Query psy13255
Match_columns 156
No_of_seqs 178 out of 1648
Neff 8.7
Searched_HMMs 46136
Date Sat Aug 17 00:04:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13255.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13255hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0249 MutS Mismatch repair A 100.0 1.6E-36 3.5E-41 260.5 3.2 134 22-156 546-695 (843)
2 TIGR01070 mutS1 DNA mismatch r 100.0 5.7E-33 1.2E-37 240.0 4.3 134 22-156 531-680 (840)
3 PRK05399 DNA mismatch repair p 100.0 2.2E-31 4.8E-36 230.9 13.3 65 92-156 631-695 (854)
4 KOG0218|consensus 100.0 6.4E-33 1.4E-37 228.9 1.2 133 23-156 768-918 (1070)
5 KOG0220|consensus 100.0 5.7E-30 1.2E-34 211.3 1.6 133 23-156 563-709 (867)
6 PF00488 MutS_V: MutS domain V 99.9 5.2E-30 1.1E-34 193.7 -2.6 113 44-156 1-131 (235)
7 KOG0217|consensus 99.9 7.9E-28 1.7E-32 204.5 6.5 65 92-156 923-987 (1125)
8 KOG0219|consensus 99.9 4E-26 8.6E-31 190.8 3.3 135 21-156 578-733 (902)
9 KOG0221|consensus 99.9 5E-26 1.1E-30 185.8 3.1 135 20-156 535-687 (849)
10 cd03286 ABC_MSH6_euk MutS6 hom 99.9 1.6E-25 3.6E-30 167.3 0.1 103 54-156 3-118 (218)
11 PRK00409 recombination and DNA 99.9 8.1E-25 1.8E-29 188.5 2.3 131 22-156 269-416 (782)
12 cd03287 ABC_MSH3_euk MutS3 hom 99.9 4.5E-24 9.8E-29 159.9 -0.7 104 53-156 3-119 (222)
13 cd03281 ABC_MSH5_euk MutS5 hom 99.8 2.8E-21 6.1E-26 144.2 -0.5 103 53-156 2-117 (213)
14 cd03282 ABC_MSH4_euk MutS4 hom 99.8 8.8E-21 1.9E-25 140.6 -0.6 102 54-156 3-117 (204)
15 cd03285 ABC_MSH2_euk MutS2 hom 99.8 3.1E-20 6.6E-25 139.4 -0.6 103 54-156 3-118 (222)
16 TIGR01069 mutS2 MutS2 family p 99.8 1.2E-19 2.6E-24 156.4 1.8 131 22-156 264-411 (771)
17 cd03284 ABC_MutS1 MutS1 homolo 99.8 8E-20 1.7E-24 136.6 -0.7 104 53-156 2-118 (216)
18 smart00534 MUTSac ATPase domai 99.7 8.2E-17 1.8E-21 117.6 5.7 74 83-156 5-87 (185)
19 COG1193 Mismatch repair ATPase 99.7 3.9E-18 8.5E-23 145.7 -1.9 127 22-156 261-404 (753)
20 TIGR01070 mutS1 DNA mismatch r 99.6 2.8E-15 6E-20 130.5 7.6 91 1-91 250-340 (840)
21 cd03243 ABC_MutS_homologs The 99.6 3.1E-16 6.8E-21 116.0 0.3 103 54-156 3-117 (202)
22 cd03280 ABC_MutS2 MutS2 homolo 99.6 3.8E-16 8.2E-21 115.4 0.6 102 54-156 3-117 (200)
23 COG0249 MutS Mismatch repair A 99.5 1.2E-14 2.5E-19 126.1 6.3 91 1-91 261-352 (843)
24 cd03283 ABC_MutS-like MutS-lik 99.5 1.9E-15 4.2E-20 111.7 1.0 99 54-156 3-114 (199)
25 PF05192 MutS_III: MutS domain 99.5 3.4E-14 7.3E-19 104.4 7.4 88 4-91 1-89 (204)
26 KOG0218|consensus 99.3 7.8E-13 1.7E-17 110.9 4.5 90 2-91 460-553 (1070)
27 smart00533 MUTSd DNA-binding d 99.0 9.9E-10 2.1E-14 85.6 5.3 71 21-91 1-71 (308)
28 KOG0221|consensus 98.9 9.9E-10 2.1E-14 91.2 2.9 141 2-144 239-395 (849)
29 KOG0219|consensus 98.4 5E-07 1.1E-11 77.4 5.0 89 2-90 290-382 (902)
30 cd03227 ABC_Class2 ABC-type Cl 98.3 7.8E-07 1.7E-11 63.5 3.9 62 82-156 26-108 (162)
31 KOG0220|consensus 98.0 2.9E-06 6.2E-11 72.0 1.4 85 1-85 260-344 (867)
32 PRK05399 DNA mismatch repair p 97.0 3.2E-05 6.9E-10 68.5 -4.2 101 22-125 545-654 (854)
33 smart00533 MUTSd DNA-binding d 96.6 0.00038 8.1E-09 54.2 -0.5 40 22-62 263-306 (308)
34 PRK00409 recombination and DNA 87.5 0.99 2.1E-05 40.2 4.7 41 23-65 13-54 (782)
35 PF13173 AAA_14: AAA domain 87.0 0.36 7.8E-06 32.7 1.4 19 83-101 8-26 (128)
36 cd03222 ABC_RNaseL_inhibitor T 84.0 4 8.6E-05 29.5 5.7 67 84-156 32-98 (177)
37 COG1373 Predicted ATPase (AAA+ 83.2 1.3 2.7E-05 36.3 3.1 22 83-104 43-64 (398)
38 cd03216 ABC_Carb_Monos_I This 80.4 2.8 6.1E-05 29.6 3.8 71 84-156 33-109 (163)
39 cd03214 ABC_Iron-Siderophores_ 76.3 3.2 6.9E-05 29.7 3.1 22 84-105 32-53 (180)
40 cd00267 ABC_ATPase ABC (ATP-bi 75.1 11 0.00023 26.2 5.4 71 84-156 32-107 (157)
41 cd03221 ABCF_EF-3 ABCF_EF-3 E 74.5 10 0.00022 26.1 5.1 65 84-156 33-97 (144)
42 smart00382 AAA ATPases associa 69.5 15 0.00032 23.7 4.9 20 84-103 9-28 (148)
43 cd03239 ABC_SMC_head The struc 65.1 20 0.00043 25.8 5.1 29 128-156 95-125 (178)
44 KOG0734|consensus 61.6 11 0.00025 32.4 3.7 22 135-156 382-405 (752)
45 PRK08939 primosomal protein Dn 58.7 7.8 0.00017 30.6 2.2 18 139-156 209-226 (306)
46 cd03247 ABCC_cytochrome_bd The 58.5 30 0.00066 24.4 5.1 31 124-156 95-125 (178)
47 KOG0217|consensus 58.1 1.4 3.1E-05 39.9 -2.2 80 23-103 830-925 (1125)
48 cd03229 ABC_Class3 This class 54.0 64 0.0014 22.8 6.2 23 134-156 105-127 (178)
49 PF00004 AAA: ATPase family as 53.4 20 0.00044 23.4 3.3 23 134-156 42-67 (132)
50 cd00009 AAA The AAA+ (ATPases 52.4 15 0.00032 24.0 2.5 20 83-102 25-44 (151)
51 cd03228 ABCC_MRP_Like The MRP 52.4 32 0.0007 24.2 4.4 22 84-105 35-56 (171)
52 cd03223 ABCD_peroxisomal_ALDP 51.2 59 0.0013 22.8 5.6 71 84-156 34-118 (166)
53 PF10035 DUF2179: Uncharacteri 49.0 26 0.00056 19.8 2.8 23 133-155 27-49 (55)
54 cd03230 ABC_DR_subfamily_A Thi 49.0 69 0.0015 22.5 5.7 19 84-102 33-51 (173)
55 TIGR01069 mutS2 MutS2 family p 47.0 33 0.00071 30.8 4.4 39 26-66 17-55 (771)
56 PRK12377 putative replication 46.0 16 0.00035 27.9 2.1 17 140-156 156-172 (248)
57 TIGR03015 pepcterm_ATPase puta 42.2 39 0.00084 25.4 3.7 17 83-99 49-65 (269)
58 PRK07952 DNA replication prote 41.5 5.6 0.00012 30.3 -1.0 17 140-156 155-171 (244)
59 PF05496 RuvB_N: Holliday junc 40.6 31 0.00066 26.3 2.8 21 136-156 90-110 (233)
60 PRK06526 transposase; Provisio 38.0 21 0.00045 27.3 1.6 15 142-156 154-168 (254)
61 TIGR01519 plasmod_dom_1 Plasmo 37.0 8 0.00017 23.5 -0.6 39 107-145 9-47 (70)
62 PF15117 UPF0697: Uncharacteri 34.0 47 0.001 21.2 2.4 47 90-139 22-68 (99)
63 TIGR02688 conserved hypothetic 32.9 10 0.00022 31.7 -0.9 17 140-156 253-269 (449)
64 cd00561 CobA_CobO_BtuR ATP:cor 31.6 70 0.0015 22.8 3.3 12 145-156 93-104 (159)
65 COG4604 CeuD ABC-type enteroch 31.5 48 0.001 25.1 2.5 52 84-147 34-85 (252)
66 TIGR00602 rad24 checkpoint pro 31.4 30 0.00064 30.4 1.6 10 147-156 195-204 (637)
67 PRK08181 transposase; Validate 29.9 26 0.00056 27.1 1.0 17 140-156 160-176 (269)
68 COG0079 HisC Histidinol-phosph 29.2 54 0.0012 26.4 2.7 21 135-155 164-184 (356)
69 PHA02972 hypothetical protein; 29.1 54 0.0012 21.1 2.1 21 135-155 88-108 (109)
70 TIGR02858 spore_III_AA stage I 28.9 60 0.0013 25.2 2.8 19 84-102 118-136 (270)
71 PF00005 ABC_tran: ABC transpo 27.8 73 0.0016 21.1 2.8 29 126-156 107-135 (137)
72 COG0488 Uup ATPase components 27.7 32 0.0007 29.4 1.2 33 84-116 355-395 (530)
73 TIGR00708 cobA cob(I)alamin ad 26.9 66 0.0014 23.3 2.6 11 146-156 96-106 (173)
74 PRK08084 DNA replication initi 26.3 48 0.001 24.9 1.8 17 84-100 52-68 (235)
75 PRK09183 transposase/IS protei 25.5 55 0.0012 25.0 2.1 17 84-100 109-125 (259)
76 PRK01688 histidinol-phosphate 24.3 82 0.0018 24.9 2.9 23 134-156 163-185 (351)
77 PF01637 Arch_ATPase: Archaeal 24.3 64 0.0014 23.2 2.2 26 131-156 102-127 (234)
78 PRK10865 protein disaggregatio 24.3 1E+02 0.0022 28.1 3.7 19 138-156 259-280 (857)
79 PF13401 AAA_22: AAA domain; P 24.2 86 0.0019 20.4 2.7 20 136-156 77-96 (131)
80 PRK05986 cob(I)alamin adenolsy 23.1 1.3E+02 0.0028 22.2 3.5 11 146-156 114-124 (191)
81 TIGR03420 DnaA_homol_Hda DnaA 22.9 46 0.00099 24.3 1.1 17 84-100 45-61 (226)
82 TIGR03346 chaperone_ClpB ATP-d 22.1 93 0.002 28.3 3.1 20 137-156 253-275 (852)
83 COG1618 Predicted nucleotide k 21.7 67 0.0014 23.4 1.7 18 139-156 91-109 (179)
84 PTZ00293 thymidine kinase; Pro 21.4 33 0.00072 25.7 0.1 22 122-143 79-100 (211)
85 PRK10787 DNA-binding ATP-depen 21.3 48 0.001 29.8 1.1 10 147-156 416-425 (784)
86 PF00571 CBS: CBS domain CBS d 20.9 1.3E+02 0.0029 16.2 2.7 21 135-155 18-38 (57)
87 TIGR03345 VI_ClpV1 type VI sec 20.7 1.7E+02 0.0036 26.8 4.4 21 136-156 266-289 (852)
88 PRK07414 cob(I)yrinic acid a,c 20.7 1.5E+02 0.0033 21.6 3.4 11 146-156 114-124 (178)
No 1
>COG0249 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.6e-36 Score=260.53 Aligned_cols=134 Identities=28% Similarity=0.429 Sum_probs=121.1
Q ss_pred ccHHHHhhHhhhhHHHHHHHccccCCCCCHH----HHHhhHHHHHHHhhchhhHHHHHHhh-hh--hhhhhhhchhH---
Q psy13255 22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNLD----AIKQRQDAISVLLDQKHITEQMRAKM-KD--LRDLERMLPSS--- 91 (156)
Q Consensus 22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~----~i~~Rhplv~~l~~~~~v~~~i~~~l-~~--~~~~~n~~gk~--- 91 (156)
...++.|| |+.+++..+...+|++|.++.. +.++|||+||..+++.+|||++...- ++ +.|+|||+|||
T Consensus 546 a~aLa~lD-~l~slA~~a~~~~y~rP~~~~~~~l~i~~gRHPvvE~~~~~~fVpNd~~L~~~~~i~lITGPNM~GKSTyl 624 (843)
T COG0249 546 AKALAELD-VLSSLAEIAAEQNYVRPEFVDSNDLEIKEGRHPVVEAVLDNGFVPNDIDLSGNRRIILITGPNMGGKSTYL 624 (843)
T ss_pred HHHHHHHH-HHHHHHHHHhhCCCCCceecCCCCEEEEecCcchhhhhccCCcccCceeeCCCceEEEEECCCCCccHHHH
Confidence 47899999 9999999999999999988644 56899999999888779999997331 11 34679999998
Q ss_pred ------HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 92 ------TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 92 ------~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|||+||||||++|.++++|+||||||+.|++..|.||||+||.|+++||++||++|||||||+
T Consensus 625 RQvali~imAQiGsfVPA~~A~i~ivD~IfTRiGa~DDL~~G~STFMvEM~Eta~IL~~AT~~SLvilDEi 695 (843)
T COG0249 625 RQVALIVILAQIGSFVPAEKARIGIVDRIFTRIGAADDLASGRSTFMVEMLETANILDNATERSLVILDEI 695 (843)
T ss_pred HHHHHHHHHHHcCCCeeHHHccccccceeeecccccchhhccccHHHHHHHHHHHHHHhCCCCcEEEEecc
Confidence 46899999999999999999999999999999999999999999999999999999999999996
No 2
>TIGR01070 mutS1 DNA mismatch repair protein MutS.
Probab=99.97 E-value=5.7e-33 Score=239.99 Aligned_cols=134 Identities=28% Similarity=0.423 Sum_probs=119.1
Q ss_pred ccHHHHhhHhhhhHHHHHHHccccCCCCCHH----HHHhhHHHHHHHhhchhhHHHHHHhhh---hhhhhhhhchhH---
Q psy13255 22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNLD----AIKQRQDAISVLLDQKHITEQMRAKMK---DLRDLERMLPSS--- 91 (156)
Q Consensus 22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~----~i~~Rhplv~~l~~~~~v~~~i~~~l~---~~~~~~n~~gk~--- 91 (156)
...++.|| |+.+++..+...+|++|.++.+ +.++|||+++......+||||+...-. -+.++|||+|||
T Consensus 531 ~~~la~lD-~l~s~A~~a~~~~~~~P~~~~~~~i~i~~~RHP~le~~~~~~~VpNdi~l~~~~~~~iITGPNmgGKSt~l 609 (840)
T TIGR01070 531 ARALAELD-VLANLAEVAETLHYTRPRFGDDPQLRIREGRHPVVEQVLRTPFVPNDLEMAHNRRMLLITGPNMGGKSTYM 609 (840)
T ss_pred HHHHHHHH-HHHHHHHHHHHCCCcCceecCCCcEEEEeeECHHHHhccCCCeEeeeeecCCCccEEEEECCCCCCchHHH
Confidence 47899999 9999999999999999998633 468999999876556789999974311 134679999998
Q ss_pred ------HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 92 ------TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 92 ------~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|||+||||||+++.+|++|+||||||+.|++..|+|||++||.+++.|+++++++||||+||+
T Consensus 610 rqvali~imAq~G~~VPA~~a~i~~~D~Iftrig~~d~i~~g~STF~~Em~e~a~IL~~at~~sLvllDE~ 680 (840)
T TIGR01070 610 RQTALIALLAQIGSFVPAESAELPLFDRIFTRIGASDDLASGRSTFMVEMTEAANILHNATENSLVLFDEI 680 (840)
T ss_pred HHHHHHHHHHhcCCCccchheEeccccEEEEecCcccchhcCcchHHHHHHHHHHHHhhCCCCEEEEEccC
Confidence 47899999999999999999999999999999999999999999999999999999999999996
No 3
>PRK05399 DNA mismatch repair protein MutS; Provisional
Probab=99.97 E-value=2.2e-31 Score=230.90 Aligned_cols=65 Identities=45% Similarity=0.724 Sum_probs=63.3
Q ss_pred HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 92 TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 92 ~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|||+||||||+++.++++|+||||||+.|++..|+|||++||.+++.|+++++++||||+||+
T Consensus 631 ~ilAq~G~~VPa~~a~i~~~d~I~triga~d~i~~g~STF~~E~~~~~~il~~at~~sLvllDE~ 695 (854)
T PRK05399 631 VLLAQIGSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMTETANILNNATERSLVLLDEI 695 (854)
T ss_pred HHHHhcCCceeccceEecccCeeeeccCcccccccCcccHHHHHHHHHHHHHhCCCCcEEEEecC
Confidence 36899999999999999999999999999999999999999999999999999999999999996
No 4
>KOG0218|consensus
Probab=99.97 E-value=6.4e-33 Score=228.94 Aligned_cols=133 Identities=28% Similarity=0.406 Sum_probs=120.4
Q ss_pred cHHHHhhHhhhhHHHHHHHccccCCCCCHH-----HHHhhHHHHHHHhhchhhHHHHHHhhh----hhhhhhhhchhH--
Q psy13255 23 TLIEQLDHCVTSFGKRMLRAQLVKPLTNLD-----AIKQRQDAISVLLDQKHITEQMRAKMK----DLRDLERMLPSS-- 91 (156)
Q Consensus 23 sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~-----~i~~Rhplv~~l~~~~~v~~~i~~~l~----~~~~~~n~~gk~-- 91 (156)
..++.+| |+.++++..-..+|+||.+..+ +.++|||.+|.++.+.+|||++...-. .+.++|||+||+
T Consensus 768 ~~LatlD-Ci~SlA~~s~n~nYvRPtfvd~~~eI~ikngRhPvIe~Ll~d~fVPNdi~ls~egerc~IITGPNMGGKSsy 846 (1070)
T KOG0218|consen 768 LNLATLD-CILSLAATSCNVNYVRPTFVDGQQEIIIKNGRHPVIESLLVDYFVPNDIMLSPEGERCNIITGPNMGGKSSY 846 (1070)
T ss_pred HHHHHHH-HHHHHHHHhccCCccCcccccchhhhhhhcCCCchHHHHhhhccCCCcceecCCCceEEEEeCCCCCCchHH
Confidence 5789999 9999999999999999999742 347999999998888899999853322 245789999997
Q ss_pred -------HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 92 -------TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 92 -------~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|||+|+||||+++.+++||+||||||+.|++..|.|||++||.+++.|+++|+++||||+||+
T Consensus 847 IrQvALitIMAQiGsfVPAeea~l~IfdgvltRmGAsDnI~~grSTFm~Emldt~eil~kat~~SlvilDEl 918 (1070)
T KOG0218|consen 847 IRQVALITIMAQIGSFVPAEEARLSIFDGVLTRMGASDNIINGRSTFMVEMLDTLEILKKATKRSLVILDEL 918 (1070)
T ss_pred HHHHHHHHHHHHhcCccchHHhhhhHHhhHHHhhccccccccchhHHHHHHHHHHHHHHhcccchhhhhHhh
Confidence 58999999999999999999999999999999999999999999999999999999999999996
No 5
>KOG0220|consensus
Probab=99.95 E-value=5.7e-30 Score=211.32 Aligned_cols=133 Identities=27% Similarity=0.370 Sum_probs=116.9
Q ss_pred cHHHHhhHhhhhHHHHHHHccccCCCCCHH--HHHhhHHHHHHHhhchhhHHHHHHhh---hhhhhhhhhchhH------
Q psy13255 23 TLIEQLDHCVTSFGKRMLRAQLVKPLTNLD--AIKQRQDAISVLLDQKHITEQMRAKM---KDLRDLERMLPSS------ 91 (156)
Q Consensus 23 sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~--~i~~Rhplv~~l~~~~~v~~~i~~~l---~~~~~~~n~~gk~------ 91 (156)
.++..|| .+++++.......+++|.+... +.++|||++++...+.++.|+....- -++.++|||+||+
T Consensus 563 e~~~~lD-~l~sfa~~~~~~~y~~P~fT~slaI~qGRHPILe~i~~ek~i~N~t~~t~~s~f~IITGPNMsGKSTYLKQv 641 (867)
T KOG0220|consen 563 EAVSMLD-MLCSFAHACTLSDYVRPEFTDSLAIKQGRHPILEKISAEKPIANNTYVTEGSNFLIITGPNMSGKSTYLKQV 641 (867)
T ss_pred HHHHHHH-HHHHHHHhhccccccccccCCceeeccCCCchhhhhcccCcccCcceeecccceEEEECCCCCcchHHHHHH
Confidence 5778899 7888999999999999998754 56799999998777766777664210 1345779999998
Q ss_pred ---HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 92 ---TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 92 ---~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|||+||||||.++++|+|++||+|||..|+++.+.|+|+.||++++.|++.++++|||++||+
T Consensus 642 Al~~IMAQIGc~IPA~YaS~pIf~RIFtRmg~nDele~NsS~F~sEMke~A~Ilq~a~~~SLiVlDEL 709 (867)
T KOG0220|consen 642 ALCQIMAQIGSYVPAEYASFRVFKRIFTRMGTNDELERNSSTFMSEMKEAAYILQNANKNSLIVLDEL 709 (867)
T ss_pred HHHHHHHHhccCcchhhccchHHHHHHHHhcCchhhhhchhHHHHHHHHHHHHHHhCCcCcEEEEhhh
Confidence 47999999999999999999999999999999999999999999999999999999999999996
No 6
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=99.95 E-value=5.2e-30 Score=193.66 Aligned_cols=113 Identities=30% Similarity=0.490 Sum_probs=84.8
Q ss_pred ccCCCCCHH----HHHhhHHHHHHHh-hchhhHHHHHHhhhh----hhhhhhhchhH---------HHHHhhCCCCCCCc
Q psy13255 44 LVKPLTNLD----AIKQRQDAISVLL-DQKHITEQMRAKMKD----LRDLERMLPSS---------TFLSFQGCRVPADS 105 (156)
Q Consensus 44 ~~~P~~~~~----~i~~Rhplv~~l~-~~~~v~~~i~~~l~~----~~~~~n~~gk~---------~~laq~g~~vpa~~ 105 (156)
|++|.+..+ +.++|||+++..+ .+.++||++...-.. +.++|||+||+ ++|||+|+||||++
T Consensus 1 y~~P~~~~~~~l~i~~~~HPll~~~~~~~~~v~ndi~~~~~~~~~~iiTGpN~sGKSt~lk~i~~~~ilaq~G~~VPA~~ 80 (235)
T PF00488_consen 1 YCRPKISEEKSLKIKEGRHPLLEEKLENKKFVPNDIELSNNKSRIIIITGPNMSGKSTFLKQIGLIVILAQIGCFVPAES 80 (235)
T ss_dssp EB-EEEESTTEEEEEEE--TTHHHHTTTSSC--EEEEESSSSSSEEEEESSTTSSHHHHHHHHHHHHHHHTTT--BSSSE
T ss_pred CcccEEcCCCCEEEEeccCCEEeccccCCceecceeecCCCceeEEEEeCCCccchhhHHHHHHHHhhhhhcCceeeecc
Confidence 678877642 4579999999875 456899988633222 45679999998 47899999999999
Q ss_pred ccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 106 LTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 106 ~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
+.++++|+||+++++.|++..|.|+|+.||.+++.|+++++++|||||||+
T Consensus 81 ~~i~~~d~I~t~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~~sLvliDE~ 131 (235)
T PF00488_consen 81 AEIPIFDRIFTRIGDDDSIESGLSTFMAEMKRLSSILRNATEKSLVLIDEL 131 (235)
T ss_dssp EEEE--SEEEEEES---SSTTSSSHHHHHHHHHHHHHHH--TTEEEEEEST
T ss_pred cccccccEEEeecccccccccccccHHHhHHHHHhhhhhcccceeeecccc
Confidence 999999999999999999999999999999999999999999999999997
No 7
>KOG0217|consensus
Probab=99.94 E-value=7.9e-28 Score=204.49 Aligned_cols=65 Identities=49% Similarity=0.910 Sum_probs=63.3
Q ss_pred HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 92 TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 92 ~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|||+||+|||+.++++++|+||||+|+.|++..|.|||+.|+.+.+.|++.+|++|||++||+
T Consensus 923 vilaq~G~~VPa~~~~~tpidrI~tRlGA~D~im~g~STF~vELsET~~IL~~aT~~SLvi~DEL 987 (1125)
T KOG0217|consen 923 VILAQIGCDVPAEVMELTPIDRIFTRLGANDDIMSGESTFFVELSETKKILKHATRHSLVIVDEL 987 (1125)
T ss_pred HHHHHhCCCccHHHhcccchHHHhhhcccccchhcCCceEEEeccchHHHHhhcCccceeeehhh
Confidence 36899999999999999999999999999999999999999999999999999999999999996
No 8
>KOG0219|consensus
Probab=99.92 E-value=4e-26 Score=190.78 Aligned_cols=135 Identities=29% Similarity=0.415 Sum_probs=111.6
Q ss_pred cccHHHHhhHhhhhHHHHHH--HccccCCCCC------HHHHHhhHHHHHHHhhchhhHHHHHHh-------------hh
Q psy13255 21 EGTLIEQLDHCVTSFGKRML--RAQLVKPLTN------LDAIKQRQDAISVLLDQKHITEQMRAK-------------MK 79 (156)
Q Consensus 21 ~~sl~~~LD~~~t~~g~~~l--~~~~~~P~~~------~~~i~~Rhplv~~l~~~~~v~~~i~~~-------------l~ 79 (156)
-+.+++.|| ++.+++..+- --.|+||.+- ....+.|||+++.=-..+++||++... +.
T Consensus 578 l~~vlAhLD-v~~SFa~~st~a~~pYvRP~~l~~gs~rl~l~~~rHp~lE~Qd~~~fIpNdv~le~~~~~~~IiTGpNMG 656 (902)
T KOG0219|consen 578 LNQVLAHLD-VFVSFAHAATVAPIPYVRPKLLPLGSKRLELKQSRHPVLEGQDEIPFIPNDVVLEKGKCRMLIITGPNMG 656 (902)
T ss_pred HHHHHHHHH-hheeehhhcccCCCCccCccccccchhHHHHHhcccchhhccccCCCCCCccccccCCceEEEEeCCCcC
Confidence 347899999 8999998887 4669999553 235679999998422236889887532 23
Q ss_pred hhhhhhhhchhHHHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 80 DLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 80 ~~~~~~n~~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++.+++|++|++++|||+||||||++|.++++|.|++|.|+.|+...|.||||+||.+.+.|++.++++||++|||+
T Consensus 657 GKSTyir~~Gvi~lmAQIGcfVPce~A~i~IvD~Il~RVGA~D~q~kG~STFM~Emleta~Ilr~at~~SliiiDEL 733 (902)
T KOG0219|consen 657 GKSTYIRQVGVIVLMAQIGCFVPCESATISIVDGILTRVGAGDSQLKGISTFMAEMLETASILRRATKNSLIIIDEL 733 (902)
T ss_pred ccchhhhhhhHHHHHHHhCCceehhhcCCchhhHHHhhhccchhhhcchHHHHHHHHHHHHHHHhcCCCcEEEEecc
Confidence 34444555555679999999999999999999999999999999999999999999999999999999999999996
No 9
>KOG0221|consensus
Probab=99.92 E-value=5e-26 Score=185.80 Aligned_cols=135 Identities=24% Similarity=0.308 Sum_probs=118.1
Q ss_pred ccccHHHHhhHhhhhHHHHHHHccccCCCCCHH-----HHHhhHHHHHHHhhchhhHHHHHHhhh----hhhhhhhhchh
Q psy13255 20 TEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLD-----AIKQRQDAISVLLDQKHITEQMRAKMK----DLRDLERMLPS 90 (156)
Q Consensus 20 ~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~-----~i~~Rhplv~~l~~~~~v~~~i~~~l~----~~~~~~n~~gk 90 (156)
+.-++...|| .+.++|..+..++|.+|....+ ++++|||+++... +.++||+....=. .+.++||.+||
T Consensus 535 ~~l~laSrld-vLls~a~~aa~~gy~~P~lv~e~~il~I~ngrh~l~e~~~-dtfvPNst~iggdkgri~vITGpNasGK 612 (849)
T KOG0221|consen 535 RVLDLASRLD-VLLSLASAAADYGYSRPRLVPEVLILRIQNGRHPLMELCA-DTFVPNSTEIGGDKGRIKVITGPNASGK 612 (849)
T ss_pred HHHHHHHHHH-HHHHHHHHHHhcCCCCCccccHHHHHHHHcCChhHHHHHH-HhcCCCceeecCCCceEEEEeCCCCCCc
Confidence 3447888999 8899999999999999988744 5689999998654 5689998753211 23567999999
Q ss_pred H---------HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 91 S---------TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 91 ~---------~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
+ ++|||+||||||++|+++++|+|||||+.-+++..++|||+.++.+++..+++||.+|||||||+
T Consensus 613 SiYlkqvglivfLahIGsFVPAe~A~IGivDrI~tri~s~esv~~gqSTFmiD~~Qva~aLr~AT~~SLvlIDEf 687 (849)
T KOG0221|consen 613 SIYLKQVGLIVFLAHIGSFVPAEEAEIGIVDRIFTRIHSCESVSLGQSTFMIDLNQVAKALRNATAQSLVLIDEF 687 (849)
T ss_pred eEEEeechhhhHHHhhccccchhhhhcchHHHHHHHhhhhhhhhhhhhHHHHhHHHHHHHHHHhhcCcEEEEhhc
Confidence 7 68999999999999999999999999999999999999999999999999999999999999997
No 10
>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=99.90 E-value=1.6e-25 Score=167.29 Aligned_cols=103 Identities=32% Similarity=0.500 Sum_probs=90.0
Q ss_pred HHhhHHHHHHHhhchhhHHHHHHhhhh----hhhhhhhchhH---------HHHHhhCCCCCCCcccccccceeeccCCc
Q psy13255 54 IKQRQDAISVLLDQKHITEQMRAKMKD----LRDLERMLPSS---------TFLSFQGCRVPADSLTLTPVDRIFTRMGA 120 (156)
Q Consensus 54 i~~Rhplv~~l~~~~~v~~~i~~~l~~----~~~~~n~~gk~---------~~laq~g~~vpa~~~~l~~~d~i~~~~~~ 120 (156)
.++|||+++....++++||++....++ .-+++|++||+ ++|||+|+||||+++.++++|+||++++.
T Consensus 3 ~~~rHPll~~~~~~~~v~ndi~l~~~~~~~~~itG~n~~gKs~~l~~i~~~~~la~~G~~vpa~~~~i~~~~~i~~~~~~ 82 (218)
T cd03286 3 EELRHPCLNASTASSFVPNDVDLGATSPRILVLTGPNMGGKSTLLRTVCLAVIMAQMGMDVPAKSMRLSLVDRIFTRIGA 82 (218)
T ss_pred ccccCCEEecccCCCeEEeeeEEeecCCcEEEEECCCCCchHHHHHHHHHHHHHHHcCCccCccccEeccccEEEEecCc
Confidence 468999997655567899998643221 23458999987 57999999999999999999999999999
Q ss_pred cccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 121 KDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 121 ~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
.|++..+.|||+.||.+++.|++.+++++||||||+
T Consensus 83 ~d~~~~~~StF~~e~~~~~~il~~~~~~sLvLlDE~ 118 (218)
T cd03286 83 RDDIMKGESTFMVELSETANILRHATPDSLVILDEL 118 (218)
T ss_pred ccccccCcchHHHHHHHHHHHHHhCCCCeEEEEecc
Confidence 999999999999999999999999999999999996
No 11
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=99.90 E-value=8.1e-25 Score=188.47 Aligned_cols=131 Identities=20% Similarity=0.303 Sum_probs=114.5
Q ss_pred ccHHHHhhHhhhhHHHHHHHccccCCCCCH----HHHHhhHHHHHHHhhchhhHHHHHHhhh-h--hhhhhhhchhH---
Q psy13255 22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL----DAIKQRQDAISVLLDQKHITEQMRAKMK-D--LRDLERMLPSS--- 91 (156)
Q Consensus 22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~----~~i~~Rhplv~~l~~~~~v~~~i~~~l~-~--~~~~~n~~gk~--- 91 (156)
...++.|| |+.++++.+...+|++|.++. .+.++|||+++. ..++||++...-. + +.++|||+||+
T Consensus 269 ~~~l~~lD-~l~a~a~~a~~~~~~~P~~~~~~~i~l~~~rHPll~~---~~~Vpndi~l~~~~~~~iITGpN~gGKTt~l 344 (782)
T PRK00409 269 NKIFDELD-FIFARARYAKALKATFPLFNDEGKIDLRQARHPLLDG---EKVVPKDISLGFDKTVLVITGPNTGGKTVTL 344 (782)
T ss_pred HHHHHHHH-HHHHHHHHHHHCCCccceEcCCCcEEEcCcCCceecc---CceECceeEECCCceEEEEECCCCCCcHHHH
Confidence 36899999 999999999999999999963 356899999853 4578999863211 1 34679999998
Q ss_pred ------HHHHhhCCCCCCCc-ccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 92 ------TFLSFQGCRVPADS-LTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 92 ------~~laq~g~~vpa~~-~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|||+|+||||.+ +.+|+||+||+++|+.|++..+.|+|+.+|.++..|+..+++++|||+||+
T Consensus 345 ktigl~~~maq~G~~vpa~~~~~i~~~~~i~~~ig~~~si~~~lStfS~~m~~~~~Il~~~~~~sLvLlDE~ 416 (782)
T PRK00409 345 KTLGLAALMAKSGLPIPANEPSEIPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVRILEKADKNSLVLFDEL 416 (782)
T ss_pred HHHHHHHHHHHhCCCcccCCCccccccceEEEecCCccchhhchhHHHHHHHHHHHHHHhCCcCcEEEecCC
Confidence 47999999999996 799999999999999999999999999999999999999999999999996
No 12
>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=99.87 E-value=4.5e-24 Score=159.93 Aligned_cols=104 Identities=32% Similarity=0.466 Sum_probs=90.1
Q ss_pred HHHhhHHHHHHHhhchhhHHHHHHhhhh----hhhhhhhchhH---------HHHHhhCCCCCCCcccccccceeeccCC
Q psy13255 53 AIKQRQDAISVLLDQKHITEQMRAKMKD----LRDLERMLPSS---------TFLSFQGCRVPADSLTLTPVDRIFTRMG 119 (156)
Q Consensus 53 ~i~~Rhplv~~l~~~~~v~~~i~~~l~~----~~~~~n~~gk~---------~~laq~g~~vpa~~~~l~~~d~i~~~~~ 119 (156)
+.++|||+++.....+++++++.....+ .-+++|++||+ ++|+|+|++|||+.++++++|+||++|+
T Consensus 3 i~~~rHPlle~~~~~~~v~n~i~~~~~~g~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~ 82 (222)
T cd03287 3 IKEGRHPMIESLLDKSFVPNDIHLSAEGGYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMG 82 (222)
T ss_pred eecccCCEEeccCCCCEEEEeEEEEecCCcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEec
Confidence 3579999998765556788887543221 23459999998 4689999999999999999999999999
Q ss_pred ccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 120 AKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 120 ~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
+.|++..+.|+|++||.+++.|++++++++|+|+||+
T Consensus 83 ~~d~~~~~~StF~~e~~~~~~il~~~~~~sLvllDE~ 119 (222)
T cd03287 83 ASDSIQHGMSTFMVELSETSHILSNCTSRSLVILDEL 119 (222)
T ss_pred CccccccccchHHHHHHHHHHHHHhCCCCeEEEEccC
Confidence 9999999999999999999999999999999999995
No 13
>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=99.80 E-value=2.8e-21 Score=144.17 Aligned_cols=103 Identities=28% Similarity=0.412 Sum_probs=88.7
Q ss_pred HHHhhHHHHHHHhhchhhHHHHHHhhh--h--hhhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCC
Q psy13255 53 AIKQRQDAISVLLDQKHITEQMRAKMK--D--LRDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMG 119 (156)
Q Consensus 53 ~i~~Rhplv~~l~~~~~v~~~i~~~l~--~--~~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~ 119 (156)
+.++|||+++.. .+.+|||++...-. + .-+++|++||++ +|+|+|++|||..+.++++|++|++++
T Consensus 2 i~~~rHPll~~~-~~~~vpnd~~l~~~~~~~~~itGpNg~GKStlLk~i~~~~~la~~G~~v~a~~~~~~~~d~i~~~l~ 80 (213)
T cd03281 2 IQGGRHPLLELF-VDSFVPNDTEIGGGGPSIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPADSATIGLVDKIFTRMS 80 (213)
T ss_pred cccccCCEEecc-CCceEcceEEecCCCceEEEEECCCCCChHHHHHHHHHHHHHHhCCCeeEcCCcEEeeeeeeeeeeC
Confidence 357899999852 34689999864311 1 235699999985 368999999999999999999999999
Q ss_pred ccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 120 AKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 120 ~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
..|++..+.|+|+.||.+++.++..+++++|+|+||+
T Consensus 81 ~~~si~~~~S~f~~el~~l~~~l~~~~~~slvllDE~ 117 (213)
T cd03281 81 SRESVSSGQSAFMIDLYQVSKALRLATRRSLVLIDEF 117 (213)
T ss_pred CccChhhccchHHHHHHHHHHHHHhCCCCcEEEeccc
Confidence 9999999999999999999999999999999999996
No 14
>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=99.79 E-value=8.8e-21 Score=140.63 Aligned_cols=102 Identities=26% Similarity=0.381 Sum_probs=86.8
Q ss_pred HHhhHHHHHHHhhchhhHHHHHHhhhh----hhhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCCc
Q psy13255 54 IKQRQDAISVLLDQKHITEQMRAKMKD----LRDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMGA 120 (156)
Q Consensus 54 i~~Rhplv~~l~~~~~v~~~i~~~l~~----~~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~~ 120 (156)
.++|||+++. ...+++++++...... .-+++|++||++ +|+|+|++|||.++.++++|+||++++.
T Consensus 3 ~~~~hpll~~-~~~~~v~~~~~~~~~~~~~~~l~G~n~~GKstll~~i~~~~~la~~G~~vpa~~~~l~~~d~I~~~~~~ 81 (204)
T cd03282 3 RDSRHPILDR-DKKNFIPNDIYLTRGSSRFHIITGPNMSGKSTYLKQIALLAIMAQIGCFVPAEYATLPIFNRLLSRLSN 81 (204)
T ss_pred ccccCCeEec-cCCcEEEeeeEEeeCCCcEEEEECCCCCCHHHHHHHHHHHHHHHHcCCCcchhhcCccChhheeEecCC
Confidence 4689999875 2345778887543221 124589999974 6899999999999999999999999999
Q ss_pred cccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 121 KDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 121 ~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
.|++..+.|+|+.||++++.+++.+++++|+|+||+
T Consensus 82 ~d~~~~~~S~fs~e~~~~~~il~~~~~~~lvllDE~ 117 (204)
T cd03282 82 DDSMERNLSTFASEMSETAYILDYADGDSLVLIDEL 117 (204)
T ss_pred ccccchhhhHHHHHHHHHHHHHHhcCCCcEEEeccc
Confidence 999999999999999999999999999999999995
No 15
>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=99.77 E-value=3.1e-20 Score=139.40 Aligned_cols=103 Identities=29% Similarity=0.420 Sum_probs=88.3
Q ss_pred HHhhHHHHHHHhhchhhHHHHHHhhhh----hhhhhhhchhH---------HHHHhhCCCCCCCcccccccceeeccCCc
Q psy13255 54 IKQRQDAISVLLDQKHITEQMRAKMKD----LRDLERMLPSS---------TFLSFQGCRVPADSLTLTPVDRIFTRMGA 120 (156)
Q Consensus 54 i~~Rhplv~~l~~~~~v~~~i~~~l~~----~~~~~n~~gk~---------~~laq~g~~vpa~~~~l~~~d~i~~~~~~ 120 (156)
.++|||+++......++++++.....+ .-+++|++||+ ++|||+|+||||+++.++++|+|+++++.
T Consensus 3 ~~~~hpll~~~~~~~~v~~~~~~~~~~~~~~~l~G~n~~GKstll~~i~~~~~la~~g~~vpa~~~~~~~~~~il~~~~l 82 (222)
T cd03285 3 KEARHPCVEAQDDVAFIPNDVTLTRGKSRFLIITGPNMGGKSTYIRQIGVIVLMAQIGCFVPCDSADIPIVDCILARVGA 82 (222)
T ss_pred cccCCCEEeccCCCCeEEeeEEEeecCCeEEEEECCCCCChHHHHHHHHHHHHHHHhCCCcCcccEEEeccceeEeeecc
Confidence 468999998654456788888643211 23458999987 46899999999999999999999999999
Q ss_pred cccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 121 KDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 121 ~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
.|++..+.|+|+.||.+++.+++.+++++|+|+||+
T Consensus 83 ~d~~~~~lS~~~~e~~~~a~il~~~~~~sLvLLDEp 118 (222)
T cd03285 83 SDSQLKGVSTFMAEMLETAAILKSATENSLIIIDEL 118 (222)
T ss_pred ccchhcCcChHHHHHHHHHHHHHhCCCCeEEEEecC
Confidence 999999999999999999999999999999999996
No 16
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=99.76 E-value=1.2e-19 Score=156.39 Aligned_cols=131 Identities=16% Similarity=0.217 Sum_probs=112.1
Q ss_pred ccHHHHhhHhhhhHHHHHHHccccCCCCCH----HHHHhhHHHHHHHhhchhhHHHHHHhhh-h--hhhhhhhchhHH--
Q psy13255 22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL----DAIKQRQDAISVLLDQKHITEQMRAKMK-D--LRDLERMLPSST-- 92 (156)
Q Consensus 22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~----~~i~~Rhplv~~l~~~~~v~~~i~~~l~-~--~~~~~n~~gk~~-- 92 (156)
...++.|| ++.+.+..+....++.|.+.. ...++|||+++. ..++|+++...-. . ..++||++||++
T Consensus 264 ~~~l~~lD-~l~a~a~~a~~~~~~~P~~~~~~~i~l~~~rhPll~~---~~~vp~di~l~~~~~~liItGpNg~GKSTlL 339 (771)
T TIGR01069 264 FKEFDFLD-SLQARARYAKAVKGEFPMPSFTGKIILENARHPLLKE---PKVVPFTLNLKFEKRVLAITGPNTGGKTVTL 339 (771)
T ss_pred HHHHHHHH-HHHHHHHHHHHCCCeeceecCCCCEEEccccCceecC---CceEeceeEeCCCceEEEEECCCCCCchHHH
Confidence 36899999 999999999999999998753 356899999852 3478888863211 1 235699999984
Q ss_pred -------HHHhhCCCCCCCc-ccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 93 -------FLSFQGCRVPADS-LTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 93 -------~laq~g~~vpa~~-~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
+|+|+|++|||.. +.+++||++|+++++.|++.++.|+|+.||.++..|+..+++++|||+||+
T Consensus 340 K~i~~~~l~aq~G~~Vpa~~~~~~~~~d~i~~~i~~~~si~~~LStfS~~m~~~~~il~~~~~~sLvLlDE~ 411 (771)
T TIGR01069 340 KTLGLLALMFQSGIPIPANEHSEIPYFEEIFADIGDEQSIEQNLSTFSGHMKNISAILSKTTENSLVLFDEL 411 (771)
T ss_pred HHHHHHHHHHHhCCCccCCccccccchhheeeecChHhHHhhhhhHHHHHHHHHHHHHHhcCCCcEEEecCC
Confidence 5899999999987 689999999999999999999999999999999999999999999999996
No 17
>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam
Probab=99.75 E-value=8e-20 Score=136.63 Aligned_cols=104 Identities=34% Similarity=0.518 Sum_probs=89.1
Q ss_pred HHHhhHHHHHHHhh-chhhHHHHHHhhh-h--hhhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCC
Q psy13255 53 AIKQRQDAISVLLD-QKHITEQMRAKMK-D--LRDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMG 119 (156)
Q Consensus 53 ~i~~Rhplv~~l~~-~~~v~~~i~~~l~-~--~~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~ 119 (156)
+.++|||+++...+ ..+++|++....+ + .-+++|++||++ +|+|+|+++||.++.+++++++|++++
T Consensus 2 i~~~~hp~~~~~~~~~~~v~n~~~l~~~~~~~~l~Gpn~sGKstllr~i~~~~~l~~~g~~vp~~~~~i~~~~~i~~~~~ 81 (216)
T cd03284 2 IEGGRHPVVEQVLDNEPFVPNDTELDPERQILLITGPNMAGKSTYLRQVALIALLAQIGSFVPASKAEIGVVDRIFTRIG 81 (216)
T ss_pred cccccCCEEeeccCCCceEeeeEEecCCceEEEEECCCCCChHHHHHHHHHHHHHhccCCeeccccceecceeeEeccCC
Confidence 34689999987654 5578888863322 1 234699999984 578999999999999999999999999
Q ss_pred ccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 120 AKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 120 ~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
..|++..|.|+|+.||.+++.++..+++++|+|+||+
T Consensus 82 ~~~~ls~g~s~f~~e~~~l~~~l~~~~~~~llllDEp 118 (216)
T cd03284 82 ASDDLAGGRSTFMVEMVETANILNNATERSLVLLDEI 118 (216)
T ss_pred chhhhccCcchHHHHHHHHHHHHHhCCCCeEEEEecC
Confidence 9999999999999999999999999999999999995
No 18
>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family.
Probab=99.67 E-value=8.2e-17 Score=117.63 Aligned_cols=74 Identities=41% Similarity=0.589 Sum_probs=69.5
Q ss_pred hhhhhchhH---------HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEe
Q psy13255 83 DLERMLPSS---------TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALV 153 (156)
Q Consensus 83 ~~~n~~gk~---------~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvli 153 (156)
+++|++||+ ++|||+|++|||+++.++++|++|++++..|++..+.|+|+.||.+++.++..+++++|+|+
T Consensus 5 tG~N~~GKst~l~~i~~~~~la~~G~~v~a~~~~~~~~d~il~~~~~~d~~~~~~s~fs~~~~~l~~~l~~~~~~~llll 84 (185)
T smart00534 5 TGPNMGGKSTYLRQVGLIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNATENSLVLL 84 (185)
T ss_pred ECCCCCcHHHHHHHHHHHHHHHHhCCCeeehheEecccceEEEEeCCCCchhccccHHHHHHHHHHHHHHhCCCCeEEEE
Confidence 467888887 46899999999999999999999999999999999999999999999999999999999999
Q ss_pred ccC
Q psy13255 154 DEL 156 (156)
Q Consensus 154 DE~ 156 (156)
||+
T Consensus 85 DEp 87 (185)
T smart00534 85 DEL 87 (185)
T ss_pred ecC
Confidence 995
No 19
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=99.66 E-value=3.9e-18 Score=145.65 Aligned_cols=127 Identities=20% Similarity=0.259 Sum_probs=108.4
Q ss_pred ccHHHHhhHhhhhHHHHHHHccccCCCCC----HHHHHhhHHHHHHHhhchhhHHHHHHhh---hhhhhhhhhchhH---
Q psy13255 22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTN----LDAIKQRQDAISVLLDQKHITEQMRAKM---KDLRDLERMLPSS--- 91 (156)
Q Consensus 22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~----~~~i~~Rhplv~~l~~~~~v~~~i~~~l---~~~~~~~n~~gk~--- 91 (156)
...++.+| ++.+..+.+.......|.++ .+..++|||++..- +++++.... .-+.++||++||+
T Consensus 261 ~~~~~~lD-~i~Ak~~~~~~~~~v~P~~~~~~~l~l~~~~HPll~~~-----v~~~i~~~~e~~~l~ITGpN~GGKtvtL 334 (753)
T COG1193 261 LEIIGELD-FIEAKVRYAKALKGVKPDFSNDGVLELLDARHPLLKED-----VPNDLELGEELDRLIITGPNTGGKTVTL 334 (753)
T ss_pred HHHhhhhH-HHHHHHHHHHhhccCCCccCCCceEEeccccCccCccc-----cccccccccccceeeEecCCCCcceehH
Confidence 36889999 89999999999889999998 34678999998742 555554321 2345789999997
Q ss_pred ------HHHHhhCCCCCCCcc-cccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 92 ------TFLSFQGCRVPADSL-TLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 92 ------~~laq~g~~vpa~~~-~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|+|.|.++||.+. .+++|+++|..||+.|++++++|||+.+|..+++|+..++ ||+++||+
T Consensus 335 KTlgl~~lm~q~gl~i~a~~gsei~~F~~i~aDIGDeQsIeqsLSTFSshm~~i~~il~~~d--sLvl~DEl 404 (753)
T COG1193 335 KTLGLLRLMAQSGLPIPALEGSELPVFVKIFADIGDEQSIEQSLSTFSSHMTNIVEILEKAD--SLVLFDEL 404 (753)
T ss_pred HHHHHHHHHHHcCCCeeccCCCcchhHHHhhhccCcHHHHHHHHhhhHHHHHHHHHHHhhcc--hhHHHHHh
Confidence 589999999999986 8999999999999999999999999999999999996666 99999996
No 20
>TIGR01070 mutS1 DNA mismatch repair protein MutS.
Probab=99.59 E-value=2.8e-15 Score=130.53 Aligned_cols=91 Identities=32% Similarity=0.511 Sum_probs=84.0
Q ss_pred CCCHHHHhhccccccCCCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhh
Q psy13255 1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKD 80 (156)
Q Consensus 1 ~id~~t~~~Lei~~~~~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~ 80 (156)
.||.+|++||||+++..+++++||++.+|+|.|++|+|+++.|+++|+.+.+.|+.||.+|+++..+......++..+++
T Consensus 250 ~lD~~t~~~LEl~~~~~~~~~gSL~~~ld~t~T~~G~RlLr~wl~~Pl~d~~~I~~Rld~Ve~l~~~~~l~~~l~~~L~~ 329 (840)
T TIGR01070 250 QLDAATRRNLELTENLRGGKQNTLFSVLDETKTAMGSRLLKRWLHRPLRDREVLEARQDTVEVLLRHFFLREGLRPLLKE 329 (840)
T ss_pred EeCHHHHHhccCCccCCCCCCCcHHHHHhhcCCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhCHHHHHHHHHHhcc
Confidence 48999999999998876667899999999999999999999999999999999999999999999887788889888999
Q ss_pred hhhhhhhchhH
Q psy13255 81 LRDLERMLPSS 91 (156)
Q Consensus 81 ~~~~~n~~gk~ 91 (156)
++|++++.+|.
T Consensus 330 i~Dlerll~ri 340 (840)
T TIGR01070 330 VGDLERLAARV 340 (840)
T ss_pred CcCHHHHHHHH
Confidence 99998888764
No 21
>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru
Probab=99.57 E-value=3.1e-16 Score=115.95 Aligned_cols=103 Identities=37% Similarity=0.510 Sum_probs=87.5
Q ss_pred HHhhHHHHHHH-hhchhhHHHHHHhhhh--hhhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCCcc
Q psy13255 54 IKQRQDAISVL-LDQKHITEQMRAKMKD--LRDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMGAK 121 (156)
Q Consensus 54 i~~Rhplv~~l-~~~~~v~~~i~~~l~~--~~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~~~ 121 (156)
.++|||+++.. ...+++|+++...-++ .-+++|++||++ +++|.|+++|+.++.++++|++|+.++..
T Consensus 3 ~~~~~p~l~~~~~~~~~~~~~~~l~~~~~~~l~G~Ng~GKStll~~i~~~~~~~~~g~~~~~~~~~i~~~dqi~~~~~~~ 82 (202)
T cd03243 3 KGGRHPVLLALTKGETFVPNDINLGSGRLLLITGPNMGGKSTYLRSIGLAVLLAQIGCFVPAESASIPLVDRIFTRIGAE 82 (202)
T ss_pred ccccCCEEeccccCCceEeeeEEEcCCeEEEEECCCCCccHHHHHHHHHHHHHHHcCCCccccccccCCcCEEEEEecCc
Confidence 46899999865 2345789988643111 234699999984 45789999999999999999999999999
Q ss_pred ccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 122 DNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 122 d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
+++..+.|+|..|++++..++..+.+.+++|+||.
T Consensus 83 d~i~~~~s~~~~e~~~l~~i~~~~~~~~llllDEp 117 (202)
T cd03243 83 DSISDGRSTFMAELLELKEILSLATPRSLVLIDEL 117 (202)
T ss_pred ccccCCceeHHHHHHHHHHHHHhccCCeEEEEecC
Confidence 99999999999999999999999999999999995
No 22
>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a
Probab=99.57 E-value=3.8e-16 Score=115.37 Aligned_cols=102 Identities=20% Similarity=0.327 Sum_probs=84.9
Q ss_pred HHhhHHHHHHHhhchhhHHHHHHhhh-h--hhhhhhhchhHH---------HHHhhCCCCCCCc-ccccccceeeccCCc
Q psy13255 54 IKQRQDAISVLLDQKHITEQMRAKMK-D--LRDLERMLPSST---------FLSFQGCRVPADS-LTLTPVDRIFTRMGA 120 (156)
Q Consensus 54 i~~Rhplv~~l~~~~~v~~~i~~~l~-~--~~~~~n~~gk~~---------~laq~g~~vpa~~-~~l~~~d~i~~~~~~ 120 (156)
.++|||+++.. ...++++++...-. + .-++||++||++ +++|+|++||+.+ ..++++|++|++++.
T Consensus 3 ~~~~hp~~~~~-~~~~~~~~~~i~~~~~~~~ltG~Ng~GKStll~~i~~~~~~~~~G~~vp~~~~~~~~~~~~~~~~lg~ 81 (200)
T cd03280 3 REARHPLLPLQ-GEKVVPLDIQLGENKRVLVITGPNAGGKTVTLKTLGLLTLMAQSGLPIPAAEGSSLPVFENIFADIGD 81 (200)
T ss_pred cccCCCEEecc-CCceEcceEEECCCceEEEEECCCCCChHHHHHHHHHHHHHHHcCCCccccccccCcCccEEEEecCc
Confidence 46899999853 44577888764321 1 134699999984 4678899999986 679999999999999
Q ss_pred cccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 121 KDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 121 ~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
.+++..+.|+|+.+|++...++..+++.+++++||.
T Consensus 82 ~~~l~~~~s~fs~g~~~~~~i~~~~~~p~llllDEp 117 (200)
T cd03280 82 EQSIEQSLSTFSSHMKNIARILQHADPDSLVLLDEL 117 (200)
T ss_pred hhhhhcCcchHHHHHHHHHHHHHhCCCCcEEEEcCC
Confidence 999999999999999999999999999999999995
No 23
>COG0249 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=99.53 E-value=1.2e-14 Score=126.11 Aligned_cols=91 Identities=34% Similarity=0.577 Sum_probs=84.5
Q ss_pred CCCHHHHhhccccccCCC-CccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhh
Q psy13255 1 ILDSTALANLHVLTNSDN-TTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMK 79 (156)
Q Consensus 1 ~id~~t~~~Lei~~~~~~-~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~ 79 (156)
.||.+|.+||||+++..+ +++|+|++.||+|.|++|+|++++|+.+|+.+.+.|+.||++|+.+..+......++..|+
T Consensus 261 ~lD~~t~~nLEl~~~~~~~~~~gSL~~~ld~t~T~mG~RlL~~wl~~PL~~~~~I~~Rld~Ve~l~~~~~l~~~L~~~L~ 340 (843)
T COG0249 261 VLDAATRRNLELFSNLRGNGKKGSLFWLLDRTVTPMGSRLLKRWLLQPLLDKEEIEERLDAVEELKDNPELREKLREMLK 340 (843)
T ss_pred EEcHHHHhcccccccCCCCCCCCcHHHHhccCCCchhHHHHHHHhhCcccCHHHHHHHHHHHHHHHhhhHHHHHHHHHHh
Confidence 489999999999988654 7888999999999999999999999999999999999999999999988778888988899
Q ss_pred hhhhhhhhchhH
Q psy13255 80 DLRDLERMLPSS 91 (156)
Q Consensus 80 ~~~~~~n~~gk~ 91 (156)
+++|++|..++.
T Consensus 341 ~v~DleRl~~Rl 352 (843)
T COG0249 341 KVPDLERLLSRL 352 (843)
T ss_pred cCcCHHHHHHHH
Confidence 999999998875
No 24
>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid
Probab=99.52 E-value=1.9e-15 Score=111.68 Aligned_cols=99 Identities=27% Similarity=0.320 Sum_probs=84.4
Q ss_pred HHhhHHHHHHHhhchhhHHHHHHhhhhh--hhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCCccc
Q psy13255 54 IKQRQDAISVLLDQKHITEQMRAKMKDL--RDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMGAKD 122 (156)
Q Consensus 54 i~~Rhplv~~l~~~~~v~~~i~~~l~~~--~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~~~d 122 (156)
.++|||+++ ++++++|++...-+++ -++||++|||+ +++|.|++|||..+.++ .+.+|.++...|
T Consensus 3 ~~~~hp~~~---~~~~v~n~i~l~~g~~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~v~a~~~~~q-~~~l~~~~~~~d 78 (199)
T cd03283 3 KNLGHPLIG---REKRVANDIDMEKKNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELP-PVKIFTSIRVSD 78 (199)
T ss_pred cccCCCeec---CCCeecceEEEcCCcEEEEECCCCCChHHHHHHHHHHHHHHHcCCEEecCccCcc-cceEEEeccchh
Confidence 468999987 4567888886432222 34699999985 45899999999999998 799999999999
Q ss_pred cccCCcCcHHHHHHHHHHHHHhcC--CCceEEeccC
Q psy13255 123 NLSGAQSTYLAELTESETIMRHAS--KYSLALVDEL 156 (156)
Q Consensus 123 ~l~~~~S~F~~e~~~~~~il~~~~--~~slvliDE~ 156 (156)
++..+.|+|..|+.++..+++.++ +.+++|+||.
T Consensus 79 ~l~~~~s~~~~e~~~~~~iL~~~~~~~p~llllDEp 114 (199)
T cd03283 79 DLRDGISYFYAELRRLKEIVEKAKKGEPVLFLLDEI 114 (199)
T ss_pred ccccccChHHHHHHHHHHHHHhccCCCCeEEEEecc
Confidence 999999999999999999999999 8899999994
No 25
>PF05192 MutS_III: MutS domain III C-terminus.; InterPro: IPR007696 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the core domain (domain 3) found in proteins of the MutS family. The core domain of MutS adopts a multi-helical structure comprised of two subdomains, which are interrupted by the clamp domain. Two of the helices in the core domain comprise the levers that extend towards the DNA. This domain is found associated with Pfam:PF00488, Pfam:PF05188, Pfam:PF01624 and Pfam:PF05190. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterised in [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2O8F_A 3THW_A 3THX_A 2O8C_A 3THY_A 2O8E_A 2O8B_A 3THZ_A 2O8D_A 1FW6_A ....
Probab=99.52 E-value=3.4e-14 Score=104.41 Aligned_cols=88 Identities=34% Similarity=0.657 Sum_probs=72.1
Q ss_pred HHHHhhccccccC-CCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhhhh
Q psy13255 4 STALANLHVLTNS-DNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLR 82 (156)
Q Consensus 4 ~~t~~~Lei~~~~-~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~~~ 82 (156)
++|+++|||+++. ++++.++|++.+|+|.|+.|+++++.|+.+|+.+.+.|+.||..|+++..++.+..++...+++++
T Consensus 1 ~~Tl~~L~i~~~~~~~~~~~sL~~~ln~t~T~~Gkr~L~~~l~~P~~d~~~I~~R~~~v~~~~~n~~~~~~~~~~l~~~~ 80 (204)
T PF05192_consen 1 ANTLKSLEIFENSRSGKKKGSLFSLLNRTSTPMGKRLLRSWLLQPLTDIEEIEKRQDAVEEFLQNEELREELRSILKKIP 80 (204)
T ss_dssp HHHHHHTTSSSBTTTSSSSTSHHHHH---SSHHHHHHHHHHHHS-BS-HHHHHHHHHHHHHHHHTHHHHHHHHHHHTTC-
T ss_pred ChhHHhccCCCCCCCCCCCCcHHHHHhcCCChHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhhhHhhhhhhhhhccc
Confidence 5899999999775 667788999999999999999999999999999999999999999999987777788887788888
Q ss_pred hhhhhchhH
Q psy13255 83 DLERMLPSS 91 (156)
Q Consensus 83 ~~~n~~gk~ 91 (156)
|+.+...+.
T Consensus 81 di~~~l~~l 89 (204)
T PF05192_consen 81 DIERILKRL 89 (204)
T ss_dssp SHHHHHHHH
T ss_pred hHHHHHHHH
Confidence 877666653
No 26
>KOG0218|consensus
Probab=99.34 E-value=7.8e-13 Score=110.86 Aligned_cols=90 Identities=36% Similarity=0.540 Sum_probs=79.0
Q ss_pred CCHHHHhhccccccC-CCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhh---chhhHHHHHHh
Q psy13255 2 LDSTALANLHVLTNS-DNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLD---QKHITEQMRAK 77 (156)
Q Consensus 2 id~~t~~~Lei~~~~-~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~---~~~v~~~i~~~ 77 (156)
|+++|+++|||++|+ +++.+|+||+.||++.|++|.|+++.|+.+|+.+.+.|++|.++|+++.. ++.+...+...
T Consensus 460 ls~ntLq~Leif~nqtd~~~kGSLfwvldhT~TsfG~RmLr~WvtkPLvd~~~I~eRLDAVeeitshssnS~vf~si~~~ 539 (1070)
T KOG0218|consen 460 LSPNTLQSLEIFTNQTDGSEKGSLFWVLDHTRTSFGLRMLREWVTKPLVDVHQIEERLDAVEEITSHSSNSIVFESINQM 539 (1070)
T ss_pred echhhhhceeeeeecCCCCcccceEEEeccchhHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHhcccchHHHHHHHHH
Confidence 689999999999885 66778999999999999999999999999999999999999999999833 34478888888
Q ss_pred hhhhhhhhhhchhH
Q psy13255 78 MKDLRDLERMLPSS 91 (156)
Q Consensus 78 l~~~~~~~n~~gk~ 91 (156)
|.+.+|+.|.+.++
T Consensus 540 l~rlpDl~rgL~rI 553 (1070)
T KOG0218|consen 540 LNRLPDLLRGLNRI 553 (1070)
T ss_pred HHhCcHhHhhHHHH
Confidence 89999987776553
No 27
>smart00533 MUTSd DNA-binding domain of DNA mismatch repair MUTS family.
Probab=98.95 E-value=9.9e-10 Score=85.62 Aligned_cols=71 Identities=38% Similarity=0.684 Sum_probs=62.8
Q ss_pred cccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhhhhhhhhhchhH
Q psy13255 21 EGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERMLPSS 91 (156)
Q Consensus 21 ~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~~~~~~n~~gk~ 91 (156)
++||++.||+|.|++|+|.++.|+++|+.+.+.|+.|+..|+++..++.+...++..+++++|++++..|.
T Consensus 1 ~~sL~~~l~~~~T~~G~r~L~~wl~~Pl~~~~~I~~R~~~v~~~~~~~~l~~~l~~~L~~~~Di~~~l~~~ 71 (308)
T smart00533 1 KGSLFELLNHTKTPMGKRLLRRWLLQPLLDLKEINERLDAVEELVENPELRQKLRQLLKRIPDLERLLSRI 71 (308)
T ss_pred CCCHHHHHccCCCcHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHhChHHHHHHHHHHccCCcHHHHHHHH
Confidence 36899999999999999999999999999999999999999999987777777777788888887666653
No 28
>KOG0221|consensus
Probab=98.88 E-value=9.9e-10 Score=91.18 Aligned_cols=141 Identities=16% Similarity=0.284 Sum_probs=92.0
Q ss_pred CCHHHHhhccccccCCC---C----cc-ccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhh--chhhH
Q psy13255 2 LDSTALANLHVLTNSDN---T----TE-GTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLD--QKHIT 71 (156)
Q Consensus 2 id~~t~~~Lei~~~~~~---~----~~-~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~--~~~v~ 71 (156)
||.+|+.+|.||++... . +. -|+|+.+|+|.+..|++.++.|+.+|+.+...+..|+.++..++. |..+.
T Consensus 239 iD~nTisaL~Ifp~e~~~~~~k~~~~~g~Slf~l~n~c~s~~g~k~Lr~Wf~nPttd~~~l~sR~~~i~~fl~~qNa~~~ 318 (849)
T KOG0221|consen 239 IDQNTISALQIFPSESHPSKVKSGLKEGLSLFGLLNRCHSKWGEKLLRLWFTNPTTDLGELSSRLDVIQFFLLPQNADMA 318 (849)
T ss_pred eccchHHHHHhcccccccchhhhhhhcchhHHHHHHHHhhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhcchhhHHH
Confidence 79999999999987432 1 22 299999999999999999999999999999999999999998876 44577
Q ss_pred HHHHHhhhhhhhhhhh-----chhHHHHHhhCCCCCCCcccccccceeeccCCcccccc-CCcCcHHHHHHHHHHHHHh
Q psy13255 72 EQMRAKMKDLRDLERM-----LPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLS-GAQSTYLAELTESETIMRH 144 (156)
Q Consensus 72 ~~i~~~l~~~~~~~n~-----~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~-~~~S~F~~e~~~~~~il~~ 144 (156)
..+...++++++.+-. +|++ -+.+.-+++..-++.+++++ +..+....-.+. .-.+-|..++.+++++...
T Consensus 319 ~~Ls~~lgr~k~~~~~~~~~~sg~t-~l~~W~~~~stv~~~~~i~~-~~rslp~s~~~~~~~~~~~~~~l~eia~~~g~ 395 (849)
T KOG0221|consen 319 QMLSRLLGRIKNVPLILKRMKSGHT-KLSDWQVLYSTVYSALGIRD-ACRSLPQSIQLFRDIAQEFSDDLHEIASLIGK 395 (849)
T ss_pred HHHHHHHhhcccHHHHHHHHhcCCc-eechHHHHHHHHHHHHHHHH-HHHhCccchhhhhHHHHHHHHHHHHHHHHhhh
Confidence 7777667776654322 2222 11222222222233333433 211111111111 1245677888888877655
No 29
>KOG0219|consensus
Probab=98.37 E-value=5e-07 Score=77.36 Aligned_cols=89 Identities=30% Similarity=0.558 Sum_probs=70.9
Q ss_pred CCHHHHhhccccccCCCC--ccccHHH-HhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHH-h
Q psy13255 2 LDSTALANLHVLTNSDNT--TEGTLIE-QLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRA-K 77 (156)
Q Consensus 2 id~~t~~~Lei~~~~~~~--~~~sl~~-~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~-~ 77 (156)
+|..|.++|++|+...+. +..+|.. .||+|.|..|.|.+..|+.+|+.+.+.++.||++|+.+..+......++. .
T Consensus 290 ld~~av~alnlf~~~~~~~~~s~~L~~~~LN~c~t~~G~rll~~w~~qpL~~~~ri~~r~d~v~~l~~~~~~rq~L~~~l 369 (902)
T KOG0219|consen 290 LDSAAVRALNLFPLPYNNPEKSNNLALSLLNHCKTLQGERLLRQWLKQPLRDIDRINERHDLVEALVEDAEIRQKLRDDL 369 (902)
T ss_pred HHHHHHHHHhhcCCCCCCccccchhhHHHHhhcccccchhhhhhhhhcchHHHHHHHHHhhhHHHHHhhhHHHHHHHHHH
Confidence 689999999999876443 3335666 89999999999999999999999999999999999998887655555543 3
Q ss_pred hhhhhhhhhhchh
Q psy13255 78 MKDLRDLERMLPS 90 (156)
Q Consensus 78 l~~~~~~~n~~gk 90 (156)
+..++++.+..-+
T Consensus 370 L~~~pdi~rl~~~ 382 (902)
T KOG0219|consen 370 LRRIPDISRLARR 382 (902)
T ss_pred hhcChhHHHhhhh
Confidence 4566676555554
No 30
>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.
Probab=98.29 E-value=7.8e-07 Score=63.54 Aligned_cols=62 Identities=34% Similarity=0.280 Sum_probs=50.8
Q ss_pred hhhhhhchhHHH---------HHh----------hCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHH
Q psy13255 82 RDLERMLPSSTF---------LSF----------QGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIM 142 (156)
Q Consensus 82 ~~~~n~~gk~~~---------laq----------~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il 142 (156)
.+++|++||+++ +++ .|+++|+.++.+ +|++++ +|....++..+++++
T Consensus 26 i~G~NgsGKS~~l~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~-----i~~~~~--------lS~G~~~~~~la~~L 92 (162)
T cd03227 26 ITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIVAAVSAEL-----IFTRLQ--------LSGGEKELSALALIL 92 (162)
T ss_pred EECCCCCCHHHHHHHHHHHHHhcchhhhccCcccCCCcceeeEEEE-----ehheee--------ccccHHHHHHHHHHH
Confidence 356999999854 466 899999888766 666554 788899999999999
Q ss_pred HhcC--CCceEEeccC
Q psy13255 143 RHAS--KYSLALVDEL 156 (156)
Q Consensus 143 ~~~~--~~slvliDE~ 156 (156)
..++ +.+++|+||+
T Consensus 93 ~~~~~~~~~llllDEp 108 (162)
T cd03227 93 ALASLKPRPLYILDEI 108 (162)
T ss_pred HhcCCCCCCEEEEeCC
Confidence 9865 7899999995
No 31
>KOG0220|consensus
Probab=97.96 E-value=2.9e-06 Score=72.02 Aligned_cols=85 Identities=29% Similarity=0.473 Sum_probs=73.4
Q ss_pred CCCHHHHhhccccccCCCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhh
Q psy13255 1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKD 80 (156)
Q Consensus 1 ~id~~t~~~Lei~~~~~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~ 80 (156)
.||..+..+||++.+.+.+...++++.+|++.++.|+|.++....+|+.+...++.|..+++++..++.....++..+++
T Consensus 260 ~id~~~~~~lelV~~~~~kn~~~l~~vl~~T~t~~g~r~lRssilqpl~d~~ti~~rleaiqeL~a~~~L~~~Lr~~~k~ 339 (867)
T KOG0220|consen 260 MIDSSSAQSLELVINNQYKNNHTLFGVLNYTKTPGGYRRLRSSILQPLTDIETINMRLEAIQELLADEELFFGLRSVIKR 339 (867)
T ss_pred eeecccccceEEechhhhhcccceeeeeeeeecccchhhHHhhhcccccchhhhhHHHHHHHHHhcCchHhhhhHHHHhh
Confidence 47899999999998877766789999999999999999999999999999999999999999998887666666655665
Q ss_pred hhhhh
Q psy13255 81 LRDLE 85 (156)
Q Consensus 81 ~~~~~ 85 (156)
..+..
T Consensus 340 ~~dld 344 (867)
T KOG0220|consen 340 FLDLD 344 (867)
T ss_pred hhhHH
Confidence 55543
No 32
>PRK05399 DNA mismatch repair protein MutS; Provisional
Probab=97.03 E-value=3.2e-05 Score=68.48 Aligned_cols=101 Identities=17% Similarity=0.179 Sum_probs=72.4
Q ss_pred ccHHHHhhHhhhhHHHHHHHccccCCCCCH----HHHHhhHHHHHHHh-hchhhHHHHHHhhh---hhhhhhhhchhHHH
Q psy13255 22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL----DAIKQRQDAISVLL-DQKHITEQMRAKMK---DLRDLERMLPSSTF 93 (156)
Q Consensus 22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~----~~i~~Rhplv~~l~-~~~~v~~~i~~~l~---~~~~~~n~~gk~~~ 93 (156)
...++.|| |+.+++..+...+|++|.+.. ++.++|||+++..+ ...++|||+...-. -+.++|||+||+++
T Consensus 545 ~~~la~lD-~l~s~A~~a~~~~~~~P~~~~~~~l~i~~~rHP~le~~~~~~~~vpnd~~l~~~~~~~iiTGpN~~GKSt~ 623 (854)
T PRK05399 545 AKALAELD-VLASLAEVAEENNYVRPEFTDDPGIDIEEGRHPVVEQVLGGEPFVPNDCDLDEERRLLLITGPNMAGKSTY 623 (854)
T ss_pred HHHHHHHH-HHHHHHHHHHHCCccccEEeCCCCEEEEeccCcEEecccCCCceEecceeeCCCCcEEEEECCCCCCcHHH
Confidence 36899999 999999999999999999863 35689999998653 35689999974311 13467999999999
Q ss_pred HHhhCCCCCCCcccccc-cceeeccCCcccccc
Q psy13255 94 LSFQGCRVPADSLTLTP-VDRIFTRMGAKDNLS 125 (156)
Q Consensus 94 laq~g~~vpa~~~~l~~-~d~i~~~~~~~d~l~ 125 (156)
|.|+|..|--. +++. +..-.+.++.-|.+.
T Consensus 624 lr~v~l~~ilA--q~G~~VPa~~a~i~~~d~I~ 654 (854)
T PRK05399 624 MRQVALIVLLA--QIGSFVPAESARIGIVDRIF 654 (854)
T ss_pred HHHHHHHHHHH--hcCCceeccceEecccCeee
Confidence 99998775322 2222 222235555556553
No 33
>smart00533 MUTSd DNA-binding domain of DNA mismatch repair MUTS family.
Probab=96.65 E-value=0.00038 Score=54.20 Aligned_cols=40 Identities=15% Similarity=0.215 Sum_probs=35.3
Q ss_pred ccHHHHhhHhhhhHHHHHHHccccCCCCCH----HHHHhhHHHHH
Q psy13255 22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL----DAIKQRQDAIS 62 (156)
Q Consensus 22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~----~~i~~Rhplv~ 62 (156)
...++.|| |+.++|..+...+|++|.++. .+.++|||+++
T Consensus 263 ~~~i~~lD-~l~s~a~~a~~~~~~~P~i~~~~~l~i~~~rHPlle 306 (308)
T smart00533 263 AEALAELD-VLLSLATLAAEGNYVRPEFVDSGELEIKNGRHPVLE 306 (308)
T ss_pred HHHHHHHH-HHHHHHHHHHHCCCcCCeeCCCCCEEEeeCCCCccc
Confidence 37899999 999999999999999999863 36789999986
No 34
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=87.48 E-value=0.99 Score=40.19 Aligned_cols=41 Identities=17% Similarity=0.331 Sum_probs=33.8
Q ss_pred cHHHHh-hHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHh
Q psy13255 23 TLIEQL-DHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLL 65 (156)
Q Consensus 23 sl~~~L-D~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~ 65 (156)
.+...| |.|.|++|++++.. ..|..+.+.++.|+..++++.
T Consensus 13 ~i~~~l~~~~~t~~Gk~~l~~--l~P~~~~~~i~~~l~~~~e~~ 54 (782)
T PRK00409 13 KIKEQLKTFAASELGKEKVLQ--LDPETDFEEVEELLEETDEAA 54 (782)
T ss_pred HHHHHHHhHcCCHHHHHHHHc--CCCCCCHHHHHHHHHHHHHHH
Confidence 344444 56999999999998 589999999999999988764
No 35
>PF13173 AAA_14: AAA domain
Probab=87.05 E-value=0.36 Score=32.69 Aligned_cols=19 Identities=16% Similarity=0.032 Sum_probs=14.8
Q ss_pred hhhhhchhHHHHHhhCCCC
Q psy13255 83 DLERMLPSSTFLSFQGCRV 101 (156)
Q Consensus 83 ~~~n~~gk~~~laq~g~~v 101 (156)
.+++.+||++++.|+....
T Consensus 8 ~G~R~vGKTtll~~~~~~~ 26 (128)
T PF13173_consen 8 TGPRGVGKTTLLKQLAKDL 26 (128)
T ss_pred ECCCCCCHHHHHHHHHHHh
Confidence 4589999999998876443
No 36
>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=84.01 E-value=4 Score=29.52 Aligned_cols=67 Identities=7% Similarity=-0.143 Sum_probs=38.1
Q ss_pred hhhhchhHHHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 84 LERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|-+||++++.-+....+..+-.+.+-..-...+ .+.. .+|.=......+++.+ +.+..++++||-
T Consensus 32 G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~--~q~~--~LSgGq~qrv~laral--~~~p~lllLDEP 98 (177)
T cd03222 32 GPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYK--PQYI--DLSGGELQRVAIAAAL--LRNATFYLFDEP 98 (177)
T ss_pred CCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEE--cccC--CCCHHHHHHHHHHHHH--hcCCCEEEEECC
Confidence 48999999988766555555554444322111111 1111 1666555555554444 356699999993
No 37
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=83.16 E-value=1.3 Score=36.33 Aligned_cols=22 Identities=14% Similarity=-0.005 Sum_probs=15.7
Q ss_pred hhhhhchhHHHHHhhCCCCCCC
Q psy13255 83 DLERMLPSSTFLSFQGCRVPAD 104 (156)
Q Consensus 83 ~~~n~~gk~~~laq~g~~vpa~ 104 (156)
.+||.+||++++.+.....+..
T Consensus 43 ~GpR~~GKTtll~~l~~~~~~~ 64 (398)
T COG1373 43 LGPRQVGKTTLLKLLIKGLLEE 64 (398)
T ss_pred ECCccccHHHHHHHHHhhCCcc
Confidence 3599999999986655554433
No 38
>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
Probab=80.37 E-value=2.8 Score=29.55 Aligned_cols=71 Identities=17% Similarity=0.004 Sum_probs=35.9
Q ss_pred hhhhchhHHHHHhhCCCCCCCcccccccceeeccCCccccccC------CcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 84 LERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSG------AQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~------~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|-+||++++.-+....|..+-.+-+-+.-.......+.... .+|.=. .+++.-...-+.+..++|+||-
T Consensus 33 G~nGsGKSTLl~~i~G~~~~~~G~v~~~g~~~~~~~~~~~~~~~i~~~~qLS~G~--~qrl~laral~~~p~illlDEP 109 (163)
T cd03216 33 GENGAGKSTLMKILSGLYKPDSGEILVDGKEVSFASPRDARRAGIAMVYQLSVGE--RQMVEIARALARNARLLILDEP 109 (163)
T ss_pred CCCCCCHHHHHHHHhCCCCCCCeEEEECCEECCcCCHHHHHhcCeEEEEecCHHH--HHHHHHHHHHhcCCCEEEEECC
Confidence 4899999999887765665555443322211111100000000 144333 3333333333567799999993
No 39
>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.
Probab=76.31 E-value=3.2 Score=29.68 Aligned_cols=22 Identities=18% Similarity=-0.047 Sum_probs=15.2
Q ss_pred hhhhchhHHHHHhhCCCCCCCc
Q psy13255 84 LERMLPSSTFLSFQGCRVPADS 105 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vpa~~ 105 (156)
++|.+||++++.-+....|..+
T Consensus 32 G~nGsGKStLl~~i~G~~~~~~ 53 (180)
T cd03214 32 GPNGAGKSTLLKTLAGLLKPSS 53 (180)
T ss_pred CCCCCCHHHHHHHHhCCCCCCC
Confidence 4899999988766644444443
No 40
>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=75.06 E-value=11 Score=26.19 Aligned_cols=71 Identities=13% Similarity=-0.051 Sum_probs=36.4
Q ss_pred hhhhchhHHHHHhhCCCCCCCcccccccceeeccCC-----ccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 84 LERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMG-----AKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~-----~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|..||++++..+....+...-++.+-..=..... ..-.....+|. .|.+++.-...-+.+..++++||.
T Consensus 32 G~nGsGKStll~~l~g~~~~~~G~i~~~~~~~~~~~~~~~~~~i~~~~qlS~--G~~~r~~l~~~l~~~~~i~ilDEp 107 (157)
T cd00267 32 GPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSG--GQRQRVALARALLLNPDLLLLDEP 107 (157)
T ss_pred CCCCCCHHHHHHHHhCCCCCCccEEEECCEEcccCCHHHHHhceEEEeeCCH--HHHHHHHHHHHHhcCCCEEEEeCC
Confidence 589999999887765555555444432211000000 00000001443 344555444444566799999994
No 41
>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.
Probab=74.48 E-value=10 Score=26.14 Aligned_cols=65 Identities=17% Similarity=0.050 Sum_probs=35.7
Q ss_pred hhhhchhHHHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 84 LERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
++|-.||++++.-+....|..+-++.+-.+. .++. ...+|.-......+.+.+ +.+..++|+||-
T Consensus 33 G~nGsGKStLl~~l~G~~~~~~G~i~~~~~~--~i~~----~~~lS~G~~~rv~laral--~~~p~illlDEP 97 (144)
T cd03221 33 GRNGAGKSTLLKLIAGELEPDEGIVTWGSTV--KIGY----FEQLSGGEKMRLALAKLL--LENPNLLLLDEP 97 (144)
T ss_pred CCCCCCHHHHHHHHcCCCCCCceEEEECCeE--EEEE----EccCCHHHHHHHHHHHHH--hcCCCEEEEeCC
Confidence 5899999998876644555454444321110 0100 001665554444444443 456799999993
No 42
>smart00382 AAA ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Probab=69.53 E-value=15 Score=23.69 Aligned_cols=20 Identities=5% Similarity=-0.213 Sum_probs=13.4
Q ss_pred hhhhchhHHHHHhhCCCCCC
Q psy13255 84 LERMLPSSTFLSFQGCRVPA 103 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vpa 103 (156)
++...||++++..+......
T Consensus 9 G~~G~GKTtl~~~l~~~~~~ 28 (148)
T smart00382 9 GPPGSGKTTLARALARELGP 28 (148)
T ss_pred CCCCCcHHHHHHHHHhccCC
Confidence 47788999877665544443
No 43
>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.
Probab=65.11 E-value=20 Score=25.76 Aligned_cols=29 Identities=17% Similarity=0.110 Sum_probs=20.4
Q ss_pred cCcHHHHHHHHHHHHHh--cCCCceEEeccC
Q psy13255 128 QSTYLAELTESETIMRH--ASKYSLALVDEL 156 (156)
Q Consensus 128 ~S~F~~e~~~~~~il~~--~~~~slvliDE~ 156 (156)
+|.=......+.+.+-. ..+..++++||.
T Consensus 95 LS~Ge~~r~~Laral~~~~~~~p~llilDEp 125 (178)
T cd03239 95 LSGGEKSLSALALIFALQEIKPSPFYVLDEI 125 (178)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCCCEEEEECC
Confidence 67766666677776643 356699999994
No 44
>KOG0734|consensus
Probab=61.61 E-value=11 Score=32.43 Aligned_cols=22 Identities=14% Similarity=0.304 Sum_probs=18.0
Q ss_pred HHHHHHHHHhcCCC--ceEEeccC
Q psy13255 135 LTESETIMRHASKY--SLALVDEL 156 (156)
Q Consensus 135 ~~~~~~il~~~~~~--slvliDE~ 156 (156)
-+++...+++|..+ +.++||||
T Consensus 382 ArRVRdLF~aAk~~APcIIFIDEi 405 (752)
T KOG0734|consen 382 ARRVRDLFAAAKARAPCIIFIDEI 405 (752)
T ss_pred HHHHHHHHHHHHhcCCeEEEEech
Confidence 46888888887664 99999997
No 45
>PRK08939 primosomal protein DnaI; Reviewed
Probab=58.65 E-value=7.8 Score=30.59 Aligned_cols=18 Identities=6% Similarity=0.287 Sum_probs=13.9
Q ss_pred HHHHHhcCCCceEEeccC
Q psy13255 139 ETIMRHASKYSLALVDEL 156 (156)
Q Consensus 139 ~~il~~~~~~slvliDE~ 156 (156)
...++...+-.|++||||
T Consensus 209 ~~~l~~l~~~dlLiIDDi 226 (306)
T PRK08939 209 KEKIDAVKEAPVLMLDDI 226 (306)
T ss_pred HHHHHHhcCCCEEEEecC
Confidence 455666777899999986
No 46
>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.
Probab=58.46 E-value=30 Score=24.45 Aligned_cols=31 Identities=16% Similarity=-0.052 Sum_probs=17.5
Q ss_pred ccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 124 LSGAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 124 l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
+...+|.-. .+++.-...-+.+..++|+||.
T Consensus 95 i~~~LS~G~--~qrv~laral~~~p~~lllDEP 125 (178)
T cd03247 95 LGRRFSGGE--RQRLALARILLQDAPIVLLDEP 125 (178)
T ss_pred hcccCCHHH--HHHHHHHHHHhcCCCEEEEECC
Confidence 334455433 3343333333567799999993
No 47
>KOG0217|consensus
Probab=58.12 E-value=1.4 Score=39.91 Aligned_cols=80 Identities=16% Similarity=0.130 Sum_probs=59.3
Q ss_pred cHHHHhhHhhhhHHHHHHH--ccccCCCCCHH--------HHHhhHHHHHHHhh-chhhHHHHHHhhh-----hhhhhhh
Q psy13255 23 TLIEQLDHCVTSFGKRMLR--AQLVKPLTNLD--------AIKQRQDAISVLLD-QKHITEQMRAKMK-----DLRDLER 86 (156)
Q Consensus 23 sl~~~LD~~~t~~g~~~l~--~~~~~P~~~~~--------~i~~Rhplv~~l~~-~~~v~~~i~~~l~-----~~~~~~n 86 (156)
..++.|| |+++++..+.. ..+|+|.+... ....|||++..-.. ..++||++..... ++-++||
T Consensus 830 ~~~a~iD-~l~sla~~s~~~~~~~Crp~i~~~~dt~~~l~~~~~~Hpcfsl~s~~~~fipN~v~~g~~~e~~~~llTGpN 908 (1125)
T KOG0217|consen 830 KALASID-CLLSLAETSKGLGGPMCRPEIVESTDTPGFLIVKGLRHPCFSLPSTGTSFIPNDVELGGAEENREGLLTGPN 908 (1125)
T ss_pred HHHHHHH-HHHHHHHhhccCCCCcccceeecccCCCceeEEecccCceeecCcCCCccccchhhccccccceeeeeccCC
Confidence 5788899 99998887755 55899977532 24689999864333 3689999864321 3457899
Q ss_pred hchhHHHHHhhCCCCCC
Q psy13255 87 MLPSSTFLSFQGCRVPA 103 (156)
Q Consensus 87 ~~gk~~~laq~g~~vpa 103 (156)
|+||+++|.|.+..|-.
T Consensus 909 mgGKSTllRq~c~~vil 925 (1125)
T KOG0217|consen 909 MGGKSTLLRQACIAVIL 925 (1125)
T ss_pred cCCchHHHHHHHHHHHH
Confidence 99999999999888743
No 48
>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=54.03 E-value=64 Score=22.78 Aligned_cols=23 Identities=17% Similarity=0.068 Sum_probs=14.8
Q ss_pred HHHHHHHHHHhcCCCceEEeccC
Q psy13255 134 ELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 134 e~~~~~~il~~~~~~slvliDE~ 156 (156)
|.+++.-...-+.+..++|+||-
T Consensus 105 ~~qr~~la~al~~~p~llilDEP 127 (178)
T cd03229 105 QQQRVALARALAMDPDVLLLDEP 127 (178)
T ss_pred HHHHHHHHHHHHCCCCEEEEeCC
Confidence 44444444444577799999993
No 49
>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport. Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....
Probab=53.41 E-value=20 Score=23.38 Aligned_cols=23 Identities=17% Similarity=0.343 Sum_probs=14.1
Q ss_pred HHHHHHHHHHhc---CCCceEEeccC
Q psy13255 134 ELTESETIMRHA---SKYSLALVDEL 156 (156)
Q Consensus 134 e~~~~~~il~~~---~~~slvliDE~ 156 (156)
....+..+++++ ...++++|||+
T Consensus 42 ~~~~i~~~~~~~~~~~~~~vl~iDe~ 67 (132)
T PF00004_consen 42 SEQKIRDFFKKAKKSAKPCVLFIDEI 67 (132)
T ss_dssp HHHHHHHHHHHHHHTSTSEEEEEETG
T ss_pred cccccccccccccccccceeeeeccc
Confidence 334444455553 33699999996
No 50
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=52.44 E-value=15 Score=24.00 Aligned_cols=20 Identities=5% Similarity=-0.287 Sum_probs=14.0
Q ss_pred hhhhhchhHHHHHhhCCCCC
Q psy13255 83 DLERMLPSSTFLSFQGCRVP 102 (156)
Q Consensus 83 ~~~n~~gk~~~laq~g~~vp 102 (156)
.++...||++++..+....+
T Consensus 25 ~G~~G~GKT~l~~~i~~~~~ 44 (151)
T cd00009 25 YGPPGTGKTTLARAIANELF 44 (151)
T ss_pred ECCCCCCHHHHHHHHHHHhh
Confidence 45888999987766655443
No 51
>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=52.35 E-value=32 Score=24.16 Aligned_cols=22 Identities=18% Similarity=-0.135 Sum_probs=14.9
Q ss_pred hhhhchhHHHHHhhCCCCCCCc
Q psy13255 84 LERMLPSSTFLSFQGCRVPADS 105 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vpa~~ 105 (156)
++|.+||++++.-+....|..+
T Consensus 35 G~nGsGKstLl~~i~G~~~~~~ 56 (171)
T cd03228 35 GPSGSGKSTLLKLLLRLYDPTS 56 (171)
T ss_pred CCCCCCHHHHHHHHHcCCCCCC
Confidence 4899999988866644444333
No 52
>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt
Probab=51.24 E-value=59 Score=22.76 Aligned_cols=71 Identities=11% Similarity=0.004 Sum_probs=35.5
Q ss_pred hhhhchhHHHHHhhCCCCCCCccccccc--cee--------eccCCccccc----cCCcCcHHHHHHHHHHHHHhcCCCc
Q psy13255 84 LERMLPSSTFLSFQGCRVPADSLTLTPV--DRI--------FTRMGAKDNL----SGAQSTYLAELTESETIMRHASKYS 149 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vpa~~~~l~~~--d~i--------~~~~~~~d~l----~~~~S~F~~e~~~~~~il~~~~~~s 149 (156)
++|-+||++++.-+....+..+-++.+- .++ +......|++ ...+|.-...-..+++.+ +.+..
T Consensus 34 G~nGsGKSTLl~~l~G~~~~~~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~~~~~LS~G~~~rv~laral--~~~p~ 111 (166)
T cd03223 34 GPSGTGKSSLFRALAGLWPWGSGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYPWDDVLSGGEQQRLAFARLL--LHKPK 111 (166)
T ss_pred CCCCCCHHHHHHHHhcCCCCCCceEEECCCceEEEECCCCccccccHHHHhhccCCCCCCHHHHHHHHHHHHH--HcCCC
Confidence 5899999988765544444333222110 001 0011222332 233555444444444433 46779
Q ss_pred eEEeccC
Q psy13255 150 LALVDEL 156 (156)
Q Consensus 150 lvliDE~ 156 (156)
++|+||-
T Consensus 112 ~lllDEP 118 (166)
T cd03223 112 FVFLDEA 118 (166)
T ss_pred EEEEECC
Confidence 9999993
No 53
>PF10035 DUF2179: Uncharacterized protein conserved in bacteria (DUF2179); InterPro: IPR019264 This entry, found mostly in hypothetical bacterial proteins, has no known function. ; PDB: 3HLU_B.
Probab=49.03 E-value=26 Score=19.83 Aligned_cols=23 Identities=17% Similarity=0.304 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHhcCCCceEEecc
Q psy13255 133 AELTESETIMRHASKYSLALVDE 155 (156)
Q Consensus 133 ~e~~~~~~il~~~~~~slvliDE 155 (156)
.|+.++++++++.+++.++.+-|
T Consensus 27 ~e~~~l~~~I~~~Dp~AFi~v~~ 49 (55)
T PF10035_consen 27 RELPKLKKIIKEIDPKAFISVSD 49 (55)
T ss_dssp CHHHHHHHHHHCC-TT-EEEE--
T ss_pred HHHHHHHHHHHHhCCCEEEEEEc
Confidence 37889999999999999998765
No 54
>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=48.99 E-value=69 Score=22.50 Aligned_cols=19 Identities=5% Similarity=-0.176 Sum_probs=13.6
Q ss_pred hhhhchhHHHHHhhCCCCC
Q psy13255 84 LERMLPSSTFLSFQGCRVP 102 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vp 102 (156)
++|-+||++++.-+....|
T Consensus 33 G~nGsGKStLl~~l~G~~~ 51 (173)
T cd03230 33 GPNGAGKTTLIKIILGLLK 51 (173)
T ss_pred CCCCCCHHHHHHHHhCCCC
Confidence 4899999988766544443
No 55
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=47.01 E-value=33 Score=30.78 Aligned_cols=39 Identities=21% Similarity=0.245 Sum_probs=33.1
Q ss_pred HHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhh
Q psy13255 26 EQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLD 66 (156)
Q Consensus 26 ~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~ 66 (156)
...+.|.|+.|++.+.. ..|..+.+.++.|+..++++..
T Consensus 17 ~l~~~~~t~~gk~~~~~--l~P~~~~~~i~~~l~~~~e~~~ 55 (771)
T TIGR01069 17 NLLKQTFTPLGKEDAIG--LKPPKSVEESKEIIIKLTALGS 55 (771)
T ss_pred HHHHHcCCHHHHHHHhc--CCCCCCHHHHHHHHHHHHHHHH
Confidence 34567999999999998 7999999999999998887654
No 56
>PRK12377 putative replication protein; Provisional
Probab=46.03 E-value=16 Score=27.90 Aligned_cols=17 Identities=24% Similarity=0.487 Sum_probs=14.0
Q ss_pred HHHHhcCCCceEEeccC
Q psy13255 140 TIMRHASKYSLALVDEL 156 (156)
Q Consensus 140 ~il~~~~~~slvliDE~ 156 (156)
.+++....-.|++||||
T Consensus 156 ~~l~~l~~~dLLiIDDl 172 (248)
T PRK12377 156 KFLQELCKVDLLVLDEI 172 (248)
T ss_pred HHHHHhcCCCEEEEcCC
Confidence 56777788899999996
No 57
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=42.22 E-value=39 Score=25.41 Aligned_cols=17 Identities=12% Similarity=-0.238 Sum_probs=12.3
Q ss_pred hhhhhchhHHHHHhhCC
Q psy13255 83 DLERMLPSSTFLSFQGC 99 (156)
Q Consensus 83 ~~~n~~gk~~~laq~g~ 99 (156)
.+++.+||++++..+..
T Consensus 49 ~G~~G~GKTtl~~~l~~ 65 (269)
T TIGR03015 49 TGEVGAGKTTLIRNLLK 65 (269)
T ss_pred EcCCCCCHHHHHHHHHH
Confidence 56899999977655433
No 58
>PRK07952 DNA replication protein DnaC; Validated
Probab=41.51 E-value=5.6 Score=30.35 Aligned_cols=17 Identities=24% Similarity=0.516 Sum_probs=13.0
Q ss_pred HHHHhcCCCceEEeccC
Q psy13255 140 TIMRHASKYSLALVDEL 156 (156)
Q Consensus 140 ~il~~~~~~slvliDE~ 156 (156)
.+++.....++++|||+
T Consensus 155 ~~l~~l~~~dlLvIDDi 171 (244)
T PRK07952 155 QLLNDLSNVDLLVIDEI 171 (244)
T ss_pred HHHHHhccCCEEEEeCC
Confidence 45666667789999996
No 59
>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.
Probab=40.60 E-value=31 Score=26.30 Aligned_cols=21 Identities=14% Similarity=0.355 Sum_probs=14.2
Q ss_pred HHHHHHHHhcCCCceEEeccC
Q psy13255 136 TESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 136 ~~~~~il~~~~~~slvliDE~ 156 (156)
.+++.++.+..++.+++|||+
T Consensus 90 ~dl~~il~~l~~~~ILFIDEI 110 (233)
T PF05496_consen 90 GDLAAILTNLKEGDILFIDEI 110 (233)
T ss_dssp HHHHHHHHT--TT-EEEECTC
T ss_pred HHHHHHHHhcCCCcEEEEech
Confidence 455667777788999999997
No 60
>PRK06526 transposase; Provisional
Probab=37.96 E-value=21 Score=27.34 Aligned_cols=15 Identities=33% Similarity=0.680 Sum_probs=10.8
Q ss_pred HHhcCCCceEEeccC
Q psy13255 142 MRHASKYSLALVDEL 156 (156)
Q Consensus 142 l~~~~~~slvliDE~ 156 (156)
++...+..++||||+
T Consensus 154 l~~l~~~dlLIIDD~ 168 (254)
T PRK06526 154 LVKLGRYPLLIVDEV 168 (254)
T ss_pred HHHhccCCEEEEccc
Confidence 444455689999996
No 61
>TIGR01519 plasmod_dom_1 Plasmodium falciparum uncharacterized domain. This model represents an uncharacterized domain present in roughly eight hypothetical proteins of the malaria parasite Plasmodium falciparum.
Probab=36.95 E-value=8 Score=23.53 Aligned_cols=39 Identities=15% Similarity=0.225 Sum_probs=31.0
Q ss_pred cccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhc
Q psy13255 107 TLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHA 145 (156)
Q Consensus 107 ~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~ 145 (156)
.+..+|+||..--...++-.+.|.|..|+.+.+-++..|
T Consensus 9 vm~~fDnifidklid~~v~nk~S~~~~~~~~n~v~l~~A 47 (70)
T TIGR01519 9 LMNIFDNIFIDKLIDNNVHNKGSIISEDVVPNSLLLSKA 47 (70)
T ss_pred HHHHHHHHHHHHHHccccccCCCcccHHHHHHHHHHHhc
Confidence 356678888776667788888899999999998888654
No 62
>PF15117 UPF0697: Uncharacterised protein family UPF0697
Probab=34.03 E-value=47 Score=21.22 Aligned_cols=47 Identities=13% Similarity=0.128 Sum_probs=34.8
Q ss_pred hHHHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHH
Q psy13255 90 SSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESE 139 (156)
Q Consensus 90 k~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~ 139 (156)
.++++...|.++.|++..-.++. ||+--....... ...|+.+|.++.
T Consensus 22 livilvS~~l~~YarrNKrkImR-ifs~ppt~~~~~--epnfyd~~~kiR 68 (99)
T PF15117_consen 22 LIVILVSFGLFMYARRNKRKIMR-IFSVPPTAETLT--EPNFYDSMSKIR 68 (99)
T ss_pred eehhHHhhHHHHhhhhcCceEEE-EEecCCCCCCCC--CCcHHHHHHHHH
Confidence 45788899999999887666654 888776666654 567888777654
No 63
>TIGR02688 conserved hypothetical protein TIGR02688. Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.
Probab=32.92 E-value=10 Score=31.66 Aligned_cols=17 Identities=12% Similarity=0.319 Sum_probs=13.5
Q ss_pred HHHHhcCCCceEEeccC
Q psy13255 140 TIMRHASKYSLALVDEL 156 (156)
Q Consensus 140 ~il~~~~~~slvliDE~ 156 (156)
+.+.......+|+|||+
T Consensus 253 ~~lg~v~~~DlLI~DEv 269 (449)
T TIGR02688 253 RQIGLVGRWDVVAFDEV 269 (449)
T ss_pred HHHhhhccCCEEEEEcC
Confidence 55666777899999996
No 64
>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.
Probab=31.62 E-value=70 Score=22.76 Aligned_cols=12 Identities=33% Similarity=0.855 Sum_probs=9.9
Q ss_pred cCCCceEEeccC
Q psy13255 145 ASKYSLALVDEL 156 (156)
Q Consensus 145 ~~~~slvliDE~ 156 (156)
.....|+|+||+
T Consensus 93 ~~~~dLlVLDEi 104 (159)
T cd00561 93 SGEYDLVILDEI 104 (159)
T ss_pred cCCCCEEEEech
Confidence 356799999996
No 65
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=31.52 E-value=48 Score=25.12 Aligned_cols=52 Identities=27% Similarity=0.186 Sum_probs=38.8
Q ss_pred hhhhchhHHHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCC
Q psy13255 84 LERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASK 147 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~ 147 (156)
+||..|||++|..+.-.++.++..+.+ |+ .++ .++=..|+.+...|+++.+.
T Consensus 34 GPNGAGKSTLLS~~sRL~~~d~G~i~i-~g--------~~~---~~~~s~~LAk~lSILkQ~N~ 85 (252)
T COG4604 34 GPNGAGKSTLLSMMSRLLKKDSGEITI-DG--------LEL---TSTPSKELAKKLSILKQENH 85 (252)
T ss_pred CCCCccHHHHHHHHHHhccccCceEEE-ee--------eec---ccCChHHHHHHHHHHHhhch
Confidence 499999999999999999888776644 32 233 33446788888899988643
No 66
>TIGR00602 rad24 checkpoint protein rad24. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.40 E-value=30 Score=30.37 Aligned_cols=10 Identities=30% Similarity=0.577 Sum_probs=8.4
Q ss_pred CCceEEeccC
Q psy13255 147 KYSLALVDEL 156 (156)
Q Consensus 147 ~~slvliDE~ 156 (156)
.+.++|||||
T Consensus 195 ~~~IILIDEi 204 (637)
T TIGR00602 195 DKKIILVEDL 204 (637)
T ss_pred ceeEEEeecc
Confidence 4579999997
No 67
>PRK08181 transposase; Validated
Probab=29.86 E-value=26 Score=27.14 Aligned_cols=17 Identities=24% Similarity=0.591 Sum_probs=12.3
Q ss_pred HHHHhcCCCceEEeccC
Q psy13255 140 TIMRHASKYSLALVDEL 156 (156)
Q Consensus 140 ~il~~~~~~slvliDE~ 156 (156)
..++......|+||||+
T Consensus 160 ~~l~~l~~~dLLIIDDl 176 (269)
T PRK08181 160 SAIAKLDKFDLLILDDL 176 (269)
T ss_pred HHHHHHhcCCEEEEecc
Confidence 34555566789999996
No 68
>COG0079 HisC Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]
Probab=29.21 E-value=54 Score=26.42 Aligned_cols=21 Identities=19% Similarity=0.311 Sum_probs=17.1
Q ss_pred HHHHHHHHHhcCCCceEEecc
Q psy13255 135 LTESETIMRHASKYSLALVDE 155 (156)
Q Consensus 135 ~~~~~~il~~~~~~slvliDE 155 (156)
-.++..+++.+..+.+|++||
T Consensus 164 ~~~l~~l~~~~~~~~~vVvDE 184 (356)
T COG0079 164 REELRALLEALPEGGLVVIDE 184 (356)
T ss_pred HHHHHHHHHhCCCCcEEEEeC
Confidence 447777788877799999999
No 69
>PHA02972 hypothetical protein; Provisional
Probab=29.08 E-value=54 Score=21.08 Aligned_cols=21 Identities=24% Similarity=0.425 Sum_probs=15.3
Q ss_pred HHHHHHHHHhcCCCceEEecc
Q psy13255 135 LTESETIMRHASKYSLALVDE 155 (156)
Q Consensus 135 ~~~~~~il~~~~~~slvliDE 155 (156)
+++++++-++.+.+|++++|-
T Consensus 88 IRev~einkkIkR~sliiLD~ 108 (109)
T PHA02972 88 IREVREINKKIKRRSLIILDK 108 (109)
T ss_pred HHHHHHHhhhhheeEEEEEeC
Confidence 445556666778899999983
No 70
>TIGR02858 spore_III_AA stage III sporulation protein AA. Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.
Probab=28.86 E-value=60 Score=25.15 Aligned_cols=19 Identities=11% Similarity=-0.097 Sum_probs=13.2
Q ss_pred hhhhchhHHHHHhhCCCCC
Q psy13255 84 LERMLPSSTFLSFQGCRVP 102 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~vp 102 (156)
+++-+||++++..+-..++
T Consensus 118 g~~g~GKttl~~~l~~~~~ 136 (270)
T TIGR02858 118 SPPQCGKTTLLRDLARILS 136 (270)
T ss_pred cCCCCCHHHHHHHHhCccC
Confidence 4899999988765544443
No 71
>PF00005 ABC_tran: ABC transporter This structure is on hold until Dec 1999; InterPro: IPR003439 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energise diverse biological systems. ABC transporters minimally consist of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain []. The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyse ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarise the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site [, , ]. The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis [, , , , , ]. The ATP-Binding Cassette (ABC) superfamily forms one of the largest of all protein families with a diversity of physiological functions []. Several studies have shown that there is a correlation between the functional characterisation and the phylogenetic classification of the ABC cassette [, ]. More than 50 subfamilies have been described based on a phylogenetic and functional classification [, , ]; (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). On the basis of sequence similarities a family of related ATP-binding proteins has been characterised [, , , , ]. The proteins belonging to this family also contain one or two copies of the 'A' consensus sequence [] or the 'P-loop' [] (see IPR001687 from INTERPRO).; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NHB_A 3NH9_A 3NHA_A 3NH6_A 1VCI_A 1V43_A 2YZ2_B 2PMK_A 2FFA_A 1XEF_D ....
Probab=27.84 E-value=73 Score=21.05 Aligned_cols=29 Identities=17% Similarity=0.037 Sum_probs=18.5
Q ss_pred CCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 126 GAQSTYLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 126 ~~~S~F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
..+|.-...-..+++.+ +.+..++|+||-
T Consensus 107 ~~LS~Ge~~rl~la~al--~~~~~llllDEP 135 (137)
T PF00005_consen 107 SSLSGGEKQRLALARAL--LKNPKLLLLDEP 135 (137)
T ss_dssp GGSCHHHHHHHHHHHHH--HTTSSEEEEEST
T ss_pred chhhHHHHHHHHHHHHH--HcCCCEEEEeCC
Confidence 45666554444444444 467799999993
No 72
>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
Probab=27.65 E-value=32 Score=29.42 Aligned_cols=33 Identities=15% Similarity=0.074 Sum_probs=21.0
Q ss_pred hhhhchhHHHHHhh--------CCCCCCCcccccccceeec
Q psy13255 84 LERMLPSSTFLSFQ--------GCRVPADSLTLTPVDRIFT 116 (156)
Q Consensus 84 ~~n~~gk~~~laq~--------g~~vpa~~~~l~~~d~i~~ 116 (156)
++|..||+++|.-+ |.........+++||+=..
T Consensus 355 G~NG~GKSTLlk~l~g~~~~~~G~v~~g~~v~igyf~Q~~~ 395 (530)
T COG0488 355 GPNGAGKSTLLKLLAGELGPLSGTVKVGETVKIGYFDQHRD 395 (530)
T ss_pred CCCCCCHHHHHHHHhhhcccCCceEEeCCceEEEEEEehhh
Confidence 49999999887654 3333333456777776543
No 73
>TIGR00708 cobA cob(I)alamin adenosyltransferase. Alternate name: corrinoid adenosyltransferase.
Probab=26.85 E-value=66 Score=23.26 Aligned_cols=11 Identities=45% Similarity=0.736 Sum_probs=9.3
Q ss_pred CCCceEEeccC
Q psy13255 146 SKYSLALVDEL 156 (156)
Q Consensus 146 ~~~slvliDE~ 156 (156)
.+..|||+||+
T Consensus 96 ~~~DlvVLDEi 106 (173)
T TIGR00708 96 PELDLVLLDEL 106 (173)
T ss_pred CCCCEEEehhh
Confidence 55699999996
No 74
>PRK08084 DNA replication initiation factor; Provisional
Probab=26.34 E-value=48 Score=24.85 Aligned_cols=17 Identities=12% Similarity=-0.070 Sum_probs=11.9
Q ss_pred hhhhchhHHHHHhhCCC
Q psy13255 84 LERMLPSSTFLSFQGCR 100 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~ 100 (156)
+|..+||+.++..++..
T Consensus 52 Gp~G~GKThLl~a~~~~ 68 (235)
T PRK08084 52 SREGAGRSHLLHAACAE 68 (235)
T ss_pred CCCCCCHHHHHHHHHHH
Confidence 47889999776555543
No 75
>PRK09183 transposase/IS protein; Provisional
Probab=25.54 E-value=55 Score=25.03 Aligned_cols=17 Identities=6% Similarity=-0.105 Sum_probs=11.9
Q ss_pred hhhhchhHHHHHhhCCC
Q psy13255 84 LERMLPSSTFLSFQGCR 100 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~ 100 (156)
++...||+.+...+|..
T Consensus 109 Gp~GtGKThLa~al~~~ 125 (259)
T PRK09183 109 GPSGVGKTHLAIALGYE 125 (259)
T ss_pred eCCCCCHHHHHHHHHHH
Confidence 48889999776655543
No 76
>PRK01688 histidinol-phosphate aminotransferase; Provisional
Probab=24.34 E-value=82 Score=24.91 Aligned_cols=23 Identities=13% Similarity=0.239 Sum_probs=17.0
Q ss_pred HHHHHHHHHHhcCCCceEEeccC
Q psy13255 134 ELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 134 e~~~~~~il~~~~~~slvliDE~ 156 (156)
...++..+++.+.++.++|+||.
T Consensus 163 ~~~~l~~l~~~~~~~~~vivDEa 185 (351)
T PRK01688 163 NPQDLRTLLELTRGKAIVVADEA 185 (351)
T ss_pred CHHHHHHHHHhCCCCcEEEEECc
Confidence 34466777777766789999994
No 77
>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP.; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.
Probab=24.32 E-value=64 Score=23.15 Aligned_cols=26 Identities=15% Similarity=0.281 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255 131 YLAELTESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 131 F~~e~~~~~~il~~~~~~slvliDE~ 156 (156)
....+.++...+.....+.+++|||+
T Consensus 102 ~~~~l~~~~~~l~~~~~~~iiviDe~ 127 (234)
T PF01637_consen 102 SFSALERLLEKLKKKGKKVIIVIDEF 127 (234)
T ss_dssp -G--HHHHHHHHHHCHCCEEEEEETG
T ss_pred HHHHHHHHHHHHHhcCCcEEEEEecH
Confidence 34556666677777666799999996
No 78
>PRK10865 protein disaggregation chaperone; Provisional
Probab=24.30 E-value=1e+02 Score=28.12 Aligned_cols=19 Identities=16% Similarity=0.354 Sum_probs=12.9
Q ss_pred HHHHHHh---cCCCceEEeccC
Q psy13255 138 SETIMRH---ASKYSLALVDEL 156 (156)
Q Consensus 138 ~~~il~~---~~~~slvliDE~ 156 (156)
++.+++. ...+.+++|||+
T Consensus 259 lk~~~~~~~~~~~~~ILfIDEi 280 (857)
T PRK10865 259 LKGVLNDLAKQEGNVILFIDEL 280 (857)
T ss_pred HHHHHHHHHHcCCCeEEEEecH
Confidence 4445543 345789999996
No 79
>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B.
Probab=24.23 E-value=86 Score=20.37 Aligned_cols=20 Identities=15% Similarity=0.127 Sum_probs=12.2
Q ss_pred HHHHHHHHhcCCCceEEeccC
Q psy13255 136 TESETIMRHASKYSLALVDEL 156 (156)
Q Consensus 136 ~~~~~il~~~~~~slvliDE~ 156 (156)
..+...+++... .+++|||+
T Consensus 77 ~~~~~~l~~~~~-~~lviDe~ 96 (131)
T PF13401_consen 77 SLLIDALDRRRV-VLLVIDEA 96 (131)
T ss_dssp HHHHHHHHHCTE-EEEEEETT
T ss_pred HHHHHHHHhcCC-eEEEEeCh
Confidence 344444444333 79999995
No 80
>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated
Probab=23.12 E-value=1.3e+02 Score=22.20 Aligned_cols=11 Identities=45% Similarity=0.866 Sum_probs=9.3
Q ss_pred CCCceEEeccC
Q psy13255 146 SKYSLALVDEL 156 (156)
Q Consensus 146 ~~~slvliDE~ 156 (156)
.+..|||+||+
T Consensus 114 ~~ydlvVLDEi 124 (191)
T PRK05986 114 ESYDLVVLDEL 124 (191)
T ss_pred CCCCEEEEehh
Confidence 45699999996
No 81
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=22.86 E-value=46 Score=24.26 Aligned_cols=17 Identities=18% Similarity=-0.087 Sum_probs=11.4
Q ss_pred hhhhchhHHHHHhhCCC
Q psy13255 84 LERMLPSSTFLSFQGCR 100 (156)
Q Consensus 84 ~~n~~gk~~~laq~g~~ 100 (156)
++..+||+++..++...
T Consensus 45 G~~G~GKT~la~~~~~~ 61 (226)
T TIGR03420 45 GESGSGKSHLLQAACAA 61 (226)
T ss_pred CCCCCCHHHHHHHHHHH
Confidence 47888998766555443
No 82
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=22.13 E-value=93 Score=28.27 Aligned_cols=20 Identities=15% Similarity=0.358 Sum_probs=13.4
Q ss_pred HHHHHHHhc---CCCceEEeccC
Q psy13255 137 ESETIMRHA---SKYSLALVDEL 156 (156)
Q Consensus 137 ~~~~il~~~---~~~slvliDE~ 156 (156)
+++.+++.+ ..+.+++|||+
T Consensus 253 ~l~~~l~~~~~~~~~~ILfIDEi 275 (852)
T TIGR03346 253 RLKAVLNEVTKSEGQIILFIDEL 275 (852)
T ss_pred HHHHHHHHHHhcCCCeEEEeccH
Confidence 445555543 45789999996
No 83
>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=21.71 E-value=67 Score=23.35 Aligned_cols=18 Identities=22% Similarity=0.409 Sum_probs=12.2
Q ss_pred HHHHHhcCCC-ceEEeccC
Q psy13255 139 ETIMRHASKY-SLALVDEL 156 (156)
Q Consensus 139 ~~il~~~~~~-slvliDE~ 156 (156)
...+++|-.. .+++|||+
T Consensus 91 ~~al~rA~~~aDvIIIDEI 109 (179)
T COG1618 91 IPALRRALEEADVIIIDEI 109 (179)
T ss_pred HHHHHHHhhcCCEEEEecc
Confidence 3445555444 89999996
No 84
>PTZ00293 thymidine kinase; Provisional
Probab=21.41 E-value=33 Score=25.67 Aligned_cols=22 Identities=14% Similarity=0.253 Sum_probs=9.2
Q ss_pred ccccCCcCcHHHHHHHHHHHHH
Q psy13255 122 DNLSGAQSTYLAELTESETIMR 143 (156)
Q Consensus 122 d~l~~~~S~F~~e~~~~~~il~ 143 (156)
|-+.-+.--|+.++.++...+.
T Consensus 79 dvI~IDEaQFf~~i~~~~~~l~ 100 (211)
T PTZ00293 79 DVIAIDEGQFFPDLVEFSEAAA 100 (211)
T ss_pred CEEEEEchHhhHhHHHHHHHHH
Confidence 3333344444444444444443
No 85
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=21.33 E-value=48 Score=29.84 Aligned_cols=10 Identities=50% Similarity=0.693 Sum_probs=8.3
Q ss_pred CCceEEeccC
Q psy13255 147 KYSLALVDEL 156 (156)
Q Consensus 147 ~~slvliDE~ 156 (156)
.+.+++|||+
T Consensus 416 ~~~villDEi 425 (784)
T PRK10787 416 KNPLFLLDEI 425 (784)
T ss_pred CCCEEEEECh
Confidence 4679999996
No 86
>PF00571 CBS: CBS domain CBS domain web page. Mutations in the CBS domain of Swiss:P35520 lead to homocystinuria.; InterPro: IPR000644 CBS (cystathionine-beta-synthase) domains are small intracellular modules, mostly found in two or four copies within a protein, that occur in a variety of proteins in bacteria, archaea, and eukaryotes [, ]. Tandem pairs of CBS domains can act as binding domains for adenosine derivatives and may regulate the activity of attached enzymatic or other domains []. In some cases, CBS domains may act as sensors of cellular energy status by being activated by AMP and inhibited by ATP []. In chloride ion channels, the CBS domains have been implicated in intracellular targeting and trafficking, as well as in protein-protein interactions, but results vary with different channels: in the CLC-5 channel, the CBS domain was shown to be required for trafficking [], while in the CLC-1 channel, the CBS domain was shown to be critical for channel function, but not necessary for trafficking []. Recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites [, ]. Crystallographic studies of CBS domains have shown that pairs of CBS sequences form a globular domain where each CBS unit adopts a beta-alpha-beta-beta-alpha pattern []. Crystal structure of the CBS domains of the AMP-activated protein kinase in complexes with AMP and ATP shows that the phosphate groups of AMP/ATP lie in a surface pocket at the interface of two CBS domains, which is lined with basic residues, many of which are associated with disease-causing mutations []. In humans, mutations in conserved residues within CBS domains cause a variety of human hereditary diseases, including (with the gene mutated in parentheses): homocystinuria (cystathionine beta-synthase); Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase); retinitis pigmentosa (IMP dehydrogenase-1); congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members).; GO: 0005515 protein binding; PDB: 3JTF_A 3TE5_C 3TDH_C 3T4N_C 2QLV_C 3OI8_A 3LV9_A 2QH1_B 1PVM_B 3LQN_A ....
Probab=20.91 E-value=1.3e+02 Score=16.22 Aligned_cols=21 Identities=43% Similarity=0.525 Sum_probs=15.8
Q ss_pred HHHHHHHHHhcCCCceEEecc
Q psy13255 135 LTESETIMRHASKYSLALVDE 155 (156)
Q Consensus 135 ~~~~~~il~~~~~~slvliDE 155 (156)
+.++...+.+.+-+.+.++||
T Consensus 18 l~~~~~~~~~~~~~~~~V~d~ 38 (57)
T PF00571_consen 18 LEEALEIMRKNGISRLPVVDE 38 (57)
T ss_dssp HHHHHHHHHHHTSSEEEEEST
T ss_pred HHHHHHHHHHcCCcEEEEEec
Confidence 556677777777788888886
No 87
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=20.75 E-value=1.7e+02 Score=26.79 Aligned_cols=21 Identities=10% Similarity=0.289 Sum_probs=13.9
Q ss_pred HHHHHHHHhc---CCCceEEeccC
Q psy13255 136 TESETIMRHA---SKYSLALVDEL 156 (156)
Q Consensus 136 ~~~~~il~~~---~~~slvliDE~ 156 (156)
.+++.+++.+ ..+..++|||+
T Consensus 266 ~~lk~ii~e~~~~~~~~ILfIDEi 289 (852)
T TIGR03345 266 NRLKSVIDEVKASPQPIILFIDEA 289 (852)
T ss_pred HHHHHHHHHHHhcCCCeEEEEeCh
Confidence 3455555543 45689999996
No 88
>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated
Probab=20.70 E-value=1.5e+02 Score=21.55 Aligned_cols=11 Identities=55% Similarity=1.002 Sum_probs=9.5
Q ss_pred CCCceEEeccC
Q psy13255 146 SKYSLALVDEL 156 (156)
Q Consensus 146 ~~~slvliDE~ 156 (156)
.+..|+|+||+
T Consensus 114 ~~~dlvVLDEi 124 (178)
T PRK07414 114 GRYSLVVLDEL 124 (178)
T ss_pred CCCCEEEEehh
Confidence 56799999996
Done!