Query psy11221
Match_columns 202
No_of_seqs 197 out of 583
Neff 3.3
Searched_HMMs 46136
Date Fri Aug 16 21:16:32 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11221.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11221hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0567 SucA 2-oxoglutarate de 100.0 1.3E-58 2.9E-63 454.7 8.2 153 6-175 170-337 (906)
2 KOG0450|consensus 100.0 1E-55 2.2E-60 428.1 8.2 151 9-175 247-413 (1017)
3 PRK12270 kgd alpha-ketoglutara 100.0 1.5E-53 3.4E-58 423.2 8.4 150 9-174 491-658 (1228)
4 TIGR00239 2oxo_dh_E1 2-oxoglut 100.0 1.6E-50 3.5E-55 400.1 9.8 149 9-174 187-354 (929)
5 cd02016 TPP_E1_OGDC_like Thiam 100.0 4.8E-45 1E-49 319.6 9.5 133 29-174 1-151 (265)
6 PRK09404 sucA 2-oxoglutarate d 100.0 1E-39 2.2E-44 323.4 9.7 149 9-174 187-353 (924)
7 KOG0451|consensus 100.0 5.6E-38 1.2E-42 300.9 5.8 143 12-174 161-330 (913)
8 PF00676 E1_dh: Dehydrogenase 98.1 8.9E-07 1.9E-11 78.3 1.3 122 27-175 7-135 (300)
9 PLN02374 pyruvate dehydrogenas 97.2 0.0003 6.5E-09 66.2 3.4 77 24-111 96-183 (433)
10 cd02000 TPP_E1_PDC_ADC_BCADC T 86.0 0.41 8.9E-06 42.1 1.6 115 28-175 10-138 (293)
11 TIGR00250 RNAse_H_YqgF RNAse H 66.6 5.8 0.00013 31.6 2.8 25 53-77 35-59 (130)
12 cd01987 USP_OKCHK USP domain i 59.7 11 0.00023 27.5 2.9 26 55-80 74-99 (124)
13 KOG4409|consensus 49.8 6.3 0.00014 37.5 0.4 36 166-202 93-128 (365)
14 PRK09982 universal stress prot 46.8 19 0.00042 27.6 2.6 26 55-81 92-117 (142)
15 cd00293 USP_Like Usp: Universa 45.9 70 0.0015 22.1 5.2 26 55-80 82-107 (130)
16 PRK15005 universal stress prot 45.2 27 0.00058 26.0 3.1 39 55-97 96-134 (144)
17 PF00582 Usp: Universal stress 44.2 36 0.00078 23.7 3.5 41 37-82 78-118 (140)
18 PF13353 Fer4_12: 4Fe-4S singl 40.9 66 0.0014 24.1 4.7 47 26-72 38-89 (139)
19 cd01988 Na_H_Antiporter_C The 39.9 38 0.00082 24.4 3.1 39 55-96 83-121 (132)
20 cd01989 STK_N The N-terminal d 37.7 41 0.00089 25.1 3.1 27 55-81 92-118 (146)
21 PRK00923 sirohydrochlorin coba 36.1 62 0.0013 24.7 3.9 44 27-73 21-66 (126)
22 PRK00865 glutamate racemase; P 35.7 83 0.0018 27.4 5.1 55 22-76 120-187 (261)
23 PLN02824 hydrolase, alpha/beta 34.2 14 0.0003 30.8 0.1 35 167-202 33-67 (294)
24 cd06533 Glyco_transf_WecG_TagA 33.5 1.8E+02 0.0039 23.7 6.5 57 27-98 60-117 (171)
25 PLN02679 hydrolase, alpha/beta 33.1 15 0.00033 32.6 0.1 35 167-202 92-126 (360)
26 PRK13586 1-(5-phosphoribosyl)- 32.8 39 0.00084 29.3 2.6 21 63-83 208-229 (232)
27 KOG3171|consensus 32.8 16 0.00035 33.4 0.3 44 44-87 170-216 (273)
28 TIGR02240 PHA_depoly_arom poly 32.6 20 0.00043 29.7 0.8 35 167-202 29-63 (276)
29 PRK00109 Holliday junction res 32.0 56 0.0012 26.3 3.2 24 54-77 42-65 (138)
30 PRK06489 hypothetical protein; 32.0 25 0.00053 31.0 1.3 37 166-202 72-117 (360)
31 PF03808 Glyco_tran_WecB: Glyc 30.0 2E+02 0.0044 23.4 6.2 48 27-74 62-109 (172)
32 PF02633 Creatininase: Creatin 29.2 83 0.0018 26.7 4.0 46 35-83 71-116 (237)
33 cd07766 DHQ_Fe-ADH Dehydroquin 25.5 2.6E+02 0.0057 24.5 6.5 45 28-73 41-86 (332)
34 PF03652 UPF0081: Uncharacteri 24.6 66 0.0014 25.8 2.4 29 55-83 40-70 (135)
35 cd03416 CbiX_SirB_N Sirohydroc 24.0 1.4E+02 0.003 21.7 3.8 43 27-72 19-63 (101)
36 COG0589 UspA Universal stress 23.7 86 0.0019 22.7 2.7 42 53-97 100-141 (154)
37 TIGR00067 glut_race glutamate 23.4 1.8E+02 0.0039 25.4 5.1 59 17-76 110-182 (251)
38 PRK03592 haloalkane dehalogena 23.4 29 0.00062 29.0 0.2 35 167-202 31-65 (295)
39 PF07273 DUF1439: Protein of u 22.3 54 0.0012 26.6 1.5 21 27-47 4-24 (152)
40 TIGR02495 NrdG2 anaerobic ribo 22.1 1.7E+02 0.0037 23.4 4.3 43 25-67 48-91 (191)
41 PRK00870 haloalkane dehalogena 22.0 32 0.00069 29.0 0.1 35 167-202 50-85 (302)
42 PF15230 SRRM_C: Serine/argini 21.2 33 0.00071 25.7 0.1 8 142-149 43-50 (66)
43 cd03412 CbiK_N Anaerobic cobal 20.4 1.1E+02 0.0024 23.9 2.9 46 27-72 20-75 (127)
No 1
>COG0567 SucA 2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, and related enzymes [Energy production and conversion]
Probab=100.00 E-value=1.3e-58 Score=454.71 Aligned_cols=153 Identities=33% Similarity=0.450 Sum_probs=142.4
Q ss_pred EecCchhhhhhhhccccccchHHHHHHhhhhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeec
Q psy11221 6 ISNSSEIVSPLLLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETT 85 (202)
Q Consensus 6 ~~~s~e~~~~ll~r~~~~~~Ae~FE~FL~~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~ 85 (202)
..+|.|++..+|-|+ +.||+||+||++||||+|||||||||||||+|+++|++|++.|+++|||||||||||||| +
T Consensus 170 ~~~~~e~k~~~l~~L---~~ae~fE~fl~~kf~g~KRFslEG~eslip~l~~~i~~~~~~G~~~vviGMaHRGRLNvL-~ 245 (906)
T COG0567 170 PTFTAEEKKAILKRL---TAAEGFERFLHTKFPGAKRFSLEGGESLIPMLDELIDRAGKQGVKEVVIGMAHRGRLNVL-V 245 (906)
T ss_pred CCCCHHHHHHHHHHH---HHHHHHHHHhhccCCCCccccccchhhHHHHHHHHHHHHHhcCcceEEecccccchHHHH-H
Confidence 357889999999999 899999999999999999999999999999999999999999999999999999999999 9
Q ss_pred ccCCCChhhhccc-CC-----CCCCCcccCceeecCCccccccccccccccCCCCceEEEeecCCCcceecCcEEE----
Q psy11221 86 GQGLQKVPRLFSQ-NP-----QNNGDIRHFVFFSSTPTFLHTFDWIKASQTQGDRGPHLTLNCWPRAMFLSTPVCI---- 155 (202)
Q Consensus 86 NVl~KP~~~IF~E-~~-----~~sGDVKYHLG~Ss~~~~le~~d~v~~~~t~~g~~vhlsL~~NPSHLEaVnPVv~---- 155 (202)
||||||++.||+| ++ ..+||||||+|+|+++ +|.+| .|||+|++||||||+|||||+
T Consensus 246 nvlgKp~~~if~eF~g~~~~~~~sGDVKYH~G~~~~~------------~~~~~-~v~l~La~NPSHLE~v~PVV~G~vR 312 (906)
T COG0567 246 NVLGKPYRDIFDEFEGKSAEPDLSGDVKYHLGFSSDR------------QTDGG-KVHLSLAFNPSHLEIVNPVVEGSVR 312 (906)
T ss_pred HHhCCCHHHHHHHhCCCCCCCCccccccccccccccc------------ccCCC-eeEEEecCCcchhhhhchhhhcchH
Confidence 9999999999999 44 2599999999999986 56666 899999999999999999999
Q ss_pred -----eccCCCCeEEEEEEeccccc
Q psy11221 156 -----LHETFRPIFTPIIFFFFALS 175 (202)
Q Consensus 156 -----~~~~~~~~v~PIlih~~~~~ 175 (202)
+.++.+++++||++||||--
T Consensus 313 a~Qd~~~d~~~~k~lpiliHGDAAf 337 (906)
T COG0567 313 AKQDRLGDTERDKVLPILIHGDAAF 337 (906)
T ss_pred hhhhhhccCccceeEEEEEecChhc
Confidence 56677889999999999864
No 2
>KOG0450|consensus
Probab=100.00 E-value=1e-55 Score=428.12 Aligned_cols=151 Identities=37% Similarity=0.550 Sum_probs=140.8
Q ss_pred CchhhhhhhhccccccchHHHHHHhhhhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeecccC
Q psy11221 9 SSEIVSPLLLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQG 88 (202)
Q Consensus 9 s~e~~~~ll~r~~~~~~Ae~FE~FL~~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl 88 (202)
|.|++..+|.|+ ++++.||+||++||++.|||||||||+|||+|++||+++++.||++|||||||||||||| +||+
T Consensus 247 s~e~k~~il~RL---~~st~FE~FLa~Kw~seKRFGLEGcE~lIP~mK~iiDrS~elGVe~iviGMpHRGRLNvL-~NVv 322 (1017)
T KOG0450|consen 247 SHEQKRVILDRL---TRSTRFEEFLATKWPSEKRFGLEGCEVLIPAMKTIIDRSSELGVESIVIGMPHRGRLNVL-ANVV 322 (1017)
T ss_pred CHHHHHHHHHHH---HHhhHHHHHHhhhCCccccccccchhhhhhHHHHHhhhhhhcCchheEecCCccchhHHH-HHHH
Confidence 456888999999 999999999999999999999999999999999999999999999999999999999999 9999
Q ss_pred CCChhhhccc-CC-----CCCCCcccCceeecCCccccccccccccccC-CCCceEEEeecCCCcceecCcEEE------
Q psy11221 89 LQKVPRLFSQ-NP-----QNNGDIRHFVFFSSTPTFLHTFDWIKASQTQ-GDRGPHLTLNCWPRAMFLSTPVCI------ 155 (202)
Q Consensus 89 ~KP~~~IF~E-~~-----~~sGDVKYHLG~Ss~~~~le~~d~v~~~~t~-~g~~vhlsL~~NPSHLEaVnPVv~------ 155 (202)
+||+++||+| ++ +||||||||||.+.++ .++ +||.|+|+|++||||||||||||+
T Consensus 323 RKpl~qIfseF~g~~~~DeGSGDVKYHLG~~~~R------------~~r~s~k~i~LslVANPSHLEA~DPVV~GKtrA~ 390 (1017)
T KOG0450|consen 323 RKPLEQIFSEFSGLEAADEGSGDVKYHLGMYYER------------PNRVSGKNITLSLVANPSHLEAVDPVVMGKTRAE 390 (1017)
T ss_pred hhHHHHHHHhccCCCCCcCCCCceeeeecccccc------------ccccCCceeEEEEecCchhhcccCceeechHHHH
Confidence 9999999999 32 4999999999998664 554 799999999999999999999999
Q ss_pred ---eccCCCCeEEEEEEeccccc
Q psy11221 156 ---LHETFRPIFTPIIFFFFALS 175 (202)
Q Consensus 156 ---~~~~~~~~v~PIlih~~~~~ 175 (202)
.+|.+++|++.|||||||--
T Consensus 391 q~y~~D~~~~k~m~ILiHGDaaF 413 (1017)
T KOG0450|consen 391 QFYTGDEEGKKVMGILIHGDAAF 413 (1017)
T ss_pred HHhccccccceeEEEEEecchhh
Confidence 57788999999999999854
No 3
>PRK12270 kgd alpha-ketoglutarate decarboxylase; Reviewed
Probab=100.00 E-value=1.5e-53 Score=423.25 Aligned_cols=150 Identities=28% Similarity=0.367 Sum_probs=136.7
Q ss_pred CchhhhhhhhccccccchHHHHHHhhhhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeecccC
Q psy11221 9 SSEIVSPLLLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQG 88 (202)
Q Consensus 9 s~e~~~~ll~r~~~~~~Ae~FE~FL~~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl 88 (202)
+.|++..+|-|+ +.||.||.|||+||+|||||||||+||+||+||++++.|++.|.++|||||||||||||| +||.
T Consensus 491 ~~~eq~~iL~~L---naaEaFEtFLqtkyvGqkRFslEG~Es~iplld~~~~~aa~~~l~evvigm~HRGRLNVL-ani~ 566 (1228)
T PRK12270 491 TREEQKRILSKL---NAAEAFETFLQTKYVGQKRFSLEGGESLIPLLDAVLDQAAEHGLDEVVIGMAHRGRLNVL-ANIV 566 (1228)
T ss_pred CHHHHHHHHHHh---hhHHHHHHHHhhhcccceeeeecchhhHHHHHHHHHHHHHhcCCceEEecccccchHHHH-HHHh
Confidence 457888999999 889999999999999999999999999999999999999999999999999999999999 9999
Q ss_pred CCChhhhccc-CC-------CCCCCcccCceeecCCccccccccccccccCCCCceEEEeecCCCcceecCcEEE-----
Q psy11221 89 LQKVPRLFSQ-NP-------QNNGDIRHFVFFSSTPTFLHTFDWIKASQTQGDRGPHLTLNCWPRAMFLSTPVCI----- 155 (202)
Q Consensus 89 ~KP~~~IF~E-~~-------~~sGDVKYHLG~Ss~~~~le~~d~v~~~~t~~g~~vhlsL~~NPSHLEaVnPVv~----- 155 (202)
||||.+||+| ++ .||||||||||++.+. .+.+|+++.++|++|||||||||||+.
T Consensus 567 gK~y~qiF~EFegn~dp~~~~GsGDVKYHlG~eG~~------------~~~~g~~~~v~laaNPSHLEavdpVleGivRa 634 (1228)
T PRK12270 567 GKPYSQIFREFEGNLDPRSAQGSGDVKYHLGAEGTF------------TQMFGDEIKVSLAANPSHLEAVDPVLEGIVRA 634 (1228)
T ss_pred cCCHHHHHHHhcCCCCccccCcCcceeeeccCceee------------eccCCCeeEEEEecCchhhhhcchHhhhhhhh
Confidence 9999999999 54 2899999999999875 455688899999999999999999998
Q ss_pred ----ec-cCCCCeEEEEEEecccc
Q psy11221 156 ----LH-ETFRPIFTPIIFFFFAL 174 (202)
Q Consensus 156 ----~~-~~~~~~v~PIlih~~~~ 174 (202)
++ ..++-.|+||+|||||-
T Consensus 635 kQd~l~~g~~~~~vlpi~~hGdaa 658 (1228)
T PRK12270 635 KQDRLDKGEEGFTVLPILLHGDAA 658 (1228)
T ss_pred hhhhhcccccCCceeEEEEecccc
Confidence 22 11246999999999986
No 4
>TIGR00239 2oxo_dh_E1 2-oxoglutarate dehydrogenase, E1 component. The E1 ortholog from Corynebacterium glutamicum is unusual in having an N-terminal extension that resembles the dihydrolipoamide succinyltransferase (E2) component of 2-oxoglutarate dehydrogenase.
Probab=100.00 E-value=1.6e-50 Score=400.06 Aligned_cols=149 Identities=31% Similarity=0.417 Sum_probs=135.0
Q ss_pred CchhhhhhhhccccccchHHHHHHhhhhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeecccC
Q psy11221 9 SSEIVSPLLLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQG 88 (202)
Q Consensus 9 s~e~~~~ll~r~~~~~~Ae~FE~FL~~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl 88 (202)
|.|++..+|-|+ ++||.||+||++||+|+|||||||||||||+|+++|++|+++||+++|+||||||||||| +||+
T Consensus 187 ~~~~k~~il~~L---~~ae~fE~fl~~kf~g~KRFslEG~eslip~l~~~i~~~~~~gv~d~v~gmaHRGRlnvL-~nv~ 262 (929)
T TIGR00239 187 NSEEKKRFLSRL---TAAEGFERFLGAKFPGAKRFSLEGLDALVPMLKEIIRHSVNSGTRDVVLGMAHRGRLNVL-VNVL 262 (929)
T ss_pred CHHHHHHHHHHH---HHHHHHHHHHHHhCCCCceeecccHHHHHHHHHHHHHHHHHcCCCeEEeccccCCcHHHH-HHHh
Confidence 668888999999 999999999999999999999999999999999999999999999999999999999999 9999
Q ss_pred CCChhhhccc-CC----C---CCCCcccCce-eecCCccccccccccccccCCCCceEEEeecCCCcceecCcEEE----
Q psy11221 89 LQKVPRLFSQ-NP----Q---NNGDIRHFVF-FSSTPTFLHTFDWIKASQTQGDRGPHLTLNCWPRAMFLSTPVCI---- 155 (202)
Q Consensus 89 ~KP~~~IF~E-~~----~---~sGDVKYHLG-~Ss~~~~le~~d~v~~~~t~~g~~vhlsL~~NPSHLEaVnPVv~---- 155 (202)
|||+++||+| .+ . ++||||||+| +|++. ++ .|+.+|++|++||||||+|||||+
T Consensus 263 gkp~~~if~ef~g~~~~~~~~g~gdvKyHlg~~~~~~------------~~-~~~~~~~~l~~npSHLeav~Pva~G~Ar 329 (929)
T TIGR00239 263 GKPPEDIFSEFAGKHKSHLPDGTGDVKYHMGRFSSDF------------TT-DGKLVHLALAFNPSHLEIVSPVVIGSTR 329 (929)
T ss_pred CCCHHHHHHHHcCCCCCcccCCCCCcCccCCCccccc------------cc-CCCcceeeecCCCcccccccchhhhHHH
Confidence 9999999999 32 1 6999999999 88775 34 455799999999999999999999
Q ss_pred ----e-cc-CCCCeEEEEEEecccc
Q psy11221 156 ----L-HE-TFRPIFTPIIFFFFAL 174 (202)
Q Consensus 156 ----~-~~-~~~~~v~PIlih~~~~ 174 (202)
. .+ +.+++.+||++|||+-
T Consensus 330 A~q~~~~~~~~~~~~v~v~~~GDgA 354 (929)
T TIGR00239 330 ARLDRLNDSPESTKVLAILIHGDAA 354 (929)
T ss_pred HHHHhcCCcccccceEEEEEecccc
Confidence 2 22 4466899999999987
No 5
>cd02016 TPP_E1_OGDC_like Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of the tricarboxylic acid cycle.
Probab=100.00 E-value=4.8e-45 Score=319.55 Aligned_cols=133 Identities=38% Similarity=0.577 Sum_probs=120.7
Q ss_pred HHHHhhhhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeecccCCCChhhhccc-CC-------
Q psy11221 29 FEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQGLQKVPRLFSQ-NP------- 100 (202)
Q Consensus 29 FE~FL~~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl~KP~~~IF~E-~~------- 100 (202)
||+||++||+|+||||+||+|++||+|+++++.++++||+++|+|||||||||+| +|++|||+++||+| .+
T Consensus 1 ~e~f~~~~f~~~krfs~eG~Es~~~~l~~~~~~~~~~~~~d~v~gm~HRgrln~L-~~~lg~~~~~if~ef~g~~~~~~~ 79 (265)
T cd02016 1 FEQFLATKFPGQKRFGLEGAESLIPALDELIDRAAELGVEEVVIGMAHRGRLNVL-ANVLGKPLEQIFSEFEGKSEFPED 79 (265)
T ss_pred ChhhHHHhcCCCeEEEecCHHHHHHHHHHHHHHHHhcCCCeEEeccCcCCcHHHH-HHHhCCCHHHHHHHhhCCCCCCCC
Confidence 8999999999999999999999999999999999999999999999999999999 99999999999999 32
Q ss_pred -CCCCCcccCceeecCCccccccccccccccCCCCceEEEeecCCCcceecCcEEE--------e-ccCCCCeEEEEEEe
Q psy11221 101 -QNNGDIRHFVFFSSTPTFLHTFDWIKASQTQGDRGPHLTLNCWPRAMFLSTPVCI--------L-HETFRPIFTPIIFF 170 (202)
Q Consensus 101 -~~sGDVKYHLG~Ss~~~~le~~d~v~~~~t~~g~~vhlsL~~NPSHLEaVnPVv~--------~-~~~~~~~v~PIlih 170 (202)
.++||||||+|++.+. ++.+|+.+|++|++||||||+++||+. . .++.+++.++|++|
T Consensus 80 ~~~~gdv~yHlg~~~~~------------~~~~~~~~~~~l~~npS~l~~~~pva~G~A~A~k~~~~~~~~~~~v~v~~~ 147 (265)
T cd02016 80 DEGSGDVKYHLGYSSDR------------KTPSGKKVHLSLAPNPSHLEAVNPVVMGKTRAKQDYRGDGERDKVLPILIH 147 (265)
T ss_pred CCCCCCcCcCCccCccc------------ccCCCCeeEEEecCCCcccccccCeehhHHHHHHHhcCCccCCCeEEEEEe
Confidence 1579999999999775 455577899999999999999999999 1 22334689999999
Q ss_pred cccc
Q psy11221 171 FFAL 174 (202)
Q Consensus 171 ~~~~ 174 (202)
||+-
T Consensus 148 GDgA 151 (265)
T cd02016 148 GDAA 151 (265)
T ss_pred cCcc
Confidence 9986
No 6
>PRK09404 sucA 2-oxoglutarate dehydrogenase E1 component; Reviewed
Probab=100.00 E-value=1e-39 Score=323.36 Aligned_cols=149 Identities=32% Similarity=0.454 Sum_probs=132.5
Q ss_pred CchhhhhhhhccccccchHHHHHHhhhhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeecccC
Q psy11221 9 SSEIVSPLLLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQG 88 (202)
Q Consensus 9 s~e~~~~ll~r~~~~~~Ae~FE~FL~~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl 88 (202)
|.|++..++-++ ++++.||+||++||+++||||+||+|++||+++++++.|+++|++++|+||+||||||+| +|++
T Consensus 187 s~e~~~~il~~m---~~~r~fE~fl~~~f~~~Krf~~eG~Ea~i~gl~~li~~a~~lg~~D~vigmaHRgrlnvL-a~v~ 262 (924)
T PRK09404 187 SAEEKKAILERL---TAAEGFERFLHTKFVGQKRFSLEGGESLIPMLDEIIRRAGKLGVKEIVIGMAHRGRLNVL-VNVL 262 (924)
T ss_pred CHHHHHHHHHHH---HHHHHHHHHHHHHhccCCcccccchhhHHHHHHHHHHHHHhCCCCCEEEecCcCchHHHH-HHhc
Confidence 445666666666 789999999999999999999999999999999999999999999999999999999999 9999
Q ss_pred CCChhhhccc-CCC-------CCCCcccCceeecCCccccccccccccccCCCCceEEEeecCCCcceecCcEEE-----
Q psy11221 89 LQKVPRLFSQ-NPQ-------NNGDIRHFVFFSSTPTFLHTFDWIKASQTQGDRGPHLTLNCWPRAMFLSTPVCI----- 155 (202)
Q Consensus 89 ~KP~~~IF~E-~~~-------~sGDVKYHLG~Ss~~~~le~~d~v~~~~t~~g~~vhlsL~~NPSHLEaVnPVv~----- 155 (202)
|||+++||+| .++ ++||||||+|++.+. +.. |+.+|++|++||||||+||||+.
T Consensus 263 G~~~~~ifaEf~Gk~~~~~~~~~GdvkyHlG~~~~~------------~g~-gg~mhi~l~~npShleav~Pva~G~A~A 329 (924)
T PRK09404 263 GKPPRDLFAEFEGKHGPDEVLGSGDVKYHLGFSSDR------------ETD-GGEVHLSLAFNPSHLEIVNPVVEGSVRA 329 (924)
T ss_pred CCCHHHHHHHHcCCCCCCCCCCCCCcccccCccccc------------cCC-CCeeEeeccCCccccccccCeehhHHHH
Confidence 9999999999 443 489999999999875 343 55899999999999999999999
Q ss_pred ----ecc-CCCCeEEEEEEecccc
Q psy11221 156 ----LHE-TFRPIFTPIIFFFFAL 174 (202)
Q Consensus 156 ----~~~-~~~~~v~PIlih~~~~ 174 (202)
..+ +++++++||++|||+-
T Consensus 330 ~q~~~~~~~~~~~~v~v~~~GDgA 353 (924)
T PRK09404 330 RQDRRGDGQDRKKVLPILIHGDAA 353 (924)
T ss_pred HHHhcCCcccccceEEEEEecCcc
Confidence 233 4567799999999986
No 7
>KOG0451|consensus
Probab=100.00 E-value=5.6e-38 Score=300.92 Aligned_cols=143 Identities=26% Similarity=0.371 Sum_probs=128.9
Q ss_pred hhhhhhhccccccchHHHHHHhhhhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeecccCCCC
Q psy11221 12 IVSPLLLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQGLQK 91 (202)
Q Consensus 12 ~~~~ll~r~~~~~~Ae~FE~FL~~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl~KP 91 (202)
++++||++| +.|++||++|||+.||||.||+|||+.++.++++.+++.+|++||||||||||||+| +.+|+.|
T Consensus 161 ~i~~Lmlks------q~fD~FlatKFpTvKRYGgEGAESM~aFF~eLl~~sa~~~ie~viigmpHRGRlnLl-t~Ll~fp 233 (913)
T KOG0451|consen 161 EIAELMLKS------QAFDNFLATKFPTVKRYGGEGAESMLAFFWELLRDSAQANIEHVIIGMPHRGRLNLL-TALLNFP 233 (913)
T ss_pred HHHHHHHhh------hhHHHHHHhccchhhhhccccHHHHHHHHHHHHHHHHhcCcceEEEeccccCcchHH-HHHhcCC
Confidence 788999988 779999999999999999999999999999999999999999999999999999999 9999999
Q ss_pred hhhhccc-CC--------CCCCCcccCceeecCCccccccccccccccCCCCceEEEeecCCCcceecCcEEE-------
Q psy11221 92 VPRLFSQ-NP--------QNNGDIRHFVFFSSTPTFLHTFDWIKASQTQGDRGPHLTLNCWPRAMFLSTPVCI------- 155 (202)
Q Consensus 92 ~~~IF~E-~~--------~~sGDVKYHLG~Ss~~~~le~~d~v~~~~t~~g~~vhlsL~~NPSHLEaVnPVv~------- 155 (202)
++.+|.+ .+ +..|||.+|+-.|-|. +. .|+++|++|++|||||||||||.|
T Consensus 234 P~~mFRK~~G~sEFpE~~~A~gDVlSHl~sS~dy------------kg-~~~~lhvtMlpNPSHLEAvNPVAmGKtR~rq 300 (913)
T KOG0451|consen 234 PAKMFRKLSGASEFPEDIEAMGDVLSHLHSSEDY------------KG-LGKKLHVTMLPNPSHLEAVNPVAMGKTRSRQ 300 (913)
T ss_pred HHHHHHHhcCcccCchhhhHHHHHHHHhhhhhhh------------cc-cCCceEEEecCChhhhhccCchhhcchhHHH
Confidence 9999999 33 2689999999877664 33 466899999999999999999999
Q ss_pred --ec---------cCCCCeEEEEEEecccc
Q psy11221 156 --LH---------ETFRPIFTPIIFFFFAL 174 (202)
Q Consensus 156 --~~---------~~~~~~v~PIlih~~~~ 174 (202)
++ ...++.|+-+++||||-
T Consensus 301 qsr~~Gdyspd~sa~~Gd~Vlnv~vHGDaa 330 (913)
T KOG0451|consen 301 QSRGEGDYSPDSSAPFGDHVLNVIVHGDAA 330 (913)
T ss_pred HhhcCCCCCCCCcCCCCCceEEEEEecchh
Confidence 11 13478999999999984
No 8
>PF00676 E1_dh: Dehydrogenase E1 component; InterPro: IPR001017 This entry includes a number of dehydrogenases all of which use thiamine pyrophosphate as a cofactor and are members of a multienzyme complex. Pyruvate dehydrogenase (1.2.4.1 from EC), a component of the multienzyme pyruvate dehydrogenase complex; 2-oxoglutarate dehydrogenase (1.2.4.2 from EC), a component of the multienzyme 2-oxoglutarate dehydrogenase which contains multiple copies of three enzymatic components: 2-oxoglutarate dehydrogenase (E1), dihydrolipoamide succinyltransferase (E2) and lipoamide dehydrogenase (E3); and 2-oxoisovalerate dehydrogenase (1.2.4.4 from EC), a component of the multienzyme branched-chain alpha-keto dehydrogenase complex all belong to this family.; GO: 0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor, 0008152 metabolic process; PDB: 1X7Y_A 1V1M_A 1X7W_A 1OLU_A 2J9F_A 2BEW_A 1V11_A 2BFE_A 1U5B_A 2BEU_A ....
Probab=98.11 E-value=8.9e-07 Score=78.35 Aligned_cols=122 Identities=20% Similarity=0.175 Sum_probs=89.2
Q ss_pred HHHHHHhhhhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeecccCCCChhhhccc-CC--CCC
Q psy11221 27 SEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQGLQKVPRLFSQ-NP--QNN 103 (202)
Q Consensus 27 e~FE~FL~~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl~KP~~~IF~E-~~--~~s 103 (202)
..||..+.++|..+||+|......-..++...+..+.+.+ +.++++ ||++.++| + .+-|+.++|+| .+ ++.
T Consensus 7 ~r~~d~~~~~~~~~~~~g~~~~~~GqEa~~v~~~~~l~~~--D~v~~~-yR~~~~~l-a--~g~~~~~~~~e~~g~~~g~ 80 (300)
T PF00676_consen 7 RRFEDERARKLQRQGRFGFYHLSAGQEAIQVAAAAALRPG--DWVFPY-YRDHGHAL-A--RGIDLEEIFAELLGKAKGH 80 (300)
T ss_dssp HHHHHHHHHHHHHTTSSSCTT-TTTCHHHHHHHHHHSCTT--SEEEEC-STTHHHHH-H--TTT-HHHHHHHHHTBTTST
T ss_pred HHHHHHHHHHHhhCCCeEEecchHHHHHHHHHHHHhccCC--CEEEec-ccchhhhh-h--ccccccchhHHhcCcccCC
Confidence 5699999999999999999988888888887777766665 877776 99999999 5 46679999999 32 234
Q ss_pred CCcccCceeecCCccccccccccccccCCCCceEEEeecCCCcceecCcEEE---e-ccCCCCeEEEEEEeccccc
Q psy11221 104 GDIRHFVFFSSTPTFLHTFDWIKASQTQGDRGPHLTLNCWPRAMFLSTPVCI---L-HETFRPIFTPIIFFFFALS 175 (202)
Q Consensus 104 GDVKYHLG~Ss~~~~le~~d~v~~~~t~~g~~vhlsL~~NPSHLEaVnPVv~---~-~~~~~~~v~PIlih~~~~~ 175 (202)
|+..+.+.++ .+..++....+|+|.+ .|++. + ....+.+.++|.+|||+-+
T Consensus 81 ~g~~~~~~~~-------------------~~~~~~~~~~~~vg~~--~p~a~G~A~a~k~~~~~~v~v~~~GDga~ 135 (300)
T PF00676_consen 81 GGGRHPLHFS-------------------DKGLNILGASSPVGAQ--VPIAAGVALAIKYRGKDGVVVCFFGDGAT 135 (300)
T ss_dssp TTTGCTTEEE-------------------BTTTTBEEEESSTTTH--HHHHHHHHHHHHHTTSSEEEEEEEETGGG
T ss_pred CCCccccccc-------------------cccceeeecccccccc--CccccchhHhhhhcCCceeEEEEecCccc
Confidence 4444312111 1234677888888888 78777 1 2234588999999999863
No 9
>PLN02374 pyruvate dehydrogenase (acetyl-transferring)
Probab=97.18 E-value=0.0003 Score=66.25 Aligned_cols=77 Identities=18% Similarity=0.291 Sum_probs=63.3
Q ss_pred cchHHHHHHhhhhcCCceeecc----cChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeecccCCCChhhhccc-
Q psy11221 24 FSNSEFEAFLAKKWSSEKRFGL----EGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQGLQKVPRLFSQ- 98 (202)
Q Consensus 24 ~~Ae~FE~FL~~KF~g~KRFsL----EG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl~KP~~~IF~E- 98 (202)
..+-.||+.+.+.|...|.||. .|.|++.+++...++. ++.+++ .||++.++| ..|.++.++|+|
T Consensus 96 ~~~R~fEe~~~~l~~~Gki~g~~h~~~GqEA~~vg~~~aL~~------~D~v~~-~yR~h~~~L---a~G~~~~~~mael 165 (433)
T PLN02374 96 VLGRSFEDMCAQMYYRGKMFGFVHLYNGQEAVSTGFIKLLKK------DDSVVS-TYRDHVHAL---SKGVPARAVMSEL 165 (433)
T ss_pred HHHHHHHHHHHHHHhCCcceeccCCCCCcHHHHHHHHHHcCC------CCEEEc-cCcChHHhh---hcCCCHHHHHHHH
Confidence 4557799999999999999887 9999998887766653 488899 999999999 679999999999
Q ss_pred CCC------CCCCcccCce
Q psy11221 99 NPQ------NNGDIRHFVF 111 (202)
Q Consensus 99 ~~~------~sGDVKYHLG 111 (202)
.++ +.|+ .+|++
T Consensus 166 ~Gk~~g~~~Grgg-smH~~ 183 (433)
T PLN02374 166 FGKATGCCRGQGG-SMHMF 183 (433)
T ss_pred cCCCCCCCCCCCC-cCccC
Confidence 332 4444 67873
No 10
>cd02000 TPP_E1_PDC_ADC_BCADC Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex (BCADC). PDC catalyzes the irreversible oxidative decarboxylation of pyruvate to produce acetyl-CoA in the bridging step between glycolysis and the citric acid cycle. ADC participates in the breakdown of acetoin while BCADC participates in the breakdown of branched chain amino acids. BCADC catalyzes the oxidative decarboxylation of 4-methyl-2-oxopentanoate, 3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate (branched chain 2-oxo acids derived from the transamination of leucine, valine and isoleucine).
Probab=86.04 E-value=0.41 Score=42.07 Aligned_cols=115 Identities=11% Similarity=-0.002 Sum_probs=76.5
Q ss_pred HHHHHhhhhcCCceeec----ccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeecccCCCChhhhccc-CCCC
Q psy11221 28 EFEAFLAKKWSSEKRFG----LEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQGLQKVPRLFSQ-NPQN 102 (202)
Q Consensus 28 ~FE~FL~~KF~g~KRFs----LEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl~KP~~~IF~E-~~~~ 102 (202)
.||.-+.+.|-..|=.+ ..|-|+.-+++...++ -++.+++ .||++-..| + .|.|+.++|+| .++.
T Consensus 10 ~~e~~~~~~~~~g~~~~~~~~~~GqEa~~vg~~~~l~------~~D~~~~-~yR~~~~~l-a--~G~~~~~~~~e~~g~~ 79 (293)
T cd02000 10 RFDERLLELYRQGKIGGFYHLSIGQEAVAVGVAAALR------PGDWVFP-TYRDHGHAL-A--RGVDLKEMLAELFGKE 79 (293)
T ss_pred HHHHHHHHHHHCCccccccCCCCChHHHHHHHHHHCC------CCCEEEe-cchhHHHHH-H--cCCCHHHHHHHHcCCC
Confidence 36666666654443333 7899999777665544 2477888 999999999 4 89999999999 3321
Q ss_pred CC-----CcccCceeecCCccccccccccccccCCCCceEEEeecCCCcceecCcEEE---ec-cCCCCeEEEEEEeccc
Q psy11221 103 NG-----DIRHFVFFSSTPTFLHTFDWIKASQTQGDRGPHLTLNCWPRAMFLSTPVCI---LH-ETFRPIFTPIIFFFFA 173 (202)
Q Consensus 103 sG-----DVKYHLG~Ss~~~~le~~d~v~~~~t~~g~~vhlsL~~NPSHLEaVnPVv~---~~-~~~~~~v~PIlih~~~ 173 (202)
.| +..+|++.. ...+....++|-..-|+.+ +. ...++.-..|.++||+
T Consensus 80 ~g~~~G~~g~~h~~~~-----------------------~~~~~~~~g~lG~~~p~a~G~a~a~k~~~~~~~vv~~~GDG 136 (293)
T cd02000 80 TGPCKGRGGSMHIGDK-----------------------EKNFFGGNGIVGGQVPLAAGAALALKYRGEDRVAVCFFGDG 136 (293)
T ss_pred CCCCCCCCCCCCCCch-----------------------hcCccccccccccchhHHHHHHHHHHHhCCCCEEEEEeCCC
Confidence 11 244555421 1235566789999999998 11 1123455789999997
Q ss_pred cc
Q psy11221 174 LS 175 (202)
Q Consensus 174 ~~ 175 (202)
-.
T Consensus 137 a~ 138 (293)
T cd02000 137 AT 138 (293)
T ss_pred cc
Confidence 64
No 11
>TIGR00250 RNAse_H_YqgF RNAse H-fold protein YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC.
Probab=66.65 E-value=5.8 Score=31.59 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHhcCCceEEeecCCc
Q psy11221 53 PAMKQVIDKSTELGVESVVMGMPHR 77 (202)
Q Consensus 53 P~L~~iI~~aa~~GV~~IViGMaHR 77 (202)
+.++++.+...+.+++.||+|+|-.
T Consensus 35 ~~~~~l~~~i~~~~~~~iVvGlP~~ 59 (130)
T TIGR00250 35 PDWSRIEELLKEWTPDKIVVGLPLN 59 (130)
T ss_pred HHHHHHHHHHHHcCCCEEEEeccCC
Confidence 3456666777789999999999975
No 12
>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.
Probab=59.67 E-value=11 Score=27.55 Aligned_cols=26 Identities=19% Similarity=0.404 Sum_probs=23.1
Q ss_pred HHHHHHHHHhcCCceEEeecCCcccc
Q psy11221 55 MKQVIDKSTELGVESVVMGMPHRGNL 80 (202)
Q Consensus 55 L~~iI~~aa~~GV~~IViGMaHRGRL 80 (202)
-+.|++.+.+.+++-||||..+|+.+
T Consensus 74 ~~~I~~~~~~~~~dllviG~~~~~~~ 99 (124)
T cd01987 74 AEAIVEFAREHNVTQIVVGKSRRSRW 99 (124)
T ss_pred HHHHHHHHHHcCCCEEEeCCCCCchH
Confidence 47788989999999999999999876
No 13
>KOG4409|consensus
Probab=49.82 E-value=6.3 Score=37.48 Aligned_cols=36 Identities=25% Similarity=0.299 Sum_probs=31.1
Q ss_pred EEEEeccccccccccceeeeeeeeEEEEEEeecCCCC
Q psy11221 166 PIIFFFFALSHVQMGSAFDIDLSISFRVIALRPTGFG 202 (202)
Q Consensus 166 PIlih~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 (202)
=|+||||+-+---.+..|| ||+--+.|.|+.+.|||
T Consensus 93 lVliHGyGAg~g~f~~Nf~-~La~~~~vyaiDllG~G 128 (365)
T KOG4409|consen 93 LVLIHGYGAGLGLFFRNFD-DLAKIRNVYAIDLLGFG 128 (365)
T ss_pred EEEEeccchhHHHHHHhhh-hhhhcCceEEecccCCC
Confidence 4689999998887888887 67778999999999998
No 14
>PRK09982 universal stress protein UspD; Provisional
Probab=46.83 E-value=19 Score=27.55 Aligned_cols=26 Identities=12% Similarity=0.185 Sum_probs=21.1
Q ss_pred HHHHHHHHHhcCCceEEeecCCccccc
Q psy11221 55 MKQVIDKSTELGVESVVMGMPHRGNLI 81 (202)
Q Consensus 55 L~~iI~~aa~~GV~~IViGMaHRGRLN 81 (202)
-++|++.|.+.+++=|||| .||+-+.
T Consensus 92 ~~~I~~~A~~~~aDLIVmG-~~~~~~~ 117 (142)
T PRK09982 92 PETLLEIMQKEQCDLLVCG-HHHSFIN 117 (142)
T ss_pred HHHHHHHHHHcCCCEEEEe-CChhHHH
Confidence 4778899999999999999 6765443
No 15
>cd00293 USP_Like Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, athough Usp lacks ATP-binding activity.
Probab=45.85 E-value=70 Score=22.12 Aligned_cols=26 Identities=31% Similarity=0.611 Sum_probs=23.4
Q ss_pred HHHHHHHHHhcCCceEEeecCCcccc
Q psy11221 55 MKQVIDKSTELGVESVVMGMPHRGNL 80 (202)
Q Consensus 55 L~~iI~~aa~~GV~~IViGMaHRGRL 80 (202)
.+++++.+.+.+++-+|+|...|+.+
T Consensus 82 ~~~i~~~~~~~~~dlvvig~~~~~~~ 107 (130)
T cd00293 82 AEAILEAAEELGADLIVMGSRGRSGL 107 (130)
T ss_pred HHHHHHHHHHcCCCEEEEcCCCCCcc
Confidence 58899999999999999999888875
No 16
>PRK15005 universal stress protein F; Provisional
Probab=45.20 E-value=27 Score=26.01 Aligned_cols=39 Identities=8% Similarity=0.136 Sum_probs=26.8
Q ss_pred HHHHHHHHHhcCCceEEeecCCccccceeecccCCCChhhhcc
Q psy11221 55 MKQVIDKSTELGVESVVMGMPHRGNLISETTGQGLQKVPRLFS 97 (202)
Q Consensus 55 L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl~KP~~~IF~ 97 (202)
-++|++.|.+.+++=||+| +||+ +.. --++|--..++..
T Consensus 96 ~~~I~~~a~~~~~DLIV~G-s~~~--~~~-~~llGS~a~~vl~ 134 (144)
T PRK15005 96 KDRILELAKKIPADMIIIA-SHRP--DIT-TYLLGSNAAAVVR 134 (144)
T ss_pred HHHHHHHHHHcCCCEEEEe-CCCC--Cch-heeecchHHHHHH
Confidence 3788999999999999999 6654 323 3345655555544
No 17
>PF00582 Usp: Universal stress protein family; InterPro: IPR006016 The universal stress protein UspA P28242 from SWISSPROT [] is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity. The crystal structure of Haemophilus influenzae UspA [] reveals an alpha/beta fold similar to that of the Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0577 protein, which binds ATP [], though UspA lacks ATP-binding activity.; GO: 0006950 response to stress; PDB: 3DLO_C 3QTB_A 2PFS_A 3TNJ_A 1JMV_D 3FH0_B 3FDX_B 3AB7_A 3AB8_A 2GM3_F ....
Probab=44.20 E-value=36 Score=23.73 Aligned_cols=41 Identities=20% Similarity=0.156 Sum_probs=30.3
Q ss_pred cCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccce
Q psy11221 37 WSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLIS 82 (202)
Q Consensus 37 F~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNV 82 (202)
.......-..| ..-+++++.+.+.+++-||+|-..|+++.=
T Consensus 78 ~~~~~~~~~~~-----~~~~~i~~~~~~~~~dliv~G~~~~~~~~~ 118 (140)
T PF00582_consen 78 GIVIEVVIESG-----DVADAIIEFAEEHNADLIVMGSRGRSGLER 118 (140)
T ss_dssp TSEEEEEEEES-----SHHHHHHHHHHHTTCSEEEEESSSTTSTTT
T ss_pred cceeEEEEEee-----ccchhhhhccccccceeEEEeccCCCCccC
Confidence 34444444444 245778899999999999999999888753
No 18
>PF13353 Fer4_12: 4Fe-4S single cluster domain; PDB: 3C8F_A 3CB8_A 3T7V_A 2YX0_A 3CAN_A.
Probab=40.91 E-value=66 Score=24.06 Aligned_cols=47 Identities=15% Similarity=0.166 Sum_probs=33.8
Q ss_pred hHHHHHHhhhh-cCCceeecccChhhHH----HHHHHHHHHHHhcCCceEEe
Q psy11221 26 NSEFEAFLAKK-WSSEKRFGLEGCEILI----PAMKQVIDKSTELGVESVVM 72 (202)
Q Consensus 26 Ae~FE~FL~~K-F~g~KRFsLEG~EslI----P~L~~iI~~aa~~GV~~IVi 72 (202)
.+.+++++..- -.+.+...+-|+|.++ |.+.++++.+.+.+...+++
T Consensus 38 ~~~~~~ii~~~~~~~~~~i~l~GGEPll~~~~~~l~~i~~~~k~~~~~~~~~ 89 (139)
T PF13353_consen 38 EEIIEEIIEELKNYGIKGIVLTGGEPLLHENYDELLEILKYIKEKFPKKIII 89 (139)
T ss_dssp HHHHHHHCHHHCCCCCCEEEEECSTGGGHHSHHHHHHHHHHHHHTT-SEEEE
T ss_pred chhhhhhhhHHhcCCceEEEEcCCCeeeeccHhHHHHHHHHHHHhCCCCeEE
Confidence 45555554433 3666889999999998 88999999999888755443
No 19
>cd01988 Na_H_Antiporter_C The C-terminal domain of a subfamily of Na+ /H+ antiporter existed in bacteria and archea . Na+/H+ exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolising cells. Na+ /H+ exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiports exchange Na+ for H+ in an electroneutral manner, and this activity is carried out by a family of Na+ /H+ exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity wit h other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the regio
Probab=39.90 E-value=38 Score=24.37 Aligned_cols=39 Identities=10% Similarity=0.122 Sum_probs=28.4
Q ss_pred HHHHHHHHHhcCCceEEeecCCccccceeecccCCCChhhhc
Q psy11221 55 MKQVIDKSTELGVESVVMGMPHRGNLISETTGQGLQKVPRLF 96 (202)
Q Consensus 55 L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl~KP~~~IF 96 (202)
-++|++.+.+.+++-||+|...|+.+. .-++|-....+.
T Consensus 83 ~~~I~~~a~~~~~dlIV~G~~~~~~~~---~~~lGs~~~~v~ 121 (132)
T cd01988 83 ASGILRTAKERQADLIIMGWHGSTSLR---DRLFGGVIDQVL 121 (132)
T ss_pred HHHHHHHHHhcCCCEEEEecCCCCCcc---ceecCchHHHHH
Confidence 377888888899999999999998872 113455555544
No 20
>cd01989 STK_N The N-terminal domain of Eukaryotic Serine Threonine kinases. The Serine Threonine kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. The N-terminal domain is homologous to the USP family which has a ATP binding fold. The N-terminal domain is predicted to be involved in ATP binding.
Probab=37.71 E-value=41 Score=25.14 Aligned_cols=27 Identities=19% Similarity=0.449 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCCceEEeecCCccccc
Q psy11221 55 MKQVIDKSTELGVESVVMGMPHRGNLI 81 (202)
Q Consensus 55 L~~iI~~aa~~GV~~IViGMaHRGRLN 81 (202)
-++|++.|.+.+++-||||=..|+.+.
T Consensus 92 ~~~I~~~a~~~~~dlIV~Gs~g~~~l~ 118 (146)
T cd01989 92 AKAIVEYVADHGITKLVMGASSDNHFS 118 (146)
T ss_pred HHHHHHHHHHcCCCEEEEeccCCCcee
Confidence 367889999999999999998888874
No 21
>PRK00923 sirohydrochlorin cobaltochelatase; Reviewed
Probab=36.10 E-value=62 Score=24.67 Aligned_cols=44 Identities=16% Similarity=0.284 Sum_probs=30.8
Q ss_pred HHHHHHhhhhcCCc-eeec-ccChhhHHHHHHHHHHHHHhcCCceEEee
Q psy11221 27 SEFEAFLAKKWSSE-KRFG-LEGCEILIPAMKQVIDKSTELGVESVVMG 73 (202)
Q Consensus 27 e~FE~FL~~KF~g~-KRFs-LEG~EslIP~L~~iI~~aa~~GV~~IViG 73 (202)
+.|.+.+.++++.. =+.+ +|.++ |.+++.++++.+.|+++|++=
T Consensus 21 ~~~~~~l~~~~~~~~v~~afle~~~---P~l~~~l~~l~~~g~~~v~vv 66 (126)
T PRK00923 21 TKIAEKIKEKHPFYIVEVGFMEFNE---PTIPEALKKLIGTGADKIIVV 66 (126)
T ss_pred HHHHHHHHHhCCCCeEEEEEEEcCC---CCHHHHHHHHHHcCCCEEEEE
Confidence 44666677776542 2334 55444 888999999999999998874
No 22
>PRK00865 glutamate racemase; Provisional
Probab=35.74 E-value=83 Score=27.37 Aligned_cols=55 Identities=15% Similarity=0.358 Sum_probs=34.3
Q ss_pred cccchHHHHHHhhhhcCCceee-------------cccChhhHHHHHHHHHHHHHhcCCceEEeecCC
Q psy11221 22 ATFSNSEFEAFLAKKWSSEKRF-------------GLEGCEILIPAMKQVIDKSTELGVESVVMGMPH 76 (202)
Q Consensus 22 ~~~~Ae~FE~FL~~KF~g~KRF-------------sLEG~EslIP~L~~iI~~aa~~GV~~IViGMaH 76 (202)
+|.++..|++.+++.-++.+=+ +..+.|.....+++.++...+.|++.||+|..|
T Consensus 120 ~Ti~s~~y~~~i~~~~~~~~v~~~~~~~lv~~ie~g~~~~~~~~~~l~~~l~~l~~~g~d~iILGCTh 187 (261)
T PRK00865 120 GTVKSAAYRDLIARFAPDCQVESLACPELVPLVEAGILGGPVTLEVLREYLAPLLAAGIDTLVLGCTH 187 (261)
T ss_pred HHhhchHHHHHHHHhCCCCEEEEecCHHHHHHHhCCCcCCHHHHHHHHHHHHHHhcCCCCEEEECCcC
Confidence 4456667777776543333311 011234455666777776667799999999988
No 23
>PLN02824 hydrolase, alpha/beta fold family protein
Probab=34.19 E-value=14 Score=30.85 Aligned_cols=35 Identities=23% Similarity=0.252 Sum_probs=25.9
Q ss_pred EEEeccccccccccceeeeeeeeEEEEEEeecCCCC
Q psy11221 167 IIFFFFALSHVQMGSAFDIDLSISFRVIALRPTGFG 202 (202)
Q Consensus 167 Ilih~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 (202)
|++||+..+.-++-.... .|+=.||||+.-..|+|
T Consensus 33 lllHG~~~~~~~w~~~~~-~L~~~~~vi~~DlpG~G 67 (294)
T PLN02824 33 VLVHGFGGNADHWRKNTP-VLAKSHRVYAIDLLGYG 67 (294)
T ss_pred EEECCCCCChhHHHHHHH-HHHhCCeEEEEcCCCCC
Confidence 789999887765544332 35556899999999987
No 24
>cd06533 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan.
Probab=33.46 E-value=1.8e+02 Score=23.73 Aligned_cols=57 Identities=14% Similarity=0.185 Sum_probs=37.5
Q ss_pred HHHHHHhhhhcCCceeec-ccChhhHHHHHHHHHHHHHhcCCceEEeecCCccccceeecccCCCChhhhccc
Q psy11221 27 SEFEAFLAKKWSSEKRFG-LEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQGLQKVPRLFSQ 98 (202)
Q Consensus 27 e~FE~FL~~KF~g~KRFs-LEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl~KP~~~IF~E 98 (202)
+.+.+.|.++||+.+=-| -.|--.... .+++++.-.+.+.+=|++|| |.|-+++|..
T Consensus 60 ~~~~~~l~~~yp~l~i~g~~~g~~~~~~-~~~i~~~I~~~~pdiv~vgl--------------G~PkQE~~~~ 117 (171)
T cd06533 60 EKAAERLRARYPGLKIVGYHHGYFGPEE-EEEIIERINASGADILFVGL--------------GAPKQELWIA 117 (171)
T ss_pred HHHHHHHHHHCCCcEEEEecCCCCChhh-HHHHHHHHHHcCCCEEEEEC--------------CCCHHHHHHH
Confidence 445677889999987444 233222211 22367777778888888887 7788888876
No 25
>PLN02679 hydrolase, alpha/beta fold family protein
Probab=33.08 E-value=15 Score=32.62 Aligned_cols=35 Identities=23% Similarity=0.333 Sum_probs=26.5
Q ss_pred EEEeccccccccccceeeeeeeeEEEEEEeecCCCC
Q psy11221 167 IIFFFFALSHVQMGSAFDIDLSISFRVIALRPTGFG 202 (202)
Q Consensus 167 Ilih~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 (202)
|++||+.-++-.....++ .|+-.|||++....|||
T Consensus 92 vllHG~~~~~~~w~~~~~-~L~~~~~via~Dl~G~G 126 (360)
T PLN02679 92 LLVHGFGASIPHWRRNIG-VLAKNYTVYAIDLLGFG 126 (360)
T ss_pred EEECCCCCCHHHHHHHHH-HHhcCCEEEEECCCCCC
Confidence 689999887765554443 35557999999999987
No 26
>PRK13586 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=32.78 E-value=39 Score=29.34 Aligned_cols=21 Identities=24% Similarity=0.502 Sum_probs=18.3
Q ss_pred HhcCCceEEeecC-Ccccccee
Q psy11221 63 TELGVESVVMGMP-HRGNLISE 83 (202)
Q Consensus 63 a~~GV~~IViGMa-HRGRLNVL 83 (202)
.+.|++-+++|+| |.|+++.+
T Consensus 208 ~~~G~~gvivg~Aly~g~~~~~ 229 (232)
T PRK13586 208 KNVGFDYIIVGMAFYLGKLRGI 229 (232)
T ss_pred HHCCCCEEEEehhhhcCccccE
Confidence 3569999999987 99999887
No 27
>KOG3171|consensus
Probab=32.77 E-value=16 Score=33.35 Aligned_cols=44 Identities=23% Similarity=0.254 Sum_probs=31.9
Q ss_pred cccChhhHHHHHHHHHHHHHh---cCCceEEeecCCccccceeeccc
Q psy11221 44 GLEGCEILIPAMKQVIDKSTE---LGVESVVMGMPHRGNLISETTGQ 87 (202)
Q Consensus 44 sLEG~EslIP~L~~iI~~aa~---~GV~~IViGMaHRGRLNVL~~NV 87 (202)
|+.|||.|--.|.-+-..+.. -.++.-++||.-|=|+|+||+=+
T Consensus 170 gi~gcealn~~~~cLAAeyP~vKFckikss~~gas~~F~~n~lP~Ll 216 (273)
T KOG3171|consen 170 GIKGCEALNSSLTCLAAEYPIVKFCKIKSSNTGASDRFSLNVLPTLL 216 (273)
T ss_pred CCchHHHHhhhHHHhhccCCceeEEEeeeccccchhhhcccCCceEE
Confidence 678999987777655332221 15677789999999999996644
No 28
>TIGR02240 PHA_depoly_arom poly(3-hydroxyalkanoate) depolymerase. This family consists of the polyhydroxyalkanoic acid (PHA) depolymerase of Pseudomonas oleovorans, Pseudomonas putida BM01, and related species. This enzyme is part of polyester storage and mobilization system as in many bacteria. However, species containing this enzyme are unusual in their capacity to produce aromatic polyesters when grown on carbon sources such as benzoic acid or phenylacetic acid.
Probab=32.62 E-value=20 Score=29.71 Aligned_cols=35 Identities=23% Similarity=0.260 Sum_probs=24.2
Q ss_pred EEEeccccccccccceeeeeeeeEEEEEEeecCCCC
Q psy11221 167 IIFFFFALSHVQMGSAFDIDLSISFRVIALRPTGFG 202 (202)
Q Consensus 167 Ilih~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 (202)
|++||+.-++-......+ .|+-.+|||++-..|+|
T Consensus 29 vllHG~~~~~~~w~~~~~-~L~~~~~vi~~Dl~G~G 63 (276)
T TIGR02240 29 LIFNGIGANLELVFPFIE-ALDPDLEVIAFDVPGVG 63 (276)
T ss_pred EEEeCCCcchHHHHHHHH-HhccCceEEEECCCCCC
Confidence 678998776654433322 25556899999999887
No 29
>PRK00109 Holliday junction resolvase-like protein; Reviewed
Probab=32.04 E-value=56 Score=26.28 Aligned_cols=24 Identities=17% Similarity=0.306 Sum_probs=19.7
Q ss_pred HHHHHHHHHHhcCCceEEeecCCc
Q psy11221 54 AMKQVIDKSTELGVESVVMGMPHR 77 (202)
Q Consensus 54 ~L~~iI~~aa~~GV~~IViGMaHR 77 (202)
.++++.+...+.+++.||+|+|-.
T Consensus 42 ~~~~l~~~i~~~~i~~iVvGlP~~ 65 (138)
T PRK00109 42 DWDRLEKLIKEWQPDGLVVGLPLN 65 (138)
T ss_pred HHHHHHHHHHHhCCCEEEEeccCC
Confidence 456677777888999999999965
No 30
>PRK06489 hypothetical protein; Provisional
Probab=32.02 E-value=25 Score=31.04 Aligned_cols=37 Identities=14% Similarity=0.043 Sum_probs=24.5
Q ss_pred EEEEecccccccccc-ceee-------e-eeeeEEEEEEeecCCCC
Q psy11221 166 PIIFFFFALSHVQMG-SAFD-------I-DLSISFRVIALRPTGFG 202 (202)
Q Consensus 166 PIlih~~~~~~~~~~-~~~~-------~-~~~~~~~~~~~~~~~~~ 202 (202)
=|++||+..++-.+- ..+. + .++-.||||+.-..|+|
T Consensus 72 lvllHG~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~Via~Dl~GhG 117 (360)
T PRK06489 72 VLVLHGTGGSGKSFLSPTFAGELFGPGQPLDASKYFIILPDGIGHG 117 (360)
T ss_pred EEEeCCCCCchhhhccchhHHHhcCCCCcccccCCEEEEeCCCCCC
Confidence 367899988875543 1111 1 12456999999999987
No 31
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=30.02 E-value=2e+02 Score=23.39 Aligned_cols=48 Identities=15% Similarity=0.225 Sum_probs=29.7
Q ss_pred HHHHHHhhhhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeec
Q psy11221 27 SEFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGM 74 (202)
Q Consensus 27 e~FE~FL~~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGM 74 (202)
+.+++.|.++||+-+=-|-.-+----...+++++.-.+.+.+=|++||
T Consensus 62 ~~~~~~l~~~yP~l~ivg~~~g~f~~~~~~~i~~~I~~~~pdiv~vgl 109 (172)
T PF03808_consen 62 EKAAANLRRRYPGLRIVGYHHGYFDEEEEEAIINRINASGPDIVFVGL 109 (172)
T ss_pred HHHHHHHHHHCCCeEEEEecCCCCChhhHHHHHHHHHHcCCCEEEEEC
Confidence 456778899999876443221100122345666666677888888886
No 32
>PF02633 Creatininase: Creatinine amidohydrolase; InterPro: IPR003785 This family includes the enzymes creatininase and 2-amino-5-formylamino-6-ribosylaminopyrimidin-4(3H)-one 5'-monophosphate deformylase, also known as formamide hydrolase. Creatinase or creatinine amidohydrolase (3.5.2.10 from EC) catalyses the hydrolysis of creatinine to creatine, which can then be metabolised to urea and sarcosine by creatinase (3.5.3.3 from EC). Creatininase is a member of the urease-related amidohydrolase superfamily []. Formamide hydrolase catalyzes the hydrolysis of the formamide of 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-monophosphate (FAPy) to form 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (APy) (3.5.1.102 from EC). ; PDB: 3A6K_F 3A6F_A 3A6D_B 1J2U_B 3A6J_C 1J2T_A 3A6G_C 3A6H_F 1Q3K_E 3A6L_C ....
Probab=29.24 E-value=83 Score=26.73 Aligned_cols=46 Identities=20% Similarity=0.349 Sum_probs=34.3
Q ss_pred hhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEEeecCCcccccee
Q psy11221 35 KKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVVMGMPHRGNLISE 83 (202)
Q Consensus 35 ~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IViGMaHRGRLNVL 83 (202)
..|||. .++. .|+++.+|.++++...++|++.+|+==.|-|-...|
T Consensus 71 ~~fpGT--isl~-~~t~~~~l~di~~sl~~~Gf~~ivivngHgGN~~~l 116 (237)
T PF02633_consen 71 MGFPGT--ISLS-PETLIALLRDILRSLARHGFRRIVIVNGHGGNIAAL 116 (237)
T ss_dssp TTSTT---BBB--HHHHHHHHHHHHHHHHHHT--EEEEEESSTTHHHHH
T ss_pred CCCCCe--EEeC-HHHHHHHHHHHHHHHHHcCCCEEEEEECCHhHHHHH
Confidence 457766 4554 599999999999999999999999999999944334
No 33
>cd07766 DHQ_Fe-ADH Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH). Dehydroquinate synthase-like. This superfamily divides into two subgroups: the dehydroquinate synthase-like, and a large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. Dehydroquinate synthase-like group includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. The alcohol dehydrogenases in this superfamily contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alc
Probab=25.53 E-value=2.6e+02 Score=24.53 Aligned_cols=45 Identities=18% Similarity=0.270 Sum_probs=33.1
Q ss_pred HHHHHhhhhcCCceeecccChhhHHHHHHHHHHHHHhcCCceEE-ee
Q psy11221 28 EFEAFLAKKWSSEKRFGLEGCEILIPAMKQVIDKSTELGVESVV-MG 73 (202)
Q Consensus 28 ~FE~FL~~KF~g~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IV-iG 73 (202)
.+++.|.+. .....|...+.|.-+-.++++++.+.+.+.+-|| +|
T Consensus 41 ~v~~~l~~~-~~~~~~~~~~~~p~~~~v~~~~~~~~~~~~d~IIaiG 86 (332)
T cd07766 41 KVADSLKKL-IAVHIFDGVGPNPTFEEVKEAVERARAAEVDAVIAVG 86 (332)
T ss_pred HHHHHHHhc-CcEEEeCCcCCCcCHHHHHHHHHHHHhcCcCEEEEeC
Confidence 345555555 5667898888898888888898888887876655 44
No 34
>PF03652 UPF0081: Uncharacterised protein family (UPF0081); InterPro: IPR005227 Holliday junction resolvases (HJRs) are key enzymes of DNA recombination. The principal HJRs are now known or confidently predicted for all bacteria and archaea whose genomes have been completely sequenced, with many species encoding multiple potential HJRs. Structural and evolutionary relationships of HJRs and related nucleases suggests that the HJR function has evolved independently from at least four distinct structural folds, namely RNase H, endonuclease, endonuclease VII-colicin E and RusA (IPR008822 from INTERPRO): The endonuclease fold, whose structural prototypes are the phage exonuclease, the very short patch repair nuclease (Vsr) and type II restriction enzymes, is shown to encompass by far a greater diversity of nucleases than previously suspected. This fold unifies archaeal HJRs (IPR002732 from INTERPRO), repair nucleases such as RecB (IPR004586 from INTERPRO) and Vsr (IPR004603 from INTERPRO), restriction enzymes and a variety of predicted nucleases whose specific activities remain to be determined. The RNase H fold characterises the RuvC family (IPR002176 from INTERPRO), which is nearly ubiquitous in bacteria, and in addition the YqgF family (IPR005227 from INTERPRO). The proteins of this family, typified by Escherichia coli YqgF, are likely to function as an alternative to RuvC in most bacteria, but could be the principal HJRs in low-GC Gram-positive bacteria and Aquifex. Endonuclease VII of phage T4 (IPR004211 from INTERPRO) is shown to serve as a structural template for many nucleases, including McrA and other type II restriction enzymes. Together with colicin E7, endonuclease VII defines a distinct metal-dependent nuclease fold. Horizontal gene transfer, lineage-specific gene loss and gene family expansion, and non-orthologous gene displacement seem to have been major forces in the evolution of HJRs and related nucleases. A remarkable case of displacement is seen in the Lyme disease spirochete Borrelia burgdorferi, which does not possess any of the typical HJRs, but instead encodes, in its chromosome and each of the linear plasmids, members of the exonuclease family predicted to function as HJRs. The diversity of HJRs and related nucleases in bacteria and archaea contrasts with their near absence in eukaryotes. The few detected eukaryotic representatives of the endonuclease fold and the RNase H fold have probably been acquired from bacteria via horizontal gene transfer. The identity of the principal HJR(s) involved in recombination in eukaryotes remains uncertain; this function could be performed by topoisomerase IB or by a novel, so far undetected, class of enzymes. Likely HJRs and related nucleases were identified in the genomes of numerous bacterial and eukaryotic DNA viruses. Gene flow between viral and cellular genomes has probably played a major role in the evolution of this class of enzymes. This family represents the YqgF family of putative Holliday junction resolvases. With the exception of the spirochetes, the YqgF family is represented in all bacterial lineages, including the mycoplasmas with their highly degenerate genomes. The RuvC resolvases are conspicuously absent in the low-GC Gram-positive bacterial lineage, with the exception of Ureaplasma parvum (Ureaplasma urealyticum biotype 1) (Q9PQY7 from SWISSPROT, []). Furthermore, loss of function ruvC mutants of E. coli show a residual HJR activity that cannot be ascribed to the prophage-encoded RusA resolvase []. This suggests that the YqgF family proteins could be alternative HJRs whose function partially overlaps with that of RuvC [].; GO: 0016788 hydrolase activity, acting on ester bonds, 0006281 DNA repair, 0006310 DNA recombination, 0006974 response to DNA damage stimulus, 0005737 cytoplasm; PDB: 1NU0_A 1OVQ_A 1NMN_B 1VHX_B 1IV0_A.
Probab=24.56 E-value=66 Score=25.77 Aligned_cols=29 Identities=17% Similarity=0.446 Sum_probs=19.6
Q ss_pred HHHHHHHHHhcCCceEEeecCCc--ccccee
Q psy11221 55 MKQVIDKSTELGVESVVMGMPHR--GNLISE 83 (202)
Q Consensus 55 L~~iI~~aa~~GV~~IViGMaHR--GRLNVL 83 (202)
++++.+-..+.+++.+|+|+|-. |+.+-.
T Consensus 40 ~~~l~~li~~~~i~~iVvGlP~~~~G~~~~~ 70 (135)
T PF03652_consen 40 IEELKKLIEEYQIDGIVVGLPLNMDGSESEQ 70 (135)
T ss_dssp HHHHHHHHHHCCECEEEEEEEBBCTSSC-CC
T ss_pred HHHHHHHHHHhCCCEEEEeCCcccCCCccHH
Confidence 44555556678999999999843 454444
No 35
>cd03416 CbiX_SirB_N Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be important for metal delivery and/or storage, and may also contain an iron-sulfur center. Both are found in a wide range of bacteria. This subgroup also contains single domain proteins from archaea and bacteria which may represent the ancestral form of class II chelatases before domain duplication occurred.
Probab=24.00 E-value=1.4e+02 Score=21.67 Aligned_cols=43 Identities=19% Similarity=0.283 Sum_probs=30.0
Q ss_pred HHHHHHhhhhcCC--ceeecccChhhHHHHHHHHHHHHHhcCCceEEe
Q psy11221 27 SEFEAFLAKKWSS--EKRFGLEGCEILIPAMKQVIDKSTELGVESVVM 72 (202)
Q Consensus 27 e~FE~FL~~KF~g--~KRFsLEG~EslIP~L~~iI~~aa~~GV~~IVi 72 (202)
+.+.+-+.++++. ...=-+|+.+ |.+++.+++..+.|+++|++
T Consensus 19 ~~l~~~l~~~~~~~~v~~afle~~~---p~~~~~l~~l~~~g~~~v~v 63 (101)
T cd03416 19 EALAERLRERLPGDEVELAFLELAE---PSLAEALDELAAQGATRIVV 63 (101)
T ss_pred HHHHHHHHhhCCCCcEEEEEEEcCC---CCHHHHHHHHHHcCCCEEEE
Confidence 4567777777642 2222266543 88888999999999999887
No 36
>COG0589 UspA Universal stress protein UspA and related nucleotide-binding proteins [Signal transduction mechanisms]
Probab=23.71 E-value=86 Score=22.71 Aligned_cols=42 Identities=14% Similarity=0.238 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhcCCceEEeecCCccccceeecccCCCChhhhcc
Q psy11221 53 PAMKQVIDKSTELGVESVVMGMPHRGNLISETTGQGLQKVPRLFS 97 (202)
Q Consensus 53 P~L~~iI~~aa~~GV~~IViGMaHRGRLNVL~~NVl~KP~~~IF~ 97 (202)
|.-+++++.+.+.+.+-||+|-..|++|.=+ ++|--.+.+..
T Consensus 100 ~~~~~i~~~a~~~~adliV~G~~g~~~l~~~---llGsvs~~v~~ 141 (154)
T COG0589 100 PSAEEILELAEEEDADLIVVGSRGRSGLSRL---LLGSVAEKVLR 141 (154)
T ss_pred CcHHHHHHHHHHhCCCEEEECCCCCccccce---eeehhHHHHHh
Confidence 4456777888888999999999888888743 34544444443
No 37
>TIGR00067 glut_race glutamate racemase. The most closely related proteins differing in function are aspartate racemases.
Probab=23.39 E-value=1.8e+02 Score=25.35 Aligned_cols=59 Identities=19% Similarity=0.287 Sum_probs=38.8
Q ss_pred hhccccccchHHHHHHhhhhcCCceeecccChhhHHH--------------HHHHHHHHHHhcCCceEEeecCC
Q psy11221 17 LLRSSATFSNSEFEAFLAKKWSSEKRFGLEGCEILIP--------------AMKQVIDKSTELGVESVVMGMPH 76 (202)
Q Consensus 17 l~r~~~~~~Ae~FE~FL~~KF~g~KRFsLEG~EslIP--------------~L~~iI~~aa~~GV~~IViGMaH 76 (202)
++--.+|.++..|++.+++.=+..+=++ ++|..+++ .++.+++...+.|++.+|+|.-|
T Consensus 110 vLAT~~Ti~s~~y~~~i~~~~~~~~v~~-~~~~~lv~~Ie~g~~~~~~~~~~l~~~l~~l~~~~~d~lILGCTh 182 (251)
T TIGR00067 110 VIATNATIKSNAYHEALKEIANDLLVEM-LACPELVPLAEAGLLGEDYALECLKRYLRPLLDTLPDTVVLGCTH 182 (251)
T ss_pred EEeCHHHHhhhHHHHHHHHhCCCCEEEe-cCCHHHHHHHHcCCcCCHHHHHHHHHHHHHHhcCCCCEEEECcCC
Confidence 3444578888899999876544444332 44444444 44555555556699999999998
No 38
>PRK03592 haloalkane dehalogenase; Provisional
Probab=23.38 E-value=29 Score=28.98 Aligned_cols=35 Identities=17% Similarity=0.072 Sum_probs=24.1
Q ss_pred EEEeccccccccccceeeeeeeeEEEEEEeecCCCC
Q psy11221 167 IIFFFFALSHVQMGSAFDIDLSISFRVIALRPTGFG 202 (202)
Q Consensus 167 Ilih~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 202 (202)
|+|||+..+.-.....+. .|+-.+|||+.-..|+|
T Consensus 31 vllHG~~~~~~~w~~~~~-~L~~~~~via~D~~G~G 65 (295)
T PRK03592 31 VFLHGNPTSSYLWRNIIP-HLAGLGRCLAPDLIGMG 65 (295)
T ss_pred EEECCCCCCHHHHHHHHH-HHhhCCEEEEEcCCCCC
Confidence 568998876655443332 24445799999999987
No 39
>PF07273 DUF1439: Protein of unknown function (DUF1439); InterPro: IPR010835 This family consists of several hypothetical bacterial proteins of around 190 residues in length. Several members of this family are annotated as being putative lipoproteins and are often known as YceB. The function of this family is unknown.; PDB: 3L6I_B.
Probab=22.30 E-value=54 Score=26.59 Aligned_cols=21 Identities=38% Similarity=0.786 Sum_probs=17.0
Q ss_pred HHHHHHhhhhcCCceeecccC
Q psy11221 27 SEFEAFLAKKWSSEKRFGLEG 47 (202)
Q Consensus 27 e~FE~FL~~KF~g~KRFsLEG 47 (202)
...+++|+++|+=+|++|+.|
T Consensus 4 ~eiq~~L~k~~~~~k~~g~~g 24 (152)
T PF07273_consen 4 QEIQQYLAKKFPYQKKVGIPG 24 (152)
T ss_dssp HHHHHHHHCC--EEEEEEETT
T ss_pred HHHHHHHHHhCChhhhcccCC
Confidence 567999999999999999876
No 40
>TIGR02495 NrdG2 anaerobic ribonucleoside-triphosphate reductase activating protein. This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD.
Probab=22.06 E-value=1.7e+02 Score=23.36 Aligned_cols=43 Identities=19% Similarity=0.223 Sum_probs=31.1
Q ss_pred chHHHHHHhhhhcCCceeecccChhhHH-HHHHHHHHHHHhcCC
Q psy11221 25 SNSEFEAFLAKKWSSEKRFGLEGCEILI-PAMKQVIDKSTELGV 67 (202)
Q Consensus 25 ~Ae~FE~FL~~KF~g~KRFsLEG~EslI-P~L~~iI~~aa~~GV 67 (202)
..+.+-+++.+.....+...+-|+|.++ |-+.++++.+.+.|.
T Consensus 48 ~~~~i~~~i~~~~~~~~~i~~sGGEPll~~~l~~li~~~~~~g~ 91 (191)
T TIGR02495 48 EVEFLLEFLRSRQGLIDGVVITGGEPTLQAGLPDFLRKVRELGF 91 (191)
T ss_pred CHHHHHHHHHHhcCCCCeEEEECCcccCcHhHHHHHHHHHHCCC
Confidence 4566777776643445678888999988 557788898887663
No 41
>PRK00870 haloalkane dehalogenase; Provisional
Probab=21.96 E-value=32 Score=29.01 Aligned_cols=35 Identities=23% Similarity=0.182 Sum_probs=23.1
Q ss_pred EEEeccccccccccceeeeeeee-EEEEEEeecCCCC
Q psy11221 167 IIFFFFALSHVQMGSAFDIDLSI-SFRVIALRPTGFG 202 (202)
Q Consensus 167 Ilih~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~ 202 (202)
|+|||+.-++-....... .|+- .|||+++-..|+|
T Consensus 50 vliHG~~~~~~~w~~~~~-~L~~~gy~vi~~Dl~G~G 85 (302)
T PRK00870 50 LLLHGEPSWSYLYRKMIP-ILAAAGHRVIAPDLIGFG 85 (302)
T ss_pred EEECCCCCchhhHHHHHH-HHHhCCCEEEEECCCCCC
Confidence 789998655443322222 3543 4999999999987
No 42
>PF15230 SRRM_C: Serine/arginine repetitive matrix protein C-terminus
Probab=21.21 E-value=33 Score=25.69 Aligned_cols=8 Identities=13% Similarity=-0.089 Sum_probs=6.5
Q ss_pred cCCCccee
Q psy11221 142 CWPRAMFL 149 (202)
Q Consensus 142 ~NPSHLEa 149 (202)
--|||||+
T Consensus 43 DSPS~lEa 50 (66)
T PF15230_consen 43 DSPSHLEA 50 (66)
T ss_pred CCccccch
Confidence 36999997
No 43
>cd03412 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity.
Probab=20.39 E-value=1.1e+02 Score=23.90 Aligned_cols=46 Identities=13% Similarity=0.221 Sum_probs=31.4
Q ss_pred HHHHHHhhhhcCCce-eeccc---------ChhhHHHHHHHHHHHHHhcCCceEEe
Q psy11221 27 SEFEAFLAKKWSSEK-RFGLE---------GCEILIPAMKQVIDKSTELGVESVVM 72 (202)
Q Consensus 27 e~FE~FL~~KF~g~K-RFsLE---------G~EslIP~L~~iI~~aa~~GV~~IVi 72 (202)
+.+++=+.++||+.. |++-= ..+--+|.+.+.+++..+.|+++|++
T Consensus 20 ~~i~~~l~~~~p~~~V~~afts~~i~~~l~~~~~~~p~~~eaL~~l~~~G~~~V~V 75 (127)
T cd03412 20 DAIEDKVRAAFPDYEVRWAFTSRMIRKKLKKRGIEVDTPEEALAKLAADGYTEVIV 75 (127)
T ss_pred HHHHHHHHHHCCCCeEEEEecHHHHHHHHHhcCCCCCCHHHHHHHHHHCCCCEEEE
Confidence 446666778888653 33321 11233588999999999999999876
Done!