Query psy5290
Match_columns 536
No_of_seqs 178 out of 343
Neff 2.5
Searched_HMMs 46136
Date Fri Aug 16 22:48:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5290.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5290hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00061 DNA-directed RNA poly 100.0 8.8E-59 1.9E-63 438.3 15.8 173 1-180 16-189 (205)
2 KOG3218|consensus 100.0 1.2E-58 2.6E-63 436.2 15.1 173 1-180 20-192 (208)
3 PLN03111 DNA-directed RNA poly 100.0 1.7E-58 3.7E-63 436.6 15.3 172 1-180 19-190 (206)
4 PF03871 RNA_pol_Rpb5_N: RNA p 99.9 2.5E-23 5.5E-28 174.7 2.1 76 1-78 18-93 (93)
5 PRK09570 rpoH DNA-directed RNA 99.9 1.7E-22 3.7E-27 168.4 4.0 59 119-180 3-61 (79)
6 PF01191 RNA_pol_Rpb5_C: RNA p 99.8 3.9E-22 8.4E-27 164.3 3.9 58 120-180 1-58 (74)
7 COG2012 RPB5 DNA-directed RNA 99.8 8.6E-22 1.9E-26 164.8 3.7 63 115-180 2-64 (80)
8 PF04471 Mrr_cat: Restriction 96.2 0.013 2.7E-07 47.4 6.0 75 42-119 37-112 (115)
9 TIGR00640 acid_CoA_mut_C methy 57.7 20 0.00044 32.4 4.9 80 3-104 25-104 (132)
10 PRK07993 DNA polymerase III su 57.6 31 0.00067 35.5 6.8 97 55-152 76-186 (334)
11 cd02072 Glm_B12_BD B12 binding 50.2 31 0.00067 31.7 4.9 70 3-94 22-91 (128)
12 PF14779 BBS1: Ciliary BBSome 49.9 11 0.00024 38.3 2.2 35 263-297 51-104 (257)
13 PRK08058 DNA polymerase III su 45.4 78 0.0017 32.1 7.3 93 58-150 83-185 (329)
14 TIGR00678 holB DNA polymerase 41.0 89 0.0019 28.3 6.3 90 59-148 70-169 (188)
15 TIGR03595 Obg_CgtA_exten Obg f 38.8 15 0.00032 30.2 0.9 49 133-181 12-64 (69)
16 cd02781 MopB_CT_Acetylene-hydr 38.0 49 0.0011 28.3 4.0 43 166-217 42-86 (130)
17 PRK06871 DNA polymerase III su 37.6 1.4E+02 0.003 31.1 7.8 91 55-146 76-178 (325)
18 cd02788 MopB_CT_NDH-1_NuoG2-N7 35.5 49 0.0011 27.7 3.5 49 151-213 28-78 (96)
19 cd02777 MopB_CT_DMSOR-like The 34.3 57 0.0012 28.1 3.8 41 166-215 43-85 (127)
20 PRK06964 DNA polymerase III su 32.7 1.9E+02 0.0042 30.3 8.0 85 64-149 111-206 (342)
21 cd02071 MM_CoA_mut_B12_BD meth 31.9 92 0.002 27.1 4.8 70 3-94 22-91 (122)
22 PF01568 Molydop_binding: Moly 31.5 51 0.0011 27.2 3.0 42 166-216 39-82 (110)
23 PRK05707 DNA polymerase III su 31.2 1.9E+02 0.004 29.9 7.5 91 55-145 74-176 (328)
24 PF01939 DUF91: Protein of unk 31.1 77 0.0017 31.9 4.7 57 55-116 150-211 (228)
25 PRK05564 DNA polymerase III su 31.0 1.7E+02 0.0037 29.1 7.0 86 61-146 69-164 (313)
26 PRK02261 methylaspartate mutas 30.6 1E+02 0.0022 28.1 4.9 69 3-93 26-94 (137)
27 PRK08769 DNA polymerase III su 30.3 1.8E+02 0.004 30.1 7.3 87 64-151 92-189 (319)
28 TIGR01501 MthylAspMutase methy 30.2 60 0.0013 30.0 3.5 70 2-93 23-92 (134)
29 COG4624 Iron only hydrogenase 30.2 39 0.00085 36.8 2.6 37 131-174 220-256 (411)
30 PF13167 GTP-bdg_N: GTP-bindin 30.1 77 0.0017 27.9 4.0 53 65-122 41-93 (95)
31 cd02792 MopB_CT_Formate-Dh-Na- 29.8 79 0.0017 26.6 3.9 42 166-216 44-87 (122)
32 cd02790 MopB_CT_Formate-Dh_H F 28.2 86 0.0019 26.0 3.8 41 166-215 44-86 (116)
33 PRK08485 DNA polymerase III su 28.2 1.4E+02 0.003 30.0 5.8 46 58-104 31-77 (206)
34 PF13156 Mrr_cat_2: Restrictio 27.8 79 0.0017 29.4 3.8 48 58-105 51-99 (129)
35 KOG0182|consensus 27.2 1.3E+02 0.0028 31.0 5.4 129 7-145 105-241 (246)
36 PF15427 S100PBPR: S100P-bindi 26.1 75 0.0016 34.3 3.7 83 130-223 29-111 (386)
37 KOG0460|consensus 25.2 97 0.0021 34.0 4.4 82 73-160 130-217 (449)
38 cd02786 MopB_CT_3 The MopB_CT_ 25.0 1E+02 0.0022 25.8 3.8 49 153-215 32-82 (116)
39 cd02067 B12-binding B12 bindin 24.5 1.9E+02 0.0042 24.4 5.4 72 2-95 21-93 (119)
40 PRK07132 DNA polymerase III su 24.4 2.9E+02 0.0062 28.4 7.4 89 62-150 66-165 (299)
41 PF09269 DUF1967: Domain of un 23.8 42 0.0009 27.6 1.2 16 166-181 49-64 (69)
42 PF11513 TA0956: Thermoplasma 23.4 2.3E+02 0.005 26.1 5.8 62 20-84 45-106 (110)
43 PRK05917 DNA polymerase III su 23.4 2.1E+02 0.0044 29.7 6.2 49 55-103 63-117 (290)
44 TIGR00459 aspS_bact aspartyl-t 23.3 1.4E+02 0.0029 33.8 5.3 26 133-158 367-392 (583)
45 cd00508 MopB_CT_Fdh-Nap-like T 22.9 1E+02 0.0022 25.6 3.3 41 166-215 44-86 (120)
46 cd02778 MopB_CT_Thiosulfate-R- 22.1 1.3E+02 0.0029 25.4 3.9 42 166-216 39-82 (123)
47 PRK07276 DNA polymerase III su 21.5 2.1E+02 0.0046 29.5 5.8 93 55-150 74-178 (290)
48 COG4012 Uncharacterized protei 21.3 9.8E+02 0.021 25.9 10.5 163 5-195 148-321 (342)
49 cd02791 MopB_CT_Nitrate-R-NapA 21.0 1.2E+02 0.0026 25.5 3.4 41 166-215 44-86 (122)
50 cd02775 MopB_CT Molybdopterin- 20.7 1.4E+02 0.003 23.9 3.6 50 154-215 23-74 (101)
No 1
>PTZ00061 DNA-directed RNA polymerase; Provisional
Probab=100.00 E-value=8.8e-59 Score=438.30 Aligned_cols=173 Identities=38% Similarity=0.642 Sum_probs=168.1
Q ss_pred CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCC-CCCcchHHHHHHHHHHhh
Q psy5290 1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPD-EPKIGIKTIKTYCQRMQE 79 (536)
Q Consensus 1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpd-E~KVGVKtIRkyiErMkE 79 (536)
+|||+||||.|+++|++||+++|+++||+++ +.|++|+|++.+.+||+++|||||++ +++||+|+||+|+++|++
T Consensus 16 ~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~----~~r~~l~~~~~~~~d~~~~i~VfF~~~~~~vgvk~ir~~~~~~~~ 91 (205)
T PTZ00061 16 CEMLEDRGYIITSQEKLETFATFKERFEENE----RLRSRMLMVASHKTDPTNRIIVYFADETKKTGVKPIRELTEKMEE 91 (205)
T ss_pred HHHHhccCCccCHHHHcCCHHHHHHHhccCc----ccHhHcEEEeecCCCCCCcEEEEeCCCCCcCCHHHHHHHHHHHhh
Confidence 5999999999999999999999999999874 57999999999999999999999998 569999999999999999
Q ss_pred cCCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccC
Q psy5290 80 ETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKR 159 (536)
Q Consensus 80 ENI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~t 159 (536)
+|++|+|||+|++|||+||++|.+++++++||+|+|+|||||||+|+|||||++||+|||++||++|+++++|||||+.+
T Consensus 92 ~n~~r~IlV~q~~ltp~Ar~~i~~~~~~~~iE~F~E~eLlvnit~H~lVPkH~~Ls~eEk~~lL~~y~i~~~qLPrI~~~ 171 (205)
T PTZ00061 92 HDIQRAILVTQNVLTPFAKDAILEAAPRHIIENFLETELLVNITKHELVPKHIPLTDDEKLNLLQRYKVKESQLPRIQSA 171 (205)
T ss_pred cCCceEEEEECCCCCHHHHHHHHhhCCCcEEEEeeehheEEecccceecCCeEEcCHHHHHHHHHHhCCCHHHCCccccc
Confidence 99999999999999999999999999889999999999999999999999999999999999999999999999999999
Q ss_pred CcccccccccCCccCcEEecC
Q psy5290 160 TGEEHFLKECSFESATVKSVY 180 (536)
Q Consensus 160 DPvavfvk~iGAKpGDVVrv~ 180 (536)
||+ ++++|+|+||||+|.
T Consensus 172 DPv---ary~g~k~G~vvkI~ 189 (205)
T PTZ00061 172 DPV---ARYFGLSKGQVVKII 189 (205)
T ss_pred Chh---hHhcCCCCCCEEEEE
Confidence 999 999999999999984
No 2
>KOG3218|consensus
Probab=100.00 E-value=1.2e-58 Score=436.16 Aligned_cols=173 Identities=54% Similarity=0.866 Sum_probs=170.2
Q ss_pred CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhc
Q psy5290 1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEE 80 (536)
Q Consensus 1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEE 80 (536)
|||||||||.|+++|++++|++|+++||+++ ++|++|+|+|.|++||+++|||||+++++||||+||.|+.+|+++
T Consensus 20 ~qMlrDRGY~vt~~el~ltLe~F~~~yg~~~----p~r~~L~~~~~~~~dp~~ki~V~F~~~~kvgvk~~k~~~~~~~~~ 95 (208)
T KOG3218|consen 20 MQMLRDRGYTVTQEELDLTLEEFKARYGDKM----PDREDLRILAAHRDDPTDKIYVFFPEEPKVGVKTMKTYVIQMQSE 95 (208)
T ss_pred HHHHHhcCccccHHHhhhhHHHHHHHhccCC----cchhhEEEEeccCCCCcCcEEEEeCCCCcccHHHHHHHHHHHHhc
Confidence 6999999999999999999999999999975 789999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCC
Q psy5290 81 TIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRT 160 (536)
Q Consensus 81 NI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tD 160 (536)
|++++|||+|++||++|++++.+++++|.||+|+|+||+||||+|+|||||++||+|||++||++|+++++|||+|+..|
T Consensus 96 ni~~~IlV~q~~mt~~A~k~i~~~~p~f~iE~F~e~eLlvNIT~H~lvPkH~vL~~eEK~~LL~ry~l~e~qLPRIq~~D 175 (208)
T KOG3218|consen 96 NIFRAILVVQNGMTPSALKALSDFTPKFTIEVFLEAELLVNITEHELVPKHQVLTDEEKEELLRRYKLKETQLPRIQKKD 175 (208)
T ss_pred CceEEEEEecCCCChHHHHHHHhcCCceEEEeeehhhheeeccceeecCceEEcCHHHHHHHHHHhcCCcccCCeeeccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccCCccCcEEecC
Q psy5290 161 GEEHFLKECSFESATVKSVY 180 (536)
Q Consensus 161 Pvavfvk~iGAKpGDVVrv~ 180 (536)
|+ ++++|+|-|+||+|-
T Consensus 176 pv---aRYyGLKrGqVVKI~ 192 (208)
T KOG3218|consen 176 PV---ARYYGLKRGQVVKII 192 (208)
T ss_pred hH---HhhhccccCcEEEEE
Confidence 99 999999999999984
No 3
>PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional
Probab=100.00 E-value=1.7e-58 Score=436.60 Aligned_cols=172 Identities=43% Similarity=0.733 Sum_probs=168.3
Q ss_pred CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhc
Q psy5290 1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEE 80 (536)
Q Consensus 1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEE 80 (536)
+|||+||||.|+++|++||+++|+++||++ ++|++|+|++.+++|++++|||||+++++||+|+||+|+++|+++
T Consensus 19 ~eMl~DRGY~V~~~el~~s~~~F~~~~~~~-----~~r~~l~~~~~~~~d~~~~i~V~F~~~~kvgvk~ir~~~~~~~~e 93 (206)
T PLN03111 19 LEMLRDRGYLVSDSELNLTLSEFREKFGEK-----PKREDLRISAPKRSDPSKKILVFFPEEEKVGVKTIKTYAERMKDE 93 (206)
T ss_pred HHHHhccCCccCHHHHcCCHHHHHHHHcCC-----cCHHHcEeeeecCCCCCCcEEEEeCCCCccCHHHHHHHHHHHhhc
Confidence 599999999999999999999999999986 579999999999999999999999999999999999999999999
Q ss_pred CCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCC
Q psy5290 81 TIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRT 160 (536)
Q Consensus 81 NI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tD 160 (536)
|++|+|||+|++|||+||+++.++++.++||+|+|+|||||||+|+|||||++||+|||++||++|+++++|||||+.+|
T Consensus 94 ~~~r~IlV~q~~itp~A~~~i~~~~~~~~iE~F~e~eLlvnit~H~lVPkH~~ls~eEk~~lL~~y~i~~~qLPrI~~~D 173 (206)
T PLN03111 94 NVSRAILVLQSKLTPFAKQALSEFNSKFKIEVFQETELLVNITKHVLVPKHQVLTDEEKKTLLKRYTVKETQLPRIQVSD 173 (206)
T ss_pred CcceEEEEECCCCCHHHHHHHHhhCcCceEEEeehhHheeccccceecCCeEEcCHHHHHHHHHHcCCCHHHCCcccccC
Confidence 99999999999999999999999988899999999999999999999999999999999999999999999999999999
Q ss_pred cccccccccCCccCcEEecC
Q psy5290 161 GEEHFLKECSFESATVKSVY 180 (536)
Q Consensus 161 Pvavfvk~iGAKpGDVVrv~ 180 (536)
|+ ++++|+|+||||+|.
T Consensus 174 Pv---ary~g~k~G~vvkI~ 190 (206)
T PLN03111 174 PI---ARYYGLKRGQVVKII 190 (206)
T ss_pred hh---hHhcCCCCCCEEEEE
Confidence 99 999999999999984
No 4
>PF03871 RNA_pol_Rpb5_N: RNA polymerase Rpb5, N-terminal domain; InterPro: IPR005571 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region, plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) (IPR000783 from INTERPRO) [, , , ]. This entry represents the N-terminal domain of eukaryotic RPB5, which has a core structure consisting of 3 layers alpha/beta/alpha []. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure []. This module is important for positioning the downstream DNA.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3H0G_Q 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E 1I50_E ....
Probab=99.87 E-value=2.5e-23 Score=174.67 Aligned_cols=76 Identities=50% Similarity=1.109 Sum_probs=62.0
Q ss_pred CcccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHh
Q psy5290 1 MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQ 78 (536)
Q Consensus 1 LEMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMk 78 (536)
+|||+||||.|+++|++||+++|+++||+++ +.++|++|+|.+.+.+||+++|+|||+++++||+|+||+|+++|+
T Consensus 18 ~eMl~DRGY~V~~~el~~s~~~F~~~~~~~~--~~~~r~~L~~~~~~~~d~~~~i~V~F~~~~kvgvk~Ir~~~~~m~ 93 (93)
T PF03871_consen 18 MEMLRDRGYLVSEEELNMSLEEFKEKYGENP--GNPDRERLTISASKRDDPSDKIFVFFPEEPKVGVKTIRKYCERMK 93 (93)
T ss_dssp CCCCCCCTEE--CCCCS--HHHHHHHCB-SS--SSB-GCCT-EEEEESCHT--EEEEEE-SSSCESCCCCHHHCHHH-
T ss_pred HHHHhcCCCccChhhhcCCHHHHHHHHcccC--CCCCHHHeeeeccCCCCCCCeEEEEeCCCCCcCHHHHHHHHHhcC
Confidence 6999999999999999999999999999864 358999999999999999999999999999999999999999985
No 5
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=99.86 E-value=1.7e-22 Score=168.43 Aligned_cols=59 Identities=25% Similarity=0.338 Sum_probs=57.5
Q ss_pred eeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecC
Q psy5290 119 LINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVY 180 (536)
Q Consensus 119 LVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~ 180 (536)
.+|||+|+|||+|++||+||+++||++|+++++|||||+.+||+ ++++|||+||||+|.
T Consensus 3 ~~nit~H~lVPkH~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv---~r~~g~k~GdVvkI~ 61 (79)
T PRK09570 3 KFDVLDHELVPEHEILSEEEAKKLLKEYGIKPEQLPKIKASDPV---VKAIGAKPGDVIKIV 61 (79)
T ss_pred ceecccccccCCeEECCHHHHHHHHHHcCCCHHHCCceeccChh---hhhcCCCCCCEEEEE
Confidence 58999999999999999999999999999999999999999999 999999999999984
No 6
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=99.85 E-value=3.9e-22 Score=164.33 Aligned_cols=58 Identities=31% Similarity=0.371 Sum_probs=49.8
Q ss_pred eccccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecC
Q psy5290 120 INITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVY 180 (536)
Q Consensus 120 VNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~ 180 (536)
+|||+|+|||+|++||+||+++||++|+++++|||||+.+||+ ++++|||+||||+|.
T Consensus 1 ~ni~~H~lVPkH~ils~eE~~~lL~~y~i~~~qLP~I~~~DPv---~r~~g~k~GdVvkI~ 58 (74)
T PF01191_consen 1 FNITKHELVPKHEILSEEEKKELLKKYNIKPEQLPKILSSDPV---ARYLGAKPGDVVKII 58 (74)
T ss_dssp S-CTSSTTC-EEEEE-HHHHHHHHHHTT--TTCSSEEETTSHH---HHHTT--TTSEEEEE
T ss_pred CCcccceecCCeEEcCHHHHHHHHHHhCCChhhCCcccccChh---hhhcCCCCCCEEEEE
Confidence 6999999999999999999999999999999999999999999 999999999999985
No 7
>COG2012 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]
Probab=99.84 E-value=8.6e-22 Score=164.77 Aligned_cols=63 Identities=30% Similarity=0.312 Sum_probs=60.8
Q ss_pred ecceeeccccccccCceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecC
Q psy5290 115 ESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVY 180 (536)
Q Consensus 115 EsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~ 180 (536)
++.+.+|+++|+|||+|++|++||++++|++|+|+++|||||+.+||+ ++++|||+||||+|-
T Consensus 2 ~~~~~~~v~~H~lVPeH~vls~eE~~~vLk~l~i~~~qLPkI~~~DPv---a~~lgak~GdvVkIv 64 (80)
T COG2012 2 ESMLKFNVLDHELVPEHEVLSEEEAKEVLKELGIEPEQLPKIKASDPV---AKALGAKPGDVVKIV 64 (80)
T ss_pred ccccceeeccccccCceEEcCHHHHHHHHHHhCCCHHHCCcccccChh---HHHccCCCCcEEEEE
Confidence 567899999999999999999999999999999999999999999999 999999999999984
No 8
>PF04471 Mrr_cat: Restriction endonuclease; InterPro: IPR007560 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. This entry represents Mrr, a type IV restriction endonuclease involved in the acceptance of modified foreign DNA, restricting both adenine- and cytosine-methylated DNA. Plasmids carrying HincII, HpaI, and TaqI R and M genes are severely restricted in Escherichia coli strains that are Mrr+ []. Mrr appears to be the final effector of the bacterial SOS response, which is not only a vital reply to DNA damage but also constitutes an essential mechanism for the generation of genetic variability that in turn fuels adaptation and resistance development in bacterial populations []. Mrr possesses a cleavage domain that is similar to that found in type II restriction enzymes, however it has an unusual glutamine residue at the central position of the (D/E)-(D/E)XK hallmark of the active site [].; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0009307 DNA restriction-modification system; PDB: 1Y88_A.
Probab=96.23 E-value=0.013 Score=47.42 Aligned_cols=75 Identities=19% Similarity=0.326 Sum_probs=42.0
Q ss_pred EEEeecCCCCCCceEEEeCC-CCCcchHHHHHHHHHHhhcCCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeeccee
Q psy5290 42 IVLVAHNDDPTDQMFVFFPD-EPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELL 119 (536)
Q Consensus 42 tfsashkdDPTdKIfVFFpd-E~KVGVKtIRkyiErMkEENI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELL 119 (536)
-+.+.+.+....+++|.+-. ..+++.+.|+.++..+...+..++|||+.+.+|+.|++.+.... .|+++..++|.
T Consensus 37 Di~~~~~~~~~~~~~vqcK~~~~~v~~~~v~~~~~~~~~~~~~~~iivt~~~~t~~a~~~~~~~~---~I~l~d~~~L~ 112 (115)
T PF04471_consen 37 DIIAEKDDLGKERILVQCKRYKKKVDVKAVRQLIGKAKKYGADKGIIVTSSGFTPEAKEFAEKFK---NIELIDGEDLQ 112 (115)
T ss_dssp EEEEEETT---EEEEEEE---S-EE-HHHHHHHHHHHGGGT-SEEEEE-SSEE-HHHHHHHH-----------------
T ss_pred EEEEEEcccCceEEEEEEEEeccccchHHHHHHhhhhhccCCCEEEEEECCcCCHHHHHHHHhhc---ccccccccccc
Confidence 34444433233467777643 35899999999999999999999999999999999998876542 57777776664
No 9
>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2.
Probab=57.67 E-value=20 Score=32.36 Aligned_cols=80 Identities=15% Similarity=0.110 Sum_probs=53.1
Q ss_pred ccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhcCC
Q psy5290 3 LCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETI 82 (536)
Q Consensus 3 MLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEENI 82 (536)
||++-||.|.+.....|-++|.+..-+.. -+ +++...- ..-.+..++..++.+++++.
T Consensus 25 ~l~~~GfeVi~lg~~~s~e~~v~aa~e~~-------ad--------------ii~iSsl-~~~~~~~~~~~~~~L~~~g~ 82 (132)
T TIGR00640 25 AYADLGFDVDVGPLFQTPEEIARQAVEAD-------VH--------------VVGVSSL-AGGHLTLVPALRKELDKLGR 82 (132)
T ss_pred HHHhCCcEEEECCCCCCHHHHHHHHHHcC-------CC--------------EEEEcCc-hhhhHHHHHHHHHHHHhcCC
Confidence 78999999999999999999998874321 11 2222222 22346678999999999888
Q ss_pred CEEEEEEcCCCCHHHHHHHhhc
Q psy5290 83 HRAIIVVQTGMTPSAKQSLVDM 104 (536)
Q Consensus 83 ~RgIIVvQqkLTPsARKAL~em 104 (536)
....+++-+.+...-...+.++
T Consensus 83 ~~i~vivGG~~~~~~~~~l~~~ 104 (132)
T TIGR00640 83 PDILVVVGGVIPPQDFDELKEM 104 (132)
T ss_pred CCCEEEEeCCCChHhHHHHHHC
Confidence 6555555555554434445444
No 10
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=57.64 E-value=31 Score=35.51 Aligned_cols=97 Identities=13% Similarity=0.179 Sum_probs=57.6
Q ss_pred eEEEeCCC--CCcchHHHHHHHHHHhh---cCCCEEEEEEc-CCCCHHHHHHHhhc---Cccce---eeEeeecceeecc
Q psy5290 55 MFVFFPDE--PKIGIKTIKTYCQRMQE---ETIHRAIIVVQ-TGMTPSAKQSLVDM---APKYI---LEYFLESELLINI 122 (536)
Q Consensus 55 IfVFFpdE--~KVGVKtIRkyiErMkE---ENI~RgIIVvQ-qkLTPsARKAL~em---spkfk---IEVFqEsELLVNI 122 (536)
+++.+++. ..|+|..||.+++.+.. ++-.|.|||.. ++||..|..++... .+... +-.-..+.||--|
T Consensus 76 ~~~i~p~~~~~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~lLpTI 155 (334)
T PRK07993 76 YYTLTPEKGKSSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALLTDAAANALLKTLEEPPENTWFFLACREPARLLATL 155 (334)
T ss_pred EEEEecccccccCCHHHHHHHHHHHhhccccCCceEEEEcchHhhCHHHHHHHHHHhcCCCCCeEEEEEECChhhChHHH
Confidence 45555654 45999999999998764 56677777775 77998776555433 22222 2222233455443
Q ss_pred c-cccccCceeecChHHHHHHHh-hcCCCCCC
Q psy5290 123 T-EHELVPEHIVLTPEEKQELLT-RYWRSCVT 152 (536)
Q Consensus 123 T-kHeLVPKHeVLS~EEKkeLLk-rY~IK~~Q 152 (536)
. +-..+ .-..+++|+..+.|. ++++..++
T Consensus 156 rSRCq~~-~~~~~~~~~~~~~L~~~~~~~~~~ 186 (334)
T PRK07993 156 RSRCRLH-YLAPPPEQYALTWLSREVTMSQDA 186 (334)
T ss_pred Hhccccc-cCCCCCHHHHHHHHHHccCCCHHH
Confidence 2 22223 233578899888885 44655443
No 11
>cd02072 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains.
Probab=50.17 E-value=31 Score=31.74 Aligned_cols=70 Identities=11% Similarity=0.137 Sum_probs=49.7
Q ss_pred ccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhcCC
Q psy5290 3 LCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETI 82 (536)
Q Consensus 3 MLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEENI 82 (536)
||++.||.|-+--++.+.++|.+..-+.. -.-+.++ .=-.-.+..++..++.++++++
T Consensus 22 ~L~~~GfeVidLG~~v~~e~~v~aa~~~~------adiVglS----------------~L~t~~~~~~~~~~~~l~~~gl 79 (128)
T cd02072 22 AFTEAGFNVVNLGVLSPQEEFIDAAIETD------ADAILVS----------------SLYGHGEIDCKGLREKCDEAGL 79 (128)
T ss_pred HHHHCCCEEEECCCCCCHHHHHHHHHHcC------CCEEEEe----------------ccccCCHHHHHHHHHHHHHCCC
Confidence 79999999999999999999999875421 1111222 1112446788999999999999
Q ss_pred CEEEEEEcCCCC
Q psy5290 83 HRAIIVVQTGMT 94 (536)
Q Consensus 83 ~RgIIVvQqkLT 94 (536)
....+++-+.+.
T Consensus 80 ~~v~vivGG~~~ 91 (128)
T cd02072 80 KDILLYVGGNLV 91 (128)
T ss_pred CCCeEEEECCCC
Confidence 666666666653
No 12
>PF14779 BBS1: Ciliary BBSome complex subunit 1
Probab=49.94 E-value=11 Score=38.30 Aligned_cols=35 Identities=43% Similarity=0.896 Sum_probs=27.3
Q ss_pred CCccccCCCCCCCcc--eeeeeccc-c----------------ccccccceeee
Q psy5290 263 NGKSLKQGVPLTDIP--VMAFYTKH-E----------------LDELKPFFKFF 297 (536)
Q Consensus 263 ~~~~~~~~~~~~~~~--~~~~~~~~-~----------------~~~~~~~~~~~ 297 (536)
+|-+|.+-.+|.|+| ++.||... | -..|||||||-
T Consensus 51 kGt~l~~E~~L~d~P~ai~sFy~d~~ep~~P~iAVA~G~~vyiYkNlkP~yKft 104 (257)
T PF14779_consen 51 KGTSLISEITLPDLPSAIVSFYMDEHEPRTPAIAVAAGPSVYIYKNLKPFYKFT 104 (257)
T ss_pred cCCChhhcccccCCCeEEEEEeccCCCCCCCeEEEEeCCEEEEEecccceeeec
Confidence 678888889999998 47888765 2 24689999984
No 13
>PRK08058 DNA polymerase III subunit delta'; Validated
Probab=45.42 E-value=78 Score=32.12 Aligned_cols=93 Identities=24% Similarity=0.207 Sum_probs=54.8
Q ss_pred EeCCCCCcchHHHHHHHHHHh---hcCCCEEEEEEc-CCCCHHHHHHHhhc---CccceeeEeee---cceeeccccccc
Q psy5290 58 FFPDEPKIGIKTIKTYCQRMQ---EETIHRAIIVVQ-TGMTPSAKQSLVDM---APKYILEYFLE---SELLINITEHEL 127 (536)
Q Consensus 58 FFpdE~KVGVKtIRkyiErMk---EENI~RgIIVvQ-qkLTPsARKAL~em---spkfkIEVFqE---sELLVNITkHeL 127 (536)
..++..++++..||..++.+. -++-.|.|||-. +.||..|..++... .+...+=+|.- +.|+--|..--.
T Consensus 83 i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~a~NaLLK~LEEPp~~~~~Il~t~~~~~ll~TIrSRc~ 162 (329)
T PRK08058 83 VAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTASAANSLLKFLEEPSGGTTAILLTENKHQILPTILSRCQ 162 (329)
T ss_pred eccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHHHHHHHHHHhcCCCCCceEEEEeCChHhCcHHHHhhce
Confidence 344566799999999999987 455567888877 67888665555433 12222222211 122222222222
Q ss_pred cCceeecChHHHHHHHhhcCCCC
Q psy5290 128 VPEHIVLTPEEKQELLTRYWRSC 150 (536)
Q Consensus 128 VPKHeVLS~EEKkeLLkrY~IK~ 150 (536)
+=.-..++++|..+.|++.++.+
T Consensus 163 ~i~~~~~~~~~~~~~L~~~gi~~ 185 (329)
T PRK08058 163 VVEFRPLPPESLIQRLQEEGISE 185 (329)
T ss_pred eeeCCCCCHHHHHHHHHHcCCCh
Confidence 22334578888888888766544
No 14
>TIGR00678 holB DNA polymerase III, delta' subunit. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.
Probab=41.05 E-value=89 Score=28.32 Aligned_cols=90 Identities=20% Similarity=0.242 Sum_probs=49.2
Q ss_pred eCCCCCcchHHHHHHHHHHhh---cCCCEEEEEEc-CCCCHHHHHHHhhcC---ccceeeEeeecc---eeecccccccc
Q psy5290 59 FPDEPKIGIKTIKTYCQRMQE---ETIHRAIIVVQ-TGMTPSAKQSLVDMA---PKYILEYFLESE---LLINITEHELV 128 (536)
Q Consensus 59 FpdE~KVGVKtIRkyiErMkE---ENI~RgIIVvQ-qkLTPsARKAL~ems---pkfkIEVFqEsE---LLVNITkHeLV 128 (536)
..+...+++..||.+++.+.. .+-.+.|||-. +.++..|..++...- +...+=+|.-++ |+--|...-.+
T Consensus 70 ~~~~~~~~~~~i~~i~~~~~~~~~~~~~kviiide~~~l~~~~~~~Ll~~le~~~~~~~~il~~~~~~~l~~~i~sr~~~ 149 (188)
T TIGR00678 70 EPEGQSIKVDQVRELVEFLSRTPQESGRRVVIIEDAERMNEAAANALLKTLEEPPPNTLFILITPSPEKLLPTIRSRCQV 149 (188)
T ss_pred ccccCcCCHHHHHHHHHHHccCcccCCeEEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhChHHHHhhcEE
Confidence 344456899999998888765 45455555543 567776544444321 222232332222 21122333322
Q ss_pred CceeecChHHHHHHHhhcCC
Q psy5290 129 PEHIVLTPEEKQELLTRYWR 148 (536)
Q Consensus 129 PKHeVLS~EEKkeLLkrY~I 148 (536)
=+-..++.+|..+.|++.++
T Consensus 150 ~~~~~~~~~~~~~~l~~~gi 169 (188)
T TIGR00678 150 LPFPPLSEEALLQWLIRQGI 169 (188)
T ss_pred eeCCCCCHHHHHHHHHHcCC
Confidence 23345788999999988743
No 15
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=38.82 E-value=15 Score=30.23 Aligned_cols=49 Identities=10% Similarity=0.068 Sum_probs=30.8
Q ss_pred ecChHHHHHHHhhcCCCCC----CccccccCCcccccccccCCccCcEEecCC
Q psy5290 133 VLTPEEKQELLTRYWRSCV----TIFWTQKRTGEEHFLKECSFESATVKSVYP 181 (536)
Q Consensus 133 VLS~EEKkeLLkrY~IK~~----QLPkIk~tDPvavfvk~iGAKpGDVVrv~~ 181 (536)
+++-+..+.+++++++.-. .|=++...-.+.--++.-||+.||.|+|..
T Consensus 12 ~V~g~~ier~~~~~~~~~~e~~~~f~~~L~~~Gv~~~L~~~G~~~GD~V~Ig~ 64 (69)
T TIGR03595 12 VVSGKKIERWVAKTPFNNDENLRRFARKLKKLGVEDALRKAGAKDGDTVRIGD 64 (69)
T ss_pred EEechHHHHHHHHcCCCCHHHHHHHHHHHHHCCHHHHHHHcCCCCCCEEEEcc
Confidence 3466667777777776642 233333333333336777999999999974
No 16
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=37.97 E-value=49 Score=28.27 Aligned_cols=43 Identities=12% Similarity=0.002 Sum_probs=29.7
Q ss_pred ccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecC--CcceeeccCCCCCC
Q psy5290 166 LKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSD--RANAVFLPQGLSTP 217 (536)
Q Consensus 166 vk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d--~~~~~~~~~~~~~~ 217 (536)
++++|++.||.|+|+-.-- . +-+.|++++ +.+.||+|.|...+
T Consensus 42 A~~~gi~~Gd~V~v~s~~G--------~-~~~~v~v~~~i~~g~v~~~~g~~~~ 86 (130)
T cd02781 42 AAKLGIADGDWVWVETPRG--------R-ARQKARLTPGIRPGVVRAEHGWWYP 86 (130)
T ss_pred HHHcCCCCCCEEEEECCCC--------E-EEEEEEECCCCCCCEEEEecccccc
Confidence 5578999999999875442 2 223445555 56889999986544
No 17
>PRK06871 DNA polymerase III subunit delta'; Validated
Probab=37.60 E-value=1.4e+02 Score=31.13 Aligned_cols=91 Identities=13% Similarity=0.199 Sum_probs=52.2
Q ss_pred eEEEeC-CCCCcchHHHHHHHHHHhh---cCCCEEEEEEc-CCCCHHHHHHHhhc---Ccccee---eEeeecceeeccc
Q psy5290 55 MFVFFP-DEPKIGIKTIKTYCQRMQE---ETIHRAIIVVQ-TGMTPSAKQSLVDM---APKYIL---EYFLESELLINIT 123 (536)
Q Consensus 55 IfVFFp-dE~KVGVKtIRkyiErMkE---ENI~RgIIVvQ-qkLTPsARKAL~em---spkfkI---EVFqEsELLVNIT 123 (536)
+++..+ +...+||..||.+++.+.. ++-.|.|||-. +.||..|..++... .+...+ -.-..+.||--|.
T Consensus 76 ~~~i~p~~~~~I~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m~~~AaNaLLKtLEEPp~~~~fiL~t~~~~~llpTI~ 155 (325)
T PRK06871 76 FHILEPIDNKDIGVDQVREINEKVSQHAQQGGNKVVYIQGAERLTEAAANALLKTLEEPRPNTYFLLQADLSAALLPTIY 155 (325)
T ss_pred EEEEccccCCCCCHHHHHHHHHHHhhccccCCceEEEEechhhhCHHHHHHHHHHhcCCCCCeEEEEEECChHhCchHHH
Confidence 343445 3457999999999888764 56667777765 67998776665433 222221 1112233443332
Q ss_pred -cccccCceeecChHHHHHHHhhc
Q psy5290 124 -EHELVPEHIVLTPEEKQELLTRY 146 (536)
Q Consensus 124 -kHeLVPKHeVLS~EEKkeLLkrY 146 (536)
+...+ .-..+++++..+.|++-
T Consensus 156 SRC~~~-~~~~~~~~~~~~~L~~~ 178 (325)
T PRK06871 156 SRCQTW-LIHPPEEQQALDWLQAQ 178 (325)
T ss_pred hhceEE-eCCCCCHHHHHHHHHHH
Confidence 11112 23356788888888753
No 18
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=35.45 E-value=49 Score=27.67 Aligned_cols=49 Identities=18% Similarity=0.090 Sum_probs=33.3
Q ss_pred CCccccccCCcccccccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecC--CcceeeccCC
Q psy5290 151 VTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSD--RANAVFLPQG 213 (536)
Q Consensus 151 ~QLPkIk~tDPvavfvk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d--~~~~~~~~~~ 213 (536)
+..-+|...| ++.+|.+.||.|+|.-.-- .+.+.|++++ +.+.||+|.|
T Consensus 28 ~~~v~inp~d-----A~~lGi~~Gd~V~v~s~~G---------~i~~~v~v~~~v~~g~V~~p~g 78 (96)
T cd02788 28 APYARLSPAD-----AARLGLADGDLVEFSLGDG---------TLTLPVQISKYLPAGVVGLPLG 78 (96)
T ss_pred CCEEEECHHH-----HHHcCCCCCCEEEEEECCe---------EEEEEEEECCCCCCCEEEEecC
Confidence 3344555544 4578999999999874432 3445667766 4578999998
No 19
>cd02777 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB hom
Probab=34.28 E-value=57 Score=28.13 Aligned_cols=41 Identities=17% Similarity=0.288 Sum_probs=29.4
Q ss_pred ccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecCC--cceeeccCCCC
Q psy5290 166 LKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDR--ANAVFLPQGLS 215 (536)
Q Consensus 166 vk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d~--~~~~~~~~~~~ 215 (536)
++++|.+.||.|+|.-.-. .+.+.|+.+|+ .+.||+|.|.-
T Consensus 43 A~~lgi~~Gd~V~v~s~~g---------~i~~~v~i~~~v~~g~v~~~~g~~ 85 (127)
T cd02777 43 AAARGIKDGDIVRVFNDRG---------AVLAGARVTDRIMPGVVALPEGAW 85 (127)
T ss_pred HHHcCCCCCCEEEEEcCCe---------EEEEEEEECCCcCCCEEEeCcccc
Confidence 5578999999999985433 34456666664 47899998753
No 20
>PRK06964 DNA polymerase III subunit delta'; Validated
Probab=32.66 E-value=1.9e+02 Score=30.28 Aligned_cols=85 Identities=16% Similarity=0.156 Sum_probs=50.8
Q ss_pred CcchHHHHHHHHHHhh---cCCCEEEEEEc-CCCCHHHHHHHhhc---Cccc---eeeEeeecceeeccc-cccccCcee
Q psy5290 64 KIGIKTIKTYCQRMQE---ETIHRAIIVVQ-TGMTPSAKQSLVDM---APKY---ILEYFLESELLINIT-EHELVPEHI 132 (536)
Q Consensus 64 KVGVKtIRkyiErMkE---ENI~RgIIVvQ-qkLTPsARKAL~em---spkf---kIEVFqEsELLVNIT-kHeLVPKHe 132 (536)
.|+|..||.+++.+.. ++-.|.+||.. +.||..|..++-.. .+.. .+-.-..+.||--|. .-..+ .-.
T Consensus 111 ~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~t~fiL~t~~~~~LLpTI~SRcq~i-~~~ 189 (342)
T PRK06964 111 EIKIEQVRALLDFCGVGTHRGGARVVVLYPAEALNVAAANALLKTLEEPPPGTVFLLVSARIDRLLPTILSRCRQF-PMT 189 (342)
T ss_pred ccCHHHHHHHHHHhccCCccCCceEEEEechhhcCHHHHHHHHHHhcCCCcCcEEEEEECChhhCcHHHHhcCEEE-Eec
Confidence 5999999999988754 45567777766 66998776555432 1221 222223344443433 11111 123
Q ss_pred ecChHHHHHHHhhcCCC
Q psy5290 133 VLTPEEKQELLTRYWRS 149 (536)
Q Consensus 133 VLS~EEKkeLLkrY~IK 149 (536)
.++.||..+.|++.++.
T Consensus 190 ~~~~~~~~~~L~~~~~~ 206 (342)
T PRK06964 190 VPAPEAAAAWLAAQGVA 206 (342)
T ss_pred CCCHHHHHHHHHHcCCC
Confidence 57889999999887654
No 21
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=31.90 E-value=92 Score=27.13 Aligned_cols=70 Identities=14% Similarity=0.037 Sum_probs=46.2
Q ss_pred ccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhcCC
Q psy5290 3 LCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETI 82 (536)
Q Consensus 3 MLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEENI 82 (536)
|+++.||.|..--.+.+.++|.+.-.+.. + +-|.+.+.. .-....++.+++.+++.+.
T Consensus 22 ~l~~~G~~vi~lG~~vp~e~~~~~a~~~~-------------------~-d~V~iS~~~--~~~~~~~~~~~~~L~~~~~ 79 (122)
T cd02071 22 ALRDAGFEVIYTGLRQTPEEIVEAAIQED-------------------V-DVIGLSSLS--GGHMTLFPEVIELLRELGA 79 (122)
T ss_pred HHHHCCCEEEECCCCCCHHHHHHHHHHcC-------------------C-CEEEEcccc--hhhHHHHHHHHHHHHhcCC
Confidence 78899999988777788889887764321 0 112222333 3456778999999999988
Q ss_pred CEEEEEEcCCCC
Q psy5290 83 HRAIIVVQTGMT 94 (536)
Q Consensus 83 ~RgIIVvQqkLT 94 (536)
....+++-+...
T Consensus 80 ~~i~i~~GG~~~ 91 (122)
T cd02071 80 GDILVVGGGIIP 91 (122)
T ss_pred CCCEEEEECCCC
Confidence 655555554443
No 22
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=31.51 E-value=51 Score=27.21 Aligned_cols=42 Identities=19% Similarity=0.271 Sum_probs=28.4
Q ss_pred ccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecCC--cceeeccCCCCC
Q psy5290 166 LKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDR--ANAVFLPQGLST 216 (536)
Q Consensus 166 vk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d~--~~~~~~~~~~~~ 216 (536)
++++|++-||.|+|.-.-- -+-+.|+.+|+ .+.|++|.|...
T Consensus 39 A~~~Gi~~Gd~V~v~s~~G---------~v~~~v~~~~~v~~g~v~~~~~~~~ 82 (110)
T PF01568_consen 39 AAKLGIKDGDWVRVSSPRG---------SVEVRVKVTDGVPPGVVFMPHGWGG 82 (110)
T ss_dssp HHHCT--TTCEEEEEETTE---------EEEEEEEEETTS-TTEEEEESTHTT
T ss_pred HHHhcCcCCCEEEEEeccc---------eEeeeeEEecCCcCCEEEEeccccc
Confidence 5678999999999975432 34466777774 578888887644
No 23
>PRK05707 DNA polymerase III subunit delta'; Validated
Probab=31.22 E-value=1.9e+02 Score=29.90 Aligned_cols=91 Identities=18% Similarity=0.227 Sum_probs=53.0
Q ss_pred eEEEeCCC--CCcchHHHHHHHHHHhh---cCCCEEEEEEc-CCCCHHHHHHHhhc---Ccc---ceeeEeeecceeecc
Q psy5290 55 MFVFFPDE--PKIGIKTIKTYCQRMQE---ETIHRAIIVVQ-TGMTPSAKQSLVDM---APK---YILEYFLESELLINI 122 (536)
Q Consensus 55 IfVFFpdE--~KVGVKtIRkyiErMkE---ENI~RgIIVvQ-qkLTPsARKAL~em---spk---fkIEVFqEsELLVNI 122 (536)
++++.+++ ..++|..||++++.+.. ++-.|.+||-. +.||..|..++... .+. +.+-.-..+.|+--|
T Consensus 74 ~~~i~~~~~~~~i~id~iR~l~~~~~~~~~~~~~kv~iI~~a~~m~~~aaNaLLK~LEEPp~~~~fiL~t~~~~~ll~TI 153 (328)
T PRK05707 74 NFVLEPEEADKTIKVDQVRELVSFVVQTAQLGGRKVVLIEPAEAMNRNAANALLKSLEEPSGDTVLLLISHQPSRLLPTI 153 (328)
T ss_pred EEEEeccCCCCCCCHHHHHHHHHHHhhccccCCCeEEEECChhhCCHHHHHHHHHHHhCCCCCeEEEEEECChhhCcHHH
Confidence 55555654 35999999999998864 56667777654 66898776555433 111 112222233444443
Q ss_pred ccccccCceeecChHHHHHHHhh
Q psy5290 123 TEHELVPEHIVLTPEEKQELLTR 145 (536)
Q Consensus 123 TkHeLVPKHeVLS~EEKkeLLkr 145 (536)
..--.+=.-..++.+|..+.|++
T Consensus 154 ~SRc~~~~~~~~~~~~~~~~L~~ 176 (328)
T PRK05707 154 KSRCQQQACPLPSNEESLQWLQQ 176 (328)
T ss_pred HhhceeeeCCCcCHHHHHHHHHH
Confidence 32211112244788888888875
No 24
>PF01939 DUF91: Protein of unknown function DUF91; InterPro: IPR002793 The function of these prokaryotic proteins is unknown. Computational analysis suggests that they may form a restriction endonuclease-like fold, similar to that found in a variety of endonucleases and DNA repair enzymes [].; PDB: 2VLD_A.
Probab=31.10 E-value=77 Score=31.89 Aligned_cols=57 Identities=19% Similarity=0.333 Sum_probs=33.9
Q ss_pred eEEEeCCC--CCcchHHHHHHHHHHhhcCC---CEEEEEEcCCCCHHHHHHHhhcCccceeeEeeec
Q psy5290 55 MFVFFPDE--PKIGIKTIKTYCQRMQEETI---HRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLES 116 (536)
Q Consensus 55 IfVFFpdE--~KVGVKtIRkyiErMkEENI---~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEs 116 (536)
+.|..--. ..=.+.++..|++.++++.. =|+|||.++ +|+.|+..+.+ ..||+...+
T Consensus 150 VVIElKR~~a~~~aV~QL~rY~~~l~~~~~~~~VRGilvA~~-i~~~a~~ll~~----~glef~~ld 211 (228)
T PF01939_consen 150 VVIELKRRRADRDAVEQLLRYVELLKRDPGLEPVRGILVAPS-ITPQARELLED----RGLEFVELD 211 (228)
T ss_dssp EEEEE-SS-B-HHHHHHHHHHHHHHHHHH--S-EEEEEEES--B-HHHHHHHHH----HT-EEEE--
T ss_pred EEEEEEeccCCHHHHHHHHHHHHHHhhccCCCceeEEEECCC-CCHHHHHHHHH----cCCEEEEec
Confidence 45566433 22446666778888876532 389999877 99999988755 357766554
No 25
>PRK05564 DNA polymerase III subunit delta'; Validated
Probab=30.96 E-value=1.7e+02 Score=29.07 Aligned_cols=86 Identities=20% Similarity=0.318 Sum_probs=49.9
Q ss_pred CCCCcchHHHHHHHHHHhh---cCCCEEEEEEc-CCCCHHHHHHHhhcC---ccceeeEeeec---ceeeccccccccCc
Q psy5290 61 DEPKIGIKTIKTYCQRMQE---ETIHRAIIVVQ-TGMTPSAKQSLVDMA---PKYILEYFLES---ELLINITEHELVPE 130 (536)
Q Consensus 61 dE~KVGVKtIRkyiErMkE---ENI~RgIIVvQ-qkLTPsARKAL~ems---pkfkIEVFqEs---ELLVNITkHeLVPK 130 (536)
+...++++.||..++.+.. ++-.|.|||.. +.||..|..++...- +...+=+|.-+ .|+--|...-.+=.
T Consensus 69 ~~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~~a~naLLK~LEepp~~t~~il~~~~~~~ll~TI~SRc~~~~ 148 (313)
T PRK05564 69 NKKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTEQAQNAFLKTIEEPPKGVFIILLCENLEQILDTIKSRCQIYK 148 (313)
T ss_pred cCCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhcCHHHHHHHHHHhcCCCCCeEEEEEeCChHhCcHHHHhhceeee
Confidence 5567999999999997654 56678888888 889987765555432 22222222211 11111221111112
Q ss_pred eeecChHHHHHHHhhc
Q psy5290 131 HIVLTPEEKQELLTRY 146 (536)
Q Consensus 131 HeVLS~EEKkeLLkrY 146 (536)
-..++++|..+.|++-
T Consensus 149 ~~~~~~~~~~~~l~~~ 164 (313)
T PRK05564 149 LNRLSKEEIEKFISYK 164 (313)
T ss_pred CCCcCHHHHHHHHHHH
Confidence 3346888888888753
No 26
>PRK02261 methylaspartate mutase subunit S; Provisional
Probab=30.58 E-value=1e+02 Score=28.11 Aligned_cols=69 Identities=10% Similarity=0.098 Sum_probs=47.6
Q ss_pred ccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhcCC
Q psy5290 3 LCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETI 82 (536)
Q Consensus 3 MLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEENI 82 (536)
||+++||.|..--.+.+.++|.+.-.+.. -+- |.+.+.. .-....++++++.+++.+.
T Consensus 26 ~lr~~G~eVi~LG~~vp~e~i~~~a~~~~------~d~--------------V~lS~~~--~~~~~~~~~~~~~L~~~~~ 83 (137)
T PRK02261 26 ALTEAGFEVINLGVMTSQEEFIDAAIETD------ADA--------------ILVSSLY--GHGEIDCRGLREKCIEAGL 83 (137)
T ss_pred HHHHCCCEEEECCCCCCHHHHHHHHHHcC------CCE--------------EEEcCcc--ccCHHHHHHHHHHHHhcCC
Confidence 78999999988878889999988754320 011 2222222 2457788999999999888
Q ss_pred CEEEEEEcCCC
Q psy5290 83 HRAIIVVQTGM 93 (536)
Q Consensus 83 ~RgIIVvQqkL 93 (536)
....+++-+.+
T Consensus 84 ~~~~i~vGG~~ 94 (137)
T PRK02261 84 GDILLYVGGNL 94 (137)
T ss_pred CCCeEEEECCC
Confidence 66666666666
No 27
>PRK08769 DNA polymerase III subunit delta'; Validated
Probab=30.25 E-value=1.8e+02 Score=30.11 Aligned_cols=87 Identities=17% Similarity=0.121 Sum_probs=50.9
Q ss_pred CcchHHHHHHHHHHhh---cCCCEEEEEEc-CCCCHHHHHHHhhc---Ccc---ceeeEeeecceeecccc-ccccCcee
Q psy5290 64 KIGIKTIKTYCQRMQE---ETIHRAIIVVQ-TGMTPSAKQSLVDM---APK---YILEYFLESELLINITE-HELVPEHI 132 (536)
Q Consensus 64 KVGVKtIRkyiErMkE---ENI~RgIIVvQ-qkLTPsARKAL~em---spk---fkIEVFqEsELLVNITk-HeLVPKHe 132 (536)
.|+|..||.+++.+.. ++-.|.|||.. +.||..|..+|... .+. |.+-.-..+.||--|.. ...+ .-.
T Consensus 92 ~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m~~~AaNaLLKtLEEPp~~~~fiL~~~~~~~lLpTIrSRCq~i-~~~ 170 (319)
T PRK08769 92 EIVIEQVREISQKLALTPQYGIAQVVIVDPADAINRAACNALLKTLEEPSPGRYLWLISAQPARLPATIRSRCQRL-EFK 170 (319)
T ss_pred cccHHHHHHHHHHHhhCcccCCcEEEEeccHhhhCHHHHHHHHHHhhCCCCCCeEEEEECChhhCchHHHhhheEe-eCC
Confidence 4899999999998765 44456776655 66997776555433 111 22222233445444332 1111 123
Q ss_pred ecChHHHHHHHhhcCCCCC
Q psy5290 133 VLTPEEKQELLTRYWRSCV 151 (536)
Q Consensus 133 VLS~EEKkeLLkrY~IK~~ 151 (536)
.++.||..+.|++.++.+.
T Consensus 171 ~~~~~~~~~~L~~~~~~~~ 189 (319)
T PRK08769 171 LPPAHEALAWLLAQGVSER 189 (319)
T ss_pred CcCHHHHHHHHHHcCCChH
Confidence 4788999999987665543
No 28
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=30.22 E-value=60 Score=29.99 Aligned_cols=70 Identities=13% Similarity=0.134 Sum_probs=48.3
Q ss_pred cccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhcC
Q psy5290 2 QLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEET 81 (536)
Q Consensus 2 EMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEEN 81 (536)
-||++.||.|-+--+..+.++|.+..-+.. -+-+.++.- -.-.+..++...+.+++++
T Consensus 23 ~~l~~~GfeVi~LG~~v~~e~~v~aa~~~~------adiVglS~l----------------~~~~~~~~~~~~~~l~~~g 80 (134)
T TIGR01501 23 HAFTNAGFNVVNLGVLSPQEEFIKAAIETK------ADAILVSSL----------------YGHGEIDCKGLRQKCDEAG 80 (134)
T ss_pred HHHHHCCCEEEECCCCCCHHHHHHHHHHcC------CCEEEEecc----------------cccCHHHHHHHHHHHHHCC
Confidence 389999999999888999999999874320 111222211 1234567888999999999
Q ss_pred CCEEEEEEcCCC
Q psy5290 82 IHRAIIVVQTGM 93 (536)
Q Consensus 82 I~RgIIVvQqkL 93 (536)
+...++|+-+.+
T Consensus 81 l~~~~vivGG~~ 92 (134)
T TIGR01501 81 LEGILLYVGGNL 92 (134)
T ss_pred CCCCEEEecCCc
Confidence 976656666653
No 29
>COG4624 Iron only hydrogenase large subunit, C-terminal domain [General function prediction only]
Probab=30.17 E-value=39 Score=36.84 Aligned_cols=37 Identities=19% Similarity=0.161 Sum_probs=33.5
Q ss_pred eeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccC
Q psy5290 131 HIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESA 174 (536)
Q Consensus 131 HeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpG 174 (536)
-.+||.+|..++|+..+|+..+||...-.+++ |+..|
T Consensus 220 D~vLTtrEL~~ml~~l~id~~~lp~~~~~s~~-------g~~sg 256 (411)
T COG4624 220 DFVLTTRELVKMLKELRIDFARLPDGHYDSPA-------GFSSG 256 (411)
T ss_pred eEEecHHHHHHHHHHhCCCHhHCCCCCccccc-------ccccc
Confidence 46899999999999999999999999999998 66666
No 30
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=30.13 E-value=77 Score=27.95 Aligned_cols=53 Identities=17% Similarity=0.346 Sum_probs=39.3
Q ss_pred cchHHHHHHHHHHhhcCCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeecc
Q psy5290 65 IGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINI 122 (536)
Q Consensus 65 VGVKtIRkyiErMkEENI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVNI 122 (536)
+|.-.+.++.+.+.+.+++ ++|+.+.+||...+.|... +.++++.-+.|+.+|
T Consensus 41 iG~GK~eei~~~~~~~~~d--~vvfd~~Lsp~Q~rNLe~~---~~~~V~DRt~LIL~I 93 (95)
T PF13167_consen 41 IGSGKVEEIKELIEELDAD--LVVFDNELSPSQQRNLEKA---LGVKVIDRTQLILEI 93 (95)
T ss_pred echhHHHHHHHHHhhcCCC--EEEECCCCCHHHHHHHHHH---HCCeeeccccHHHHH
Confidence 5566666666666667774 5566678999888888765 478999999888776
No 31
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=29.78 E-value=79 Score=26.58 Aligned_cols=42 Identities=14% Similarity=0.101 Sum_probs=30.2
Q ss_pred ccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecCC--cceeeccCCCCC
Q psy5290 166 LKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDR--ANAVFLPQGLST 216 (536)
Q Consensus 166 vk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d~--~~~~~~~~~~~~ 216 (536)
++.+|++.||.|+|.-.-- .+.+-|+++++ ...|++|.|...
T Consensus 44 A~~lgi~~Gd~V~v~s~~G---------~~~~~v~v~~~i~~g~v~~~~g~~~ 87 (122)
T cd02792 44 AAERGIKNGDMVWVSSPRG---------KIKVKALVTDRVKPHEVGIPYHWGG 87 (122)
T ss_pred HHHcCCCCCCEEEEEcCCc---------eEEEEEEECCCcCCCEEEEecccCc
Confidence 5578999999999975432 34566777664 468899987643
No 32
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=28.20 E-value=86 Score=26.03 Aligned_cols=41 Identities=17% Similarity=0.229 Sum_probs=29.1
Q ss_pred ccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecC--CcceeeccCCCC
Q psy5290 166 LKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSD--RANAVFLPQGLS 215 (536)
Q Consensus 166 vk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d--~~~~~~~~~~~~ 215 (536)
++.+|++.||.|+|.-.-- .+-+-|++++ +.+.|++|.|..
T Consensus 44 A~~lgi~~Gd~V~v~~~~G---------~~~~~v~i~~~i~~g~v~~~~g~~ 86 (116)
T cd02790 44 AKRLGIEDGEKVRVSSRRG---------SVEVRARVTDRVPEGVVFMPFHFA 86 (116)
T ss_pred HHHcCCCCCCEEEEEcCCE---------EEEEEEEECCCcCCCEEEEecCcC
Confidence 4568999999999986542 2445666665 457888998853
No 33
>PRK08485 DNA polymerase III subunit delta'; Validated
Probab=28.19 E-value=1.4e+02 Score=29.97 Aligned_cols=46 Identities=17% Similarity=0.288 Sum_probs=31.7
Q ss_pred EeCCCCCcchHHHHHHHHHHhhc-CCCEEEEEEcCCCCHHHHHHHhhc
Q psy5290 58 FFPDEPKIGIKTIKTYCQRMQEE-TIHRAIIVVQTGMTPSAKQSLVDM 104 (536)
Q Consensus 58 FFpdE~KVGVKtIRkyiErMkEE-NI~RgIIVvQqkLTPsARKAL~em 104 (536)
||..+ .+||..||.+++.+.-. +-.+.||.--+.||..|..++-..
T Consensus 31 ~f~~~-~i~Vd~iReii~~~~~~~~~~k~iI~~a~~l~~~A~NaLLK~ 77 (206)
T PRK08485 31 FFIKE-EFKIEDAKEVIAEAYIAESEEKIIVIAAPSYGIEAQNALLKI 77 (206)
T ss_pred EECCC-CCCHHHHHHHHHHHhhCCCCcEEEEEchHhhCHHHHHHHHHH
Confidence 34433 69999999999987543 344556665677998887666543
No 34
>PF13156 Mrr_cat_2: Restriction endonuclease
Probab=27.83 E-value=79 Score=29.42 Aligned_cols=48 Identities=17% Similarity=0.340 Sum_probs=39.6
Q ss_pred EeCCCCCcchHHHHHHHHHHhhcCCCEEEEEEcC-CCCHHHHHHHhhcC
Q psy5290 58 FFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQT-GMTPSAKQSLVDMA 105 (536)
Q Consensus 58 FFpdE~KVGVKtIRkyiErMkEENI~RgIIVvQq-kLTPsARKAL~ems 105 (536)
||..+.+|..+.|-.|+.......+.+.|||.-. +++..|.++|..-.
T Consensus 51 fY~~~~~I~k~didSF~s~sgk~~f~~rliisTt~~~s~nAe~~l~~q~ 99 (129)
T PF13156_consen 51 FYDPDHTIQKSDIDSFFSASGKSRFSRRLIISTTDKWSKNAEKALENQS 99 (129)
T ss_pred eeCCCceEcHHHhhHHHHhcCCccccCcEEEEcCcHhhHHHHHHHHcCC
Confidence 5677779999999999999888888877777664 78999999887643
No 35
>KOG0182|consensus
Probab=27.20 E-value=1.3e+02 Score=31.01 Aligned_cols=129 Identities=19% Similarity=0.301 Sum_probs=71.4
Q ss_pred CCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEE-eecCCCCC----CceEEEeC-CCCCcchHHHHH--HHHHHh
Q psy5290 7 RGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVL-VAHNDDPT----DQMFVFFP-DEPKIGIKTIKT--YCQRMQ 78 (536)
Q Consensus 7 RGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~Ltfs-ashkdDPT----dKIfVFFp-dE~KVGVKtIRk--yiErMk 78 (536)
-||.+..+-|.-+..+-.+.|..+... ++--=.|++. +.....|. |-.-.|+. .-...|+|+.+. |+|+
T Consensus 105 ~Gyemp~DiL~k~~Ad~~QvytQ~a~m-Rplg~~~~~i~~D~E~gP~vYk~DpAGyy~g~kAtaaG~Kq~e~tsfLEK-- 181 (246)
T KOG0182|consen 105 YGYEMPCDILAKRMADKSQVYTQNAAM-RPLGVAATLIGVDEERGPSVYKTDPAGYYYGFKATAAGVKQQEATSFLEK-- 181 (246)
T ss_pred cCCCCCHHHHHHHHhhHHHHHhhhhhh-cccceeEEEEEeccccCcceEeecCccccccceeeecccchhhHHHHHHH--
Confidence 489999988888888888888765221 1111112222 22222222 11222221 123588887665 5554
Q ss_pred hcCCCEEEEEEcCCCCHHHHHHHhhcCccceeeEeeecceeeccccccccCceeecChHHHHHHHhh
Q psy5290 79 EETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTR 145 (536)
Q Consensus 79 EENI~RgIIVvQqkLTPsARKAL~emspkfkIEVFqEsELLVNITkHeLVPKHeVLS~EEKkeLLkr 145 (536)
+++.-+.-+-...--.|..+|.+... .-|.-+||-|-+..-. -|+-.+||.||.++.|..
T Consensus 182 --k~Kk~~~~t~~e~ve~ai~al~~sl~----~Dfk~se~EVgvv~~~-~p~f~~Ls~~eie~hL~~ 241 (246)
T KOG0182|consen 182 --KYKKDIDLTFEETVETAISALQSSLG----IDFKSSELEVGVVTVD-NPEFRILSAEEIEEHLQA 241 (246)
T ss_pred --hhccCccchHHHHHHHHHHHHHHHHh----cccCCcceEEEEEEcC-CcceeeccHHHHHHHHHH
Confidence 33333332222222344445544322 3578888888776543 689999999999999874
No 36
>PF15427 S100PBPR: S100P-binding protein
Probab=26.09 E-value=75 Score=34.32 Aligned_cols=83 Identities=27% Similarity=0.177 Sum_probs=48.0
Q ss_pred ceeecChHHHHHHHhhcCCCCCCccccccCCcccccccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecCCcceee
Q psy5290 130 EHIVLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSDRANAVF 209 (536)
Q Consensus 130 KHeVLS~EEKkeLLkrY~IK~~QLPkIk~tDPvavfvk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d~~~~~~ 209 (536)
-|--.|+||+++||+.=....+|+.+=...|-.- .-+.|.+-..|.--.|.=+ .-++-|--...-+...-
T Consensus 29 ghfs~TEEEIqeLLkdDd~s~e~~~~~~~~d~~~--~~ek~~~~s~i~~dtpqek--------nsl~Slgp~Aet~~~~k 98 (386)
T PF15427_consen 29 GHFSYTEEEIQELLKDDDPSNEQSSGGLLKDDGG--HVEKGERGSQILLDTPQEK--------NSLYSLGPVAETPGLFK 98 (386)
T ss_pred CCccccHHHHHHHHccccccchhhcccccccccc--cccccCCCccccCCCchhc--------ccccccccccCCccccc
Confidence 4667899999999998888878877733222221 1223444444433333322 22222222233344455
Q ss_pred ccCCCCCCCCCCCC
Q psy5290 210 LPQGLSTPESHPPV 223 (536)
Q Consensus 210 ~~~~~~~~~~~~~~ 223 (536)
||| |+|+-+|-|.
T Consensus 99 LPQ-lst~~gh~p~ 111 (386)
T PF15427_consen 99 LPQ-LSTSVGHGPT 111 (386)
T ss_pred Ccc-ccccCCCCCC
Confidence 787 8999999775
No 37
>KOG0460|consensus
Probab=25.18 E-value=97 Score=34.03 Aligned_cols=82 Identities=22% Similarity=0.287 Sum_probs=58.0
Q ss_pred HHHHHhh--cCCCEEEEEEcC--CCCHHHHHHHhhcCccceeeEeeecceeeccccccccCceeecC--hHHHHHHHhhc
Q psy5290 73 YCQRMQE--ETIHRAIIVVQT--GMTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLT--PEEKQELLTRY 146 (536)
Q Consensus 73 yiErMkE--ENI~RgIIVvQq--kLTPsARKAL~emspkfkIEVFqEsELLVNITkHeLVPKHeVLS--~EEKkeLLkrY 146 (536)
|+..|-. ...+-+|||+.. +.-|+.|..|.- +....| +.+.|=|.+-.+|++-+.|. +-|.++||..|
T Consensus 130 YIKNMItGaaqMDGaILVVaatDG~MPQTrEHlLL-ArQVGV-----~~ivvfiNKvD~V~d~e~leLVEmE~RElLse~ 203 (449)
T KOG0460|consen 130 YIKNMITGAAQMDGAILVVAATDGPMPQTREHLLL-ARQVGV-----KHIVVFINKVDLVDDPEMLELVEMEIRELLSEF 203 (449)
T ss_pred HHHHhhcCccccCceEEEEEcCCCCCcchHHHHHH-HHHcCC-----ceEEEEEecccccCCHHHHHHHHHHHHHHHHHc
Confidence 5555533 467789999873 334677776643 333333 55666677788887777764 77899999999
Q ss_pred CCCCCCccccccCC
Q psy5290 147 WRSCVTIFWTQKRT 160 (536)
Q Consensus 147 ~IK~~QLPkIk~tD 160 (536)
+.+=+..|.|..+-
T Consensus 204 gf~Gd~~PvI~GSA 217 (449)
T KOG0460|consen 204 GFDGDNTPVIRGSA 217 (449)
T ss_pred CCCCCCCCeeecch
Confidence 99999999998763
No 38
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=24.96 E-value=1e+02 Score=25.80 Aligned_cols=49 Identities=12% Similarity=0.120 Sum_probs=31.8
Q ss_pred ccccccCCcccccccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecC--CcceeeccCCCC
Q psy5290 153 IFWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSD--RANAVFLPQGLS 215 (536)
Q Consensus 153 LPkIk~tDPvavfvk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d--~~~~~~~~~~~~ 215 (536)
.-+|...| ++++|.+.||.|+|.-.- -.+-+-|+.++ |.+.||+|.|.-
T Consensus 32 ~v~i~p~d-----A~~lgi~~Gd~V~v~s~~---------G~~~~~v~~~~~i~~g~v~~~~g~~ 82 (116)
T cd02786 32 TLLIHPAD-----AAARGIADGDLVVVFNDR---------GSVTLRAKVTDDVPPGVVVAEGGWW 82 (116)
T ss_pred EEEECHHH-----HHHcCCCCCCEEEEEcCC---------eEEEEEEEECCCCCCCEEEeecccc
Confidence 34555444 447899999999886432 23345566666 457889888754
No 39
>cd02067 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins.
Probab=24.47 E-value=1.9e+02 Score=24.44 Aligned_cols=72 Identities=14% Similarity=0.155 Sum_probs=46.1
Q ss_pred cccCCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhcC
Q psy5290 2 QLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEET 81 (536)
Q Consensus 2 EMLRDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEEN 81 (536)
.+|+..||.|..-..+++.++|.+...+. +| .+.++... ..-....++.+++.+++.+
T Consensus 21 ~~l~~~G~~V~~lg~~~~~~~l~~~~~~~-------------------~p--dvV~iS~~-~~~~~~~~~~~i~~l~~~~ 78 (119)
T cd02067 21 RALRDAGFEVIDLGVDVPPEEIVEAAKEE-------------------DA--DAIGLSGL-LTTHMTLMKEVIEELKEAG 78 (119)
T ss_pred HHHHHCCCEEEECCCCCCHHHHHHHHHHc-------------------CC--CEEEEecc-ccccHHHHHHHHHHHHHcC
Confidence 36888999997766778888988876432 11 02222221 2235688899999999887
Q ss_pred C-CEEEEEEcCCCCH
Q psy5290 82 I-HRAIIVVQTGMTP 95 (536)
Q Consensus 82 I-~RgIIVvQqkLTP 95 (536)
- +-.|+|--...+.
T Consensus 79 ~~~~~i~vGG~~~~~ 93 (119)
T cd02067 79 LDDIPVLVGGAIVTR 93 (119)
T ss_pred CCCCeEEEECCCCCh
Confidence 6 4445555555554
No 40
>PRK07132 DNA polymerase III subunit delta'; Validated
Probab=24.38 E-value=2.9e+02 Score=28.45 Aligned_cols=89 Identities=10% Similarity=0.051 Sum_probs=52.0
Q ss_pred CCCcchHHHHHHHHHHhhc----CCCEEEEEEc-CCCCHHHHHHHhhc---CccceeeEeeecc---eeeccccccccCc
Q psy5290 62 EPKIGIKTIKTYCQRMQEE----TIHRAIIVVQ-TGMTPSAKQSLVDM---APKYILEYFLESE---LLINITEHELVPE 130 (536)
Q Consensus 62 E~KVGVKtIRkyiErMkEE----NI~RgIIVvQ-qkLTPsARKAL~em---spkfkIEVFqEsE---LLVNITkHeLVPK 130 (536)
+..+++..||..++.+.-. +-.|.|||-. ++||..|..++... .+...+=+|..++ |+--|...-.+=+
T Consensus 66 g~~i~vd~Ir~l~~~~~~~~~~~~~~KvvII~~~e~m~~~a~NaLLK~LEEPp~~t~~il~~~~~~kll~TI~SRc~~~~ 145 (299)
T PRK07132 66 DKDLSKSEFLSAINKLYFSSFVQSQKKILIIKNIEKTSNSLLNALLKTIEEPPKDTYFLLTTKNINKVLPTIVSRCQVFN 145 (299)
T ss_pred CCcCCHHHHHHHHHHhccCCcccCCceEEEEecccccCHHHHHHHHHHhhCCCCCeEEEEEeCChHhChHHHHhCeEEEE
Confidence 4679999999999998543 4677888877 77888665554432 2333443342221 1111222222223
Q ss_pred eeecChHHHHHHHhhcCCCC
Q psy5290 131 HIVLTPEEKQELLTRYWRSC 150 (536)
Q Consensus 131 HeVLS~EEKkeLLkrY~IK~ 150 (536)
-..+++++..+.|.+-++.+
T Consensus 146 f~~l~~~~l~~~l~~~~~~~ 165 (299)
T PRK07132 146 VKEPDQQKILAKLLSKNKEK 165 (299)
T ss_pred CCCCCHHHHHHHHHHcCCCh
Confidence 34578888887777655443
No 41
>PF09269 DUF1967: Domain of unknown function (DUF1967); InterPro: IPR015349 The Obg family comprises a group of ancient P-loop small G proteins (GTPases) belonging to the TRAFAC (for translation factors) class and can be subdivided into several distinct protein subfamilies []. OBG GTPases have been found in both prokaryotes and eukaryotes []. The structure of the OBG GTPase from Thermus thermophilus has been determined []. This entry represents a C-terminal domain found in certain OBG GTPases. This domain contains a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. It is predominantly found in the bacterial GTP-binding protein Obg, and is functionally uncharacterised. ; GO: 0000166 nucleotide binding; PDB: 1UDX_A.
Probab=23.78 E-value=42 Score=27.58 Aligned_cols=16 Identities=6% Similarity=0.104 Sum_probs=10.9
Q ss_pred ccccCCccCcEEecCC
Q psy5290 166 LKECSFESATVKSVYP 181 (536)
Q Consensus 166 vk~iGAKpGDVVrv~~ 181 (536)
++.-|++.||.|+|..
T Consensus 49 L~~~G~~~GD~V~Ig~ 64 (69)
T PF09269_consen 49 LRKAGAKEGDTVRIGD 64 (69)
T ss_dssp HHTTT--TT-EEEETT
T ss_pred HHHcCCCCCCEEEEcC
Confidence 6778999999999864
No 42
>PF11513 TA0956: Thermoplasma acidophilum protein TA0956; InterPro: IPR021595 TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. ; PDB: 2K24_A 2JMK_A.
Probab=23.44 E-value=2.3e+02 Score=26.09 Aligned_cols=62 Identities=15% Similarity=0.194 Sum_probs=32.8
Q ss_pred HHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhcCCCE
Q psy5290 20 LDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIHR 84 (536)
Q Consensus 20 LEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEENI~R 84 (536)
+.+|.++|..... -.|.-+..-|.+- +...+-+-|-|.+-..==.+.||++++..++.|++.
T Consensus 45 lmdFIsryARTDE-ImPEDKTvGFvvi--N~dKK~mSvsFsdideNmK~~i~ei~kkykd~Gykv 106 (110)
T PF11513_consen 45 LMDFISRYARTDE-IMPEDKTVGFVVI--NKDKKMMSVSFSDIDENMKNSIEEIVKKYKDSGYKV 106 (110)
T ss_dssp HHHHHHHH---S----TTSEEEEEEEE--ETTTTEEEEEE-S--CCHHHHHHHHHHHHHCCS-EE
T ss_pred HHHHHHHhhcccc-cCCCCceeEEEEE--ecCCeEEEEEecchhHHHHHHHHHHHHHhhcCCcee
Confidence 8899999974321 1122233444443 333345677788553222778888998888777653
No 43
>PRK05917 DNA polymerase III subunit delta'; Validated
Probab=23.43 E-value=2.1e+02 Score=29.68 Aligned_cols=49 Identities=18% Similarity=0.213 Sum_probs=35.1
Q ss_pred eEEEeCCCC--CcchHHHHHHHHHHhh---cCCCEEEEEEc-CCCCHHHHHHHhh
Q psy5290 55 MFVFFPDEP--KIGIKTIKTYCQRMQE---ETIHRAIIVVQ-TGMTPSAKQSLVD 103 (536)
Q Consensus 55 IfVFFpdE~--KVGVKtIRkyiErMkE---ENI~RgIIVvQ-qkLTPsARKAL~e 103 (536)
+++.+++.. .++|.+||.+.+.+.. ++-.+.+||.. ++||..|..++..
T Consensus 63 ~~~i~p~~~~~~I~idqiR~l~~~~~~~p~e~~~kv~ii~~ad~mt~~AaNaLLK 117 (290)
T PRK05917 63 IHEFSPQGKGRLHSIETPRAIKKQIWIHPYESPYKIYIIHEADRMTLDAISAFLK 117 (290)
T ss_pred EEEEecCCCCCcCcHHHHHHHHHHHhhCccCCCceEEEEechhhcCHHHHHHHHH
Confidence 555567654 3899999999888764 46667766665 7799877666553
No 44
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=23.28 E-value=1.4e+02 Score=33.80 Aligned_cols=26 Identities=19% Similarity=0.072 Sum_probs=17.2
Q ss_pred ecChHHHHHHHhhcCCCCCCcccccc
Q psy5290 133 VLTPEEKQELLTRYWRSCVTIFWTQK 158 (536)
Q Consensus 133 VLS~EEKkeLLkrY~IK~~QLPkIk~ 158 (536)
.+++++.++|.+..++++..+=.+.+
T Consensus 367 ~~~~~~~~~l~~~~~~~~gd~~~~~a 392 (583)
T TIGR00459 367 FLDEKKGKILLERTDAQNGDILLFGA 392 (583)
T ss_pred hcCHHHHHHHHHHhCCCCCCEEEEec
Confidence 46778888888866666655544443
No 45
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=22.88 E-value=1e+02 Score=25.63 Aligned_cols=41 Identities=15% Similarity=0.267 Sum_probs=28.9
Q ss_pred ccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecC--CcceeeccCCCC
Q psy5290 166 LKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSD--RANAVFLPQGLS 215 (536)
Q Consensus 166 vk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d--~~~~~~~~~~~~ 215 (536)
++.+|++.||.|+|+-.-- -+.+-|++++ +.+.||+|.|..
T Consensus 44 A~~lgi~~Gd~V~v~~~~G---------~~~~~v~~~~~i~~g~v~~~~~~~ 86 (120)
T cd00508 44 AARLGIKDGDLVRVSSRRG---------SVVVRARVTDRVRPGTVFMPFHWG 86 (120)
T ss_pred HHHcCCCCCCEEEEEeCCE---------EEEEEEEECCCcCCCEEEEecccC
Confidence 5578999999999986443 2445566655 456889987754
No 46
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=22.08 E-value=1.3e+02 Score=25.36 Aligned_cols=42 Identities=14% Similarity=0.270 Sum_probs=29.3
Q ss_pred ccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecC--CcceeeccCCCCC
Q psy5290 166 LKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSD--RANAVFLPQGLST 216 (536)
Q Consensus 166 vk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d--~~~~~~~~~~~~~ 216 (536)
++.+|++.||.|+|.-.-- .+.+-|+.++ +.+.||+|.|...
T Consensus 39 A~~~gi~~Gd~V~v~s~~G---------~i~~~v~v~~~v~~g~v~~~~g~g~ 82 (123)
T cd02778 39 AARLGIKDGDRVEVSSARG---------KVTGKARLTEGIRPDTVFMPHGFGH 82 (123)
T ss_pred HHHcCCCCCCEEEEEeCCC---------cEEEEEEEcCCcCCCEEEEeccCCc
Confidence 4467999999999864332 3445666666 3578999988643
No 47
>PRK07276 DNA polymerase III subunit delta'; Validated
Probab=21.45 E-value=2.1e+02 Score=29.47 Aligned_cols=93 Identities=20% Similarity=0.208 Sum_probs=54.7
Q ss_pred eEEEeCCCCCcchHHHHHHHHHHhh---cCCCEEEEEEc-CCCCHHHHHHHhhc---CccceeeEee----ecceeeccc
Q psy5290 55 MFVFFPDEPKIGIKTIKTYCQRMQE---ETIHRAIIVVQ-TGMTPSAKQSLVDM---APKYILEYFL----ESELLINIT 123 (536)
Q Consensus 55 IfVFFpdE~KVGVKtIRkyiErMkE---ENI~RgIIVvQ-qkLTPsARKAL~em---spkfkIEVFq----EsELLVNIT 123 (536)
++++.++...|++..||.+++.+.. ++-.|.+||-. +.||..|..++... .+... =+|. .+.||--|.
T Consensus 74 ~~~i~p~~~~I~idqIR~l~~~~~~~p~~~~~kV~II~~ad~m~~~AaNaLLKtLEEPp~~t-~~iL~t~~~~~lLpTI~ 152 (290)
T PRK07276 74 VTVIEPQGQVIKTDTIRELVKNFSQSGYEGKQQVFIIKDADKMHVNAANSLLKVIEEPQSEI-YIFLLTNDENKVLPTIK 152 (290)
T ss_pred eeeecCCCCcCCHHHHHHHHHHHhhCcccCCcEEEEeehhhhcCHHHHHHHHHHhcCCCCCe-EEEEEECChhhCchHHH
Confidence 5555666677999999999888765 55567777765 67998776555433 22212 1222 233443332
Q ss_pred -cccccCceeecChHHHHHHHhhcCCCC
Q psy5290 124 -EHELVPEHIVLTPEEKQELLTRYWRSC 150 (536)
Q Consensus 124 -kHeLVPKHeVLS~EEKkeLLkrY~IK~ 150 (536)
+...++= .. ++++..++|++.++..
T Consensus 153 SRcq~i~f-~~-~~~~~~~~L~~~g~~~ 178 (290)
T PRK07276 153 SRTQIFHF-PK-NEAYLIQLLEQKGLLK 178 (290)
T ss_pred HcceeeeC-CC-cHHHHHHHHHHcCCCh
Confidence 2222221 11 5778888888777654
No 48
>COG4012 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.29 E-value=9.8e+02 Score=25.86 Aligned_cols=163 Identities=17% Similarity=0.232 Sum_probs=85.5
Q ss_pred CCCCCcCChhhHhcCHHHHHHHhCCCCCCCCCCCCceEEEeecCCCCCCceEEEeCCCCCcchHHHHHHHHHHhhcCCCE
Q psy5290 5 HDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDPTDQMFVFFPDEPKIGIKTIKTYCQRMQEETIHR 84 (536)
Q Consensus 5 RDRGYlVsEeELnMSLEEFkekYgd~p~~GspdRe~LtfsashkdDPTdKIfVFFpdE~KVGVKtIRkyiErMkEENI~R 84 (536)
+|-||--..+.-+--++-|++..+.++. |+ =++|+.++.-=.-.-||.-++.+.+.. +
T Consensus 148 QDHG~~pd~snRvfRFelfrelL~~ng~-----~e---------------~f~fl~~eiPe~FtRMraaa~sal~~~--t 205 (342)
T COG4012 148 QDHGYHPDYSNRVFRFELFRELLGANGC-----RE---------------DFMFLDDEIPESFTRMRAAAMSALSAG--T 205 (342)
T ss_pred eccCCCCcccchhhHHHHHHHHHcCCCC-----cc---------------cceecCCcCchhHHHHHHHHHHHHhcC--c
Confidence 4555555444444445556665554321 12 245666554334455555444444333 3
Q ss_pred EEEEEcCCCCHHHHHHHhhcC-cc---------ceeeEeeecceeeccccccccCceeecChHHHHHHHhhcCCCCCCcc
Q psy5290 85 AIIVVQTGMTPSAKQSLVDMA-PK---------YILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVTIF 154 (536)
Q Consensus 85 gIIVvQqkLTPsARKAL~ems-pk---------fkIEVFqEsELLVNITkHeLVPKHeVLS~EEKkeLLkrY~IK~~QLP 154 (536)
..++...+..+-+--.++..+ +. ..--+|.|+ =++-|.+|. -..|++|+.+.++.|+-.-+-.-=
T Consensus 206 ~av~mDskfaav~gal~dpaa~palvVd~GngHttaalvded-RI~gv~EHH----T~~Lspekled~I~rf~~GeL~ne 280 (342)
T COG4012 206 DAVAMDSKFAAVMGALVDPAADPALVVDYGNGHTTAALVDED-RIVGVYEHH----TIRLSPEKLEDQIIRFVEGELENE 280 (342)
T ss_pred eEEEEcchhHhhhhcccCcccCceEEEEccCCceEEEEecCC-eEEEEeecc----cccCCHHHHHHHHHHHHhcccccc
Confidence 355666654332222221111 11 112334554 556666773 357899999999998876653333
Q ss_pred ccccCCcc-cccccccCCccCcEEecCCCCchhhhhhccCcE
Q psy5290 155 WTQKRTGE-EHFLKECSFESATVKSVYPSLKAPIFQLLQQPL 195 (536)
Q Consensus 155 kIk~tDPv-avfvk~iGAKpGDVVrv~~~~~~~~~~~~~~~~ 195 (536)
-+..+-.- ++.+.-|||++=.-+-..++.| |.++++.||-
T Consensus 281 eV~~DgGHGch~~evvd~eev~~iv~tgpk~-p~levg~Dpe 321 (342)
T COG4012 281 EVYRDGGHGCHNVEVVDWEEVEDIVSTGPKK-PELEVGRDPE 321 (342)
T ss_pred eeecCCCCceeeecccCchhhhhhccCCCCC-chhhhCCCch
Confidence 34433322 4555556776654444556654 8899888874
No 49
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=20.97 E-value=1.2e+02 Score=25.53 Aligned_cols=41 Identities=20% Similarity=0.298 Sum_probs=27.8
Q ss_pred ccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecC--CcceeeccCCCC
Q psy5290 166 LKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSD--RANAVFLPQGLS 215 (536)
Q Consensus 166 vk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d--~~~~~~~~~~~~ 215 (536)
++++|.+.||.|+|.-.-- ++ -+-|++++ +.+.|++|.|..
T Consensus 44 A~~lgi~~Gd~V~v~~~~G--------~~-~~~v~~~~~i~~g~v~~~~g~~ 86 (122)
T cd02791 44 AARLGLKEGDLVRVTSRRG--------EV-VLRVRVTDRVRPGEVFVPMHWG 86 (122)
T ss_pred HHHcCCCCCCEEEEEcCCE--------EE-EEEEEECCCcCCCeEEEecccC
Confidence 5578999999999875443 33 24455555 457888888753
No 50
>cd02775 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is
Probab=20.68 E-value=1.4e+02 Score=23.93 Aligned_cols=50 Identities=18% Similarity=0.244 Sum_probs=34.0
Q ss_pred cccccCCcccccccccCCccCcEEecCCCCchhhhhhccCcEEEEEEecC--CcceeeccCCCC
Q psy5290 154 FWTQKRTGEEHFLKECSFESATVKSVYPSLKAPIFQLLQQPLFLLVKTSD--RANAVFLPQGLS 215 (536)
Q Consensus 154 PkIk~tDPvavfvk~iGAKpGDVVrv~~~~~~~~~~~~~~~~fllv~~~d--~~~~~~~~~~~~ 215 (536)
+.+..+... ++.+|++.||.|.|.-... . +-+-|++++ +.+.||+|.|..
T Consensus 23 ~~v~~~~~d---a~~lgl~~Gd~v~v~~~~g--------~-~~~~v~~~~~v~~g~v~~~~~~~ 74 (101)
T cd02775 23 PVVEINPED---AAALGIKDGDLVRVESRRG--------S-VVLRAKVTDGVPPGVVFLPHGWG 74 (101)
T ss_pred CEEEECHHH---HHHcCCCCCCEEEEEcCCc--------E-EEEEEEECCCcCCCEEEeeCccC
Confidence 444444445 6778999999999886654 3 335556666 467888888754
Done!