Query 041357
Match_columns 169
No_of_seqs 107 out of 176
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 06:18:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041357.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041357hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3471 RNA polymerase II tran 100.0 2.3E-73 5.1E-78 509.9 14.7 167 3-169 268-463 (465)
2 TIGR00625 tfb2 Transcription f 100.0 1.7E-70 3.6E-75 497.0 18.3 167 3-169 256-448 (448)
3 COG5144 TFB2 RNA polymerase II 100.0 1.2E-63 2.7E-68 439.2 10.9 165 4-168 256-445 (447)
4 PF03849 Tfb2: Transcription f 100.0 4.6E-38 9.9E-43 278.9 8.5 81 3-83 256-366 (366)
5 PF13625 Helicase_C_3: Helicas 99.2 1.3E-10 2.8E-15 88.9 10.4 112 22-135 2-115 (129)
6 TIGR00603 rad25 DNA repair hel 88.0 5.6 0.00012 39.4 10.7 90 17-112 20-109 (732)
7 KOG2036 Predicted P-loop ATPas 63.1 5.9 0.00013 39.9 2.6 58 33-101 529-605 (1011)
8 PF04491 Pox_T4_N: Poxvirus T4 63.0 9.4 0.0002 25.4 2.8 26 10-35 14-45 (46)
9 cd06836 PLPDE_III_ODC_DapDC_li 58.7 1.3E+02 0.0028 26.8 10.2 95 27-146 27-128 (379)
10 PRK06015 keto-hydroxyglutarate 58.2 66 0.0014 27.0 7.8 126 19-166 28-164 (201)
11 PRK13761 hypothetical protein; 57.0 5.5 0.00012 34.8 1.2 23 60-82 12-35 (248)
12 PF06992 Phage_lambda_P: Repli 56.8 35 0.00077 29.6 6.0 88 42-139 40-139 (233)
13 COG4109 Predicted transcriptio 52.7 16 0.00035 34.1 3.5 34 55-101 290-323 (432)
14 TIGR01182 eda Entner-Doudoroff 51.2 96 0.0021 26.0 7.7 125 20-166 33-168 (204)
15 PRK07114 keto-hydroxyglutarate 48.9 1.7E+02 0.0036 24.9 9.1 128 19-166 39-180 (222)
16 PF02244 Propep_M14: Carboxype 48.2 82 0.0018 21.1 6.3 46 122-167 6-55 (74)
17 COG1701 Uncharacterized protei 40.0 15 0.00032 32.1 1.1 22 61-82 15-37 (256)
18 PF01081 Aldolase: KDPG and KH 38.6 35 0.00075 28.5 3.1 126 19-166 32-168 (196)
19 PRK05718 keto-hydroxyglutarate 37.4 45 0.00097 28.0 3.6 125 20-166 40-175 (212)
20 TIGR01615 A_thal_3542 uncharac 37.1 12 0.00025 29.9 0.1 39 19-63 48-87 (131)
21 PRK08508 biotin synthase; Prov 37.0 2.4E+02 0.0051 24.1 8.1 96 41-139 76-180 (279)
22 PF10566 Glyco_hydro_97: Glyco 34.8 40 0.00087 29.6 3.1 25 123-147 71-97 (273)
23 PF02784 Orn_Arg_deC_N: Pyrido 33.9 2.1E+02 0.0045 23.6 7.1 94 30-146 24-117 (251)
24 PRK14529 adenylate kinase; Pro 33.5 79 0.0017 26.7 4.5 81 49-138 22-103 (223)
25 PF13496 DUF4120: Domain of un 32.1 38 0.00083 25.5 2.1 17 123-139 4-20 (95)
26 KOG0287 Postreplication repair 31.7 77 0.0017 29.6 4.4 90 47-136 237-359 (442)
27 PF02787 CPSase_L_D3: Carbamoy 31.7 39 0.00085 26.0 2.2 37 65-108 15-52 (123)
28 PF11849 DUF3369: Domain of un 31.4 57 0.0012 25.9 3.2 35 9-48 122-156 (174)
29 PF00406 ADK: Adenylate kinase 30.1 1.7E+02 0.0038 21.9 5.6 74 50-132 19-94 (151)
30 PF09419 PGP_phosphatase: Mito 29.6 1.5E+02 0.0033 24.1 5.5 114 40-166 5-129 (168)
31 PF13833 EF-hand_8: EF-hand do 28.7 37 0.00079 21.2 1.4 17 59-75 3-20 (54)
32 PF08671 SinI: Anti-repressor 28.6 30 0.00066 20.9 0.9 13 66-78 9-21 (30)
33 cd06568 GH20_SpHex_like A subg 28.3 58 0.0013 28.8 3.0 24 118-141 68-91 (329)
34 PF00571 CBS: CBS domain CBS d 27.9 59 0.0013 20.0 2.2 31 41-71 20-56 (57)
35 PF13707 RloB: RloB-like prote 27.6 1.3E+02 0.0027 23.5 4.5 56 91-146 38-99 (183)
36 cd02742 GH20_hexosaminidase Be 26.1 63 0.0014 28.0 2.8 26 117-142 64-89 (303)
37 cd06569 GH20_Sm-chitobiase-lik 25.5 69 0.0015 29.7 3.1 25 117-141 89-113 (445)
38 cd06564 GH20_DspB_LnbB-like Gl 24.7 74 0.0016 27.8 3.0 25 117-141 74-98 (326)
39 cd06562 GH20_HexA_HexB-like Be 24.3 67 0.0015 28.5 2.7 23 119-141 64-86 (348)
40 cd06570 GH20_chitobiase-like_1 23.3 85 0.0018 27.7 3.1 24 118-141 61-84 (311)
41 cd06563 GH20_chitobiase-like T 23.2 71 0.0015 28.3 2.6 25 117-141 78-102 (357)
42 PF12513 SUV3_C: Mitochondrial 22.6 52 0.0011 21.2 1.2 19 41-59 9-27 (49)
43 TIGR03551 F420_cofH 7,8-dideme 22.5 3.5E+02 0.0075 23.7 6.8 97 41-139 104-222 (343)
44 PF12818 Tegument_dsDNA: dsDNA 22.1 1.1E+02 0.0023 27.0 3.5 66 30-105 140-214 (282)
45 cd07241 Glo_EDI_BRP_like_3 Thi 21.3 2.1E+02 0.0046 19.6 4.3 38 120-157 77-120 (125)
46 cd00452 KDPG_aldolase KDPG and 21.2 1.9E+02 0.0042 23.0 4.6 44 28-73 30-76 (190)
47 PF13344 Hydrolase_6: Haloacid 20.4 1.2E+02 0.0026 22.0 2.9 9 147-155 31-39 (101)
48 cd06565 GH20_GcnA-like Glycosy 20.2 1.1E+02 0.0024 26.6 3.2 24 119-142 54-77 (301)
49 cd03082 TRX_Fd_NuoE_W_FDH_beta 20.0 84 0.0018 21.7 2.0 20 54-73 48-72 (72)
No 1
>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=2.3e-73 Score=509.87 Aligned_cols=167 Identities=41% Similarity=0.722 Sum_probs=161.5
Q ss_pred ccccCccceeece---------------------eCCCceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEEEe
Q 041357 3 IQSRKESWFIPTI---------------------ADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAI 61 (169)
Q Consensus 3 ~~k~k~~~f~pT~---------------------~~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg~i 61 (169)
+||+|+++||||+ .++.|||||||||||||||+||||+|||+|||++.|||||||||+|
T Consensus 268 Qrk~k~~rfyptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~riYAYT~S~lQiAvi~LF~~l~~rf~nlvvG~i 347 (465)
T KOG3471|consen 268 QRKIKILRFYPTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNYRIYAYTNSPLQIAVIALFTELTYRFPNLVVGVI 347 (465)
T ss_pred HhhhhhheecchhhhhccchhhhhhhhhhhcccccccCceEEEEeccEEEEecCCHHHHHHHHHHHHHHhhccccceeee
Confidence 6899999999999 3456999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHcCCCccc------cccChhhhhcC--CCCChhHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHH
Q 041357 62 TKESLYNAFENGITTEQ------QNAHPRVADKI--PSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDY 133 (169)
Q Consensus 62 TR~Sv~~Al~~GITA~Q------~~aHp~m~~~~--p~iP~tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~y 133 (169)
||||||+||++||||+| +||||||+... |+|||||+|||+|||+||||+.+++|+||++|+|..||+.+++|
T Consensus 348 TreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQIrLWElernR~~~~~g~LYs~Fls~~df~~l~ey 427 (465)
T KOG3471|consen 348 TRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQIRLWELERNRLRMTEGYLYSDFLSLSDFQLLLEY 427 (465)
T ss_pred eHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHHHHHHHhhcceecccchhHHhhhhhhhHHHHHHH
Confidence 99999999999999999 99999998876 89999999999999999999999999999999999999999999
Q ss_pred HHHcCeEEeecCCccEEEEecccchHHHHHHhhccC
Q 041357 134 ARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 169 (169)
Q Consensus 134 A~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~~~~ 169 (169)
|+++|+|+|+|+.||+|||+.+||++|++|||+++|
T Consensus 428 a~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k 463 (465)
T KOG3471|consen 428 AREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK 463 (465)
T ss_pred HHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence 999999999999999999999999999999999654
No 2
>TIGR00625 tfb2 Transcription factor tfb2. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.7e-70 Score=496.97 Aligned_cols=167 Identities=38% Similarity=0.711 Sum_probs=161.4
Q ss_pred ccccCccceeece------------e-------CCCceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEEEeCH
Q 041357 3 IQSRKESWFIPTI------------A-------DNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITK 63 (169)
Q Consensus 3 ~~k~k~~~f~pT~------------~-------~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg~iTR 63 (169)
++++++++||||| + .++|||||||||||||||+||||+|||+|||++.||||||+||.|||
T Consensus 256 ~~~~~~~~fYPTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~~il~lF~~~~~r~pnlvvg~iTr 335 (448)
T TIGR00625 256 QRKRKSRRFYPTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQIALIALFSELLARFPNMVVGQITR 335 (448)
T ss_pred EecCCCCcccchHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCceEEEEecH
Confidence 5788999999999 1 35799999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcCCCccc------cccChhhh-hcCCCCChhHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHH
Q 041357 64 ESLYNAFENGITTEQ------QNAHPRVA-DKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARD 136 (169)
Q Consensus 64 ~Sv~~Al~~GITA~Q------~~aHp~m~-~~~p~iP~tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~ 136 (169)
+||++|+++|||||| +||||+|+ +..|+|||||+|||+|||.||||+++++|+||++|.|+.||+++++||++
T Consensus 336 ~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l~~~f~s~~~y~~~~~ya~~ 415 (448)
T TIGR00625 336 ESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVLYNDFLTQVDFELLLAYARE 415 (448)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEeecceeeeecCCHHHHHHHHHHHHH
Confidence 999999999999999 99999998 47899999999999999999999999999999999999999999999999
Q ss_pred cCeEEeecCCccEEEEecccchHHHHHHhhccC
Q 041357 137 QSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 169 (169)
Q Consensus 137 ~g~llw~~~~kr~~~V~~~~h~~vr~f~k~~~~ 169 (169)
+|+|+|+|+.||+|||+.+||++||+|||++|+
T Consensus 416 ~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~ 448 (448)
T TIGR00625 416 LGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH 448 (448)
T ss_pred cCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence 999999999999999999999999999999985
No 3
>COG5144 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]
Probab=100.00 E-value=1.2e-63 Score=439.21 Aligned_cols=165 Identities=35% Similarity=0.621 Sum_probs=159.5
Q ss_pred cccCccceeece-------------------eCCCceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEEEeCHH
Q 041357 4 QSRKESWFIPTI-------------------ADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKE 64 (169)
Q Consensus 4 ~k~k~~~f~pT~-------------------~~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg~iTR~ 64 (169)
++-.+.+||||+ .++.||||||||||+|||||||||+|+++|||++.+||||||+|+||||
T Consensus 256 ~~i~~~~fYpt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplqiavi~LF~nl~arf~Nlv~GiITre 335 (447)
T COG5144 256 LGILRKIFYPTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRE 335 (447)
T ss_pred hccchhhccccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHHHHHHHHhhhhhcccchhhhhhccHH
Confidence 456677899999 4567999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCCCccc------cccChhhhhcCCCCChhHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHHcC
Q 041357 65 SLYNAFENGITTEQ------QNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQS 138 (169)
Q Consensus 65 Sv~~Al~~GITA~Q------~~aHp~m~~~~p~iP~tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~~g 138 (169)
||++||.+||||+| +||||||+++.|.+|||++|||+|||+||||+...||+||+||.+.++|+.+++||.+.|
T Consensus 336 SirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~pG~LysdFlt~s~y~~~~eya~~~g 415 (447)
T COG5144 336 SIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYSDFLTLSDYQKVLEYAIRGG 415 (447)
T ss_pred HHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEeecchHHhhhhchhhHHHHHHHHHhcC
Confidence 99999999999999 999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeecCCccEEEEecccchHHHHHHhhcc
Q 041357 139 GLLWEDSKKMRLVVNAEIHMHMREFLRGQN 168 (169)
Q Consensus 139 ~llw~~~~kr~~~V~~~~h~~vr~f~k~~~ 168 (169)
+|+|+|..||||||+.+||.+|++|.|++-
T Consensus 416 vLvw~d~~Krmffi~~eG~s~v~~f~Kr~l 445 (447)
T COG5144 416 VLVWSDVDKRMFFIKLEGHSLVKEFVKRIL 445 (447)
T ss_pred eEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence 999999999999999999999999999864
No 4
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=100.00 E-value=4.6e-38 Score=278.93 Aligned_cols=81 Identities=49% Similarity=0.889 Sum_probs=77.4
Q ss_pred ccccCccceeece------------------------eCCCceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEE
Q 041357 3 IQSRKESWFIPTI------------------------ADNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIV 58 (169)
Q Consensus 3 ~~k~k~~~f~pT~------------------------~~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvv 58 (169)
++|+++++||||| +.++|||||||||||||||+||||+|||+|||++.||||||+|
T Consensus 256 ~~~~~~~~fypT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~s~l~iaiL~lF~~~~~r~pnlvv 335 (366)
T PF03849_consen 256 QRKRKSRRFYPTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTNSPLQIAILSLFCELKYRFPNLVV 335 (366)
T ss_pred EecCCCCeEechHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecCCHHHHHHHHHHHHHHhcCCCeEE
Confidence 5788999999999 1358999999999999999999999999999999999999999
Q ss_pred EEeCHHHHHHHHHcCCCccc------cccCh
Q 041357 59 GAITKESLYNAFENGITTEQ------QNAHP 83 (169)
Q Consensus 59 g~iTR~Sv~~Al~~GITA~Q------~~aHp 83 (169)
|+||||||++|+++|||||| +||||
T Consensus 336 g~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp 366 (366)
T PF03849_consen 336 GQITRESVRRALKNGITADQIISFLRSHAHP 366 (366)
T ss_pred EEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence 99999999999999999999 99998
No 5
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=99.22 E-value=1.3e-10 Score=88.95 Aligned_cols=112 Identities=19% Similarity=0.265 Sum_probs=91.5
Q ss_pred EEEEeCceEEEEcCCH--hHHHHHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccccccChhhhhcCCCCChhHHHH
Q 041357 22 VVVETNFKMYAYSTSK--LHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQ 99 (169)
Q Consensus 22 IIvETNfRvYAYT~S~--LqiaiL~lF~~l~~r~PNlvvg~iTR~Sv~~Al~~GITA~Q~~aHp~m~~~~p~iP~tV~dQ 99 (169)
+||+.||.|.+.+.+| -+...|..|+++ .+..+|.+..||+.|+.+|++.|+|+++..+-=+-.. ..-||+||..+
T Consensus 2 liVqpd~~I~v~~~~~~~~~~~~L~~fae~-~s~~~~~~yrlT~~Sl~~A~~~G~~~e~i~~~L~~~S-~~~lP~~v~~~ 79 (129)
T PF13625_consen 2 LIVQPDFEILVEPGHPSPADAWFLARFAEL-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEFLERYS-KNPLPQNVEQS 79 (129)
T ss_pred EEECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHHHHHHc-CCCCCHHHHHH
Confidence 6899999999977766 455899999999 6779999999999999999999999999222111111 23589999999
Q ss_pred HHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHH
Q 041357 100 IRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYAR 135 (169)
Q Consensus 100 IrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~ 135 (169)
|+-|...-.++++.++.++-...+.+..+.+.+..+
T Consensus 80 i~~w~~~~g~v~l~~~~~~l~~~d~~~l~~l~~~~~ 115 (129)
T PF13625_consen 80 IEDWARRYGRVRLYKGAYLLECDDPELLDELLADPE 115 (129)
T ss_pred HHHHHHhcCCEEEecCeEEEEECCHHHHHHHHhChh
Confidence 999999999999999777778888887777665433
No 6
>TIGR00603 rad25 DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=88.04 E-value=5.6 Score=39.42 Aligned_cols=90 Identities=20% Similarity=0.230 Sum_probs=69.4
Q ss_pred CCCceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccccccChhhhhcCCCCChhH
Q 041357 17 DNCGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNV 96 (169)
Q Consensus 17 ~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg~iTR~Sv~~Al~~GITA~Q~~aHp~m~~~~p~iP~tV 96 (169)
..+|.|++||--.+|. -=-..|.-|+|+..|--+|-...||-=|+-+|...|+++++...--.-.+ ...||++|
T Consensus 20 ~~d~~i~lE~~~p~~~-----~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~s-k~~~p~~i 93 (732)
T TIGR00603 20 APDGHIFLESFSPLYK-----QAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLS-KTPIPKGI 93 (732)
T ss_pred cCCCeEEEEeCCccHH-----HHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHh-CCCCCHHH
Confidence 3468888888433321 11378899999999999999999999999999999999999222111111 24799999
Q ss_pred HHHHHHHHHhcCceee
Q 041357 97 CDQIRLWESDLNRVET 112 (169)
Q Consensus 97 ~dQIrLWE~Er~Rl~~ 112 (169)
++.|+.+-.--.++++
T Consensus 94 ~~~i~~~~~~ygk~kl 109 (732)
T TIGR00603 94 IEFIRLCTQSYGKVKL 109 (732)
T ss_pred HHHHHHHHHhcCcEEE
Confidence 9999999999888777
No 7
>KOG2036 consensus Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]
Probab=63.08 E-value=5.9 Score=39.88 Aligned_cols=58 Identities=24% Similarity=0.483 Sum_probs=43.0
Q ss_pred EcCCHhHHHHHH------HHHhh------hhccCceEE-------EEeCHHHHHHHHHcCCCccccccChhhhhcCCCCC
Q 041357 33 YSTSKLHCEILR------LFSKI------EYQLPNLIV-------GAITKESLYNAFENGITTEQQNAHPRVADKIPSVP 93 (169)
Q Consensus 33 YT~S~LqiaiL~------lF~~l------~~r~PNlvv-------g~iTR~Sv~~Al~~GITA~Q~~aHp~m~~~~p~iP 93 (169)
|.|||-.+.+|+ |||=+ .-.+|..++ |.|+|+|+...|..|=.| + ...||
T Consensus 529 YKNSPNDLQllsDAPaH~LFvLl~PVd~~~~~iPdvlcviQv~lEG~isr~si~~sL~~G~~a-----~------GdlIp 597 (1011)
T KOG2036|consen 529 YKNSPNDLQLLSDAPAHHLFVLLGPVDPSQNAIPDVLCVIQVCLEGRISRQSIENSLRRGKRA-----A------GDLIP 597 (1011)
T ss_pred ccCCchhhhhhccCcccceEEEecCcCcccCCCCcceEEEEEeecceecHHHHHHHHhccccc-----c------CCccc
Confidence 789998888885 77744 356777432 999999999999999443 2 45677
Q ss_pred hhHHHHHH
Q 041357 94 KNVCDQIR 101 (169)
Q Consensus 94 ~tV~dQIr 101 (169)
=+|+.|.+
T Consensus 598 W~vseQf~ 605 (1011)
T KOG2036|consen 598 WTVSEQFQ 605 (1011)
T ss_pred eehhhhhc
Confidence 77777764
No 8
>PF04491 Pox_T4_N: Poxvirus T4 protein, N terminus; InterPro: IPR007580 Poxvirus T4 protein is thought to be secreted or retained in the endoplasmic reticulum if the protein also contains an additional C-terminal region (IPR007579 from INTERPRO). M-T4 of myxoma virus (O55698 from SWISSPROT) is thought to protect infected lymphocytes from apoptosis and modulate the inflammatory response to virus infection [].
Probab=62.99 E-value=9.4 Score=25.41 Aligned_cols=26 Identities=27% Similarity=0.369 Sum_probs=19.6
Q ss_pred ceeece-----eCCCceEEEEeC-ceEEEEcC
Q 041357 10 WFIPTI-----ADNCGFVVVETN-FKMYAYST 35 (169)
Q Consensus 10 ~f~pT~-----~~~~g~IIvETN-fRvYAYT~ 35 (169)
-|||.+ ....|-+|.|-| |||.||++
T Consensus 14 ~f~~~~t~C~~~~~~GGLItegNGfki~~hD~ 45 (46)
T PF04491_consen 14 DFKSSRTGCHRPQGPGGLITEGNGFKIFAHDE 45 (46)
T ss_pred eEEeecCCcccccCCCcEEeeCCcEEEEEecc
Confidence 477776 344567899998 99999874
No 9
>cd06836 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases. This subfamily contains uncharacterized proteins with similarity to ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarbo
Probab=58.71 E-value=1.3e+02 Score=26.76 Aligned_cols=95 Identities=13% Similarity=0.079 Sum_probs=66.8
Q ss_pred Cce-EEEEcCCHhHHHHHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccc-cccChhhhhcCCCCChhHHHHHHHHH
Q 041357 27 NFK-MYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQ-QNAHPRVADKIPSVPKNVCDQIRLWE 104 (169)
Q Consensus 27 NfR-vYAYT~S~LqiaiL~lF~~l~~r~PNlvvg~iTR~Sv~~Al~~GITA~Q-~~aHp~m~~~~p~iP~tV~dQIrLWE 104 (169)
|++ .||...+|. .+||+++.+.- +-+=.-+..-++.|++.|+..++ ...+|. -+..-.++.
T Consensus 27 ~~~~~yAvKaN~~-~~il~~l~~~G-----~g~DvaS~~El~~al~~G~~~~~Ii~~gp~-------K~~~~L~~a---- 89 (379)
T cd06836 27 PVLHTFAVKANPL-VPVLRLLAEAG-----AGAEVASPGELELALAAGFPPERIVFDSPA-------KTRAELREA---- 89 (379)
T ss_pred CcEEEEEEecCCC-HHHHHHHHHcC-----CcEEEcCHHHHHHHHHcCCChhhEEEeCCC-------CCHHHHHHH----
Confidence 455 489988876 46777777653 34455678889999999999999 566653 333322222
Q ss_pred HhcCceeecCceeecCCCCHHHHHHHHHHHHH-----cCeEEeecCC
Q 041357 105 SDLNRVETTPAHYYDEFPSRDVFEAACDYARD-----QSGLLWEDSK 146 (169)
Q Consensus 105 ~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~-----~g~llw~~~~ 146 (169)
. ..|+++ .++|..+.+.+.+.|++ ..+++.=++.
T Consensus 90 i-------~~gv~i-~iDS~~El~~i~~~a~~~~~~~~~v~lRvnp~ 128 (379)
T cd06836 90 L-------ELGVAI-NIDNFQELERIDALVAEFKEASSRIGLRVNPQ 128 (379)
T ss_pred H-------HCCCEE-EECCHHHHHHHHHHHHHhcCCCceEEEEECCC
Confidence 2 347766 79999999999999876 3577776653
No 10
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=58.18 E-value=66 Score=26.95 Aligned_cols=126 Identities=14% Similarity=0.215 Sum_probs=82.3
Q ss_pred CceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEE---EeCHHHHHHHHHcCCCccc-cccChhhhh-----cC
Q 041357 19 CGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGITTEQ-QNAHPRVAD-----KI 89 (169)
Q Consensus 19 ~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg---~iTR~Sv~~Al~~GITA~Q-~~aHp~m~~-----~~ 89 (169)
.|.=++|-.++ +|-= +..+.++..++|++.|| ++|.+.+++|.+.|-.-== -+..|.+.+ ..
T Consensus 28 gGi~~iEit~~------tp~a---~~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aGA~FivSP~~~~~vi~~a~~~~i 98 (201)
T PRK06015 28 GGLPAIEITLR------TPAA---LDAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAGSRFIVSPGTTQELLAAANDSDV 98 (201)
T ss_pred CCCCEEEEeCC------CccH---HHHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence 45666776665 4433 34445567778999996 6899999999999954222 344444432 34
Q ss_pred CCCCh--hHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHHcCeEEeecCCccEEEEecccchHHHHHHhh
Q 041357 90 PSVPK--NVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRG 166 (169)
Q Consensus 90 p~iP~--tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~ 166 (169)
|.+|= |..+=...|+.=-+-+++.|+-++- . .+|.+.+...+ +.-++|-+..=.-+++.+|++.
T Consensus 99 ~~iPG~~TptEi~~A~~~Ga~~vK~FPa~~~G---G-------~~yikal~~pl---p~~~l~ptGGV~~~n~~~~l~a 164 (201)
T PRK06015 99 PLLPGAATPSEVMALREEGYTVLKFFPAEQAG---G-------AAFLKALSSPL---AGTFFCPTGGISLKNARDYLSL 164 (201)
T ss_pred CEeCCCCCHHHHHHHHHCCCCEEEECCchhhC---C-------HHHHHHHHhhC---CCCcEEecCCCCHHHHHHHHhC
Confidence 77775 7778888999999999998864431 0 24455555444 4556665555555778888764
No 11
>PRK13761 hypothetical protein; Provisional
Probab=57.02 E-value=5.5 Score=34.75 Aligned_cols=23 Identities=39% Similarity=0.576 Sum_probs=19.9
Q ss_pred EeCHHHHHHHHHcCCCccc-cccC
Q 041357 60 AITKESLYNAFENGITTEQ-QNAH 82 (169)
Q Consensus 60 ~iTR~Sv~~Al~~GITA~Q-~~aH 82 (169)
.+|||.+-+++..||+|.| ..||
T Consensus 12 L~~Rekiveg~~~Gi~a~qGLIAh 35 (248)
T PRK13761 12 LLTREKIVEGVEKGITAKQGLIAH 35 (248)
T ss_pred HHHHHHHHHHHHcCcccccchhhc
Confidence 3789999999999999999 4554
No 12
>PF06992 Phage_lambda_P: Replication protein P; InterPro: IPR009731 This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin [].; GO: 0006270 DNA-dependent DNA replication initiation
Probab=56.80 E-value=35 Score=29.57 Aligned_cols=88 Identities=28% Similarity=0.311 Sum_probs=56.2
Q ss_pred HHHHHHhhhhccCceEEEEeCHHHHH--------HHHHcCCCc-cccccChhh--hhcCCCCChhHHHHHHHHHHhcCce
Q 041357 42 ILRLFSKIEYQLPNLIVGAITKESLY--------NAFENGITT-EQQNAHPRV--ADKIPSVPKNVCDQIRLWESDLNRV 110 (169)
Q Consensus 42 iL~lF~~l~~r~PNlvvg~iTR~Sv~--------~Al~~GITA-~Q~~aHp~m--~~~~p~iP~tV~dQIrLWE~Er~Rl 110 (169)
|=.||.+|..-||-- .+.-+.+.+. .-..+|||. +|..+==.+ .+..|.+|+ +-|+--|..+-+--
T Consensus 40 vd~lF~~L~aifPa~-~a~~~~~~~~~aKr~Wi~~f~engI~t~eQv~~Gm~~aR~~~spF~PS--~GqFI~WCk~~~~~ 116 (233)
T PF06992_consen 40 VDRLFRQLKAIFPAW-RANPDQEELNEAKRQWIKAFAENGITTMEQVRAGMRRARASESPFWPS--PGQFIAWCKPGDYE 116 (233)
T ss_pred HHHHHHHHHHhCchh-ccCCCHHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHhcCCCCCCC--hhHHHHHHhcchHH
Confidence 557999999999984 3446666654 346799966 772211111 123688887 67888898764421
Q ss_pred eecCceeecCCCCH-HHHHHHHHHHHHcCe
Q 041357 111 ETTPAHYYDEFPSR-DVFEAACDYARDQSG 139 (169)
Q Consensus 111 ~~~~g~ly~~f~s~-~~f~~~~~yA~~~g~ 139 (169)
. ...++. +.|+.+..|+...|.
T Consensus 117 ------~-lGLP~~del~~~~~~y~~~rg~ 139 (233)
T PF06992_consen 117 ------A-LGLPSVDELYQRYKRYCRYRGF 139 (233)
T ss_pred ------h-cCCCCHHHHHHHHHHHHHHhCC
Confidence 1 145564 457778888887774
No 13
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=52.67 E-value=16 Score=34.08 Aligned_cols=34 Identities=26% Similarity=0.582 Sum_probs=28.1
Q ss_pred ceEEEEeCHHHHHHHHHcCCCccccccChhhhhcCCCCChhHHHHHH
Q 041357 55 NLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIR 101 (169)
Q Consensus 55 Nlvvg~iTR~Sv~~Al~~GITA~Q~~aHp~m~~~~p~iP~tV~dQIr 101 (169)
|=.+|+|||..|-+|+ ||....|-+++|+.|||-
T Consensus 290 ~~llGiitR~dvlk~l-------------q~~q~qpqvget~~d~I~ 323 (432)
T COG4109 290 NTLLGIITRQDVLKSL-------------QMIQRQPQVGETISDQIA 323 (432)
T ss_pred ceEEEEEEHHHHHHHH-------------HHhccCCcccccHHHHHH
Confidence 3457999999999999 355557889999999995
No 14
>TIGR01182 eda Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida
Probab=51.20 E-value=96 Score=25.99 Aligned_cols=125 Identities=16% Similarity=0.292 Sum_probs=82.7
Q ss_pred ceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEE---EeCHHHHHHHHHcCCCccc-cccChhhhh-----cCC
Q 041357 20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGITTEQ-QNAHPRVAD-----KIP 90 (169)
Q Consensus 20 g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg---~iTR~Sv~~Al~~GITA~Q-~~aHp~m~~-----~~p 90 (169)
|.=++|.-+ ++|--... +.++..++|++.|| ++|.+.++.|.+.|-.-=- -+..|.+.+ ..|
T Consensus 33 Gi~~iEit~------~t~~a~~~---i~~l~~~~~~~~vGAGTVl~~~~a~~a~~aGA~FivsP~~~~~v~~~~~~~~i~ 103 (204)
T TIGR01182 33 GLRVLEVTL------RTPVALDA---IRLLRKEVPDALIGAGTVLNPEQLRQAVDAGAQFIVSPGLTPELAKHAQDHGIP 103 (204)
T ss_pred CCCEEEEeC------CCccHHHH---HHHHHHHCCCCEEEEEeCCCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCc
Confidence 444556555 35555444 44455678999996 6899999999999854332 233333322 247
Q ss_pred CCCh--hHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHHcCeEEeecCCccEEEEecccchHHHHHHhh
Q 041357 91 SVPK--NVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRG 166 (169)
Q Consensus 91 ~iP~--tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~ 166 (169)
.+|= |-.+=...|+.=-+-+++.|+-.+. . .+|.+++...+ +.-++|.+..=.-+++.+|++.
T Consensus 104 ~iPG~~TptEi~~A~~~Ga~~vKlFPA~~~G---G-------~~yikal~~pl---p~i~~~ptGGV~~~N~~~~l~a 168 (204)
T TIGR01182 104 IIPGVATPSEIMLALELGITALKLFPAEVSG---G-------VKMLKALAGPF---PQVRFCPTGGINLANVRDYLAA 168 (204)
T ss_pred EECCCCCHHHHHHHHHCCCCEEEECCchhcC---C-------HHHHHHHhccC---CCCcEEecCCCCHHHHHHHHhC
Confidence 7774 6777778999999999998865441 0 35666666655 5666676655555889999874
No 15
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=48.93 E-value=1.7e+02 Score=24.88 Aligned_cols=128 Identities=15% Similarity=0.195 Sum_probs=81.9
Q ss_pred CceEEEEeCceEEEEcCCHhHHHHHHHHH-hhhhccCceEEE---EeCHHHHHHHHHcCCCccc-cccChhhhh-----c
Q 041357 19 CGFVVVETNFKMYAYSTSKLHCEILRLFS-KIEYQLPNLIVG---AITKESLYNAFENGITTEQ-QNAHPRVAD-----K 88 (169)
Q Consensus 19 ~g~IIvETNfRvYAYT~S~LqiaiL~lF~-~l~~r~PNlvvg---~iTR~Sv~~Al~~GITA~Q-~~aHp~m~~-----~ 88 (169)
.|.-++|-=|| +|-=...+..+. +...++|++.|| ++|.+.++.|.+.|-.-== -+..|.+.+ .
T Consensus 39 gGi~~iEiT~~------tp~a~~~i~~l~~~~~~~~p~~~vGaGTVl~~e~a~~a~~aGA~FiVsP~~~~~v~~~~~~~~ 112 (222)
T PRK07114 39 GGARVFEFTNR------GDFAHEVFAELVKYAAKELPGMILGVGSIVDAATAALYIQLGANFIVTPLFNPDIAKVCNRRK 112 (222)
T ss_pred CCCCEEEEeCC------CCcHHHHHHHHHHHHHhhCCCeEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcC
Confidence 35555665554 444444444443 445679999996 6899999999999954222 344444432 3
Q ss_pred CCCCCh--hHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHHcCeEEeecCCccEEEEecccc--hHHHHHH
Q 041357 89 IPSVPK--NVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIH--MHMREFL 164 (169)
Q Consensus 89 ~p~iP~--tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~~g~llw~~~~kr~~~V~~~~h--~~vr~f~ 164 (169)
.|.+|= |..+=...|+.=-+-+++.|+-.+ . ..|.+.+...+ +.-+++-+..=.- +++.+|+
T Consensus 113 i~~iPG~~TpsEi~~A~~~Ga~~vKlFPA~~~----G-------~~~ikal~~p~---p~i~~~ptGGV~~~~~n~~~yl 178 (222)
T PRK07114 113 VPYSPGCGSLSEIGYAEELGCEIVKLFPGSVY----G-------PGFVKAIKGPM---PWTKIMPTGGVEPTEENLKKWF 178 (222)
T ss_pred CCEeCCCCCHHHHHHHHHCCCCEEEECccccc----C-------HHHHHHHhccC---CCCeEEeCCCCCcchhcHHHHH
Confidence 577775 677778899999999999885433 1 45666666655 5555555443332 6788888
Q ss_pred hh
Q 041357 165 RG 166 (169)
Q Consensus 165 k~ 166 (169)
+.
T Consensus 179 ~a 180 (222)
T PRK07114 179 GA 180 (222)
T ss_pred hC
Confidence 63
No 16
>PF02244 Propep_M14: Carboxypeptidase activation peptide; InterPro: IPR003146 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The peptidases are synthesised as inactive molecules, zymogens, with propeptides that must be removed by proteolytic cleavage to activate the enzyme. Structural studies of carboxypeptidases A and B reveal the propeptide to exist as a globular domain, followed by an extended alpha-helix; this shields the catalytic site, without specifically binding to it, while the substrate-binding site is blocked by making specific contacts [, ]. Members of this propeptide family are found in the metallocarboxypeptidases: A1, A2 [], A3, A4, A5, A6, U, insect gut carboxypeptidase and B [], and and are associated with peptidases belonging to MEROPS peptidase family M14A. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase.; GO: 0004180 carboxypeptidase activity, 0006508 proteolysis; PDB: 3D68_C 3D67_B 3D66_A 1PBA_A 3GLJ_A 1NSA_A 1KWM_A 2BOA_B 1PYT_A 1JQG_A ....
Probab=48.21 E-value=82 Score=21.09 Aligned_cols=46 Identities=13% Similarity=0.320 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHHHHHcCeEEeecCC---c-cEEEEecccchHHHHHHhhc
Q 041357 122 PSRDVFEAACDYARDQSGLLWEDSK---K-MRLVVNAEIHMHMREFLRGQ 167 (169)
Q Consensus 122 ~s~~~f~~~~~yA~~~g~llw~~~~---k-r~~~V~~~~h~~vr~f~k~~ 167 (169)
.+.++.+.+.+.....++-.|+.+. . --+.|.++..+.+.++++..
T Consensus 6 ~t~~q~~~L~~L~~~~~~dfW~~~~~~~~~~dv~V~p~~~~~f~~~L~~~ 55 (74)
T PF02244_consen 6 KTEEQLELLQELEQSNELDFWKEPSSVGRPVDVMVPPEKLEEFEELLKEH 55 (74)
T ss_dssp SSHHHHHHHHHHHHHSTEEEEESSSSTTSEEEEEEEGGGHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHhcccceeeecCCCCCCCeEEEEECHHHHHHHHHHHHHC
Confidence 3567888899999999999999887 2 24677899999999998864
No 17
>COG1701 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.97 E-value=15 Score=32.10 Aligned_cols=22 Identities=41% Similarity=0.649 Sum_probs=18.8
Q ss_pred eCHHHHHHHHHcCCCccc-cccC
Q 041357 61 ITKESLYNAFENGITTEQ-QNAH 82 (169)
Q Consensus 61 iTR~Sv~~Al~~GITA~Q-~~aH 82 (169)
+.|+.+-.++..|||+.| ..||
T Consensus 15 l~Reki~eg~~~Gi~~~qGLIAh 37 (256)
T COG1701 15 LIREKIIEGFEKGITVPQGLIAH 37 (256)
T ss_pred HHHHHHHHHHHcCcccccchhhc
Confidence 679999999999999999 4444
No 18
>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....
Probab=38.57 E-value=35 Score=28.45 Aligned_cols=126 Identities=18% Similarity=0.288 Sum_probs=76.1
Q ss_pred CceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEE---EeCHHHHHHHHHcCCCccc-cccChhhhh-----cC
Q 041357 19 CGFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGITTEQ-QNAHPRVAD-----KI 89 (169)
Q Consensus 19 ~g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg---~iTR~Sv~~Al~~GITA~Q-~~aHp~m~~-----~~ 89 (169)
.|.=++|--|| +|-=. ..+..+..++|+|.|| ++|.+.+++|.+.|-.-== -+..|.+.+ ..
T Consensus 32 gGi~~iEiT~~------t~~a~---~~I~~l~~~~p~~~vGAGTV~~~e~a~~a~~aGA~FivSP~~~~~v~~~~~~~~i 102 (196)
T PF01081_consen 32 GGIRAIEITLR------TPNAL---EAIEALRKEFPDLLVGAGTVLTAEQAEAAIAAGAQFIVSPGFDPEVIEYAREYGI 102 (196)
T ss_dssp TT--EEEEETT------STTHH---HHHHHHHHHHTTSEEEEES--SHHHHHHHHHHT-SEEEESS--HHHHHHHHHHTS
T ss_pred CCCCEEEEecC------CccHH---HHHHHHHHHCCCCeeEEEeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence 45667777776 34323 3345566688999997 6899999999999843222 344444433 34
Q ss_pred CCCCh--hHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHHcCeEEeecCCccEEEEecccchHHHHHHhh
Q 041357 90 PSVPK--NVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRG 166 (169)
Q Consensus 90 p~iP~--tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~ 166 (169)
|.+|= |..+=...|+.=.+-+++.|+-.+- =.+|.+++...+ +.-++|.+..=.-+++.+|++.
T Consensus 103 ~~iPG~~TptEi~~A~~~G~~~vK~FPA~~~G----------G~~~ik~l~~p~---p~~~~~ptGGV~~~N~~~~l~a 168 (196)
T PF01081_consen 103 PYIPGVMTPTEIMQALEAGADIVKLFPAGALG----------GPSYIKALRGPF---PDLPFMPTGGVNPDNLAEYLKA 168 (196)
T ss_dssp EEEEEESSHHHHHHHHHTT-SEEEETTTTTTT----------HHHHHHHHHTTT---TT-EEEEBSS--TTTHHHHHTS
T ss_pred cccCCcCCHHHHHHHHHCCCCEEEEecchhcC----------cHHHHHHHhccC---CCCeEEEcCCCCHHHHHHHHhC
Confidence 77773 6677778899999999999876542 034555554432 4456666555556789999874
No 19
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=37.37 E-value=45 Score=27.98 Aligned_cols=125 Identities=18% Similarity=0.260 Sum_probs=79.7
Q ss_pred ceEEEEeCceEEEEcCCHhHHHHHHHHHhhhhccCceEEE---EeCHHHHHHHHHcCCCccc-cccChhhhh-----cCC
Q 041357 20 GFVVVETNFKMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGITTEQ-QNAHPRVAD-----KIP 90 (169)
Q Consensus 20 g~IIvETNfRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg---~iTR~Sv~~Al~~GITA~Q-~~aHp~m~~-----~~p 90 (169)
|.=++|--++ +|- =+..+.++..+||++.|| ++|.+.++.|++.|-.-== -+..|.+.+ ..+
T Consensus 40 Gi~~iEitl~------~~~---~~~~I~~l~~~~p~~~IGAGTVl~~~~a~~a~~aGA~FivsP~~~~~vi~~a~~~~i~ 110 (212)
T PRK05718 40 GLPVLEVTLR------TPA---ALEAIRLIAKEVPEALIGAGTVLNPEQLAQAIEAGAQFIVSPGLTPPLLKAAQEGPIP 110 (212)
T ss_pred CCCEEEEecC------Ccc---HHHHHHHHHHHCCCCEEEEeeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCC
Confidence 5556676543 443 344455666789999996 7899999999999843222 233333322 357
Q ss_pred CCCh--hHHHHHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHHcCeEEeecCCccEEEEecccchHHHHHHhh
Q 041357 91 SVPK--NVCDQIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRG 166 (169)
Q Consensus 91 ~iP~--tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~ 166 (169)
.+|- |..+=...|+.--+-+++.|+-.+- =.+|.+.+...+ +.-+++.+..=.-+++.+|++.
T Consensus 111 ~iPG~~TptEi~~a~~~Ga~~vKlFPa~~~g----------g~~~lk~l~~p~---p~~~~~ptGGV~~~ni~~~l~a 175 (212)
T PRK05718 111 LIPGVSTPSELMLGMELGLRTFKFFPAEASG----------GVKMLKALAGPF---PDVRFCPTGGISPANYRDYLAL 175 (212)
T ss_pred EeCCCCCHHHHHHHHHCCCCEEEEccchhcc----------CHHHHHHHhccC---CCCeEEEeCCCCHHHHHHHHhC
Confidence 7775 4466334899999999986643220 145666666654 4567777666666889999874
No 20
>TIGR01615 A_thal_3542 uncharacterized plant-specific domain TIGR01615. of a number of uncharacterized plant proteins. The domain is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.
Probab=37.06 E-value=12 Score=29.87 Aligned_cols=39 Identities=18% Similarity=0.385 Sum_probs=28.2
Q ss_pred CceEEEEeCceEEEEcCCHhHHH-HHHHHHhhhhccCceEEEEeCH
Q 041357 19 CGFVVVETNFKMYAYSTSKLHCE-ILRLFSKIEYQLPNLIVGAITK 63 (169)
Q Consensus 19 ~g~IIvETNfRvYAYT~S~Lqia-iL~lF~~l~~r~PNlvvg~iTR 63 (169)
..-+|||.||| +.+.|| ==.-+..+...||.+.||...|
T Consensus 48 ~~R~iVd~dFr------~~FeiARpt~~Y~~ll~~LP~vFVG~~~r 87 (131)
T TIGR01615 48 EMRVIIDLDFR------SEFEIARPTEEYKRLLESLPEVFVGTTER 87 (131)
T ss_pred cceEEEeccch------hhceecCCCHHHHHHHHhCCcceECCHHH
Confidence 35799999999 655542 1123567778999999997755
No 21
>PRK08508 biotin synthase; Provisional
Probab=36.97 E-value=2.4e+02 Score=24.13 Aligned_cols=96 Identities=10% Similarity=0.014 Sum_probs=65.0
Q ss_pred HHHHHHHhhhhccCceEE----EEeCHHHHHHHHHcCCCcccc---ccChhhhhc-CC-CCChhHHHHHHHHHHhcCcee
Q 041357 41 EILRLFSKIEYQLPNLIV----GAITKESLYNAFENGITTEQQ---NAHPRVADK-IP-SVPKNVCDQIRLWESDLNRVE 111 (169)
Q Consensus 41 aiL~lF~~l~~r~PNlvv----g~iTR~Sv~~Al~~GITA~Q~---~aHp~m~~~-~p-~iP~tV~dQIrLWE~Er~Rl~ 111 (169)
-++.++..++.++|++.+ |.+|+|.+++-.+.|+++=.. -+ +...++ .+ -=+..+.+-|+.. .+. -+.
T Consensus 76 ~~~ei~~~ik~~~p~l~i~~s~G~~~~e~l~~Lk~aGld~~~~~lEt~-~~~~~~i~~~~~~~~~l~~i~~a-~~~-Gi~ 152 (279)
T PRK08508 76 YVAEAAKAVKKEVPGLHLIACNGTASVEQLKELKKAGIFSYNHNLETS-KEFFPKICTTHTWEERFQTCENA-KEA-GLG 152 (279)
T ss_pred HHHHHHHHHHhhCCCcEEEecCCCCCHHHHHHHHHcCCCEEcccccch-HHHhcCCCCCCCHHHHHHHHHHH-HHc-CCe
Confidence 456677778888898643 999999999988999966540 01 111111 11 1123344455543 333 489
Q ss_pred ecCceeecCCCCHHHHHHHHHHHHHcCe
Q 041357 112 TTPAHYYDEFPSRDVFEAACDYARDQSG 139 (169)
Q Consensus 112 ~~~g~ly~~f~s~~~f~~~~~yA~~~g~ 139 (169)
++-|+++---++.+|-...+.+.++++.
T Consensus 153 v~sg~I~GlGEt~ed~~~~l~~lr~L~~ 180 (279)
T PRK08508 153 LCSGGIFGLGESWEDRISFLKSLASLSP 180 (279)
T ss_pred ecceeEEecCCCHHHHHHHHHHHHcCCC
Confidence 9999999988888999999999999985
No 22
>PF10566 Glyco_hydro_97: Glycoside hydrolase 97 ; InterPro: IPR019563 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This is the 97th family of glycosidases, in this case bacterial. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands []. ; PDB: 2JKP_A 2JKE_A 2D73_B 2ZQ0_B 2JKA_A 3A24_A.
Probab=34.79 E-value=40 Score=29.61 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=19.2
Q ss_pred CHHHHHHHHHHHHHcC--eEEeecCCc
Q 041357 123 SRDVFEAACDYARDQS--GLLWEDSKK 147 (169)
Q Consensus 123 s~~~f~~~~~yA~~~g--~llw~~~~k 147 (169)
...+-+.|++||+++| ++||.+...
T Consensus 71 ~~~dl~elv~Ya~~KgVgi~lw~~~~~ 97 (273)
T PF10566_consen 71 PDFDLPELVDYAKEKGVGIWLWYHSET 97 (273)
T ss_dssp TT--HHHHHHHHHHTT-EEEEEEECCH
T ss_pred CccCHHHHHHHHHHcCCCEEEEEeCCc
Confidence 3578899999999999 788877654
No 23
>PF02784 Orn_Arg_deC_N: Pyridoxal-dependent decarboxylase, pyridoxal binding domain; InterPro: IPR022644 These enzymes are collectively known as group IV decarboxylases []. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [, ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region [].; GO: 0003824 catalytic activity; PDB: 2OO0_A 2ON3_A 1D7K_B 3VAB_A 2J66_A 3C5Q_A 2QGH_A 1TWI_B 1TUF_A 3N2O_A ....
Probab=33.90 E-value=2.1e+02 Score=23.57 Aligned_cols=94 Identities=12% Similarity=0.067 Sum_probs=62.9
Q ss_pred EEEEcCCHhHHHHHHHHHhhhhccCceEEEEeCHHHHHHHHHcCCCccccccChhhhhcCCCCChhHHHHHHHHHHhcCc
Q 041357 30 MYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNR 109 (169)
Q Consensus 30 vYAYT~S~LqiaiL~lF~~l~~r~PNlvvg~iTR~Sv~~Al~~GITA~Q~~aHp~m~~~~p~iP~tV~dQIrLWE~Er~R 109 (169)
.||...++. .+||+.+.+.- +-+=.-|...+..|++.|+..++...+ .|.-++.-.+... +.
T Consensus 24 ~yA~KaN~~-~~vl~~l~~~g-----~g~dv~S~~El~~a~~~g~~~~~Ii~~------gp~k~~~~l~~a~----~~-- 85 (251)
T PF02784_consen 24 FYAVKANPN-PAVLKILAEEG-----CGFDVASPGELELALKAGFPPDRIIFT------GPGKSDEELEEAI----EN-- 85 (251)
T ss_dssp EEEGGGS---HHHHHHHHHTT-----CEEEESSHHHHHHHHHTTTTGGGEEEE------CSS--HHHHHHHH----HH--
T ss_pred EEEECcCCC-HHHHHHHHHcC-----CceEEecccchHHHHhhhccccceeEe------cCcccHHHHHHHH----hC--
Confidence 377777776 57788877764 455677899999999999999994433 3334443433333 22
Q ss_pred eeecCceeecCCCCHHHHHHHHHHHHHcCeEEeecCC
Q 041357 110 VETTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDSK 146 (169)
Q Consensus 110 l~~~~g~ly~~f~s~~~f~~~~~yA~~~g~llw~~~~ 146 (169)
|+..-.++|..+.+.+.+.|.+..++|-=++.
T Consensus 86 -----~~~~i~vDs~~el~~l~~~~~~~~v~lRin~~ 117 (251)
T PF02784_consen 86 -----GVATINVDSLEELERLAELAPEARVGLRINPG 117 (251)
T ss_dssp -----TESEEEESSHHHHHHHHHHHCTHEEEEEBE-S
T ss_pred -----CceEEEeCCHHHHHHHhccCCCceeeEEEeec
Confidence 44444788999999999999988777655444
No 24
>PRK14529 adenylate kinase; Provisional
Probab=33.46 E-value=79 Score=26.66 Aligned_cols=81 Identities=21% Similarity=0.297 Sum_probs=51.8
Q ss_pred hhhccCceEEEEeCHHHHHHHHHcCCCccccccChhhhhcCCCCChhHHHHHHHHHHhcCceeecCceeecCCCCHHHH-
Q 041357 49 IEYQLPNLIVGAITKESLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRDVF- 127 (169)
Q Consensus 49 l~~r~PNlvvg~iTR~Sv~~Al~~GITA~Q~~aHp~m~~~~p~iP~tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~~f- 127 (169)
-.+.+|.+.+|.+.|+.+.. |-...+ -+..-| .+...+|..++-++-.+.+...- ..|++++.|+-..+.
T Consensus 22 ~~~~~~~is~gdllr~~i~~----~t~lg~-~i~~~i-~~G~lvpdei~~~lv~~~l~~~~---~~g~iLDGfPRt~~Qa 92 (223)
T PRK14529 22 KKYDLAHIESGAIFREHIGG----GTELGK-KAKEYI-DRGDLVPDDITIPMILETLKQDG---KNGWLLDGFPRNKVQA 92 (223)
T ss_pred HHHCCCCcccchhhhhhccC----CChHHH-HHHHHH-hccCcchHHHHHHHHHHHHhccC---CCcEEEeCCCCCHHHH
Confidence 34678998899999987642 222111 011112 34678999999999888887653 789999999986433
Q ss_pred HHHHHHHHHcC
Q 041357 128 EAACDYARDQS 138 (169)
Q Consensus 128 ~~~~~yA~~~g 138 (169)
+.+-+...+.|
T Consensus 93 ~~l~~~l~~~~ 103 (223)
T PRK14529 93 EKLWEALQKEG 103 (223)
T ss_pred HHHHHHHHhcC
Confidence 33333443433
No 25
>PF13496 DUF4120: Domain of unknown function (DUF4120)
Probab=32.13 E-value=38 Score=25.53 Aligned_cols=17 Identities=12% Similarity=0.401 Sum_probs=15.0
Q ss_pred CHHHHHHHHHHHHHcCe
Q 041357 123 SRDVFEAACDYARDQSG 139 (169)
Q Consensus 123 s~~~f~~~~~yA~~~g~ 139 (169)
-++.|+.|++||+++|-
T Consensus 4 cqEhy~kvv~yA~sI~D 20 (95)
T PF13496_consen 4 CQEHYDKVVQYAESIGD 20 (95)
T ss_pred hHHHHHHHHHHHHHhcc
Confidence 37899999999999985
No 26
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=31.74 E-value=77 Score=29.59 Aligned_cols=90 Identities=13% Similarity=0.273 Sum_probs=66.1
Q ss_pred HhhhhccCceEEEEeCHHHHHHHHH-cCCCccc-------cccChhhhhc------CCCCChhHHHHHHHHHHhcCceee
Q 041357 47 SKIEYQLPNLIVGAITKESLYNAFE-NGITTEQ-------QNAHPRVADK------IPSVPKNVCDQIRLWESDLNRVET 112 (169)
Q Consensus 47 ~~l~~r~PNlvvg~iTR~Sv~~Al~-~GITA~Q-------~~aHp~m~~~------~p~iP~tV~dQIrLWE~Er~Rl~~ 112 (169)
+.-..|||-++-..+|..-|++-|. .|.+.+= -|+|-.|.=+ .|+=-.+++.||.=||.-++++..
T Consensus 237 ~~~r~rLPK~~y~lls~s~ik~KLse~GLst~G~kQ~likRh~~~v~lyNsncD~l~Pvs~ael~rql~~we~t~~k~~~ 316 (442)
T KOG0287|consen 237 VHKRKRLPKTVYNLLSDSDIKKKLSEHGLSTQGNKQQLIKRHQEFVHLYNSNCDALHPVSAAELVRQLENWEKTRMKLEA 316 (442)
T ss_pred HhhcccCchhhHhhccHHHHHHHHHHcCCCCcchHHHHHHHHHHHHHHHhccccccCCcCHHHHHHHHHHHHHHhhcccc
Confidence 5667899999999999999988775 6776543 6666665422 366666899999999999999966
Q ss_pred cCce----eecCCCC---------------HHHHHHHHHHHHH
Q 041357 113 TPAH----YYDEFPS---------------RDVFEAACDYARD 136 (169)
Q Consensus 113 ~~g~----ly~~f~s---------------~~~f~~~~~yA~~ 136 (169)
..|+ +|..-.. ..||..+++-|+.
T Consensus 317 ~~g~ek~mv~~~d~~~~~~~~i~~~w~k~~~~dFa~LI~~Ak~ 359 (442)
T KOG0287|consen 317 SKGNEKVMVFTKDQTEKEIDEIHSKWRKKHKSDFALLIDQAKK 359 (442)
T ss_pred ccCceeeEeecCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 6654 4433211 2688888888875
No 27
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=31.73 E-value=39 Score=26.02 Aligned_cols=37 Identities=14% Similarity=0.271 Sum_probs=22.7
Q ss_pred HHHHHHHcCCCccccccChhhhhcCCCCChhHHHHHH-HHHHhcC
Q 041357 65 SLYNAFENGITTEQQNAHPRVADKIPSVPKNVCDQIR-LWESDLN 108 (169)
Q Consensus 65 Sv~~Al~~GITA~Q~~aHp~m~~~~p~iP~tV~dQIr-LWE~Er~ 108 (169)
.|.+||++|+|.++.|..- -|-|=+.+||+ |-+.|++
T Consensus 15 ~i~eAlrrG~sveeI~e~T-------~ID~wFL~~i~~Iv~~e~~ 52 (123)
T PF02787_consen 15 AIAEALRRGYSVEEIHELT-------KIDPWFLEQIKNIVDMEKE 52 (123)
T ss_dssp HHHHHHHTTB-HHHHHHHH----------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH-------CccHHHHHHHHHHHHHHHH
Confidence 3689999999999944422 23344777776 6666543
No 28
>PF11849 DUF3369: Domain of unknown function (DUF3369); InterPro: IPR021800 This domain is functionally uncharacterised. This domain is found in bacteria. This presumed domain is about 170 amino acids in length.
Probab=31.37 E-value=57 Score=25.93 Aligned_cols=35 Identities=14% Similarity=0.334 Sum_probs=28.1
Q ss_pred cceeeceeCCCceEEEEeCceEEEEcCCHhHHHHHHHHHh
Q 041357 9 SWFIPTIADNCGFVVVETNFKMYAYSTSKLHCEILRLFSK 48 (169)
Q Consensus 9 ~~f~pT~~~~~g~IIvETNfRvYAYT~S~LqiaiL~lF~~ 48 (169)
.-|+||....++.|.||+.-. =++.+..+|.+||.
T Consensus 122 ~ly~~~~~g~~~~iyl~~~~~-----l~~~d~~LlevF~~ 156 (174)
T PF11849_consen 122 VLYFPSSSGRESLIYLEGDRP-----LSETDRQLLEVFCN 156 (174)
T ss_pred EEEEecCCCCEEEEEEeCCCC-----CCHHHHHHHHHHHH
Confidence 356788888889999999843 36789999999996
No 29
>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....
Probab=30.09 E-value=1.7e+02 Score=21.85 Aligned_cols=74 Identities=19% Similarity=0.208 Sum_probs=43.7
Q ss_pred hhccCceEEEEeCHHHHHHHHHcCCCc-cccccChhhhhcCCCCChhHHHHHHHHHHhcCceeecCceeecCCCCHH-HH
Q 041357 50 EYQLPNLIVGAITKESLYNAFENGITT-EQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVETTPAHYYDEFPSRD-VF 127 (169)
Q Consensus 50 ~~r~PNlvvg~iTR~Sv~~Al~~GITA-~Q~~aHp~m~~~~p~iP~tV~dQIrLWE~Er~Rl~~~~g~ly~~f~s~~-~f 127 (169)
.|.|+.+.+|.+=|+ ++..+-.. ++... +..+...||..++-++-.++++.. ....|++.+.|+... +.
T Consensus 19 ~~~~~~is~~~llr~----~~~~~s~~g~~i~~---~l~~g~~vp~~~v~~ll~~~l~~~--~~~~g~ildGfPrt~~Qa 89 (151)
T PF00406_consen 19 RYGLVHISVGDLLRE----EIKSDSELGKQIQE---YLDNGELVPDELVIELLKERLEQP--PCNRGFILDGFPRTLEQA 89 (151)
T ss_dssp HHTSEEEEHHHHHHH----HHHTTSHHHHHHHH---HHHTTSS--HHHHHHHHHHHHHSG--GTTTEEEEESB-SSHHHH
T ss_pred hcCcceechHHHHHH----HHhhhhHHHHHHHH---HHHhhccchHHHHHHHHHHHHhhh--cccceeeeeeccccHHHH
Confidence 355665655555444 44433211 11111 333567899999999998988877 667899999999853 34
Q ss_pred HHHHH
Q 041357 128 EAACD 132 (169)
Q Consensus 128 ~~~~~ 132 (169)
+.+.+
T Consensus 90 ~~l~~ 94 (151)
T PF00406_consen 90 EALEE 94 (151)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 44443
No 30
>PF09419 PGP_phosphatase: Mitochondrial PGP phosphatase; InterPro: IPR010021 This group of hypothetical proteins is a part of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterised members of this subfamily and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs [], all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, Gram-positive bacteria and Deinococcus. There is presently no characterisation of any sequence in this family.
Probab=29.56 E-value=1.5e+02 Score=24.10 Aligned_cols=114 Identities=15% Similarity=0.176 Sum_probs=72.9
Q ss_pred HHHHHHHHhhhhccCceEEEEeCHHHHHH--HHHcCCCc-----cccccChhhhhcCCCCChhHHHHHHHHHHhcCceee
Q 041357 40 CEILRLFSKIEYQLPNLIVGAITKESLYN--AFENGITT-----EQQNAHPRVADKIPSVPKNVCDQIRLWESDLNRVET 112 (169)
Q Consensus 40 iaiL~lF~~l~~r~PNlvvg~iTR~Sv~~--Al~~GITA-----~Q~~aHp~m~~~~p~iP~tV~dQIrLWE~Er~Rl~~ 112 (169)
.+++.+|.+...-.|++.|-.|..=++.. --+.||.+ |.+.+.|. ...+|+.+. -|=.|..+.-.
T Consensus 5 ~~~~~~~~~p~l~~P~l~V~si~~I~~~~~~Lk~~Gik~li~DkDNTL~~~~----~~~i~~~~~----~~~~~l~~~~~ 76 (168)
T PF09419_consen 5 LAVFRLLRNPSLLLPHLYVPSIRDIDFEANHLKKKGIKALIFDKDNTLTPPY----EDEIPPEYA----EWLNELKKQFG 76 (168)
T ss_pred HHHHHHHcCccccCCCEEcCChhhCCcchhhhhhcCceEEEEcCCCCCCCCC----cCcCCHHHH----HHHHHHHHHCC
Confidence 47888999999999999998776666666 66778876 33555443 455666544 35444444433
Q ss_pred c-CceeecCCC-CH--HHHHHHHHHHHHcCeEEeecCCccEEEEecccchHHHHHHhh
Q 041357 113 T-PAHYYDEFP-SR--DVFEAACDYARDQSGLLWEDSKKMRLVVNAEIHMHMREFLRG 166 (169)
Q Consensus 113 ~-~g~ly~~f~-s~--~~f~~~~~yA~~~g~llw~~~~kr~~~V~~~~h~~vr~f~k~ 166 (169)
. .-+++++-. +. .+++.+...++.+|+-+-....|+ +.+.+.+.+|++.
T Consensus 77 ~~~v~IvSNsaGs~~d~~~~~a~~~~~~lgIpvl~h~~kK-----P~~~~~i~~~~~~ 129 (168)
T PF09419_consen 77 KDRVLIVSNSAGSSDDPDGERAEALEKALGIPVLRHRAKK-----PGCFREILKYFKC 129 (168)
T ss_pred CCeEEEEECCCCcccCccHHHHHHHHHhhCCcEEEeCCCC-----CccHHHHHHHHhh
Confidence 3 246777663 22 257888999999998654333331 3555667767654
No 31
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=28.65 E-value=37 Score=21.21 Aligned_cols=17 Identities=41% Similarity=0.702 Sum_probs=13.9
Q ss_pred EEeCHHHHHHHHHc-CCC
Q 041357 59 GAITKESLYNAFEN-GIT 75 (169)
Q Consensus 59 g~iTR~Sv~~Al~~-GIT 75 (169)
|.||++.++.|+.. |+.
T Consensus 3 G~i~~~~~~~~l~~~g~~ 20 (54)
T PF13833_consen 3 GKITREEFRRALSKLGIK 20 (54)
T ss_dssp SEEEHHHHHHHHHHTTSS
T ss_pred CEECHHHHHHHHHHhCCC
Confidence 78999999999965 544
No 32
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=28.56 E-value=30 Score=20.88 Aligned_cols=13 Identities=31% Similarity=0.552 Sum_probs=9.9
Q ss_pred HHHHHHcCCCccc
Q 041357 66 LYNAFENGITTEQ 78 (169)
Q Consensus 66 v~~Al~~GITA~Q 78 (169)
|+.|...|||.+|
T Consensus 9 i~eA~~~Gls~ee 21 (30)
T PF08671_consen 9 IKEAKESGLSKEE 21 (30)
T ss_dssp HHHHHHTT--HHH
T ss_pred HHHHHHcCCCHHH
Confidence 6899999999988
No 33
>cd06568 GH20_SpHex_like A subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the N-acetylhexosaminidase from Streptomyces plicatus (SpHex). SpHex catalyzes the hydrolysis of N-acetyl-beta-hexosaminides. An Asp residue within the active site plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Proteins belonging to this subgroup lack the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases.
Probab=28.28 E-value=58 Score=28.79 Aligned_cols=24 Identities=8% Similarity=0.217 Sum_probs=21.2
Q ss_pred ecCCCCHHHHHHHHHHHHHcCeEE
Q 041357 118 YDEFPSRDVFEAACDYARDQSGLL 141 (169)
Q Consensus 118 y~~f~s~~~f~~~~~yA~~~g~ll 141 (169)
...|.|++|+..+++||++.|+-|
T Consensus 68 ~~~~YT~~di~elv~yA~~rgI~v 91 (329)
T cd06568 68 PGGYYTQEDYKDIVAYAAERHITV 91 (329)
T ss_pred CCCcCCHHHHHHHHHHHHHcCCEE
Confidence 456889999999999999999965
No 34
>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=27.88 E-value=59 Score=20.01 Aligned_cols=31 Identities=29% Similarity=0.425 Sum_probs=21.4
Q ss_pred HHHHHHHhhhhc-c-----CceEEEEeCHHHHHHHHH
Q 041357 41 EILRLFSKIEYQ-L-----PNLIVGAITKESLYNAFE 71 (169)
Q Consensus 41 aiL~lF~~l~~r-~-----PNlvvg~iTR~Sv~~Al~ 71 (169)
.++..|.+-.++ + .+=++|+||+.++.+++.
T Consensus 20 ~~~~~~~~~~~~~~~V~d~~~~~~G~is~~dl~~~l~ 56 (57)
T PF00571_consen 20 EALEIMRKNGISRLPVVDEDGKLVGIISRSDLLKALL 56 (57)
T ss_dssp HHHHHHHHHTSSEEEEESTTSBEEEEEEHHHHHHHHH
T ss_pred HHHHHHHHcCCcEEEEEecCCEEEEEEEHHHHHhhhh
Confidence 455555555443 2 456889999999999873
No 35
>PF13707 RloB: RloB-like protein
Probab=27.55 E-value=1.3e+02 Score=23.48 Aligned_cols=56 Identities=14% Similarity=0.090 Sum_probs=39.0
Q ss_pred CCChhHHHHHH-HHHHhcCceeecCceeecCCC----CHHHHHHHHHHHHHcCe-EEeecCC
Q 041357 91 SVPKNVCDQIR-LWESDLNRVETTPAHYYDEFP----SRDVFEAACDYARDQSG-LLWEDSK 146 (169)
Q Consensus 91 ~iP~tV~dQIr-LWE~Er~Rl~~~~g~ly~~f~----s~~~f~~~~~yA~~~g~-llw~~~~ 146 (169)
.-|.++++.+. .-+.+.+.-.+...++.-|.. ....|+.+.+.|++.++ ++|++|-
T Consensus 38 ~~p~~lv~~a~~~~~~~~~~~~~d~v~~V~D~D~~~~~~~~~~~~~~~a~~~~i~l~~SnPc 99 (183)
T PF13707_consen 38 SDPSSLVEKAKKKRKKKKNDNEYDEVWCVFDRDQNDFEHEKLEEAIKKAKRNKINLAVSNPC 99 (183)
T ss_pred CCHHHHHHHHHHHHhhhccccCCCEEEEEEeCCCCcCcHHHHHHHHHhccccCeEEEEecCc
Confidence 45777777664 222234455666666666777 67899999999999988 6677763
No 36
>cd02742 GH20_hexosaminidase Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself.
Probab=26.13 E-value=63 Score=27.97 Aligned_cols=26 Identities=12% Similarity=0.050 Sum_probs=22.4
Q ss_pred eecCCCCHHHHHHHHHHHHHcCeEEe
Q 041357 117 YYDEFPSRDVFEAACDYARDQSGLLW 142 (169)
Q Consensus 117 ly~~f~s~~~f~~~~~yA~~~g~llw 142 (169)
-...+.|++|+..+++||+++|+-|-
T Consensus 64 ~~~~~yT~~di~elv~yA~~rgI~vi 89 (303)
T cd02742 64 SPGGFYTYAQLKDIIEYAAARGIEVI 89 (303)
T ss_pred CCCCeECHHHHHHHHHHHHHcCCEEE
Confidence 44568899999999999999999763
No 37
>cd06569 GH20_Sm-chitobiase-like The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=25.49 E-value=69 Score=29.73 Aligned_cols=25 Identities=16% Similarity=0.115 Sum_probs=22.0
Q ss_pred eecCCCCHHHHHHHHHHHHHcCeEE
Q 041357 117 YYDEFPSRDVFEAACDYARDQSGLL 141 (169)
Q Consensus 117 ly~~f~s~~~f~~~~~yA~~~g~ll 141 (169)
-+..|-|++|+..+++||+++||-|
T Consensus 89 ~~~g~YT~~di~eiv~yA~~rgI~V 113 (445)
T cd06569 89 SGSGYYSRADYIEILKYAKARHIEV 113 (445)
T ss_pred ccCCccCHHHHHHHHHHHHHcCCEE
Confidence 3456889999999999999999976
No 38
>cd06564 GH20_DspB_LnbB-like Glycosyl hydrolase family 20 (GH20) catalytic domain of dispersin B (DspB), lacto-N-biosidase (LnbB) and related proteins. Dispersin B is a soluble beta-N-acetylglucosamidase found in bacteria that hydrolyzes the beta-1,6-linkages of PGA (poly-beta-(1,6)-N-acetylglucosamine), a major component of the extracellular polysaccharide matrix. Lacto-N-biosidase hydrolyzes lacto-N-biose (LNB) type I oligosaccharides at the nonreducing terminus to produce lacto-N-biose as part of the GNB/LNB (galacto-N-biose/lacto-N-biose I) degradation pathway. The lacto-N-biosidase from Bifidobacterium bifidum has this GH20 domain, a carbohydrate binding module 32, and a bacterial immunoglobulin-like domain 2, as well as a YSIRK signal peptide and a G5 membrane anchor at the N and C termini, respectively. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=24.72 E-value=74 Score=27.77 Aligned_cols=25 Identities=20% Similarity=0.387 Sum_probs=22.0
Q ss_pred eecCCCCHHHHHHHHHHHHHcCeEE
Q 041357 117 YYDEFPSRDVFEAACDYARDQSGLL 141 (169)
Q Consensus 117 ly~~f~s~~~f~~~~~yA~~~g~ll 141 (169)
-...+.+++|+..+++||++.|+-+
T Consensus 74 ~~~~~YT~~di~eiv~yA~~rgI~v 98 (326)
T cd06564 74 ANDGYYTKEEFKELIAYAKDRGVNI 98 (326)
T ss_pred CCCCcccHHHHHHHHHHHHHcCCeE
Confidence 3467889999999999999999976
No 39
>cd06562 GH20_HexA_HexB-like Beta-N-acetylhexosaminidases catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. The hexA and hexB genes encode the alpha- and beta-subunits of the two major beta-N-acetylhexosaminidase isoenzymes, N-acetyl-beta-D-hexosaminidase A (HexA) and beta-N-acetylhexosaminidase B (HexB). Both the alpha and the beta catalytic subunits have a TIM-barrel fold and belong to the glycosyl hydrolase family 20 (GH20). The HexA enzyme is a heterodimer containing one alpha and one beta subunit while the HexB enzyme is a homodimer containing two beta-subunits. Hexosaminidase mutations cause an inability to properly hydrolyze certain sphingolipids which accumulate in lysosomes within the brain, resulting in the lipid storage disorders Tay-Sachs and Sandhoff. Mutations in the alpha subunit cause in a deficiency in the HexA enzyme and result in
Probab=24.30 E-value=67 Score=28.49 Aligned_cols=23 Identities=17% Similarity=0.185 Sum_probs=20.6
Q ss_pred cCCCCHHHHHHHHHHHHHcCeEE
Q 041357 119 DEFPSRDVFEAACDYARDQSGLL 141 (169)
Q Consensus 119 ~~f~s~~~f~~~~~yA~~~g~ll 141 (169)
..|.+++|+..+++||++.|+-|
T Consensus 64 ~~~YT~~di~eiv~yA~~rgI~v 86 (348)
T cd06562 64 SEVYTPEDVKEIVEYARLRGIRV 86 (348)
T ss_pred CceECHHHHHHHHHHHHHcCCEE
Confidence 35779999999999999999976
No 40
>cd06570 GH20_chitobiase-like_1 A functionally uncharacterized subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the chitobiase of Serratia marcescens, a beta-N-1,4-acetylhexosaminidase that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This subgroup lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=23.29 E-value=85 Score=27.69 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=21.2
Q ss_pred ecCCCCHHHHHHHHHHHHHcCeEE
Q 041357 118 YDEFPSRDVFEAACDYARDQSGLL 141 (169)
Q Consensus 118 y~~f~s~~~f~~~~~yA~~~g~ll 141 (169)
+..|.+++|+..+++||++.|+-+
T Consensus 61 ~~~~yT~~di~elv~yA~~rgI~v 84 (311)
T cd06570 61 DGLYYTQEQIREVVAYARDRGIRV 84 (311)
T ss_pred CCCccCHHHHHHHHHHHHHcCCEE
Confidence 346789999999999999999966
No 41
>cd06563 GH20_chitobiase-like The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This GH20 domain family includes an N-acetylglucosamidase (GlcNAcase A) from Pseudoalteromonas piscicida and an N-acetylhexosaminidase (SpHex) from Streptomyces plicatus. SpHex lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=23.20 E-value=71 Score=28.33 Aligned_cols=25 Identities=16% Similarity=0.297 Sum_probs=21.6
Q ss_pred eecCCCCHHHHHHHHHHHHHcCeEE
Q 041357 117 YYDEFPSRDVFEAACDYARDQSGLL 141 (169)
Q Consensus 117 ly~~f~s~~~f~~~~~yA~~~g~ll 141 (169)
-...|.+++|+..+++||++.|+-|
T Consensus 78 ~~~~~YT~~di~eiv~yA~~rgI~V 102 (357)
T cd06563 78 PYGGFYTQEEIREIVAYAAERGITV 102 (357)
T ss_pred ccCceECHHHHHHHHHHHHHcCCEE
Confidence 3456789999999999999999965
No 42
>PF12513 SUV3_C: Mitochondrial degradasome RNA helicase subunit C terminal; InterPro: IPR022192 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00271 from PFAM. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 3RC8_A 3RC3_A.
Probab=22.57 E-value=52 Score=21.22 Aligned_cols=19 Identities=21% Similarity=0.644 Sum_probs=15.7
Q ss_pred HHHHHHHhhhhccCceEEE
Q 041357 41 EILRLFSKIEYQLPNLIVG 59 (169)
Q Consensus 41 aiL~lF~~l~~r~PNlvvg 59 (169)
.+|.+++=+.+|||++.+.
T Consensus 9 k~l~lYlWLs~Rfp~~F~d 27 (49)
T PF12513_consen 9 KVLDLYLWLSYRFPDVFPD 27 (49)
T ss_dssp HHHHHHHHHHCC-TTTSTT
T ss_pred HHHHHHHHHHHHcccccCC
Confidence 6899999999999998653
No 43
>TIGR03551 F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit. This enzyme, together with CofG, complete the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the chromophore of coenzyme F420. The chromophore is also used in cyanobacteria DNA photolyases.
Probab=22.46 E-value=3.5e+02 Score=23.72 Aligned_cols=97 Identities=14% Similarity=0.161 Sum_probs=66.4
Q ss_pred HHHHHHHhhhhccCceE---------------EEEeCHHHHHHHHHcCCCccc----cccChhhhhc-CC--CCChhHHH
Q 041357 41 EILRLFSKIEYQLPNLI---------------VGAITKESLYNAFENGITTEQ----QNAHPRVADK-IP--SVPKNVCD 98 (169)
Q Consensus 41 aiL~lF~~l~~r~PNlv---------------vg~iTR~Sv~~Al~~GITA~Q----~~aHp~m~~~-~p--~iP~tV~d 98 (169)
.++.++..++..+|++- +|.+++|.+++--+.|++.=. ...+|.+++. +| .-.....+
T Consensus 104 ~~~~i~~~Ik~~~~~i~~~~~t~~ei~~~~~~~g~~~~e~l~~LkeAGl~~i~~~~~E~~~~~v~~~i~~~~~~~~~~~~ 183 (343)
T TIGR03551 104 FYLDILRAVKEEVPGMHIHAFSPMEVYYGARNSGLSVEEALKRLKEAGLDSMPGTAAEILDDEVRKVICPDKLSTAEWIE 183 (343)
T ss_pred HHHHHHHHHHHHCCCceEEecCHHHHHHHHHHcCCCHHHHHHHHHHhCcccccCcchhhcCHHHHHhcCCCCCCHHHHHH
Confidence 34788888888899874 467788888888888887432 3334555543 22 12234566
Q ss_pred HHHHHHHhcCceeecCceeecCCCCHHHHHHHHHHHHHcCe
Q 041357 99 QIRLWESDLNRVETTPAHYYDEFPSRDVFEAACDYARDQSG 139 (169)
Q Consensus 99 QIrLWE~Er~Rl~~~~g~ly~~f~s~~~f~~~~~yA~~~g~ 139 (169)
-|++...- -+.+.-|+++--=.+.++....+.++++++.
T Consensus 184 ~i~~a~~~--Gi~v~s~~i~G~~Et~ed~~~~l~~lr~l~~ 222 (343)
T TIGR03551 184 IIKTAHKL--GIPTTATIMYGHVETPEHWVDHLLILREIQE 222 (343)
T ss_pred HHHHHHHc--CCcccceEEEecCCCHHHHHHHHHHHHHhhH
Confidence 66655444 4567778888856788999999999999885
No 44
>PF12818 Tegument_dsDNA: dsDNA viral tegument protein; InterPro: IPR024346 This entry represents the N-terminal domain of tegument proteins from double-stranded DNA herpesvirus.
Probab=22.10 E-value=1.1e+02 Score=27.04 Aligned_cols=66 Identities=21% Similarity=0.337 Sum_probs=43.7
Q ss_pred EEEEcCCHhHH----HHHHHHHhhhhccCceEEEEeC---HHHHHHHHHcCCCccccccChhhhhc--CCCCChhHHHHH
Q 041357 30 MYAYSTSKLHC----EILRLFSKIEYQLPNLIVGAIT---KESLYNAFENGITTEQQNAHPRVADK--IPSVPKNVCDQI 100 (169)
Q Consensus 30 vYAYT~S~Lqi----aiL~lF~~l~~r~PNlvvg~iT---R~Sv~~Al~~GITA~Q~~aHp~m~~~--~p~iP~tV~dQI 100 (169)
=|.|.+|++.+ +.|++|.++.. +..|+|.+. +.||.+.|. ...|| +.-. .+-||++|++++
T Consensus 140 p~~y~dS~~~~~~i~~aL~~f~~~~~--~~cis~~~r~~~~~sv~~~L~-------aL~~~-~G~~l~lS~LP~~i~~~L 209 (282)
T PF12818_consen 140 PYTYRDSGLEQNKILQALQQFYSTLE--SPCISGSIRPPGPASVKEHLL-------ALCHP-GGARLDLSALPQEIVSQL 209 (282)
T ss_pred CcccccCHHHHHHHHHHHHHHHHhcC--CCcEEeecCCCCchhHHHHHH-------HhcCC-CceEEEhhcCCHHHHHHh
Confidence 48899999986 45677776653 468888864 456665553 33333 2221 478999999999
Q ss_pred HHHHH
Q 041357 101 RLWES 105 (169)
Q Consensus 101 rLWE~ 105 (169)
+=|--
T Consensus 210 ~~~~~ 214 (282)
T PF12818_consen 210 KRSPP 214 (282)
T ss_pred ccCCc
Confidence 85543
No 45
>cd07241 Glo_EDI_BRP_like_3 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=21.31 E-value=2.1e+02 Score=19.55 Aligned_cols=38 Identities=11% Similarity=0.180 Sum_probs=27.8
Q ss_pred CCCCHHHHHHHHHHHHHcCeEEeecC-----Cc-cEEEEecccc
Q 041357 120 EFPSRDVFEAACDYARDQSGLLWEDS-----KK-MRLVVNAEIH 157 (169)
Q Consensus 120 ~f~s~~~f~~~~~yA~~~g~llw~~~-----~k-r~~~V~~~~h 157 (169)
...+.++.+.+.+.+++.|+-++..+ .. .++|.+++|+
T Consensus 77 ~v~~~~~v~~~~~~l~~~g~~~~~~~~~~~~g~~~~~~~DPdG~ 120 (125)
T cd07241 77 SVGSKEAVDELTERLRADGYLIIGEPRTTGDGYYESVILDPEGN 120 (125)
T ss_pred ECCCHHHHHHHHHHHHHCCCEEEeCceecCCCeEEEEEECCCCC
Confidence 55667899999999999999776533 12 3556678876
No 46
>cd00452 KDPG_aldolase KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.
Probab=21.20 E-value=1.9e+02 Score=22.99 Aligned_cols=44 Identities=16% Similarity=0.300 Sum_probs=0.0
Q ss_pred ceEEEEcCCHhHHHHHHHHHhhhhccCceEEE---EeCHHHHHHHHHcC
Q 041357 28 FKMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENG 73 (169)
Q Consensus 28 fRvYAYT~S~LqiaiL~lF~~l~~r~PNlvvg---~iTR~Sv~~Al~~G 73 (169)
+++-.+|.+... -+..+..+..++|++.+| ++|++.+..|+..|
T Consensus 30 ~~~vev~~~~~~--~~~~i~~l~~~~~~~~iGag~v~~~~~~~~a~~~G 76 (190)
T cd00452 30 IRAIEITLRTPG--ALEAIRALRKEFPEALIGAGTVLTPEQADAAIAAG 76 (190)
T ss_pred CCEEEEeCCChh--HHHHHHHHHHHCCCCEEEEEeCCCHHHHHHHHHcC
No 47
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=20.41 E-value=1.2e+02 Score=22.00 Aligned_cols=9 Identities=11% Similarity=0.135 Sum_probs=3.3
Q ss_pred ccEEEEecc
Q 041357 147 KMRLVVNAE 155 (169)
Q Consensus 147 kr~~~V~~~ 155 (169)
++.+|++..
T Consensus 31 ~~~~~lTNn 39 (101)
T PF13344_consen 31 KPVVFLTNN 39 (101)
T ss_dssp SEEEEEES-
T ss_pred CCEEEEeCC
Confidence 333444433
No 48
>cd06565 GH20_GcnA-like Glycosyl hydrolase family 20 (GH20) catalytic domain of N-acetyl-beta-D-glucosaminidase (GcnA, also known as BhsA) and related proteins. GcnA is an exoglucosidase which cleaves N-acetyl-beta-D-galactosamine (NAG) and N-acetyl-beta-D-galactosamine residues from 4-methylumbelliferylated (4MU) substrates, as well as cleaving NAG from chito-oligosaccharides (i.e. NAG polymers). In contrast, sulfated forms of the substrate are unable to be cleaved and act instead as mild competitive inhibitors. Additionally, the enzyme is known to be poisoned by several first-row transition metals as well as by mercury. GcnA forms a homodimer with subunits comprised of three domains, an N-terminal zincin-like domain, this central catalytic GH20 domain, and a C-terminal alpha helical domain. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=20.21 E-value=1.1e+02 Score=26.55 Aligned_cols=24 Identities=13% Similarity=0.063 Sum_probs=21.3
Q ss_pred cCCCCHHHHHHHHHHHHHcCeEEe
Q 041357 119 DEFPSRDVFEAACDYARDQSGLLW 142 (169)
Q Consensus 119 ~~f~s~~~f~~~~~yA~~~g~llw 142 (169)
..+.|++|+..+++||++.|+-|-
T Consensus 54 ~~~yT~~ei~ei~~yA~~~gI~vI 77 (301)
T cd06565 54 RGAYTKEEIREIDDYAAELGIEVI 77 (301)
T ss_pred CCCcCHHHHHHHHHHHHHcCCEEE
Confidence 567899999999999999999763
No 49
>cd03082 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH is a heterodimeric NAD-dependent enzyme catalyzing the conversion of formate to carbon dioxide. The beta subunit is a fusion protein containing an N-terminal NuoE domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. Similarly, the beta subunit of W-FDH is most likely involved in the electron transport chain during the NAD-dependen
Probab=20.04 E-value=84 Score=21.75 Aligned_cols=20 Identities=30% Similarity=0.448 Sum_probs=16.5
Q ss_pred CceEE-----EEeCHHHHHHHHHcC
Q 041357 54 PNLIV-----GAITKESLYNAFENG 73 (169)
Q Consensus 54 PNlvv-----g~iTR~Sv~~Al~~G 73 (169)
|+|.| +.+|.+++.++++.|
T Consensus 48 P~v~V~~~~~~~~t~~~i~~~~~~~ 72 (72)
T cd03082 48 PAALVGQRPVDGATPAAVAAAVEAG 72 (72)
T ss_pred CeEEECCEEeCCcCHHHHHHHHhcC
Confidence 77765 578999999999876
Done!