vsr; InterPro: IPR004603 This entry represents VSR (very short patch repair) endonucleases, which occur in a variety of bacteria. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine . GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine . The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer alpha/beta/alpha topology . ; GO: 0004519 endonuclease activity, 0006298 mismatch repair.
Probab=89.26 E-value=0.23 Score=29.90 Aligned_cols=84 Identities=13% Similarity=-0.037 Sum_probs=56.0
Q ss_pred CCCH-HCCHHHHHHHHHHHHHHCCCEEE----EEECCCCCCCCCEEEEECCCCEEEE--------EEECCCCCCCHHHHH
Q ss_conf 9501-20599999999999997898899----9714898876627999159919999--------972789886989999
Q gi|254781194|r 1 MRTD-YLSEAKLEKRLVKGSKKLDCLVF----KTQFINQRGCPDRLIITPNGAHFWV--------EMKTSRGRLSNAQKR 67 (98)
Q Consensus 1 ~~~~-~m~E~~ie~~i~~~~k~~g~~~~----k~~~~g~~G~PDli~~~~~g~~~fI--------EvK~~~gkls~~Q~~ 67 (98)
|+.. .-+...+|+.|..+|-++|-.+. +-...|-.|-||+.+ ..-.-++|| .+-.-+-.|..+...
T Consensus 32 M~a~s~~~~T~pE~~l~s~L~~lGlryRkdfl~~~~~G~~g~PD~vf-~~~k~~iFidGCFWHg~~C~~~~~~p~s~~~f 110 (143)
T TIGR00632 32 MQAVSRSKGTKPEKALASLLFALGLRYRKDFLLRDKDGLPGTPDIVF-KEYKVVIFIDGCFWHGHDCDILGKVPKSRKDF 110 (143)
T ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEE-CCCEEEEEECCCEECCCCCCCCCCCCCCCHHC
T ss_conf 88764157981789999999998899888987523689854675443-47358886027300587674014788664230
Q ss_pred HHHH--------------HHHCCCEEEEECCH
Q ss_conf 9999--------------99789869998398
Q gi|254781194|r 68 VIAT--------------LLLYHQKVQVLSST 85 (98)
Q Consensus 68 ~~~~--------------l~~~G~~~~Vv~s~ 85 (98)
|+.+ |.+.|+.|++|+.-
T Consensus 111 W~~Ki~~N~~RD~~~~~~L~~~GWrv~~vW~~ 142 (143)
T TIGR00632 111 WSPKIEKNVERDRRVNDALAEEGWRVLRVWEC 142 (143)
T ss_pred CHHHHHHHHHCCCCHHHHHHHCCCEEEEEECC
T ss_conf 36888742530311789998459989896137
No 15
>PRK12497 hypothetical protein; Reviewed
Probab=89.10 E-value=2.3 Score=23.99 Aligned_cols=61 Identities=18% Similarity=0.165 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCC--------CCCHHHHHHHHH
Q ss_conf 99999999999789889997148988766279991599199999727898--------869899999999
Q gi|254781194|r 10 KLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRG--------RLSNAQKRVIAT 71 (98)
Q Consensus 10 ~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~g--------kls~~Q~~~~~~ 71 (98)
.=|.....+|++.|+..+.--.-.+.|==|||... ++...|||||+-.+ .+++.|...+.+
T Consensus 11 ~gE~~A~~~L~~~Gy~Il~rN~r~~~GEIDiIa~~-~~~lvFVEVK~R~~~~~g~~~eav~~~K~~ri~~ 79 (118)
T PRK12497 11 AGEDLAARYLESKGLRILARNFRCRFGEIDLIARD-GDTLVFVEVKTRRSDLFGGAAEAVTPRKQRRIRR 79 (118)
T ss_pred HHHHHHHHHHHHCCCEEEEEEEECCCCCCCEEEEE-CCEEEEEEEECCCCCCCCCHHHHCCHHHHHHHHH
T ss_conf 99999999999879999998500489950589996-9999999982155789889789599999999999
No 16
>PRK04247 hypothetical protein; Provisional
Probab=88.41 E-value=2.3 Score=24.03 Aligned_cols=90 Identities=23% Similarity=0.224 Sum_probs=60.4
Q ss_pred HCCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCH-HH-HHHHHHHHHC-CCE-
Q ss_conf 205999999999999978--98899971489887662799915991999997278988698-99-9999999978-986-
Q gi|254781194|r 5 YLSEAKLEKRLVKGSKKL--DCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSN-AQ-KRVIATLLLY-HQK- 78 (98)
Q Consensus 5 ~m~E~~ie~~i~~~~k~~--g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~-~Q-~~~~~~l~~~-G~~- 78 (98)
...|+++|..|.+..... |.....--.+...|.=|++.-..+|....||+|+-++-+.. .| .++.+.|++- +.+
T Consensus 127 ~G~Ea~l~~llae~p~~ie~G~~~v~rE~~T~~G~VDil~~D~~G~~V~VEvKR~ra~idaV~QL~RYve~l~~~~~~~V 206 (250)
T PRK04247 127 TGSEADMVDAILENPDLIEEGFRPVAREYETPAGIIDILGRDKEGNLVVLELKRRRAGLSAVSQLKRYVEAYREELGAKV 206 (250)
T ss_pred EEEHHHHHHHHHHCHHHHCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf 73199999999859053258988998887359884648998799899999997133781479999999999876369982
Q ss_pred --EEEECC-HHHHHHHHHH
Q ss_conf --999839-8999999998
Q gi|254781194|r 79 --VQVLSS-TEEVDGFLRM 94 (98)
Q Consensus 79 --~~Vv~s-~e~v~~~i~~ 94 (98)
++++-+ .++++.++++
T Consensus 207 RGIlvAp~It~~Ar~Ll~d 225 (250)
T PRK04247 207 RGILVAPSITERARRLLEK 225 (250)
T ss_pred EEEEECCCCCHHHHHHHHH
T ss_conf 1999988589879999997
No 17
>PRK03298 hypothetical protein; Provisional
Probab=87.81 E-value=2.8 Score=23.49 Aligned_cols=88 Identities=22% Similarity=0.226 Sum_probs=58.0
Q ss_pred CCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCH-HH-HHHHHHHHHCCC----
Q ss_conf 05999999999999978--98899971489887662799915991999997278988698-99-999999997898----
Q gi|254781194|r 6 LSEAKLEKRLVKGSKKL--DCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSN-AQ-KRVIATLLLYHQ---- 77 (98)
Q Consensus 6 m~E~~ie~~i~~~~k~~--g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~-~Q-~~~~~~l~~~G~---- 77 (98)
..|+++|..|.+.-... |.....--.+...|.=|++.-..+|....||+|+ ++-+.. .| ..+.+.|++-..
T Consensus 103 G~Eadl~~llae~P~~ie~Gf~~v~rE~~T~~G~VDll~~D~~G~~V~VEiKR-ra~idaV~QL~RYve~l~rd~~~~~V 181 (224)
T PRK03298 103 GVEAHLQELLAEHIELLGEGYTLVRREYMTAIGPVDLLCRDADGATVAVEIKR-RGEIDGVEQLTRYLELLNRDPLLAPV 181 (224)
T ss_pred ECHHHHHHHHHHCCHHHCCCCEEEEEEECCCCCCEEEEEECCCCCEEEEEEEE-CCCHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf 01999999987592421589898778731798835389987999999999983-06810899999999998557588851
Q ss_pred -EEEEECC-HHHHHHHHHH
Q ss_conf -6999839-8999999998
Q gi|254781194|r 78 -KVQVLSS-TEEVDGFLRM 94 (98)
Q Consensus 78 -~~~Vv~s-~e~v~~~i~~ 94 (98)
-.+++-| .++++.++++
T Consensus 182 RGIlvAp~It~~Ar~Ll~d 200 (224)
T PRK03298 182 RGVFAAQQIKPQARTLATD 200 (224)
T ss_pred EEEEECCCCCHHHHHHHHH
T ss_conf 4999987478879999997
No 18
>pfam01939 DUF91 Protein of unknown function DUF91. The function of this prokaryotic protein is unknown.
Probab=86.59 E-value=3.1 Score=23.22 Aligned_cols=90 Identities=23% Similarity=0.240 Sum_probs=60.9
Q ss_pred HCCHHHHHHHHHHHHHHC--CCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCH-HH-HHHHHHHHHC--CCE
Q ss_conf 205999999999999978--98899971489887662799915991999997278988698-99-9999999978--986
Q gi|254781194|r 5 YLSEAKLEKRLVKGSKKL--DCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSN-AQ-KRVIATLLLY--HQK 78 (98)
Q Consensus 5 ~m~E~~ie~~i~~~~k~~--g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~-~Q-~~~~~~l~~~--G~~ 78 (98)
...|+++|..|.+.-... |.....--.+...|.=|++.-..+|....||+|+-.+-+.. .| ..+.+.|++- ..+
T Consensus 103 ~G~Eadl~~~l~~~P~~ie~G~~~v~rE~~T~~G~VDil~~D~~G~~VvVEvKRr~a~idaV~QL~RYve~l~rd~~~~~ 182 (228)
T pfam01939 103 TGSEAEMAALIFEHPQLIEEGFKPVRREYQIAHGIVDILGKDEDGNIVILELKRRKADLHAVSQLKRYVDSLKEDYVEAK 182 (228)
T ss_pred EEEHHHHHHHHHHCHHHHCCCCEEEEEEEECCCCCEEEEEECCCCCEEEEEEEEECCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 73199999999859153248989998885258873668998799999999997403782079999999999865548886
Q ss_pred ---EEEECC-HHHHHHHHHH
Q ss_conf ---999839-8999999998
Q gi|254781194|r 79 ---VQVLSS-TEEVDGFLRM 94 (98)
Q Consensus 79 ---~~Vv~s-~e~v~~~i~~ 94 (98)
++|+-| .++++.++++
T Consensus 183 VRGIlvAp~It~~Ar~Ll~d 202 (228)
T pfam01939 183 VRGVLVAPSITEGAKKLLEE 202 (228)
T ss_pred CEEEEECCCCCHHHHHHHHH
T ss_conf 03999998589889999997
No 19
>pfam03852 Vsr DNA mismatch endonuclease Vsr.
Probab=83.14 E-value=2.7 Score=23.61 Aligned_cols=44 Identities=18% Similarity=0.035 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEE
Q ss_conf 5999999999999978988999714898876627999159919999
Q gi|254781194|r 7 SEAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWV 52 (98)
Q Consensus 7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fI 52 (98)
+....|..+.+.+.+.|-++.+ ....-+|-||+ ++.+-.-++||
T Consensus 19 k~TkpE~~vr~~L~~~G~ryr~-~~~~lpG~PDi-v~~~~k~aIFv 62 (75)
T pfam03852 19 KGTKPELALRSLLFGLGLRYRK-NDKSLPGKPDI-VFPKYKLAVFI 62 (75)
T ss_pred CCCHHHHHHHHHHHHCCCEEEE-CCCCCCCCCCE-EECCCCEEEEE
T ss_conf 9976999999999988988997-37878999999-76687789994
No 20
>COG3727 Vsr DNA G:T-mismatch repair endonuclease [DNA replication, recombination, and repair]
Probab=82.98 E-value=4.9 Score=22.10 Aligned_cols=80 Identities=23% Similarity=0.175 Sum_probs=49.4
Q ss_pred CCHHCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCC-EEEEE--------E---ECCCCC-------CC
Q ss_conf 50120599999999999997898899971489887662799915991-99999--------7---278988-------69
Q gi|254781194|r 2 RTDYLSEAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGA-HFWVE--------M---KTSRGR-------LS 62 (98)
Q Consensus 2 ~~~~m~E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~-~~fIE--------v---K~~~gk-------ls 62 (98)
+.-.-++..+|..+...+-..|-.+.. .--.-+|-||+.+ |+-+ ++|+- + |.|+.+ .+
T Consensus 15 ~rIrs~dTkpE~~lr~~L~~~G~rfR~-~~~~lpGkPDiVl--~~y~~viFvHGCFWh~H~c~~a~vPksnt~fWleKi~ 91 (150)
T COG3727 15 RRIRSRDTKPEKRLRSLLTGQGLRFRV-QDKDLPGKPDIVL--PKYRCVIFVHGCFWHGHHCYLAKVPKSNTEFWLEKIG 91 (150)
T ss_pred HHHHCCCCCHHHHHHHHHHHCCEEEEE-CCCCCCCCCCEEE--CCCEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf 998814766899999998536627885-3788999998852--3733899985100257744445688742388999986
Q ss_pred HH---HHHHHHHHHHCCCEEEEECC
Q ss_conf 89---99999999978986999839
Q gi|254781194|r 63 NA---QKRVIATLLLYHQKVQVLSS 84 (98)
Q Consensus 63 ~~---Q~~~~~~l~~~G~~~~Vv~s 84 (98)
.| -+.-+.+|+.+|+.+-||+-
T Consensus 92 kNveRD~r~~~~L~~~GwrvlvVWE 116 (150)
T COG3727 92 KNVERDERDIKRLQQLGWRVLVVWE 116 (150)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEEE
T ss_conf 6666548999999975975999986
No 21
>COG1637 Predicted nuclease of the RecB family [DNA replication, recombination, and repair]
Probab=77.39 E-value=7.5 Score=21.00 Aligned_cols=90 Identities=23% Similarity=0.205 Sum_probs=58.8
Q ss_pred HCCHHHHHHHHHHHHHHCCCEEEEE--ECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHH-H-HHHHHHHHHCCCE--
Q ss_conf 2059999999999999789889997--14898876627999159919999972789886989-9-9999999978986--
Q gi|254781194|r 5 YLSEAKLEKRLVKGSKKLDCLVFKT--QFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNA-Q-KRVIATLLLYHQK-- 78 (98)
Q Consensus 5 ~m~E~~ie~~i~~~~k~~g~~~~k~--~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~-Q-~~~~~~l~~~G~~-- 78 (98)
.++|.++++.|...-.-++-...-+ -.+...|.-|++....+|++..||+|+-++.+++. | +...+.+++-...
T Consensus 128 ~g~E~~m~~~I~e~P~lleeG~~~v~~E~~t~~G~vDilg~De~G~~viiElKR~ka~~~Av~QL~RYv~~l~~~~~~~V 207 (253)
T COG1637 128 DGSEADMQELIAENPQLLEEGFRPVAREYQTAIGKVDILGRDERGNIVIIELKRRKAGLSAVSQLKRYVELLREDTGDKV 207 (253)
T ss_pred CCHHHHHHHHHHHCHHHHHCCCEEEEEEEECCCCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCEE
T ss_conf 04099998787659466757543312652137425679988689999999994254771089999999997053468607
Q ss_pred --EEEECC-HHHHHHHHHH
Q ss_conf --999839-8999999998
Q gi|254781194|r 79 --VQVLSS-TEEVDGFLRM 94 (98)
Q Consensus 79 --~~Vv~s-~e~v~~~i~~ 94 (98)
..|+.| .+++..++++
T Consensus 208 RGiLvAp~it~~a~~ll~~ 226 (253)
T COG1637 208 RGILVAPSITEQARRLLED 226 (253)
T ss_pred EEEEECCCCCHHHHHHHHH
T ss_conf 8999866440889999997
No 22
>pfam07711 RabGGT_insert Rab geranylgeranyl transferase alpha-subunit, insert domain. Rab geranylgeranyl transferase (RabGGT) catalyses the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking. This domain is inserted between pfam01239 repeats. This domain adopts an Ig-like fold and is thought to be involved in protein-protein interactions and might be involved in the recognition and binding of REP.
Probab=77.20 E-value=3.8 Score=22.74 Aligned_cols=45 Identities=20% Similarity=0.210 Sum_probs=36.9
Q ss_pred HCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHH
Q ss_conf 7898899971489887662799915991999997278988698999
Q gi|254781194|r 21 KLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQK 66 (98)
Q Consensus 21 ~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~ 66 (98)
..++...-|.-|-..|.-+|++.. ||...++|-.+|.++.++.|.
T Consensus 11 ~e~~lsv~FSrpv~v~~~~L~Lv~-Dg~p~~veWrt~~~r~r~s~v 55 (102)
T pfam07711 11 DEGCVSVAFSRPVLVGMVGLLLVL-DGQPQAVEWRTAHPRLRHSPV 55 (102)
T ss_pred CCCEEEEEECCEEEECCCEEEEEE-CCCCEEEEEECCCCCCCCCCE
T ss_conf 678499996141540332689996-798079997689997675827
No 23
>PRK02234 recU Holliday junction-specific endonuclease; Reviewed
Probab=76.19 E-value=8.1 Score=20.80 Aligned_cols=77 Identities=13% Similarity=-0.000 Sum_probs=59.0
Q ss_pred CCHHHHHHHHHHHHHHCCCEEEEEECC---------C------------CCCCCCEEEEECCCCEEEEEEECCCC-----
Q ss_conf 059999999999999789889997148---------9------------88766279991599199999727898-----
Q gi|254781194|r 6 LSEAKLEKRLVKGSKKLDCLVFKTQFI---------N------------QRGCPDRLIITPNGAHFWVEMKTSRG----- 59 (98)
Q Consensus 6 m~E~~ie~~i~~~~k~~g~~~~k~~~~---------g------------~~G~PDli~~~~~g~~~fIEvK~~~g----- 59 (98)
-.|.+|.....-++..-=+++.|-.+| - ++--.|...++. |+++..|.|.-.+
T Consensus 31 ~LE~~IN~tN~yY~~~~iAvIhKkPTPIqivkVdypkRs~a~I~eAyf~~~STtDY~Gvyk-G~yIdFEAKET~nktsFp 109 (199)
T PRK02234 31 SLEKDINETNDYYLSNGIAVIHKKPTPIQIVKVDYPKRSKAVIKEAYFRQASTTDYNGVYK-GKYIDFEAKETKNKTSFP 109 (199)
T ss_pred HHHHHHHHHHHHHHHCCEEEEEECCCCEEEEECCCCCCCCCHHHHHEECCCCCCCCCCEEC-CEEEEEECCCCCCCCCCC
T ss_conf 5999999999999877978998358880699615544330010010235778777432567-889888754557877447
Q ss_pred --CCCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf --869899999999997898699983
Q gi|254781194|r 60 --RLSNAQKRVIATLLLYHQKVQVLS 83 (98)
Q Consensus 60 --kls~~Q~~~~~~l~~~G~~~~Vv~ 83 (98)
...++|...++++...|+.+|++=
T Consensus 110 l~Nih~HQi~hl~~~~~qgGI~F~iI 135 (199)
T PRK02234 110 LKNFHEHQIEHMKQVLAQGGICFVII 135 (199)
T ss_pred HHHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf 23403899999999997799799999
No 24
>cd01037 Restriction_endonuclease_like Superfamily of nucleases including Short Patch Repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI
Probab=75.14 E-value=8.7 Score=20.63 Aligned_cols=70 Identities=21% Similarity=0.043 Sum_probs=47.2
Q ss_pred HHHHHHHHHHHCCCEEEEEE--CCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHH------HHHHHHHHCCCEEEEE
Q ss_conf 99999999997898899971--489887662799915991999997278988698999------9999999789869998
Q gi|254781194|r 11 LEKRLVKGSKKLDCLVFKTQ--FINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQK------RVIATLLLYHQKVQVL 82 (98)
Q Consensus 11 ie~~i~~~~k~~g~~~~k~~--~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~------~~~~~l~~~G~~~~Vv 82 (98)
.|..+...+.+.+....++. .+..++.||.. + + ...+.||+|.........+. .....+...|..+.++
T Consensus 2 ~E~~l~~~l~~~~~~~~~~~~~~~~~~~~pDf~-~-~-~~~l~iE~k~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~ 78 (80)
T cd01037 2 AERLLWKLLRAKGLAVRRFRRQVPIGSYIPDFV-C-P-SAKLVIELKGTFHDGLLRKLRTSEKQERIAFLEADGKKVLRF 78 (80)
T ss_pred HHHHHHHHHHHCCCCCCEEEECCCCCCEEEEEE-C-C-CCCEEEEECCCHHCCCHHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf 799999999855878870571375078877577-2-5-448799914512153135554411778999999889989974
Q ss_pred C
Q ss_conf 3
Q gi|254781194|r 83 S 83 (98)
Q Consensus 83 ~ 83 (98)
.
T Consensus 79 ~ 79 (80)
T cd01037 79 W 79 (80)
T ss_pred C
T ss_conf 3
No 25
>PRK09225 threonine synthase; Validated
Probab=74.85 E-value=5.1 Score=22.00 Aligned_cols=40 Identities=15% Similarity=0.278 Sum_probs=30.6
Q ss_pred CCCCCCCHHHHHHHHHHHHCCCEEEEEC-CHHHHHHHHHHH
Q ss_conf 7898869899999999997898699983-989999999986
Q gi|254781194|r 56 TSRGRLSNAQKRVIATLLLYHQKVQVLS-STEEVDGFLRML 95 (98)
Q Consensus 56 ~~~gkls~~Q~~~~~~l~~~G~~~~Vv~-s~e~v~~~i~~l 95 (98)
-|.|+.|+-|+.++.....-...+.-|+ ++||++.+++.+
T Consensus 164 yP~g~vS~iQ~~QMtt~~~~NV~~i~v~G~FDDcQ~lVK~~ 204 (465)
T PRK09225 164 YPKGKVSPVQEKQMTTLQGDNIHVVAVEGDFDDCQALVKAA 204 (465)
T ss_pred ECCCCCCHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHHHH
T ss_conf 07999997799986221799779998468767899999999
No 26
>cd01560 Thr-synth_2 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria, archaebacteria and eubacterial groups. This CD, Thr-synth_2, includes enzymes from fungi and eubacterial groups, as well as, metazoan threonine synthase-like proteins.
Probab=74.65 E-value=4.6 Score=22.22 Aligned_cols=40 Identities=18% Similarity=0.268 Sum_probs=30.1
Q ss_pred CCCCCCCHHHHHHHHHHHHCCCEEEEE-CCHHHHHHHHHHH
Q ss_conf 789886989999999999789869998-3989999999986
Q gi|254781194|r 56 TSRGRLSNAQKRVIATLLLYHQKVQVL-SSTEEVDGFLRML 95 (98)
Q Consensus 56 ~~~gkls~~Q~~~~~~l~~~G~~~~Vv-~s~e~v~~~i~~l 95 (98)
-|.|+.|+-|+.++.........+.-| -++||++.+++.+
T Consensus 163 yP~g~vS~iQ~~QMtT~~~~NV~~iav~G~FDDcQ~~VK~~ 203 (460)
T cd01560 163 YPKGGVSPIQELQMTTLPADNVHVVAVEGDFDDCQSLVKAL 203 (460)
T ss_pred CCCCCCCHHHHHHHHCCCCCCEEEEEECCCCHHHHHHHHHH
T ss_conf 48888998899986254789779999648808889999999
No 27
>COG0792 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=74.16 E-value=9.2 Score=20.49 Aligned_cols=52 Identities=15% Similarity=0.072 Sum_probs=36.7
Q ss_pred CHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCC
Q ss_conf 59999999999999789889997148988766279991599199999727898
Q gi|254781194|r 7 SEAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRG 59 (98)
Q Consensus 7 ~E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~g 59 (98)
....-|..-..+|++.|...+.--.-.+-|==|||.- .++...|||||+-.+
T Consensus 4 ~G~~~E~~A~~~L~~~G~~iL~rN~r~r~GEIDlIa~-~~~~ivFVEVK~R~~ 55 (114)
T COG0792 4 LGAAGEDLAARFLESKGLRILARNWRCRYGEIDLIAR-DGDTVVFVEVKYRRN 55 (114)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHCCCCCCCEEEEEE-CCCEEEEEEEEEECC
T ss_conf 4778999999999976930255530378874689996-599899999974126
No 28
>pfam06319 DUF1052 Protein of unknown function (DUF1052). This family consists of several bacterial proteins of unknown function.
Probab=74.00 E-value=9.3 Score=20.46 Aligned_cols=54 Identities=17% Similarity=0.228 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCC
Q ss_conf 999999999999978988999714898876627999159919999972789886
Q gi|254781194|r 8 EAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRL 61 (98)
Q Consensus 8 E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkl 61 (98)
-..|.+.+...+..+|..++.-.++..--=-|++.+-+.|.++.||+|....-.
T Consensus 21 a~~i~RGv~Rll~~~g~a~l~E~~L~~GrRaDl~al~~kGei~IVEiKSs~aDF 74 (158)
T pfam06319 21 ALAVRRGVQRLLMELGHAVLPELPLASGRRADLIALSPKGEIWIVEIKSSIEDF 74 (158)
T ss_pred HHHHHHHHHHHHHHCCCCEEEEECCCCCCEEEEEEECCCCCEEEEEEECCHHHH
T ss_conf 999999999999977996335663799977779988799959999983678884
No 29
>TIGR00252 TIGR00252 conserved hypothetical protein TIGR00252; InterPro: IPR003509 The function of this family is unknown. Members include several bacterial hypothetical proteins..
Probab=73.09 E-value=3.3 Score=23.10 Aligned_cols=48 Identities=15% Similarity=0.167 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCE-EEEEEECC
Q ss_conf 9999999999978988999714898876627999159919-99997278
Q gi|254781194|r 10 KLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAH-FWVEMKTS 57 (98)
Q Consensus 10 ~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~-~fIEvK~~ 57 (98)
-.|......|+..|+...---.-.+-|==|||.-.||++. .|||||.=
T Consensus 22 a~E~~ar~wLE~kGl~fiaa~~~~~~GEiDLI~~fPd~~~i~FVEVr~R 70 (141)
T TIGR00252 22 AFESQARAWLEQKGLKFIAANVNSKWGEIDLIMRFPDKKTIVFVEVRTR 70 (141)
T ss_pred HHHHHHHHHHHHCCHHHHHHHCCCCCCCEEEECCCCCCCEEEEEEEECC
T ss_conf 1799999987733157667530689981221111899726888875105
No 30
>pfam08378 NERD Nuclease-related domain. The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing.
Probab=72.99 E-value=2.4 Score=23.85 Aligned_cols=88 Identities=16% Similarity=0.214 Sum_probs=47.0
Q ss_pred HHCCHHHHHHHHHHHHHH-CCCEEEEEE-CC---CCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCE
Q ss_conf 120599999999999997-898899971-48---9887662799915991999997278988698999999999978986
Q gi|254781194|r 4 DYLSEAKLEKRLVKGSKK-LDCLVFKTQ-FI---NQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQK 78 (98)
Q Consensus 4 ~~m~E~~ie~~i~~~~k~-~g~~~~k~~-~~---g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~ 78 (98)
++.-|..+-..|...+.. .++.++.-. -+ |+..-=|.+++.|+| ++.||+|.-.|........|.. ..+..
T Consensus 4 G~~gE~~v~~~L~~~~~~~~~~~vl~n~~l~~~~~~~~eID~lvi~~~g-i~vvE~K~~~G~i~~~~~~W~~---~~~~~ 79 (123)
T pfam08378 4 GAEGEKLVARALKKLLPDDYEYFVLHNLRLPTHGGSTTEIDHLVISPDG-IFVIEVKNYKGTIIADGGKWTQ---TIGGR 79 (123)
T ss_pred HHHHHHHHHHHHHHHCCCCCCEEEEECEEECCCCCCEEEEEEEEECCCE-EEEEEECCCCEEEEECCCEEEE---EECCC
T ss_conf 7999999999999637888988999543962699978897799994891-9999946862489962763999---86995
Q ss_pred EEEEC-CHHHHHHHHHHH
Q ss_conf 99983-989999999986
Q gi|254781194|r 79 VQVLS-STEEVDGFLRML 95 (98)
Q Consensus 79 ~~Vv~-s~e~v~~~i~~l 95 (98)
..... -+.|+..-...|
T Consensus 80 ~~~~~nPi~Q~~~~~~~l 97 (123)
T pfam08378 80 KEEFKNPLLQAYRHAKLL 97 (123)
T ss_pred EEECCCHHHHHHHHHHHH
T ss_conf 588689999999999999
No 31
>pfam06250 DUF1016 Protein of unknown function (DUF1016). Family of uncharacterized proteins found in viruses, archaea and bacteria.
Probab=66.25 E-value=9.7 Score=20.35 Aligned_cols=59 Identities=24% Similarity=0.236 Sum_probs=41.9
Q ss_pred HHCCHHHHHHHHHHHHHHC-----CCEEE-----EEECCCCCCCCCEEEEEC-CCCEEEEEEECCCCCCC
Q ss_conf 1205999999999999978-----98899-----971489887662799915-99199999727898869
Q gi|254781194|r 4 DYLSEAKLEKRLVKGSKKL-----DCLVF-----KTQFINQRGCPDRLIITP-NGAHFWVEMKTSRGRLS 62 (98)
Q Consensus 4 ~~m~E~~ie~~i~~~~k~~-----g~~~~-----k~~~~g~~G~PDli~~~~-~g~~~fIEvK~~~gkls 62 (98)
+...|+++|+.|++.+.+. .|.+| ++...|.-=+.||+.+.- =..++.||+|+..=++.
T Consensus 180 ~~~~E~dLE~ali~~i~~FLLELG~GFaFvgrQ~ri~v~~~dfyiDLlFYh~~L~c~V~IELK~g~f~pe 249 (320)
T pfam06250 180 DLYSEKDLEKALINHLEKFLLELGAGFAFVGRQKRIQVDDEDFYIDLLFYHRKLRCLVAVDLKIGKFKPE 249 (320)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCCEEEHHHHHHHHHCCCEEEEEECCCCCCHH
T ss_conf 6648899999999999999998189816754557888779323404766634114136776415876778
No 32
>pfam09520 RE_MjaII MjaII restriction endonuclease. This family includes the MjaII (recognizes GGNCC but the cleavage site is unknown) restriction endonuclease.
Probab=64.32 E-value=13 Score=19.56 Aligned_cols=22 Identities=18% Similarity=0.484 Sum_probs=19.0
Q ss_pred CCCEEEEECCCCEEEEEEECCC
Q ss_conf 6627999159919999972789
Q gi|254781194|r 37 CPDRLIITPNGAHFWVEMKTSR 58 (98)
Q Consensus 37 ~PDli~~~~~g~~~fIEvK~~~ 58 (98)
+.|+.+..+||.-+|+|+|+|+
T Consensus 144 v~Dlyi~~kdg~e~~feIKT~K 165 (252)
T pfam09520 144 VADLYVQRKDGRELYFEIKSPK 165 (252)
T ss_pred EEEEEEECCCCCEEEEEECCCC
T ss_conf 7789998279958999835779
No 33
>PRK13731 conjugal transfer surface exclusion protein TraT; Provisional
Probab=63.04 E-value=16 Score=19.09 Aligned_cols=53 Identities=11% Similarity=0.206 Sum_probs=40.1
Q ss_pred CCCCEEEEEC-CCCEEEEEEECCCCCCC-HHHHHHHHHHHHCCCEEEEECCHHHHHH
Q ss_conf 7662799915-99199999727898869-8999999999978986999839899999
Q gi|254781194|r 36 GCPDRLIITP-NGAHFWVEMKTSRGRLS-NAQKRVIATLLLYHQKVQVLSSTEEVDG 90 (98)
Q Consensus 36 G~PDli~~~~-~g~~~fIEvK~~~gkls-~~Q~~~~~~l~~~G~~~~Vv~s~e~v~~ 90 (98)
-..|=|.+.| ..+..||.+|.-.++.. ..|......|...| +-|+++++++.=
T Consensus 38 kMS~TIfLdP~s~ktVyv~vrNTS~~~~~~l~~~i~~~L~akG--Y~iv~~P~~A~Y 92 (243)
T PRK13731 38 QMSETIWLEPASERTVFLQIKNTSDKDMSGLQGKIADAVKAKG--YQVVTSPDKAYY 92 (243)
T ss_pred EECCCEEECCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCC--EEEECCHHHCEE
T ss_conf 0004388668545579999851787724567899999998589--098678657607
No 34
>TIGR00260 thrC threonine synthase; InterPro: IPR004450 Threonine synthase () is involved in threonine biosynthesis. It catalyses the conversion of O-phospho-L-homoserine and water into L-threonine and orthophosphate, using pyridoxal phosphate as a cofactor. The pyridoxal-phosphate binding site is a Lys (K) residue. The enzyme is distantly related to the serine/threonine dehydratases which are also pyridoxal-phosphate dependent enzymes .; GO: 0004795 threonine synthase activity, 0009088 threonine biosynthetic process.
Probab=62.90 E-value=5.3 Score=21.89 Aligned_cols=41 Identities=22% Similarity=0.362 Sum_probs=36.5
Q ss_pred CCCCCCCHHHHHHHHHHHHCCCEEEEEC-CHHHHHHHHHHHH
Q ss_conf 7898869899999999997898699983-9899999999862
Q gi|254781194|r 56 TSRGRLSNAQKRVIATLLLYHQKVQVLS-STEEVDGFLRMLE 96 (98)
Q Consensus 56 ~~~gkls~~Q~~~~~~l~~~G~~~~Vv~-s~e~v~~~i~~l~ 96 (98)
-|.||.+|.|+..+-+--..|..+.-++ ++||++++++.+.
T Consensus 114 ~P~Gki~p~Q~~Kl~~~~~~n~~v~~i~G~FDda~~~v~~~~ 155 (423)
T TIGR00260 114 YPAGKISPLQLGKLAQALIYNAKVIAIDGNFDDAQRLVKELF 155 (423)
T ss_pred ECCCCCCHHHCCCEEEEECCCCEEEEEECCHHHHHHHHHHHH
T ss_conf 328853330215301332378389998278799999999986
No 35
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=57.24 E-value=20 Score=18.49 Aligned_cols=84 Identities=15% Similarity=0.184 Sum_probs=54.6
Q ss_pred HHHHHHHHHHHHHCCCEEEEE-----------------ECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHH
Q ss_conf 999999999999789889997-----------------148988766279991599199999727898869899999999
Q gi|254781194|r 9 AKLEKRLVKGSKKLDCLVFKT-----------------QFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIAT 71 (98)
Q Consensus 9 ~~ie~~i~~~~k~~g~~~~k~-----------------~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~ 71 (98)
.++=++|.+.+|+. .+.+. .-|--+|+-| +.|.|+-.=..||++.|+--.........+-
T Consensus 25 ~~li~~iAk~ikKR--IviRpdpsil~~~e~a~~~I~~ivPeeA~i~~-i~FD~~~gEV~Iea~kPg~viGk~g~~l~eI 101 (145)
T cd02410 25 GDLVKDLAKDLRKR--IVIRPDPSVLKPPEEAIKIILEIVPEEAGITD-IYFDDDTGEVIIEAEKPGLVIGKGGSTLREI 101 (145)
T ss_pred CHHHHHHHHHHHCE--EEECCCHHHCCCHHHHHHHHHHHCCCCCCCEE-EEECCCCCEEEEEECCCEEEECCCCHHHHHH
T ss_conf 40999999987202--79738803418999999999985896468446-8974888579999779777972761679999
Q ss_pred HHHCCCEEEEECC-------HHHHHHHHHHH
Q ss_conf 9978986999839-------89999999986
Q gi|254781194|r 72 LLLYHQKVQVLSS-------TEEVDGFLRML 95 (98)
Q Consensus 72 l~~~G~~~~Vv~s-------~e~v~~~i~~l 95 (98)
....||..-|+++ ++++++++...
T Consensus 102 ~~~tGW~p~v~RtPpi~S~ti~~IR~~l~~~ 132 (145)
T cd02410 102 TRETGWAPKVVRTPPIQSRTVKSIRRFLRRE 132 (145)
T ss_pred HHHHCCEEEEEECCCCCHHHHHHHHHHHHHH
T ss_conf 9973981578865999617899999999980
No 36
>pfam03460 NIR_SIR_ferr Nitrite/Sulfite reductase ferredoxin-like half domain. Sulfite and Nitrite reductases are key to both biosynthetic assimilation of sulfur and nitrogen and dissimilation of oxidized anions for energy transduction. Two copies of this repeat are found in Nitrite and Sulfite reductases and form a single structural domain.
Probab=55.14 E-value=22 Score=18.29 Aligned_cols=52 Identities=23% Similarity=0.453 Sum_probs=38.4
Q ss_pred CCCCEEEEEEECCCCCCCHHHHHHHHHHHH-CC-CEEEEE--------C-CHHHHHHHHHHHHC
Q ss_conf 599199999727898869899999999997-89-869998--------3-98999999998623
Q gi|254781194|r 45 PNGAHFWVEMKTSRGRLSNAQKRVIATLLL-YH-QKVQVL--------S-STEEVDGFLRMLEC 97 (98)
Q Consensus 45 ~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~-~G-~~~~Vv--------~-s~e~v~~~i~~l~~ 97 (98)
++| .+++-++.|+|++++.|...+..+.+ .| ....+. + ..+++.+++++|+-
T Consensus 4 ~~g-~~~vri~~p~G~lt~~ql~~la~ia~~yg~g~i~lT~rq~i~l~~i~~~~~~~v~~~L~~ 66 (67)
T pfam03460 4 KDG-DYMVRVRVPGGRLTAEQLRALADIAEKYGDGEIRLTTRQNLELHGVPEEDLPELLEELAE 66 (67)
T ss_pred CCC-CEEEEEECCCCEECHHHHHHHHHHHHHHCCCCEEECCCCCEEECCCCHHHHHHHHHHHHC
T ss_conf 678-689999618908489999999999998379958787987579679898999999999970
No 37
>pfam06555 consensus
Probab=54.62 E-value=22 Score=18.23 Aligned_cols=12 Identities=17% Similarity=0.050 Sum_probs=4.8
Q ss_pred HHHHHHHCCCEE
Q ss_conf 999999789889
Q gi|254781194|r 15 LVKGSKKLDCLV 26 (98)
Q Consensus 15 i~~~~k~~g~~~ 26 (98)
+++.+++.|--+
T Consensus 3 ~i~~L~~~~f~~ 14 (200)
T pfam06555 3 TVENLEKNNFEA 14 (200)
T ss_pred HHHHHHHCCCEE
T ss_conf 799999789879
No 38
>pfam05818 TraT Enterobacterial TraT complement resistance protein. The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between an Escherichia coli and its surroundings.
Probab=54.12 E-value=23 Score=18.19 Aligned_cols=52 Identities=10% Similarity=0.326 Sum_probs=38.4
Q ss_pred CCEEEEEC---CCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCHHHHHHH
Q ss_conf 62799915---9919999972789886989999999999789869998398999999
Q gi|254781194|r 38 PDRLIITP---NGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQKVQVLSSTEEVDGF 91 (98)
Q Consensus 38 PDli~~~~---~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~e~v~~~ 91 (98)
.+=|.+.| +.+..||.+|...++--..+......|...| +-|+++++++.=+
T Consensus 9 S~TIfLdPV~~~~ktVyv~vrNTSd~~i~l~~~i~~~L~akG--Y~iv~~P~~A~Y~ 63 (215)
T pfam05818 9 SQTIFLDPVAPEQRTVYLSIRNTSDKNVNLEQKLISALQAKG--YKVVDDPDKAHYW 63 (215)
T ss_pred ECCEEECCCCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHCC--CEEECCHHHCEEE
T ss_conf 032886788800377999985388776673389999998489--3886796577077
No 39
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=53.57 E-value=23 Score=18.13 Aligned_cols=30 Identities=30% Similarity=0.325 Sum_probs=21.1
Q ss_pred HHHHHHHHHCCCEEEEEC--CHHHHHHHHHHH
Q ss_conf 999999997898699983--989999999986
Q gi|254781194|r 66 KRVIATLLLYHQKVQVLS--STEEVDGFLRML 95 (98)
Q Consensus 66 ~~~~~~l~~~G~~~~Vv~--s~e~v~~~i~~l 95 (98)
...+++|+.+|.++++.+ |++++.+-|+.+
T Consensus 90 ~~~~~~L~~~GI~v~~~~~~sl~di~~~i~~l 121 (265)
T PRK03379 90 ERQVDQLASLGIKVMWVDATSIEQIADALRQL 121 (265)
T ss_pred HHHHHHHHHCCCEEEECCCCCHHHHHHHHHHH
T ss_conf 89999998169758835999999999999999
No 40
>pfam08011 DUF1703 Protein of unknown function (DUF1703). This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches. DUF1703 has the predicted secondary structure pattern of the restriction endonuclease-like fold core and contains an additional beta-strand at the C-terminus.
Probab=53.42 E-value=23 Score=18.12 Aligned_cols=70 Identities=10% Similarity=-0.001 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCC--CCCHHHHHHHHHHHHCCCE
Q ss_conf 9999999999999789889997148988766279991599199999727898--8698999999999978986
Q gi|254781194|r 8 EAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRG--RLSNAQKRVIATLLLYHQK 78 (98)
Q Consensus 8 E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~g--kls~~Q~~~~~~l~~~G~~ 78 (98)
|.-++.-+-..+...|.. .+.-.-...|-+|+++...++..+.+|+|..+. .+......=++++++.++.
T Consensus 3 E~~Y~~~~~~~~~~~~y~-v~se~es~~GR~Di~l~p~~~~~~IiE~K~~~~~~~~~~~~~~Al~QI~~k~Y~ 74 (101)
T pfam08011 3 EGYYASVFYAYFASLGYE-VISEDETNKGRIDLTLKPTYTYIYIFEFKYIKVKDSDKEIAEEALEQIKEYGYA 74 (101)
T ss_pred CHHHHHHHHHHHHHCCCE-EEECCCCCCCCEEEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHCCCH
T ss_conf 400899999999988979-998145699946499997488199999996386431015689999999976740
No 41
>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]
Probab=53.11 E-value=23 Score=18.09 Aligned_cols=37 Identities=8% Similarity=0.075 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHH
Q ss_conf 8698999999999978986999839899999999862
Q gi|254781194|r 60 RLSNAQKRVIATLLLYHQKVQVLSSTEEVDGFLRMLE 96 (98)
Q Consensus 60 kls~~Q~~~~~~l~~~G~~~~Vv~s~e~v~~~i~~l~ 96 (98)
+|...-....+.+...|+.++.+.+.||+.++|.++.
T Consensus 62 nLd~~l~~~~~~v~~~Gg~vy~A~~aedA~~ii~~iv 98 (459)
T COG1139 62 NLDEYLEQLEENVTRNGGHVYFAKDAEDAREIIGEIV 98 (459)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHH
T ss_conf 2899999999999971987998378899999999997
No 42
>pfam06616 BsuBI_PstI_RE BsuBI/PstI restriction endonuclease C-terminus. This family represents the C-terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (EC:3.1.21.4). The enzymes of the BsuBI restriction/modification (R/M) system recognize the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system.
Probab=52.98 E-value=24 Score=18.08 Aligned_cols=63 Identities=17% Similarity=0.220 Sum_probs=44.4
Q ss_pred CCCCCCEEEEECCCCE-EEEEEECCCCCCCHHHHHHHHHHHHC--CCEEEEEC--CHHHHHHHHHHHH
Q ss_conf 8876627999159919-99997278988698999999999978--98699983--9899999999862
Q gi|254781194|r 34 QRGCPDRLIITPNGAH-FWVEMKTSRGRLSNAQKRVIATLLLY--HQKVQVLS--STEEVDGFLRMLE 96 (98)
Q Consensus 34 ~~G~PDli~~~~~g~~-~fIEvK~~~gkls~~Q~~~~~~l~~~--G~~~~Vv~--s~e~v~~~i~~l~ 96 (98)
+.-.||+++...+..+ +|||.=+..|-.++.-+..+.+|-.. ...+||-- +....++++.+|+
T Consensus 212 h~klPDvVl~d~~~~wL~liEaVtS~GPv~~~R~~eL~~l~~~~~~~lvfVTAF~dR~~fkk~~~eiA 279 (306)
T pfam06616 212 HGKLPDIVLYDLGKKWLVLVEVVASDGPVDGKRHEELAKLFADAPAGLVFVTAFPDRSAFKKYLAEIA 279 (306)
T ss_pred CCCCCCEEEEECCCCEEEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHHHHC
T ss_conf 56899789984689969999997377998989999999998538888699995589899999988732
No 43
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=52.80 E-value=24 Score=18.06 Aligned_cols=48 Identities=23% Similarity=0.257 Sum_probs=34.4
Q ss_pred EEEEEEECCCCCCCHHHHHHHHHHHHCCCEE----EEECCHHHHHHHHHHHH
Q ss_conf 9999972789886989999999999789869----99839899999999862
Q gi|254781194|r 49 HFWVEMKTSRGRLSNAQKRVIATLLLYHQKV----QVLSSTEEVDGFLRMLE 96 (98)
Q Consensus 49 ~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~----~Vv~s~e~v~~~i~~l~ 96 (98)
+++-++=.+.+..-..|...+..|+.+|+++ .++.+.+++.++++.+.
T Consensus 213 f~~y~~~~~~~~~~~t~~e~l~~L~~~GF~~~~~~~~~~~~~~~~~~~~~~~ 264 (307)
T cd00114 213 FFIYGLGEAEGLGPKTQSEALAFLKEWGFPVSPETRLCKNIEEVLAFYDEIE 264 (307)
T ss_pred EEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHHHH
T ss_conf 7899855257888677899999999779966886189799999999999999
No 44
>TIGR02291 rimK_rel_E_lig alpha-L-glutamate ligase homolog; InterPro: IPR011758 Members of this protein family contain a region of homology to the RimK family of alpha-L-glutamate ligases (IPR004666 from INTERPRO), various members of which modify the Glu-Glu C-terminus of ribosomal protein S6, or tetrahydromethanopterin, or a form of coenzyme F420 derivative. Members of this family are found so far in various Vibrio and Pseudomonas species and some other gamma and beta Proteobacteria. The function is unknown..
Probab=52.48 E-value=14 Score=19.32 Aligned_cols=60 Identities=22% Similarity=0.315 Sum_probs=37.0
Q ss_pred HHCCHHHHHHHHHHHH---HHCCCE--------------EEEEECCCCCCCCCEEEEECCCCEEE--EEE--ECCCCCCC
Q ss_conf 1205999999999999---978988--------------99971489887662799915991999--997--27898869
Q gi|254781194|r 4 DYLSEAKLEKRLVKGS---KKLDCL--------------VFKTQFINQRGCPDRLIITPNGAHFW--VEM--KTSRGRLS 62 (98)
Q Consensus 4 ~~m~E~~ie~~i~~~~---k~~g~~--------------~~k~~~~g~~G~PDli~~~~~g~~~f--IEv--K~~~gkls 62 (98)
..++|.+||.++=..| -++||. +|+..|+ .||||+=++.=.|-.+. +=+ ...+||..
T Consensus 108 ~~i~~eeiE~hvSniL~GLySLGG~~D~AliEyrvkfDp~F~~~SY--eGVPDiRiIVf~GyPVmaM~RlpTr~SdGKAN 185 (320)
T TIGR02291 108 ALISKEEIERHVSNILAGLYSLGGKRDRALIEYRVKFDPLFESVSY--EGVPDIRIIVFKGYPVMAMLRLPTRASDGKAN 185 (320)
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCCCCCCCCCC--CCCCCEEEEEECCCCHHHHCCCCCCCCCCCCC
T ss_conf 1015456778888888777650799773688532010534477111--34587268964186102100276567888302
Q ss_pred HHH
Q ss_conf 899
Q gi|254781194|r 63 NAQ 65 (98)
Q Consensus 63 ~~Q 65 (98)
-+|
T Consensus 186 LHQ 188 (320)
T TIGR02291 186 LHQ 188 (320)
T ss_pred CCC
T ss_conf 124
No 45
>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]
Probab=50.50 E-value=25 Score=17.92 Aligned_cols=35 Identities=20% Similarity=0.269 Sum_probs=25.3
Q ss_pred CCCCCEEEEECCCCE-EEEEEECCCCCCCH--HHHHHHH
Q ss_conf 876627999159919-99997278988698--9999999
Q gi|254781194|r 35 RGCPDRLIITPNGAH-FWVEMKTSRGRLSN--AQKRVIA 70 (98)
Q Consensus 35 ~G~PDli~~~~~g~~-~fIEvK~~~gkls~--~Q~~~~~ 70 (98)
.=.||+.++. +|-+ +.||+|+|...... +|....+
T Consensus 124 ~~rpDvvlfI-NGiPlv~iElK~~~~~~~~a~~Qi~~Y~ 161 (962)
T COG0610 124 KRRPDVVLFI-NGLPLVTIELKNPGVENNEAFNQIKRYQ 161 (962)
T ss_pred CCCCCEEEEE-CCCEEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf 8787569998-6865687750687535699999998861
No 46
>KOG2364 consensus
Probab=49.30 E-value=27 Score=17.73 Aligned_cols=59 Identities=20% Similarity=0.191 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHHHHHHC-CCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHH
Q ss_conf 05999999999999978-98899971489887662799915991999997278988698999
Q gi|254781194|r 6 LSEAKLEKRLVKGSKKL-DCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQK 66 (98)
Q Consensus 6 m~E~~ie~~i~~~~k~~-g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~ 66 (98)
..|.-++..|++.++.. +.--..|.+.|+--+-=++ +..||.+.+|+++|+...--.|.
T Consensus 231 l~enSveE~i~dhl~~~F~a~d~~F~sSGREDvDVRm--LG~GRPFvlEl~N~rr~~~~~q~ 290 (433)
T KOG2364 231 LKENSVEEDIKDHLKEFFSADDVVFISSGREDVDVRM--LGTGRPFVLELKNPRRNLGFEQL 290 (433)
T ss_pred CCCCCHHHHHHHHHHHHCCCCCEEECCCCCCCEEEEE--CCCCCCEEEECCCCCCCCHHHHH
T ss_conf 4455488999999986437001465147875301475--05898359985785412137776
No 47
>pfam04313 HSDR_N Type I restriction enzyme R protein N terminus (HSDR_N). This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA.
Probab=47.61 E-value=20 Score=18.50 Aligned_cols=23 Identities=30% Similarity=0.515 Sum_probs=17.8
Q ss_pred CCCCCCEEEEECCCCE-EEEEEECC
Q ss_conf 8876627999159919-99997278
Q gi|254781194|r 34 QRGCPDRLIITPNGAH-FWVEMKTS 57 (98)
Q Consensus 34 ~~G~PDli~~~~~g~~-~fIEvK~~ 57 (98)
+..-||+.++. +|-+ .+||+|++
T Consensus 17 ~~~r~Divlfi-NGlPl~~iE~K~~ 40 (90)
T pfam04313 17 QKRRPDYVLFV-NGLPLAVIELKRT 40 (90)
T ss_pred CCCCCCEEEEE-CCCEEEEEEECCC
T ss_conf 06656699998-8969999997588
No 48
>pfam05116 S6PP Sucrose-6F-phosphate phosphohydrolase. This family consists of Sucrose-6F-phosphate phosphohydrolase proteins found in plants and cyanobacteria. Sucrose-6(F)-phosphate phosphohydrolase catalyses the final step in the pathway of sucrose biosynthesis.
Probab=47.26 E-value=29 Score=17.54 Aligned_cols=35 Identities=23% Similarity=0.394 Sum_probs=17.0
Q ss_pred HHHHHHHHCCCEEEEEECCCCC-----------C--CCCEEEEECCCCEEE
Q ss_conf 9999999789889997148988-----------7--662799915991999
Q gi|254781194|r 14 RLVKGSKKLDCLVFKTQFINQR-----------G--CPDRLIITPNGAHFW 51 (98)
Q Consensus 14 ~i~~~~k~~g~~~~k~~~~g~~-----------G--~PDli~~~~~g~~~f 51 (98)
+..+.+++.|..+.= +.||+ | .||.+++. +|...+
T Consensus 26 ~al~~l~~~Gi~vvi--aTGR~~~~~~~~~~~l~l~~p~~~I~~-nG~~I~ 73 (247)
T pfam05116 26 QLLEAQYRPDSLLVF--ATGRSLDSAKELLKEKPLPTPDVLITS-VGTEIY 73 (247)
T ss_pred HHHHHHHHCCCEEEE--ECCCCHHHHHHHHHHCCCCCCCEEEEC-CCEEEE
T ss_conf 999999958988999--889999999999997598999989975-975999
No 49
>pfam04471 Mrr_cat Restriction endonuclease. Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA.
Probab=46.66 E-value=30 Score=17.48 Aligned_cols=77 Identities=17% Similarity=0.132 Sum_probs=45.0
Q ss_pred HHHHHHCCCEE-EEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHH-HHHHHHHCCCEEEEE--CC--HHHHH
Q ss_conf 99999789889-99714898876627999159919999972789886989999-999999789869998--39--89999
Q gi|254781194|r 16 VKGSKKLDCLV-FKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKR-VIATLLLYHQKVQVL--SS--TEEVD 89 (98)
Q Consensus 16 ~~~~k~~g~~~-~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~-~~~~l~~~G~~~~Vv--~s--~e~v~ 89 (98)
.+.+++.|+.- ......|--|+ |++...+++.-+.|++|.-++........ ++..+...++.-.++ .| .+++.
T Consensus 2 ~~ll~~~G~~~v~~t~~~~D~Gi-Dvia~~~~~~~~~VQ~K~~~~~vg~~~v~~l~~~~~~~~~~~~i~vTt~~fT~~A~ 80 (98)
T pfam04471 2 AELLEALGYREVELTGKSGDGGI-DVVATTSDGERIVVQAKRYRSTVGRPVIQELLGAKAGYGADKGVVVTTSGFTSAAR 80 (98)
T ss_pred HHHHHHCCCCEEEECCCCCCCCE-EEEEEECCCCEEEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHH
T ss_conf 68897679988997889898845-89999379989999999878989989999996027761898799998774398899
Q ss_pred HHHH
Q ss_conf 9999
Q gi|254781194|r 90 GFLR 93 (98)
Q Consensus 90 ~~i~ 93 (98)
++-+
T Consensus 81 ~~A~ 84 (98)
T pfam04471 81 ELAE 84 (98)
T ss_pred HHHH
T ss_conf 9997
No 50
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=45.38 E-value=27 Score=17.78 Aligned_cols=27 Identities=19% Similarity=0.099 Sum_probs=16.2
Q ss_pred HHHHHCCCEEEEECCHHHHHHHHHHHH
Q ss_conf 999978986999839899999999862
Q gi|254781194|r 70 ATLLLYHQKVQVLSSTEEVDGFLRMLE 96 (98)
Q Consensus 70 ~~l~~~G~~~~Vv~s~e~v~~~i~~l~ 96 (98)
--++..|..+|-+.+.|++.+.|+.|+
T Consensus 16 lgF~~lG~dvfpv~~~eEa~~~l~~La 42 (104)
T PRK01395 16 LPFKALGFDVFPVIEEQEARNTLRKLA 42 (104)
T ss_pred HHHHHCCEEEEECCCHHHHHHHHHHHH
T ss_conf 888865804785488799999999998
No 51
>PRK09534 btuF corrinoid ABC transporter substrate-binding protein; Reviewed
Probab=44.57 E-value=32 Score=17.29 Aligned_cols=30 Identities=13% Similarity=-0.002 Sum_probs=23.7
Q ss_pred HHHHHHHHHCCCEEEEEC---CHHHHHHHHHHH
Q ss_conf 999999997898699983---989999999986
Q gi|254781194|r 66 KRVIATLLLYHQKVQVLS---STEEVDGFLRML 95 (98)
Q Consensus 66 ~~~~~~l~~~G~~~~Vv~---s~e~v~~~i~~l 95 (98)
...+++|+++|..++++. |+|++-+-|+.|
T Consensus 131 ~~~v~~L~~~GI~V~v~~~a~SiddV~~~I~~i 163 (364)
T PRK09534 131 NDTVTRLRSAGITVFQFRAATSIDGVVEKTATI 163 (364)
T ss_pred HHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHH
T ss_conf 678999997699699918988999999999999
No 52
>pfam09588 YqaJ YqaJ-like viral recombinase domain. This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit.
Probab=42.10 E-value=35 Score=17.06 Aligned_cols=50 Identities=22% Similarity=0.185 Sum_probs=28.6
Q ss_pred HHHHHHHHHH-HHCCCEEEEE----EC---CCCCCCCCEEEEECCCCEEEEEEECCCCC
Q ss_conf 9999999999-9789889997----14---89887662799915991999997278988
Q gi|254781194|r 10 KLEKRLVKGS-KKLDCLVFKT----QF---INQRGCPDRLIITPNGAHFWVEMKTSRGR 60 (98)
Q Consensus 10 ~ie~~i~~~~-k~~g~~~~k~----~~---~g~~G~PDli~~~~~g~~~fIEvK~~~gk 60 (98)
..|..+.... +..|..+... .. +...+-||-++..+++. ..+|+|.|..+
T Consensus 56 ~~E~~a~~~~~~~~g~~v~~~~~~~~~~~~~~~~aSpDg~~~~~~~~-~~lEiK~~~~~ 113 (141)
T pfam09588 56 ELEPLARAEYEERTGIKVREVGGLLQHPEDPFLGASPDGLVVDGDGG-GILEIKTPFET 113 (141)
T ss_pred HHHHHHHHHHHHHHCCEEEEECEEEECCCCCEEEECCCEEECCCCCC-EEEEEECCCHH
T ss_conf 40399999999997998985033896378882677288744048876-37998468627
No 53
>PRK10767 chaperone protein DnaJ; Provisional
Probab=41.73 E-value=36 Score=17.03 Aligned_cols=60 Identities=18% Similarity=0.139 Sum_probs=35.2
Q ss_pred CCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHH-CCCEEEEECC------HHHHHHHHHHH
Q ss_conf 8766279991599199999727898869899999999997-8986999839------89999999986
Q gi|254781194|r 35 RGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLL-YHQKVQVLSS------TEEVDGFLRML 95 (98)
Q Consensus 35 ~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~-~G~~~~Vv~s------~e~v~~~i~~l 95 (98)
.|+|+.=--..+-.++-+.|+-|. +||+.|+..+++|++ .|-......+ ++-+.++.++|
T Consensus 308 ~Gmp~~~~~~~GDl~V~~~V~~P~-~Ls~~Qk~ll~el~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 374 (376)
T PRK10767 308 KGVKSVRGGAQGDLLCRVVVETPV-GLNEKQKQLLQELQESFGGPTGEKNSPRSKSFFDGVKKFFDDL 374 (376)
T ss_pred CCCCCCCCCCCCCEEEEEEEECCC-CCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf 898989979977889999998999-9999999999999997467666767854478899999998751
No 54
>PRK00453 rpsF 30S ribosomal protein S6; Reviewed
Probab=40.64 E-value=37 Score=16.93 Aligned_cols=56 Identities=11% Similarity=0.050 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHH
Q ss_conf 99999999999789889997148988766279991599199999727898869899
Q gi|254781194|r 10 KLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQ 65 (98)
Q Consensus 10 ~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q 65 (98)
.+.+.+.+.+.+.||.+.+....|.+-.+=-|-=...|.++++.+..+...++...
T Consensus 21 ~~~~~~~~~i~~~gg~v~~~~~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el~ 76 (95)
T PRK00453 21 ALVERYKGVITKNGGEIHKVEDWGRRRLAYPINKLRKGHYVLLNFEADPAAIAELE 76 (95)
T ss_pred HHHHHHHHHHHHCCCEEEEEECCCCCCCCCEECCCCEEEEEEEEEEECHHHHHHHH
T ss_conf 99999999999799889998502120044230667589999999998988999999
No 55
>pfam09564 RE_NgoBV NgoBV restriction endonuclease. This family includes the NgoBV (recognizes GGNNCC but cleavage site is unknown) restriction endonuclease.
Probab=40.59 E-value=37 Score=16.92 Aligned_cols=61 Identities=13% Similarity=0.046 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHCCCEEEEEE-CCCCCCCCCEEEEECCCCEEEEEEECCCC--CCCHHH---HHHHHHHH
Q ss_conf 999999999997898899971-48988766279991599199999727898--869899---99999999
Q gi|254781194|r 10 KLEKRLVKGSKKLDCLVFKTQ-FINQRGCPDRLIITPNGAHFWVEMKTSRG--RLSNAQ---KRVIATLL 73 (98)
Q Consensus 10 ~ie~~i~~~~k~~g~~~~k~~-~~g~~G~PDli~~~~~g~~~fIEvK~~~g--kls~~Q---~~~~~~l~ 73 (98)
.||..+..++.+.. .+|. ++|++-.||+++=..+..--.+|+|+-+. .|+=.- +.+.+.+.
T Consensus 46 iiQ~WL~~~L~~~~---I~f~~~~nTQ~pPDf~Ln~~~~~e~llEIK~Fn~~~sP~FDIA~f~ay~~~l~ 112 (194)
T pfam09564 46 IIQEWLGGWLRKRE---IEFDVSTNTQMPPDFFLNKKDRSRELLEVKAFNRNACPGFDIADFKMYSDEIF 112 (194)
T ss_pred HHHHHHHHHHHHCC---EEECCCCCCCCCCCEEECCCCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHH
T ss_conf 99999999876445---55148999878985465567675550888764278998642677999999885
No 56
>pfam10313 DUF2415 Uncharacterized protein domain (DUF2415). This is a short, 30 residue domain, from a family of proteins conserved in fungi. The function is unknown. There is a characteristic DLL sequence motif.
Probab=38.06 E-value=41 Score=16.69 Aligned_cols=30 Identities=27% Similarity=0.269 Sum_probs=23.2
Q ss_pred EEEEEECCCCCCCCCEEEEEC-CCCEEEEEEEC
Q ss_conf 899971489887662799915-99199999727
Q gi|254781194|r 25 LVFKTQFINQRGCPDRLIITP-NGAHFWVEMKT 56 (98)
Q Consensus 25 ~~~k~~~~g~~G~PDli~~~~-~g~~~fIEvK~ 56 (98)
++.||... +|.+||+++-. .|++-.+.+++
T Consensus 4 R~~kFSp~--~~~~DLLv~sE~~Grvhv~DlR~ 34 (43)
T pfam10313 4 RVCKFSPE--NGLNDLLVISEHVGRVHVADLRT 34 (43)
T ss_pred EEEEECCC--CCCCCEEEEEECCCEEEEEECCC
T ss_conf 79996698--99763799991687388999000
No 57
>PRK09566 nirA ferredoxin-nitrite reductase; Reviewed
Probab=36.49 E-value=43 Score=16.54 Aligned_cols=48 Identities=23% Similarity=0.457 Sum_probs=33.8
Q ss_pred EEEEEEECCCCCCCHHHHHHHHHHHH-CC--CEEEEEC---------CHHHHHHHHHHHH
Q ss_conf 99999727898869899999999997-89--8699983---------9899999999862
Q gi|254781194|r 49 HFWVEMKTSRGRLSNAQKRVIATLLL-YH--QKVQVLS---------STEEVDGFLRMLE 96 (98)
Q Consensus 49 ~~fIEvK~~~gkls~~Q~~~~~~l~~-~G--~~~~Vv~---------s~e~v~~~i~~l~ 96 (98)
++.+=+|-|+|.+|+.|...+..+.+ .| +...+.. ..+++-++++.|+
T Consensus 65 ~FMlRvriPgG~lt~~Q~r~la~ia~~yg~~G~~~iTTRQniQlh~I~~~d~~~i~~~L~ 124 (513)
T PRK09566 65 KFMLRLRVPNGILTSQQLRVLASIVQRYGEDGSADITTRQNLQLRGILLEDLPEILNRLK 124 (513)
T ss_pred CEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHCCCCHHHHHHHHHHHH
T ss_conf 468896678975599999999999998689985999737112115877788999999999
No 58
>TIGR01213 TIGR01213 conserved hypothetical protein TIGR01213; InterPro: IPR005912 The members of this family of conserved hypothetical proteins show a low level of similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs. .
Probab=36.38 E-value=43 Score=16.53 Aligned_cols=62 Identities=19% Similarity=0.124 Sum_probs=43.0
Q ss_pred HHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHH-CCCE-EEEEC
Q ss_conf 99789889997148988766279991599199999727898869899999999997-8986-99983
Q gi|254781194|r 19 SKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLL-YHQK-VQVLS 83 (98)
Q Consensus 19 ~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~-~G~~-~~Vv~ 83 (98)
++..||.-..|+..||==+==+ ++-+||.|-||+|.|+.|--+.-. ..+++++ +.+. |.|..
T Consensus 254 ~~~~~G~~~~fHGaGREDvDvR--MLG~GRPFVlEv~~Pr~R~~dl~~-l~~eiN~~a~GkGVEv~~ 317 (450)
T TIGR01213 254 LKATGGTDAVFHGAGREDVDVR--MLGTGRPFVLEVKEPRKRKIDLDE-LEEEINKGASGKGVEVLG 317 (450)
T ss_pred HHHCCCEEEEEEECCCCCEEEE--CCCCCCCEEEEECCCCCCCCCHHH-HHHHHCCCCCCCEEEEEE
T ss_conf 6422880699962566400010--178888359972588658888789-999954678853489973
No 59
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=35.17 E-value=35 Score=17.09 Aligned_cols=50 Identities=22% Similarity=0.484 Sum_probs=30.4
Q ss_pred CCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHH-HHH----HCCCEEEEECCHH-----HHHHHHHHHH
Q ss_conf 76627999159919999972789886989999999-999----7898699983989-----9999999862
Q gi|254781194|r 36 GCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIA-TLL----LYHQKVQVLSSTE-----EVDGFLRMLE 96 (98)
Q Consensus 36 G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~-~l~----~~G~~~~Vv~s~e-----~v~~~i~~l~ 96 (98)
-.||++.+.|+|.. ....|.+-+. .+. ..++.++|++..| -++.+|+-|+
T Consensus 76 ~HPD~~~i~p~~~~-----------i~idqiR~L~~~~~~~p~~g~~KV~II~~Ae~m~~~AaNALLKtLE 135 (329)
T PRK08058 76 NHPDVHLVAPDGQS-----------IKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLE 135 (329)
T ss_pred CCCCEEEECCCCCC-----------CCHHHHHHHHHHHCCCCCCCCCEEEEEECHHHHCHHHHHHHHHHHH
T ss_conf 99976774566140-----------7799999999996438757886799973477629999999999864
No 60
>PRK09567 nirA ferredoxin-nitrite reductase; Reviewed
Probab=33.66 E-value=48 Score=16.26 Aligned_cols=26 Identities=19% Similarity=0.231 Sum_probs=13.8
Q ss_pred EEEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf 99999727898869899999999997
Q gi|254781194|r 49 HFWVEMKTSRGRLSNAQKRVIATLLL 74 (98)
Q Consensus 49 ~~fIEvK~~~gkls~~Q~~~~~~l~~ 74 (98)
.+.+=+|-|+|.+|+.|...+..+.+
T Consensus 113 ~FMlRiRiPgG~lt~~Q~r~la~iA~ 138 (591)
T PRK09567 113 SYMCRLRIPNGILTHWQLAGLADLAD 138 (591)
T ss_pred CEEEEECCCCCCCCHHHHHHHHHHHH
T ss_conf 04899536896359999999999999
No 61
>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family; InterPro: IPR004473 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities , . The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. This entry represents the R subunit (HsdR) of type I restriction endonucleases such as EcoRI (3.1.21.3 from EC), which recognises the DNA sequence 5'-GAATTC; the R protein (HsdR) is required for both nuclease and ATPase activity , , , .; GO: 0003677 DNA binding, 0005524 ATP binding, 0009035 Type I site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system.
Probab=33.52 E-value=48 Score=16.25 Aligned_cols=26 Identities=23% Similarity=0.325 Sum_probs=20.8
Q ss_pred CCC---CCCEEEEECCCCE-EEEEEECCCCC
Q ss_conf 887---6627999159919-99997278988
Q gi|254781194|r 34 QRG---CPDRLIITPNGAH-FWVEMKTSRGR 60 (98)
Q Consensus 34 ~~G---~PDli~~~~~g~~-~fIEvK~~~gk 60 (98)
..| .||++++. ||-+ .-||+|.|=++
T Consensus 133 ~~~kfRrpD~~lfv-NGiPLv~iElKkp~~~ 162 (813)
T TIGR00348 133 ENIKFRRPDVTLFV-NGIPLVIIELKKPLKE 162 (813)
T ss_pred CCCCEECCCEEEEE-CCCEEEEEECCCCCCC
T ss_conf 88866457047875-2211253230686663
No 62
>PRK10361 DNA recombination protein RmuC; Provisional
Probab=33.35 E-value=48 Score=16.28 Aligned_cols=25 Identities=24% Similarity=0.446 Sum_probs=21.7
Q ss_pred CCCCCCCEEEEECCCCEEEEEEECC
Q ss_conf 9887662799915991999997278
Q gi|254781194|r 33 NQRGCPDRLIITPNGAHFWVEMKTS 57 (98)
Q Consensus 33 g~~G~PDli~~~~~g~~~fIEvK~~ 57 (98)
|.+--||.+|-+|+|+.+.|--|.|
T Consensus 236 g~r~rPDvIV~LP~~k~iVIDSKvs 260 (475)
T PRK10361 236 RSRMQPDVIVRLPQGKDVVIDAKMT 260 (475)
T ss_pred CCCCCCCEEEECCCCCEEEEECCCC
T ss_conf 8822897689878997588862788
No 63
>COG1258 Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis]
Probab=31.07 E-value=53 Score=16.01 Aligned_cols=81 Identities=20% Similarity=0.188 Sum_probs=50.2
Q ss_pred HHHHHHHHHH-HHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEEC---
Q ss_conf 9999999999-999789889997148988766279991599199999727898869899999999997898699983---
Q gi|254781194|r 8 EAKLEKRLVK-GSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQKVQVLS--- 83 (98)
Q Consensus 8 E~~ie~~i~~-~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~--- 83 (98)
..-++.-|.. ..+..|+.-.+|+..|+--+-=+| +.+|+.+-+|+|.|..|--+. ......++.-| .|.|.+
T Consensus 190 ~~sve~~i~~~~~~~f~g~~~~fhgAGREDvDvRM--LG~GRPfVlEvk~Pr~R~~dl-~~l~~~in~~~-~vev~~l~f 265 (398)
T COG1258 190 PESVEELIKQPIKEAFGGLDAKFHGAGREDVDVRM--LGTGRPFVLEVKEPRRRNVDL-DELEEEINRGG-KVEVFDLEF 265 (398)
T ss_pred CCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCEEE--ECCCCCEEEEECCCCCCCCCH-HHHHHHHCCCC-CEEEEEEEE
T ss_conf 44199998789998606850699716877663466--058983699923742256886-78899763588-589998774
Q ss_pred -CHHHHHHHH
Q ss_conf -989999999
Q gi|254781194|r 84 -STEEVDGFL 92 (98)
Q Consensus 84 -s~e~v~~~i 92 (98)
+.++++.+-
T Consensus 266 ~~~e~v~~ik 275 (398)
T COG1258 266 VGREEVEEIK 275 (398)
T ss_pred CCHHHHHHHH
T ss_conf 4799999987
No 64
>TIGR00678 holB DNA polymerase III, delta' subunit; InterPro: IPR004622 DNA-directed DNA polymerase (2.7.7.7 from EC) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. DNA polymerase III is a complex, multi-chain enzyme responsible for most of the replicative synthesis in bacteria. The enzyme also has 3' to 5' exonuclease activity. It has a core composed of alpha, epsilon and theta chains, that associate with a tau subunit which allows the core dimerisation to form the PolIII' complex. PolIII' associates with the gamma complex (gamma, delta, delta', psi and chi chains) and with the beta chain. This domain is the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tightly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classified as delta'. The noise cut-off is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits.; GO: 0003887 DNA-directed DNA polymerase activity, 0008408 3'-5' exonuclease activity, 0006260 DNA replication.
Probab=29.03 E-value=53 Score=16.04 Aligned_cols=60 Identities=17% Similarity=0.252 Sum_probs=36.2
Q ss_pred CCCCEEEEECCCCEEE-------------EEEECC-----CCCCCHHHHHHHHHHHHCCCEEEEECCHHH-----HHHHH
Q ss_conf 7662799915991999-------------997278-----988698999999999978986999839899-----99999
Q gi|254781194|r 36 GCPDRLIITPNGAHFW-------------VEMKTS-----RGRLSNAQKRVIATLLLYHQKVQVLSSTEE-----VDGFL 92 (98)
Q Consensus 36 G~PDli~~~~~g~~~f-------------IEvK~~-----~gkls~~Q~~~~~~l~~~G~~~~Vv~s~e~-----v~~~i 92 (98)
-.||+..+.|+|..-- .. +++ -+..+..+......=...|+.|+|++..|. ++.+|
T Consensus 62 ~HPD~~~~~P~~~~~~~~~de~~~~~~g~a~-~~~~~~Ik~dq~R~l~~~~~~~~~~~~~rVviI~~Ae~mn~~AANALL 140 (216)
T TIGR00678 62 NHPDLHRLEPEGQSKSLTADEAAEGEEGSAK-RRALPQIKVDQVRELVEFLSLTPQESGRRVVIIEDAERMNEAAANALL 140 (216)
T ss_pred CCCCEEEEEEECCCCCCCHHHHHHHHCCCCC-CCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCHHHCCHHHHHHHH
T ss_conf 9982378742347777776458976256421-136787872789999999860642147517997673232589898651
Q ss_pred HHHH
Q ss_conf 9862
Q gi|254781194|r 93 RMLE 96 (98)
Q Consensus 93 ~~l~ 96 (98)
+-||
T Consensus 141 KtLE 144 (216)
T TIGR00678 141 KTLE 144 (216)
T ss_pred HHEE
T ss_conf 0101
No 65
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=28.57 E-value=59 Score=15.75 Aligned_cols=41 Identities=12% Similarity=0.182 Sum_probs=28.1
Q ss_pred EEECCCCCCCHHHHHHHHHHHHCCCEEEEE-CCHHHHHHHHHHHH
Q ss_conf 972789886989999999999789869998-39899999999862
Q gi|254781194|r 53 EMKTSRGRLSNAQKRVIATLLLYHQKVQVL-SSTEEVDGFLRMLE 96 (98)
Q Consensus 53 EvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv-~s~e~v~~~i~~l~ 96 (98)
-+=-|.|+.++.|+.++..+. ..+.-+ -++||++++++++.
T Consensus 153 ~Vl~P~g~vs~~k~~q~~~~g---a~~i~v~G~fDda~~~vk~~~ 194 (411)
T COG0498 153 FVLYPKGKVSPGKLAQMLTLG---AHVIAVDGNFDDAQELVKEAA 194 (411)
T ss_pred EEEECCCCCCHHHHHHHHHCC---CEEEEECCCHHHHHHHHHHHH
T ss_conf 999459878878899997538---889997596899999999999
No 66
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate. DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately. This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=27.52 E-value=61 Score=15.64 Aligned_cols=40 Identities=23% Similarity=0.226 Sum_probs=28.9
Q ss_pred CCCCCEEEE---ECCCCEEEEEEECCCCCCCHHHHHHHHHHHHC
Q ss_conf 876627999---15991999997278988698999999999978
Q gi|254781194|r 35 RGCPDRLII---TPNGAHFWVEMKTSRGRLSNAQKRVIATLLLY 75 (98)
Q Consensus 35 ~G~PDli~~---~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~ 75 (98)
.|+|++--- ..+-.++-|.|-.|+. ||..|+.-+++|...
T Consensus 343 kG~p~~~~~~Fk~~GDl~v~V~v~~P~~-Ls~~q~~lLe~l~~~ 385 (386)
T TIGR02349 343 KGVPRLRGSNFKGRGDLLVTVKVETPKN-LSKEQKELLEELAEA 385 (386)
T ss_pred CCCCCCCCCCCCCCCCEEEEEEEEECCC-CCHHHHHHHHHHHHC
T ss_conf 7501468876763366699999985898-788899999999732
No 67
>COG5321 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.38 E-value=56 Score=15.87 Aligned_cols=43 Identities=16% Similarity=0.275 Sum_probs=27.9
Q ss_pred HHHHHHHHHCCCEEEEEE--CCCCCCCCCEEEEECCCCEEEEEEECC
Q ss_conf 999999997898899971--489887662799915991999997278
Q gi|254781194|r 13 KRLVKGSKKLDCLVFKTQ--FINQRGCPDRLIITPNGAHFWVEMKTS 57 (98)
Q Consensus 13 ~~i~~~~k~~g~~~~k~~--~~g~~G~PDli~~~~~g~~~fIEvK~~ 57 (98)
+.+..-+-..|.-++--. ..|+ -.|||.+-|.|..+.||+|+.
T Consensus 26 RGvqrLl~~mg~a~LpEltLasGR--RADLials~kGeiwIiEiKss 70 (164)
T COG5321 26 RGVQRLLMAMGHAVLPELTLASGR--RADLIALSPKGEIWIIEIKSS 70 (164)
T ss_pred HHHHHHHHHHCCCCCCCCCCCCCC--CCCEEEECCCCCEEEEEEECC
T ss_conf 869999998234547433146786--200025557785899996234
No 68
>smart00532 LIGANc Ligase N family.
Probab=25.42 E-value=67 Score=15.41 Aligned_cols=34 Identities=18% Similarity=0.163 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHCCCEE----EEECCHHHHHHHHHHHH
Q ss_conf 89999999999789869----99839899999999862
Q gi|254781194|r 63 NAQKRVIATLLLYHQKV----QVLSSTEEVDGFLRMLE 96 (98)
Q Consensus 63 ~~Q~~~~~~l~~~G~~~----~Vv~s~e~v~~~i~~l~ 96 (98)
..|...++.|+..|+++ .++.+.+++.++++.+.
T Consensus 231 ~t~~e~l~~L~~~GF~v~~~~~~~~~~~ev~~~~~~~~ 268 (441)
T smart00532 231 KTQSEALKWLKELGFPVSPHTRLCKNADEVIEYYEEWE 268 (441)
T ss_pred CCHHHHHHHHHHCCCCCCCCEEEECCHHHHHHHHHHHH
T ss_conf 68999999999779924876199689999999999999
No 69
>cd01473 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions.
Probab=24.74 E-value=69 Score=15.34 Aligned_cols=66 Identities=12% Similarity=0.140 Sum_probs=37.0
Q ss_pred CCCCCCCCCEEEEECCCCE-----------------EEEEEECC-CCCCCHHHHHHHHHH--HHCCCEEEEECCHHHHHH
Q ss_conf 4898876627999159919-----------------99997278-988698999999999--978986999839899999
Q gi|254781194|r 31 FINQRGCPDRLIITPNGAH-----------------FWVEMKTS-RGRLSNAQKRVIATL--LLYHQKVQVLSSTEEVDG 90 (98)
Q Consensus 31 ~~g~~G~PDli~~~~~g~~-----------------~fIEvK~~-~gkls~~Q~~~~~~l--~~~G~~~~Vv~s~e~v~~ 90 (98)
.+.++|+|.+++..-||+. ..|++-+= -|.....|...+.-. ....|+.+...+++.+..
T Consensus 102 ~g~R~~vpkv~IvlTDG~s~~~~~~~~~~~a~~lr~~gV~i~avGVg~~~~~eL~~iag~~~~~~~c~~~~~~~fd~l~~ 181 (192)
T cd01473 102 GNRRKDAPKVTMLFTDGNDTSASKKELQDISLLYKEENVKLLVVGVGAASENKLKLLAGCDINNDNCPNVIKTEWNNLNG 181 (192)
T ss_pred CCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCHHHHHHHHCCCCCCCCCCEEEECCHHHHHH
T ss_conf 78888997499999569988731678999999999879789999806379999999869998899775799479789999
Q ss_pred HHHHHH
Q ss_conf 999862
Q gi|254781194|r 91 FLRMLE 96 (98)
Q Consensus 91 ~i~~l~ 96 (98)
+++.|.
T Consensus 182 i~~~l~ 187 (192)
T cd01473 182 ISKFLT 187 (192)
T ss_pred HHHHHH
T ss_conf 999999
No 70
>pfam01250 Ribosomal_S6 Ribosomal protein S6.
Probab=23.85 E-value=72 Score=15.23 Aligned_cols=59 Identities=15% Similarity=0.105 Sum_probs=39.0
Q ss_pred CCHHH---HHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHH
Q ss_conf 05999---999999999978988999714898876627999159919999972789886989
Q gi|254781194|r 6 LSEAK---LEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNA 64 (98)
Q Consensus 6 m~E~~---ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~ 64 (98)
+.|.+ +.+.+.+.+.+.||.+.+....|.+-.+=-|-=...|.++++.+..+...+...
T Consensus 13 l~~~~~~~~~~~~~~~i~~~gg~i~~~e~~G~r~LAY~I~k~~~G~Y~~~~f~~~~~~i~el 74 (92)
T pfam01250 13 LSEEEVKALIEKYKKLIEENGGEVVKVEDWGKRKLAYPIKKKREGYYVLINFEAEPEAIAEL 74 (92)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCEEEEEECCCEEECCCCCCCCCEEEEEEEEEEECHHHHHHH
T ss_conf 99899999999999999878988999851310003304377889999999999998899999
No 71
>TIGR00963 secA preprotein translocase, SecA subunit; InterPro: IPR000185 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component. . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion . SecA is a cytoplasmic protein of 800 to 960 amino acid residues. Homologs of secA are also encoded in the chloroplast genome of some algae as well as in the nuclear genome of plants . It could be involved in the intraorganellar protein transport into thylakoids.; GO: 0005524 ATP binding, 0006605 protein targeting, 0006886 intracellular protein transport.
Probab=23.69 E-value=72 Score=15.21 Aligned_cols=53 Identities=21% Similarity=0.235 Sum_probs=39.1
Q ss_pred CCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECC-CCCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf 98899971489887662799915991999997278-988698999999999978986999839
Q gi|254781194|r 23 DCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTS-RGRLSNAQKRVIATLLLYHQKVQVLSS 84 (98)
Q Consensus 23 g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~-~gkls~~Q~~~~~~l~~~G~~~~Vv~s 84 (98)
|=+.|++.-.|- ++++ +|. ..||||+ |..|++-.-..+..|..-|.++--|+.
T Consensus 58 G~r~fDVQliGg------~~LH-~G~--IAEMkTGEGKTL~AtLpaYLNAL~GkGVHvVTVNd 111 (904)
T TIGR00963 58 GLRPFDVQLIGG------IVLH-KGK--IAEMKTGEGKTLVATLPAYLNALTGKGVHVVTVND 111 (904)
T ss_pred CCCCHHHHHHHH------HHHC-CCC--EEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEECC
T ss_conf 785618999999------9980-896--67831488628999999998765179627996350
No 72
>COG3331 PrfA Penicillin-binding protein-related factor A, putative recombinase [General function prediction only]
Probab=23.40 E-value=73 Score=15.18 Aligned_cols=77 Identities=14% Similarity=0.035 Sum_probs=58.4
Q ss_pred CCHHHHHHHHHHHHHHCCCEEEEEECC---------CC------------CCCCCEEEEECCCCEEEEEEECCCCC----
Q ss_conf 059999999999999789889997148---------98------------87662799915991999997278988----
Q gi|254781194|r 6 LSEAKLEKRLVKGSKKLDCLVFKTQFI---------NQ------------RGCPDRLIITPNGAHFWVEMKTSRGR---- 60 (98)
Q Consensus 6 m~E~~ie~~i~~~~k~~g~~~~k~~~~---------g~------------~G~PDli~~~~~g~~~fIEvK~~~gk---- 60 (98)
..|++|++.+.-++.+--.+..|-.+| -+ +---|...++. |.++-.|.|..+++
T Consensus 9 ~lE~~In~T~~~y~~~~~a~i~Kk~tPVqiv~v~yp~rs~a~i~eayf~~kSttDY~GvYk-G~yidFEaKeTknktsFp 87 (177)
T COG3331 9 SLEADINKTNDYYLAHDIAVIHKKPTPVQIVNVDYPKRSGAVIKEAYFRQKSTTDYYGVYK-GYYIDFEAKETKNKTSFP 87 (177)
T ss_pred CHHHHHHHHHHHHHHCCCEEEEECCCCCEEEEECCCCCCCCHHHHHHCCCCCCCEEEEEEC-CEEEEEEECCCCCCCCCC
T ss_conf 3899999899887635736886047662378704720032011233405788630456850-279755600135666473
Q ss_pred ---CCHHHHHHHHHHHHCCCEEEEEC
Q ss_conf ---69899999999997898699983
Q gi|254781194|r 61 ---LSNAQKRVIATLLLYHQKVQVLS 83 (98)
Q Consensus 61 ---ls~~Q~~~~~~l~~~G~~~~Vv~ 83 (98)
..++|...+..+...|+.+++.-
T Consensus 88 l~ni~~HQi~hlk~v~~q~Gi~Flli 113 (177)
T COG3331 88 LKNIHPHQIEHLKNVLQQGGISFLLI 113 (177)
T ss_pred HHHCCHHHHHHHHHHHHCCCCEEEEE
T ss_conf 45438889999999985698389999
No 73
>TIGR02502 type_III_YscX type III secretion protein, YscX family; InterPro: IPR012672 Members of this family are encoded within bacterial type III secretion gene clusters. Among all species with type III secretion, those with this protein are found among those that target animal rather than plant cells. The member of this family in Yersinia was shown by mutation to be required for type III secretion of Yops effector proteins and therefore is believed to be part of the secretion machinery ..
Probab=23.24 E-value=25 Score=17.93 Aligned_cols=17 Identities=24% Similarity=0.593 Sum_probs=15.0
Q ss_pred CCCCCCEEEEECCCCEE
Q ss_conf 88766279991599199
Q gi|254781194|r 34 QRGCPDRLIITPNGAHF 50 (98)
Q Consensus 34 ~~G~PDli~~~~~g~~~ 50 (98)
..++||+..+.|||+.+
T Consensus 24 ~~~LP~Ry~L~PDG~~V 40 (126)
T TIGR02502 24 DTDLPERYALLPDGQPV 40 (126)
T ss_pred CCCCCCCCCCCCCCCCH
T ss_conf 89876112688767862
No 74
>pfam06241 DUF1012 Protein of unknown function (DUF1012). Family of uncharacterized proteins found in both eukaryotes and bacteria.
Probab=23.09 E-value=61 Score=15.65 Aligned_cols=18 Identities=11% Similarity=0.263 Sum_probs=14.3
Q ss_pred CCCCCCEEEE--ECCCCEEE
Q ss_conf 8876627999--15991999
Q gi|254781194|r 34 QRGCPDRLII--TPNGAHFW 51 (98)
Q Consensus 34 ~~G~PDli~~--~~~g~~~f 51 (98)
++|+||..+| +++|+..|
T Consensus 111 Rrgf~e~VVCGl~rnGki~F 130 (208)
T pfam06241 111 RLGFQEVVVCGILRDGKVNF 130 (208)
T ss_pred HHCCCCEEEEEEECCCCCCC
T ss_conf 72688607997751896230
No 75
>pfam08608 Wyosine_form Wyosine base formation. Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW.
Probab=22.58 E-value=36 Score=16.97 Aligned_cols=26 Identities=23% Similarity=0.279 Sum_probs=14.6
Q ss_pred CCEEEEEEECCC--C----CCCHHHHHHHHHH
Q ss_conf 919999972789--8----8698999999999
Q gi|254781194|r 47 GAHFWVEMKTSR--G----RLSNAQKRVIATL 72 (98)
Q Consensus 47 g~~~fIEvK~~~--g----kls~~Q~~~~~~l 72 (98)
+...|||+|++. | +++..-.-+|+++
T Consensus 2 a~P~fVEvKay~~~G~S~~rLt~~nmp~heeV 33 (62)
T pfam08608 2 AEPDFVELKAYMHVGYSRNRLTMGNMPAHEEV 33 (62)
T ss_pred CCCCEEEEEEEEEECCCCCCCCHHHCCCHHHH
T ss_conf 99998988318986158887771339988999
No 76
>TIGR02258 2_5_ligase 2'-5' RNA ligase; InterPro: IPR004175 Members of this entry are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known . They belong to the 2H phosphoeseterase superfamily . They share a common active site, characterised by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.; GO: 0008664 2'-5'-RNA ligase activity, 0016070 RNA metabolic process.
Probab=22.26 E-value=77 Score=15.05 Aligned_cols=63 Identities=13% Similarity=0.101 Sum_probs=44.1
Q ss_pred HHHHHHHHHCCCEE--EEEECCCCCCCCCEEEEECCCCEEEEEEECCCC-CCCHHHHHHHHHHHHCCCE-E
Q ss_conf 99999999789889--997148988766279991599199999727898-8698999999999978986-9
Q gi|254781194|r 13 KRLVKGSKKLDCLV--FKTQFINQRGCPDRLIITPNGAHFWVEMKTSRG-RLSNAQKRVIATLLLYHQK-V 79 (98)
Q Consensus 13 ~~i~~~~k~~g~~~--~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~g-kls~~Q~~~~~~l~~~G~~-~ 79 (98)
..|.+++.+..--- |.+.--|--.||+. .+-|++|+.++.+.+ .|+..|....+.+..+|+. .
T Consensus 55 ~~l~~~L~~~~~~~~~F~l~l~g~G~F~~~----~~pRvlWaGv~~~~~~~L~~L~~~~~~~l~~~G~~~~ 121 (189)
T TIGR02258 55 EELEDALAKIAEPPEPFTLKLEGVGVFGNP----KSPRVLWAGVEESEEKELTQLQEELERALAKAGFSRK 121 (189)
T ss_pred HHHHHHHHHHHCCCCCCEEEEEEECCCCCC----CCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 999998887503899734787521027888----8876899843899615789999999999996488889
No 77
>TIGR03081 metmalonyl_epim methylmalonyl-CoA epimerase. Members of this protein family are the enzyme methylmalonyl-CoA epimerase (EC 5.1.99.1), also called methylmalonyl-CoA racemase. This enzyme converts (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, which is then a substrate for methylmalonyl-CoA mutase (TIGR00642). It is known in bacteria, archaea, and as a mitochondrial protein in animals. It is closely related to lactoylglutathione lyase (TIGR00068), which is also called glyoxylase I, and is also a homodimer.
Probab=22.25 E-value=78 Score=15.04 Aligned_cols=85 Identities=15% Similarity=0.153 Sum_probs=48.4
Q ss_pred CCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHHHHHHCCCEEEEECCH
Q ss_conf 05999999999999978988999714898876627999159919999972789886989999999999789869998398
Q gi|254781194|r 6 LSEAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIATLLLYHQKVQVLSST 85 (98)
Q Consensus 6 m~E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~~l~~~G~~~~Vv~s~ 85 (98)
+.=+++++.+.-|.+.+|..+.........|+= +++.+.|. ..+|+=.|.+.-++... +++. .-++..++|..+
T Consensus 7 i~V~Dld~a~~fy~~~lG~~~~~~~~~~~~~~~--~~~~~~g~-~~ieL~~~~~~~~~~~~-~l~~--~g~G~~Hiaf~V 80 (128)
T TIGR03081 7 IAVPDLEEAAKLYEDVLGAHVSHIEEVPEQGVK--VVFIALGN-TKVELLEPLGEDSPIAK-FLEK--NGGGIHHIAIEV 80 (128)
T ss_pred EECCCHHHHHHHHHHHHCCCEEECCCCCCCCEE--EEEEECCC-CCEEEEEECCCCCCHHH-HCCC--CCCCCEEEEEEC
T ss_conf 980999999999999709956531115667959--99994689-71788630578985344-1114--699856999987
Q ss_pred HHHHHHHHHHH
Q ss_conf 99999999862
Q gi|254781194|r 86 EEVDGFLRMLE 96 (98)
Q Consensus 86 e~v~~~i~~l~ 96 (98)
++++..++.|+
T Consensus 81 ~Di~~~~~~l~ 91 (128)
T TIGR03081 81 DDIEAALETLK 91 (128)
T ss_pred CCHHHHHHHHH
T ss_conf 99999999999
No 78
>TIGR03675 arCOG00543 arCOG01782 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=22.10 E-value=78 Score=15.03 Aligned_cols=84 Identities=14% Similarity=0.164 Sum_probs=53.2
Q ss_pred HHHHHHHHHHHHHHCCCEEEEE-----------------ECCCCCCCCCEEEEECCCCEEEEEEECCCCCCCHHHHHHHH
Q ss_conf 9999999999999789889997-----------------14898876627999159919999972789886989999999
Q gi|254781194|r 8 EAKLEKRLVKGSKKLDCLVFKT-----------------QFINQRGCPDRLIITPNGAHFWVEMKTSRGRLSNAQKRVIA 70 (98)
Q Consensus 8 E~~ie~~i~~~~k~~g~~~~k~-----------------~~~g~~G~PDli~~~~~g~~~fIEvK~~~gkls~~Q~~~~~ 70 (98)
..++-++|.+.+|+. .+.+. .-|-.+|+-|+ .|.++-.-..||.|.|+--.-.......+
T Consensus 41 ~~~~i~~~a~~~kkr--i~ir~d~~~~~~~~~a~~~i~~~vp~~a~i~~~-~fd~~~~ev~i~~~kpg~~~g~~g~~~~~ 117 (630)
T TIGR03675 41 DDDLVKELAKKLRKR--IVIRPDPSVLLPPEEAIEKIKEIVPEEAGITDI-YFDDVTGEVIIEAEKPGLVIGKGGSTLRE 117 (630)
T ss_pred CCHHHHHHHHHHCCE--EEECCCCHHCCCHHHHHHHHHHHCCCCCCCEEE-EECCCCCEEEEEECCCEEEECCCCHHHHH
T ss_conf 741999999986043--898279033189999999999758953584158-97489727999977963676475167999
Q ss_pred HHHHCCCEEEEECC-------HHHHHHHHHH
Q ss_conf 99978986999839-------8999999998
Q gi|254781194|r 71 TLLLYHQKVQVLSS-------TEEVDGFLRM 94 (98)
Q Consensus 71 ~l~~~G~~~~Vv~s-------~e~v~~~i~~ 94 (98)
-....||..-|+++ ++++++++..
T Consensus 118 i~~~~gw~~~v~r~p~~~s~~~~~ir~~~~~ 148 (630)
T TIGR03675 118 ITAETGWTPKVVRTPPIESKTIKNIREYLRS 148 (630)
T ss_pred HHHHHCCEEEEEECCCCCHHHHHHHHHHHHH
T ss_conf 9997497468886599970789999999997
No 79
>pfam09521 RE_NgoPII NgoPII restriction endonuclease. This family includes the NgoPII (recognizes and cleaves GG^CC) restriction endonuclease.
Probab=21.88 E-value=79 Score=15.00 Aligned_cols=40 Identities=33% Similarity=0.302 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEECCCCEEEEEEECC
Q ss_conf 99999999999997898899971489887662799915991999997278
Q gi|254781194|r 8 EAKLEKRLVKGSKKLDCLVFKTQFINQRGCPDRLIITPNGAHFWVEMKTS 57 (98)
Q Consensus 8 E~~ie~~i~~~~k~~g~~~~k~~~~g~~G~PDli~~~~~g~~~fIEvK~~ 57 (98)
+++.+++...+-+...+ .++..-.||+|+ .+|. .||+|.-
T Consensus 49 ~~d~~~r~~~~~~~fsy------~Gn~nnpPD~il--k~Gd--aiEvKKi 88 (263)
T pfam09521 49 ENDEEKKDEIYSEVFSY------LGNQNNPPDMIL--KNGD--AVEVKKI 88 (263)
T ss_pred HHHHHHHHHHHHHHHEE------CCCCCCCCHHHE--ECCC--EEEEEEE
T ss_conf 22188999998877231------267799942320--0787--2567772
No 80
>pfam04720 DUF506 Protein of unknown function (DUF506). Family of uncharacterized plant proteins.
Probab=21.81 E-value=79 Score=14.99 Aligned_cols=73 Identities=16% Similarity=0.294 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHCCCEEE----EEECCCCCCCCCEEEEECCCCEEEEEEECC---------------------CCCCCH
Q ss_conf 9999999999997898899----971489887662799915991999997278---------------------988698
Q gi|254781194|r 9 AKLEKRLVKGSKKLDCLVF----KTQFINQRGCPDRLIITPNGAHFWVEMKTS---------------------RGRLSN 63 (98)
Q Consensus 9 ~~ie~~i~~~~k~~g~~~~----k~~~~g~~G~PDli~~~~~g~~~fIEvK~~---------------------~gkls~ 63 (98)
+.+.+.++..|+..|.-+- ||... .++| .|.+-||+|-.+ -.|+|+
T Consensus 87 s~lrr~v~~~Lr~~GydAaiCkSkW~~s--~~~p-------~G~yeYiDVv~~~~~~~~~~R~iVd~dFrs~FEiARpt~ 157 (218)
T pfam04720 87 SCLRRKVMSLLRELGYDAAICKSKWESS--GKVP-------AGEYEYIDVVDGGESKKQEVRLIVDLDFRSEFEIARPTE 157 (218)
T ss_pred HHHHHHHHHHHHHCCCCEEEEECCCCCC--CCCC-------CCCCEEEEEEECCCCCCCCEEEEEECCCHHHEEEECCCH
T ss_conf 8999999999986698841333306788--9978-------976148999822788887505999456557523436858
Q ss_pred HHHHHHHHHHHCCCEEEEECCHHHHHHHHHHH
Q ss_conf 99999999997898699983989999999986
Q gi|254781194|r 64 AQKRVIATLLLYHQKVQVLSSTEEVDGFLRML 95 (98)
Q Consensus 64 ~Q~~~~~~l~~~G~~~~Vv~s~e~v~~~i~~l 95 (98)
.=+..++.| -.+| |-+.|...++|+-+
T Consensus 158 ~Y~~ll~~L----P~vf-VG~~~rL~~iv~im 184 (218)
T pfam04720 158 EYKRILQSL----PRVF-VGKVERLKQLVRIM 184 (218)
T ss_pred HHHHHHHHC----CCEE-EECHHHHHHHHHHH
T ss_conf 999999969----9847-72799999999999
No 81
>cd03008 TryX_like_RdCVF Tryparedoxin (TryX)-like family, Rod-derived cone viability factor (RdCVF) subfamily; RdCVF is a thioredoxin (TRX)-like protein specifically expressed in photoreceptors. RdCVF was isolated and identified as a factor that supports cone survival in retinal cultures. Cone photoreceptor loss is responsible for the visual handicap resulting from the inherited disease, retinitis pigmentosa. RdCVF shows 33% similarity to TRX but does not exhibit any detectable thiol oxidoreductase activity.
Probab=20.85 E-value=83 Score=14.87 Aligned_cols=39 Identities=15% Similarity=0.251 Sum_probs=27.4
Q ss_pred HHHHHHHHHHCC--CEEEEEEC---------CCCCCCCCEEEEECCCCEE
Q ss_conf 999999999789--88999714---------8988766279991599199
Q gi|254781194|r 12 EKRLVKGSKKLD--CLVFKTQF---------INQRGCPDRLIITPNGAHF 50 (98)
Q Consensus 12 e~~i~~~~k~~g--~~~~k~~~---------~g~~G~PDli~~~~~g~~~ 50 (98)
|.....+.+... |+++.+.. .+-+|+|-|+++.|+|.++
T Consensus 77 e~~f~~y~~~MP~~WlAlPf~d~~~~~L~~~f~V~gIPtLVil~~dG~vi 126 (146)
T cd03008 77 EQQQESFLKDMPKKWLFLPFEDEFRRELEAQFSVEELPTVVVLKPDGDVL 126 (146)
T ss_pred HHHHHHHHHHCCCCEEECCCCCHHHHHHHHHCCCCCCCEEEEECCCCCEE
T ss_conf 99999999977987266576968999999985998788899998999897
No 82
>pfam09491 RE_AlwI AlwI restriction endonuclease. This family includes the AlwI (recognizes GGATC), Bsp6I (recognizes GC^NGC), BstNBI (recognizes GASTC), PleI(recognizes GAGTC) and MlyI (recognizes GAGTC) restriction endonucleases.
Probab=20.32 E-value=85 Score=14.81 Aligned_cols=54 Identities=13% Similarity=0.078 Sum_probs=34.2
Q ss_pred ECCCCCCCCCEEEEECCCCEEEEEEECCCCC------CCHHHHHHHHHHHHCC----CEEEEECCHH
Q ss_conf 1489887662799915991999997278988------6989999999999789----8699983989
Q gi|254781194|r 30 QFINQRGCPDRLIITPNGAHFWVEMKTSRGR------LSNAQKRVIATLLLYH----QKVQVLSSTE 86 (98)
Q Consensus 30 ~~~g~~G~PDli~~~~~g~~~fIEvK~~~gk------ls~~Q~~~~~~l~~~G----~~~~Vv~s~e 86 (98)
++|| |.||+++.+.+ ..+.||++...|+ -.|-+++.-+.-...+ +..+|+-+++
T Consensus 333 ~A~g--~~~DI~~~~~d-~~~iiEvTl~~~~~Q~~~E~~pv~rHl~~~~~~~~~~~~y~lFiAp~I~ 396 (429)
T pfam09491 333 TAGG--NKPDIEIEYDD-FSLLIEVTLSKGSTQSNMEGEPVSRHLKELKKKYPNKNVYGLFIAPKIH 396 (429)
T ss_pred CCCC--CCCCEEEEECC-EEEEEEEEEECCCHHHHHCCCCHHHHHHHHHHHCCCCCEEEEEECCCCC
T ss_conf 7899--99888999578-1799999860673587706896789999999847998505999735205
Done!