Query psy6796
Match_columns 123
No_of_seqs 124 out of 739
Neff 2.5
Searched_HMMs 46136
Date Fri Aug 16 18:34:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6796.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6796hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00413 lipoate synthase; Pro 100.0 3.9E-29 8.5E-34 213.7 5.7 90 24-116 296-394 (398)
2 PLN02428 lipoic acid synthase 100.0 3.9E-29 8.5E-34 208.6 5.0 78 38-118 271-348 (349)
3 COG0320 LipA Lipoate synthase 100.0 2.9E-29 6.3E-34 209.2 3.8 61 46-108 244-304 (306)
4 TIGR00510 lipA lipoate synthas 99.9 7.3E-29 1.6E-33 201.8 4.8 71 39-112 232-302 (302)
5 KOG2672|consensus 99.9 1.2E-26 2.7E-31 195.9 3.7 71 46-118 287-357 (360)
6 PRK12928 lipoyl synthase; Prov 99.9 1.7E-26 3.7E-31 185.9 3.9 61 39-102 229-289 (290)
7 PRK05481 lipoyl synthase; Prov 99.6 2.7E-16 5.7E-21 126.0 4.5 65 39-106 221-285 (289)
8 PTZ00445 p36-lilke protein; Pr 62.9 20 0.00044 29.6 5.3 61 50-113 60-128 (219)
9 PRK05672 dnaE2 error-prone DNA 46.1 13 0.00028 36.1 1.9 46 13-58 335-387 (1046)
10 PRK07279 dnaE DNA polymerase I 41.1 16 0.00035 35.8 1.6 47 12-58 282-336 (1034)
11 TIGR00594 polc DNA-directed DN 40.6 17 0.00036 35.2 1.7 47 12-58 344-398 (1022)
12 cd08784 Death_DRs Death Domain 39.4 24 0.00051 23.7 1.9 16 73-88 11-26 (79)
13 PTZ00122 phosphoglycerate muta 36.8 39 0.00085 27.8 3.1 93 4-101 61-170 (299)
14 cd08777 Death_RIP1 Death Domai 36.1 23 0.0005 24.5 1.4 17 74-90 14-30 (86)
15 PRK05673 dnaE DNA polymerase I 36.0 25 0.00053 34.6 2.0 46 12-57 340-393 (1135)
16 PRK07135 dnaE DNA polymerase I 35.9 20 0.00044 34.8 1.5 46 13-58 275-328 (973)
17 smart00354 HTH_LACI helix_turn 35.2 40 0.00088 21.6 2.4 22 66-87 25-46 (70)
18 PRK09532 DNA polymerase III su 34.7 24 0.00051 33.7 1.7 46 13-58 350-403 (874)
19 TIGR01626 ytfJ_HI0045 conserve 34.4 15 0.00032 28.8 0.2 20 37-56 13-32 (184)
20 PRK07374 dnaE DNA polymerase I 33.9 26 0.00057 34.6 1.9 46 13-58 352-405 (1170)
21 PRK06920 dnaE DNA polymerase I 33.8 24 0.00052 34.7 1.6 47 12-58 325-379 (1107)
22 PRK05898 dnaE DNA polymerase I 33.5 27 0.00058 34.2 1.9 47 12-58 276-330 (971)
23 PRK06826 dnaE DNA polymerase I 31.5 32 0.0007 33.9 2.1 46 13-58 341-394 (1151)
24 PF11243 DUF3045: Protein of u 30.5 94 0.002 22.8 3.9 40 78-117 40-85 (89)
25 cd08804 Death_ank2 Death domai 29.5 34 0.00073 23.4 1.4 14 75-88 17-30 (84)
26 cd08315 Death_TRAILR_DR4_DR5 D 29.2 42 0.00091 23.6 1.8 16 73-88 19-34 (96)
27 PRK09121 5-methyltetrahydropte 28.8 33 0.00072 28.6 1.5 52 47-100 6-69 (339)
28 PF10728 DUF2520: Domain of un 28.6 1.1E+02 0.0023 22.6 4.0 41 69-109 9-49 (132)
29 TIGR02021 BchM-ChlM magnesium 28.5 75 0.0016 23.7 3.2 37 62-101 179-215 (219)
30 COG0482 TrmU Predicted tRNA(5- 28.4 26 0.00057 30.6 0.8 33 69-101 101-133 (356)
31 COG2221 DsrA Dissimilatory sul 28.2 43 0.00094 29.1 2.1 29 68-96 75-103 (317)
32 COG0587 DnaE DNA polymerase II 28.0 40 0.00087 33.6 2.0 50 13-71 343-394 (1139)
33 cd08318 Death_NMPP84 Death dom 27.8 42 0.00091 22.9 1.6 15 74-88 19-33 (86)
34 PF01402 RHH_1: Ribbon-helix-h 27.0 49 0.0011 18.7 1.6 19 67-85 5-23 (39)
35 PF00356 LacI: Bacterial regul 26.4 65 0.0014 20.0 2.1 21 66-86 24-44 (46)
36 cd02742 GH20_hexosaminidase Be 24.9 67 0.0014 26.0 2.5 25 64-88 65-89 (303)
37 PF02679 ComA: (2R)-phospho-3- 24.8 60 0.0013 26.9 2.3 24 68-91 81-104 (244)
38 PF00220 Hormone_4: Neurohypop 24.7 35 0.00075 15.9 0.5 6 24-29 4-9 (9)
39 PF12162 STAT1_TAZ2bind: STAT1 24.6 63 0.0014 18.6 1.7 12 68-79 10-21 (23)
40 smart00258 SAND SAND domain. 24.4 40 0.00087 23.5 1.0 20 66-85 33-52 (73)
41 PRK03482 phosphoglycerate muta 24.2 73 0.0016 23.8 2.5 18 83-100 46-63 (215)
42 TIGR03849 arch_ComA phosphosul 23.8 61 0.0013 26.8 2.1 24 68-91 68-91 (237)
43 cd06563 GH20_chitobiase-like T 23.6 98 0.0021 25.7 3.3 28 61-88 76-103 (357)
44 PRK13877 conjugal transfer rel 23.6 86 0.0019 23.1 2.7 37 61-97 10-52 (114)
45 COG1809 (2R)-phospho-3-sulfola 23.5 60 0.0013 27.8 2.0 27 65-91 84-110 (258)
46 cd08313 Death_TNFR1 Death doma 23.4 63 0.0014 22.4 1.8 15 73-87 11-25 (80)
47 PF02222 ATP-grasp: ATP-grasp 23.3 49 0.0011 25.3 1.4 30 61-90 5-34 (172)
48 PRK06520 5-methyltetrahydropte 23.0 41 0.00088 28.4 1.0 54 45-100 9-74 (368)
49 PF08108 Antimicrobial13: Halo 22.8 31 0.00067 18.1 0.1 9 22-30 5-13 (15)
50 KOG0840|consensus 22.8 26 0.00055 30.1 -0.2 10 22-31 127-136 (275)
51 smart00005 DEATH DEATH domain, 22.8 59 0.0013 20.9 1.5 15 72-86 16-30 (88)
52 PF06627 DUF1153: Protein of u 22.7 41 0.00089 24.7 0.8 17 68-84 61-77 (90)
53 cd01670 Death Death Domain: a 22.5 63 0.0014 20.3 1.6 14 74-87 11-24 (79)
54 PF01342 SAND: SAND domain; I 22.3 51 0.0011 22.8 1.2 16 65-80 41-56 (82)
55 TIGR03841 F420_Rv3093c probabl 22.1 1.1E+02 0.0025 24.4 3.3 29 64-92 3-31 (301)
56 PF05265 DUF723: Protein of un 22.0 55 0.0012 22.3 1.3 23 3-27 35-57 (60)
57 PRK06233 hypothetical protein; 21.9 59 0.0013 27.4 1.7 58 46-107 11-80 (372)
58 cd03311 CIMS_C_terminal_like C 21.8 46 0.00099 26.7 1.0 51 48-100 4-66 (332)
59 COG1519 KdtA 3-deoxy-D-manno-o 21.8 76 0.0016 28.5 2.4 23 69-91 269-291 (419)
60 cd04906 ACT_ThrD-I_1 First of 21.6 87 0.0019 20.7 2.2 56 27-89 12-71 (85)
61 PF00406 ADK: Adenylate kinase 21.5 43 0.00094 23.5 0.7 25 77-101 14-38 (151)
62 PF02775 TPP_enzyme_C: Thiamin 21.1 36 0.00079 24.1 0.3 23 24-46 21-43 (153)
63 cd02002 TPP_BFDC Thiamine pyro 21.1 57 0.0012 23.5 1.3 32 14-46 31-64 (178)
64 cd01986 Alpha_ANH_like Adenine 21.0 58 0.0013 21.7 1.3 65 24-92 3-69 (103)
65 TIGR01501 MthylAspMutase methy 21.0 1E+02 0.0022 23.1 2.7 25 68-92 94-118 (134)
66 TIGR01915 npdG NADPH-dependent 21.0 60 0.0013 24.6 1.5 47 51-99 146-196 (219)
67 TIGR03848 MSMEG_4193 probable 20.4 87 0.0019 23.2 2.2 18 83-100 45-62 (204)
68 cd06564 GH20_DspB_LnbB-like Gl 20.3 93 0.002 25.4 2.5 26 63-88 74-99 (326)
69 PF07733 DNA_pol3_alpha: Bacte 20.1 50 0.0011 28.9 0.9 41 18-58 52-99 (426)
No 1
>PTZ00413 lipoate synthase; Provisional
Probab=99.95 E-value=3.9e-29 Score=213.65 Aligned_cols=90 Identities=37% Similarity=0.678 Sum_probs=77.4
Q ss_pred ccCCCCccccchhh---------hhhhccccccccccccCCCCCCCccccceecChHHHHHHHHHHHhcCCceeeecccc
Q psy6796 24 LNCPGGLSSMGSKL---------AYSMGFALNCPVVEYVTPEKYAHWEKVVEYVTPEKYAHWEKVGNSMGFLYTASGPLV 94 (123)
Q Consensus 24 ~~~~~~~~~~~~~~---------~~~~~~a~~lTIGQYLqPSk~~~HlpV~rYVtPEeF~~~k~~a~~mGF~~VaSGPLV 94 (123)
..|-|++-.||-.. .+..| .-.+|||||||||++ |+||+|||+||||+.|+++|++|||++|+|||||
T Consensus 296 ~tcSGiIVGLGET~eEvie~m~dLrelG-VDivtIGQYL~Ps~~--h~~V~~yv~P~~F~~~~~~a~~~Gf~~v~sgPlV 372 (398)
T PTZ00413 296 LTKSSIMLGLGETEEEVRQTLRDLRTAG-VSAVTLGQYLQPTKT--RLKVSRYAHPKEFEMWEEEAMKMGFLYCASGPLV 372 (398)
T ss_pred eEeeeeEecCCCCHHHHHHHHHHHHHcC-CcEEeeccccCCCcc--cCCceeccCHHHHHHHHHHHHHcCCceEEecCcc
Confidence 36888888888643 23333 235699999999999 9999999999999999999999999999999999
Q ss_pred ccchhhhHHHHHHHHHHHHHHH
Q psy6796 95 RSSYKAGEFFIGSVLRNRKAAA 116 (123)
Q Consensus 95 RSSY~A~e~~~~~~l~~~~~~~ 116 (123)
||||||+|.+.+++++.|+...
T Consensus 373 RSSY~A~e~~~~~~~~~r~~~~ 394 (398)
T PTZ00413 373 RSSYRAGEYYIKNLVKQRRKAK 394 (398)
T ss_pred ccchhccHHHHHHHHHhhhhhc
Confidence 9999999998888887777654
No 2
>PLN02428 lipoic acid synthase
Probab=99.95 E-value=3.9e-29 Score=208.57 Aligned_cols=78 Identities=51% Similarity=0.853 Sum_probs=71.1
Q ss_pred hhhhccccccccccccCCCCCCCccccceecChHHHHHHHHHHHhcCCceeeeccccccchhhhHHHHHHHHHHHHHHHH
Q psy6796 38 AYSMGFALNCPVVEYVTPEKYAHWEKVVEYVTPEKYAHWEKVGNSMGFLYTASGPLVRSSYKAGEFFIGSVLRNRKAAAE 117 (123)
Q Consensus 38 ~~~~~~a~~lTIGQYLqPSk~~~HlpV~rYVtPEeF~~~k~~a~~mGF~~VaSGPLVRSSY~A~e~~~~~~l~~~~~~~~ 117 (123)
....|+-. +|||||||||+. |+||.+||+||+|++|+++|++|||++|+|||||||||||+|.+.++++++++++++
T Consensus 271 Lrelgvd~-vtigqyL~Ps~~--h~~v~~~v~p~~f~~~~~~~~~~gf~~v~sgp~vrssy~a~~~~~~~~~~~~~~~~~ 347 (349)
T PLN02428 271 LRAAGVDV-VTFGQYLRPTKR--HLPVKEYVTPEKFEFWREYGEEMGFRYVASGPLVRSSYKAGEFFIKSMIREDRAKAA 347 (349)
T ss_pred HHHcCCCE-EeeccccCCCcc--eeeeecccCHHHHHHHHHHHHHcCCceEEecCcccchhhhHHHHHHHHHHhhccccc
Confidence 34555544 799999999999 999999999999999999999999999999999999999999999999999987665
Q ss_pred H
Q psy6796 118 A 118 (123)
Q Consensus 118 ~ 118 (123)
+
T Consensus 348 ~ 348 (349)
T PLN02428 348 A 348 (349)
T ss_pred c
Confidence 4
No 3
>COG0320 LipA Lipoate synthase [Coenzyme metabolism]
Probab=99.95 E-value=2.9e-29 Score=209.19 Aligned_cols=61 Identities=44% Similarity=0.685 Sum_probs=58.2
Q ss_pred ccccccccCCCCCCCccccceecChHHHHHHHHHHHhcCCceeeeccccccchhhhHHHHHHH
Q psy6796 46 NCPVVEYVTPEKYAHWEKVVEYVTPEKYAHWEKVGNSMGFLYTASGPLVRSSYKAGEFFIGSV 108 (123)
Q Consensus 46 ~lTIGQYLqPSk~~~HlpV~rYVtPEeF~~~k~~a~~mGF~~VaSGPLVRSSY~A~e~~~~~~ 108 (123)
-||||||||||++ |+||+|||+||||+.|+++|++|||++|+|||||||||||++.|.++.
T Consensus 244 ilTiGQYlqPS~~--HlpV~ryv~PeeF~~~~~~a~~~GF~~v~sgPlvRSSYhA~~~~~~~~ 304 (306)
T COG0320 244 ILTIGQYLQPSRK--HLPVQRYVTPEEFDELEEVAEEMGFLHVASGPLVRSSYHADEQFAEAE 304 (306)
T ss_pred EEEeccccCCccc--cCCceeccCHHHHHHHHHHHHHccchhhccCcccccccchHHHHHHhh
Confidence 3799999999999 999999999999999999999999999999999999999999997663
No 4
>TIGR00510 lipA lipoate synthase. The family shows strong sequence conservation.
Probab=99.95 E-value=7.3e-29 Score=201.80 Aligned_cols=71 Identities=34% Similarity=0.576 Sum_probs=64.8
Q ss_pred hhhccccccccccccCCCCCCCccccceecChHHHHHHHHHHHhcCCceeeeccccccchhhhHHHHHHHHHHH
Q psy6796 39 YSMGFALNCPVVEYVTPEKYAHWEKVVEYVTPEKYAHWEKVGNSMGFLYTASGPLVRSSYKAGEFFIGSVLRNR 112 (123)
Q Consensus 39 ~~~~~a~~lTIGQYLqPSk~~~HlpV~rYVtPEeF~~~k~~a~~mGF~~VaSGPLVRSSY~A~e~~~~~~l~~~ 112 (123)
..+|+ -.+|||||||||++ |+||.+||+|++|+.|+++|++|||++|+|||||||||||+|.+.+++++++
T Consensus 232 relg~-d~v~igqYl~p~~~--~~~v~~~~~p~~f~~~~~~a~~~gf~~v~~~p~vrssy~a~~~~~~~~~~~~ 302 (302)
T TIGR00510 232 RDHGV-TMVTLGQYLRPSRR--HLPVKRYVSPEEFDYYRSVALEMGFLHAACGPFVRSSYHADSLFAAGRLVKT 302 (302)
T ss_pred HhcCC-CEEEeecccCCCCC--CCccccCCCHHHHHHHHHHHHHcCChheEecccchhhhhHHHHHHHHHhccC
Confidence 34444 35899999999999 9999999999999999999999999999999999999999999999987653
No 5
>KOG2672|consensus
Probab=99.93 E-value=1.2e-26 Score=195.89 Aligned_cols=71 Identities=54% Similarity=0.913 Sum_probs=67.4
Q ss_pred ccccccccCCCCCCCccccceecChHHHHHHHHHHHhcCCceeeeccccccchhhhHHHHHHHHHHHHHHHHH
Q psy6796 46 NCPVVEYVTPEKYAHWEKVVEYVTPEKYAHWEKVGNSMGFLYTASGPLVRSSYKAGEFFIGSVLRNRKAAAEA 118 (123)
Q Consensus 46 ~lTIGQYLqPSk~~~HlpV~rYVtPEeF~~~k~~a~~mGF~~VaSGPLVRSSY~A~e~~~~~~l~~~~~~~~~ 118 (123)
-+|+||||||+++ |++|++||+||.|+.|++++++|||.||+|||||||||+|+|+|+++++++|+.....
T Consensus 287 v~t~gqym~ptkr--hl~v~eyvtpekf~~w~~~~~~lgf~y~AsgplvrSsykage~~i~~~l~~r~~~~~s 357 (360)
T KOG2672|consen 287 VVTFGQYMQPTKR--HLKVKEYVTPEKFDYWKEYGEELGFLYVASGPLVRSSYKAGEYFIKNVLEKRKSKNSS 357 (360)
T ss_pred EEecccccCCccc--cceeEEeeCHHHHHHHHHHhhhcceEEeccCceeechhhhhHHHHHHHHHhcccCCCc
Confidence 4699999999999 9999999999999999999999999999999999999999999999999999876543
No 6
>PRK12928 lipoyl synthase; Provisional
Probab=99.92 E-value=1.7e-26 Score=185.90 Aligned_cols=61 Identities=36% Similarity=0.591 Sum_probs=56.8
Q ss_pred hhhccccccccccccCCCCCCCccccceecChHHHHHHHHHHHhcCCceeeeccccccchhhhH
Q psy6796 39 YSMGFALNCPVVEYVTPEKYAHWEKVVEYVTPEKYAHWEKVGNSMGFLYTASGPLVRSSYKAGE 102 (123)
Q Consensus 39 ~~~~~a~~lTIGQYLqPSk~~~HlpV~rYVtPEeF~~~k~~a~~mGF~~VaSGPLVRSSY~A~e 102 (123)
-..++ ..+|||||||||++ |+||.|||+|++|++|+++|++|||++|+|||||||||||+|
T Consensus 229 rel~~-d~v~i~~Yl~p~~~--~~~v~~~~~~~~f~~~~~~~~~~g~~~~~~~p~~rssy~a~~ 289 (290)
T PRK12928 229 RAVGC-DRLTIGQYLRPSLA--HLPVQRYWTPEEFEALGQIARELGFSHVRSGPLVRSSYHAGE 289 (290)
T ss_pred HhcCC-CEEEEEcCCCCCcc--CCceeeccCHHHHHHHHHHHHHcCCceeEecCcccccccCCC
Confidence 34454 57899999999999 999999999999999999999999999999999999999986
No 7
>PRK05481 lipoyl synthase; Provisional
Probab=99.62 E-value=2.7e-16 Score=126.00 Aligned_cols=65 Identities=38% Similarity=0.625 Sum_probs=58.7
Q ss_pred hhhccccccccccccCCCCCCCccccceecChHHHHHHHHHHHhcCCceeeeccccccchhhhHHHHH
Q psy6796 39 YSMGFALNCPVVEYVTPEKYAHWEKVVEYVTPEKYAHWEKVGNSMGFLYTASGPLVRSSYKAGEFFIG 106 (123)
Q Consensus 39 ~~~~~a~~lTIGQYLqPSk~~~HlpV~rYVtPEeF~~~k~~a~~mGF~~VaSGPLVRSSY~A~e~~~~ 106 (123)
-.++| ..+.|+||++|+.+ |++|.+++.++.|+++.++++++||++|+|||||||||+|++.+..
T Consensus 221 rel~~-d~v~if~Ys~pa~k--~~~v~~~~k~~r~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~ 285 (289)
T PRK05481 221 RAAGV-DILTIGQYLQPSRK--HLPVERYVTPEEFDEYKEIALELGFLHVASGPLVRSSYHADEQAAG 285 (289)
T ss_pred HhcCC-CEEEEEccCCCccc--cCCCCCcCCHHHHHHHHHHHHHcCchheEecCccccchhhHHHHhh
Confidence 34555 57899999999997 7899999999999999999999999999999999999999997543
No 8
>PTZ00445 p36-lilke protein; Provisional
Probab=62.87 E-value=20 Score=29.59 Aligned_cols=61 Identities=20% Similarity=0.305 Sum_probs=47.3
Q ss_pred ccccCCCCCCCccccceecChHHHHHHHHHHHhcCCceeee---c-----cccccchhhhHHHHHHHHHHHH
Q psy6796 50 VEYVTPEKYAHWEKVVEYVTPEKYAHWEKVGNSMGFLYTAS---G-----PLVRSSYKAGEFFIGSVLRNRK 113 (123)
Q Consensus 50 GQYLqPSk~~~HlpV~rYVtPEeF~~~k~~a~~mGF~~VaS---G-----PLVRSSY~A~e~~~~~~l~~~~ 113 (123)
|.|.+|... =.-|...++|| |..|-+..++.||+.+.. - +--|..|-+++..+++.+++-+
T Consensus 60 gG~~~~~~~--~~~~~~~~tpe-fk~~~~~l~~~~I~v~VVTfSd~~~~~~~~~~~~Isg~~li~~~lk~s~ 128 (219)
T PTZ00445 60 GGYIDPDND--DIRVLTSVTPD-FKILGKRLKNSNIKISVVTFSDKELIPSENRPRYISGDRMVEAALKKSK 128 (219)
T ss_pred ccccCCCcc--hhhhhccCCHH-HHHHHHHHHHCCCeEEEEEccchhhccccCCcceechHHHHHHHHHhcC
Confidence 459999844 46788899998 999999999999987642 1 2367788889888888777543
No 9
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=46.14 E-value=13 Score=36.10 Aligned_cols=46 Identities=26% Similarity=0.491 Sum_probs=38.5
Q ss_pred hhHhh-hhccccccCCCCccccchhhhhhhcc------ccccccccccCCCCC
Q psy6796 13 LWDEV-WQGSMGLNCPGGLSSMGSKLAYSMGF------ALNCPVVEYVTPEKY 58 (123)
Q Consensus 13 ~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~------a~~lTIGQYLqPSk~ 58 (123)
+||=| |--+.|+-|||==|.-||-+||.+|+ .++|-+--+|-|.+.
T Consensus 335 V~D~i~~Ak~~gi~vpGRGSaAGSLVaY~LgIT~VDPl~~~LlFERFLnpeR~ 387 (1046)
T PRK05672 335 VHDIVRFARSQGILCQGRGSAANSAVCYALGITEVDPVQSGLLFERFLSPERD 387 (1046)
T ss_pred HHHHHHHHHHCCceeCCCChHHHHHHHHHhCCCccCccccCCchhhccCCccc
Confidence 47766 88899999999999999999999997 467777778877664
No 10
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=41.06 E-value=16 Score=35.78 Aligned_cols=47 Identities=28% Similarity=0.511 Sum_probs=38.1
Q ss_pred hhhHhh-hhccccccC-CCCccccchhhhhhhcc------ccccccccccCCCCC
Q psy6796 12 LLWDEV-WQGSMGLNC-PGGLSSMGSKLAYSMGF------ALNCPVVEYVTPEKY 58 (123)
Q Consensus 12 ~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~------a~~lTIGQYLqPSk~ 58 (123)
++||=| |--+.|+-| ||-=|.-||-+||.+|. .++|=+--+|-|.+.
T Consensus 282 IV~D~i~~Ak~~gI~vGPGRGSaAGSLVaY~LgIT~vDPl~y~LlFERFLNpeR~ 336 (1034)
T PRK07279 282 IVWDLLRFGRSQGYYMGMGRGSAAGSLVAYALDITGIDPVKHNLLFERFLNKERY 336 (1034)
T ss_pred HHHHHHHHHHhCCceeCCCCchHHHHHHHHHhcCCccCccccCccHHhhcCccCC
Confidence 357776 888999888 99999999999999997 456667777777655
No 11
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.60 E-value=17 Score=35.22 Aligned_cols=47 Identities=28% Similarity=0.644 Sum_probs=38.5
Q ss_pred hhhHhh-hhccccccC-CCCccccchhhhhhhcc------ccccccccccCCCCC
Q psy6796 12 LLWDEV-WQGSMGLNC-PGGLSSMGSKLAYSMGF------ALNCPVVEYVTPEKY 58 (123)
Q Consensus 12 ~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~------a~~lTIGQYLqPSk~ 58 (123)
++||=| |--+.|+-| ||==|.-||-+||.+|+ .++|-+--+|-|.+.
T Consensus 344 IV~D~v~~Ar~~gI~vGpGRGSaAgSlVaY~LgIT~VDPl~~~LlFERFLnpeR~ 398 (1022)
T TIGR00594 344 IVWDFIKWAKDHGIPVGPGRGSAAGSLVAYALKITDIDPIKHGLLFERFLNPERI 398 (1022)
T ss_pred HHHHHHHHHHHCCCeeCCCCChHHHHHHHHHhcCCccCccccCCchhhccCCCCC
Confidence 357766 888999988 99999999999999997 467777777777664
No 12
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=39.36 E-value=24 Score=23.72 Aligned_cols=16 Identities=6% Similarity=0.239 Sum_probs=13.8
Q ss_pred HHHHHHHHHhcCCcee
Q psy6796 73 YAHWEKVGNSMGFLYT 88 (123)
Q Consensus 73 F~~~k~~a~~mGF~~V 88 (123)
|+.|+++|+.|||+..
T Consensus 11 ~~~Wk~laR~LGls~~ 26 (79)
T cd08784 11 FDQHKRFFRKLGLSDN 26 (79)
T ss_pred HHHHHHHHHHcCCCHH
Confidence 6789999999999754
No 13
>PTZ00122 phosphoglycerate mutase; Provisional
Probab=36.79 E-value=39 Score=27.84 Aligned_cols=93 Identities=13% Similarity=0.116 Sum_probs=50.0
Q ss_pred Cccchheehh-----hHhhhhccccccCCCCccccchhhhhhhccccccccccccCCCCCCCccccc-eecChHHHHHHH
Q psy6796 4 PIHGTVEFLL-----WDEVWQGSMGLNCPGGLSSMGSKLAYSMGFALNCPVVEYVTPEKYAHWEKVV-EYVTPEKYAHWE 77 (123)
Q Consensus 4 ~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~lTIGQYLqPSk~~~HlpV~-rYVtPEeF~~~k 77 (123)
|.+.+-++.. |++.|.|.. -+||+--.---+|=+------.=|==|||-... |.... +..++.=-+.-+
T Consensus 61 ~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~L~LVRHGq~~~~~----~~d~~~~~LTe~G~~QA~ 135 (299)
T PTZ00122 61 YAKENFGYYKTWGVPWNEDWDGNY-KHRPKARGKRADKSASHQRQIILVRHGQYINES----SNDDNIKRLTELGKEQAR 135 (299)
T ss_pred ccccceeEEeecCCCCcccccccc-ccChhhcccccCCCCCceeEEEEEECCCCCCCC----CCCcccCCCCHHHHHHHH
Confidence 4566777777 999999865 344432111111111000011113347865432 33333 556776555555
Q ss_pred HHHHh---c--------CCceeeeccccccchhhh
Q psy6796 78 KVGNS---M--------GFLYTASGPLVRSSYKAG 101 (123)
Q Consensus 78 ~~a~~---m--------GF~~VaSGPLVRSSY~A~ 101 (123)
+.|.. + .|..|.|+||.|.-=-|.
T Consensus 136 ~lg~~L~~~~~~~~~~~~~d~IysSPL~RA~qTAe 170 (299)
T PTZ00122 136 ITGKYLKEQFGEILVDKKVKAIYHSDMTRAKETAE 170 (299)
T ss_pred HHHHHHHHhhccccccCCCCEEEEcCcHHHHHHHH
Confidence 55543 2 699999999999854443
No 14
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=36.14 E-value=23 Score=24.47 Aligned_cols=17 Identities=18% Similarity=0.614 Sum_probs=14.0
Q ss_pred HHHHHHHHhcCCceeee
Q psy6796 74 AHWEKVGNSMGFLYTAS 90 (123)
Q Consensus 74 ~~~k~~a~~mGF~~VaS 90 (123)
..|+++|.+|||+...-
T Consensus 14 ~~Wk~lar~LG~s~~eI 30 (86)
T cd08777 14 KKWKRCARKLGFTESEI 30 (86)
T ss_pred HHHHHHHHHcCCCHHHH
Confidence 47999999999987543
No 15
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=35.97 E-value=25 Score=34.58 Aligned_cols=46 Identities=28% Similarity=0.613 Sum_probs=37.2
Q ss_pred hhhHhh-hhccccccC-CCCccccchhhhhhhccc------cccccccccCCCC
Q psy6796 12 LLWDEV-WQGSMGLNC-PGGLSSMGSKLAYSMGFA------LNCPVVEYVTPEK 57 (123)
Q Consensus 12 ~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~a------~~lTIGQYLqPSk 57 (123)
++||=| |--..|+-| ||==|.-||-+||.+|.. ++|-+--+|-|.+
T Consensus 340 IV~D~i~~Ak~~gI~vGpGRGSaAGSLVaY~LgIT~vDPl~y~LlFERFLNpeR 393 (1135)
T PRK05673 340 IVADFIQWAKDNGIPVGPGRGSGAGSLVAYALGITDLDPLRFGLLFERFLNPER 393 (1135)
T ss_pred HHHHHHHHHHHCCCeeCCCCchHHHHHHHHHhcCCccCccccCCCceeecCCCC
Confidence 357766 888899988 999999999999999974 6666777777765
No 16
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=35.95 E-value=20 Score=34.85 Aligned_cols=46 Identities=22% Similarity=0.586 Sum_probs=38.2
Q ss_pred hhHhh-hhccccccC-CCCccccchhhhhhhccc------cccccccccCCCCC
Q psy6796 13 LWDEV-WQGSMGLNC-PGGLSSMGSKLAYSMGFA------LNCPVVEYVTPEKY 58 (123)
Q Consensus 13 ~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~a------~~lTIGQYLqPSk~ 58 (123)
+||=| |--+.|+-| ||-=|.-||-+||.+|+. ++|-+--+|-|.+.
T Consensus 275 V~D~v~~Ak~~gI~vGpGRGSaAGSLVaY~LgIT~VDPl~y~LlFERFLnpeR~ 328 (973)
T PRK07135 275 IWDFIKWARKNKISIGPGRGSASGSLVSYLLNITSVNPLKYDLLFERFLNPDRI 328 (973)
T ss_pred HHHHHHHHHHCCceeCCCCcchHHHHHHHHhcCCccCccccCccHHHhcCCCCC
Confidence 57766 888899998 999999999999999974 67777777877665
No 17
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=35.23 E-value=40 Score=21.63 Aligned_cols=22 Identities=14% Similarity=0.160 Sum_probs=19.7
Q ss_pred eecChHHHHHHHHHHHhcCCce
Q psy6796 66 EYVTPEKYAHWEKVGNSMGFLY 87 (123)
Q Consensus 66 rYVtPEeF~~~k~~a~~mGF~~ 87 (123)
.+|+|+.-++..+.+.++||..
T Consensus 25 ~~v~~~t~~~i~~~~~~~gy~~ 46 (70)
T smart00354 25 GRVSEETREKVLAAMEELGYIP 46 (70)
T ss_pred CCCCHHHHHHHHHHHHHhCCCC
Confidence 4689999999999999999954
No 18
>PRK09532 DNA polymerase III subunit alpha; Reviewed
Probab=34.74 E-value=24 Score=33.73 Aligned_cols=46 Identities=24% Similarity=0.512 Sum_probs=37.1
Q ss_pred hhHhh-hhccccccC-CCCccccchhhhhhhccc------cccccccccCCCCC
Q psy6796 13 LWDEV-WQGSMGLNC-PGGLSSMGSKLAYSMGFA------LNCPVVEYVTPEKY 58 (123)
Q Consensus 13 ~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~a------~~lTIGQYLqPSk~ 58 (123)
+||=| |--+.|+-| ||==|.-||-+||.+|.. ++|-+--+|-|.+.
T Consensus 350 V~D~v~~Ar~~gi~VGpGRGSAAGSLVaY~LgIT~VDPl~~~LlFERFLnpeR~ 403 (874)
T PRK09532 350 VWDYIKYARDNNIPVGPGRGSAAGSLVAYCLKITNIDPVHHGLLFERFLNPERK 403 (874)
T ss_pred HHHHHHHHHhCCceecCCcccHHHHHHHHHhcCCccCccccCCcHhhccCCcCC
Confidence 47776 888899888 998999999999999974 66667777777654
No 19
>TIGR01626 ytfJ_HI0045 conserved hypothetical protein YtfJ-family, TIGR01626. This model represents sequences from gamma proteobacteria that are related to the E. coli protein, YtfJ.
Probab=34.35 E-value=15 Score=28.85 Aligned_cols=20 Identities=25% Similarity=0.139 Sum_probs=15.9
Q ss_pred hhhhhccccccccccccCCC
Q psy6796 37 LAYSMGFALNCPVVEYVTPE 56 (123)
Q Consensus 37 ~~~~~~~a~~lTIGQYLqPS 56 (123)
+.-++.||||+++||=+.|-
T Consensus 13 ~~~~~~~a~~~~~~~~~p~v 32 (184)
T TIGR01626 13 IFPSSAWAHNLQVEQSVPSV 32 (184)
T ss_pred HhHHHHhhhhhhcCCcCCce
Confidence 34467899999999999773
No 20
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=33.87 E-value=26 Score=34.65 Aligned_cols=46 Identities=28% Similarity=0.615 Sum_probs=37.0
Q ss_pred hhHhh-hhccccccC-CCCccccchhhhhhhccc------cccccccccCCCCC
Q psy6796 13 LWDEV-WQGSMGLNC-PGGLSSMGSKLAYSMGFA------LNCPVVEYVTPEKY 58 (123)
Q Consensus 13 ~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~a------~~lTIGQYLqPSk~ 58 (123)
+||=| |--..|+-| ||==|.-||-+||.+|+. ++|-+=-+|-|.+.
T Consensus 352 V~D~i~~Ak~~gI~vGPGRGSaAGSLVaY~LgIT~VDPl~y~LlFERFLNpeR~ 405 (1170)
T PRK07374 352 VWDYIRFAREQGIPVGPGRGSAAGSLVAYALGITNIDPVKNGLLFERFLNPERK 405 (1170)
T ss_pred HHHHHHHHHHCCCeeCCCCchHHHHHHHHHhcCCccCccccCCchhhccCCCCC
Confidence 57766 888889888 999999999999999974 56666777777655
No 21
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=33.80 E-value=24 Score=34.73 Aligned_cols=47 Identities=21% Similarity=0.485 Sum_probs=37.9
Q ss_pred hhhHhh-hhccccccC-CCCccccchhhhhhhccc------cccccccccCCCCC
Q psy6796 12 LLWDEV-WQGSMGLNC-PGGLSSMGSKLAYSMGFA------LNCPVVEYVTPEKY 58 (123)
Q Consensus 12 ~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~a------~~lTIGQYLqPSk~ 58 (123)
++||=| |--..|+-| ||==|.-||-.||.+|.. ++|-+--+|-|.+.
T Consensus 325 IV~D~i~~Ak~~gI~VGPGRGSaAGSLVaY~LgIT~VDPl~y~LlFERFLNpeR~ 379 (1107)
T PRK06920 325 IVWDFMKYAHENHILTGPGRGSAAGSLVSYVLEITDIDPIEYDLLFERFLNPERV 379 (1107)
T ss_pred HHHHHHHHHHHCCCEeCCCcchHHHHHHHHHhCCCccCccccCCcHHhhcCCCCC
Confidence 357776 778899988 999999999999999974 67777777777654
No 22
>PRK05898 dnaE DNA polymerase III DnaE; Validated
Probab=33.54 E-value=27 Score=34.17 Aligned_cols=47 Identities=26% Similarity=0.463 Sum_probs=39.1
Q ss_pred hhhHhh-hhccccccC-CCCccccchhhhhhhcc------ccccccccccCCCCC
Q psy6796 12 LLWDEV-WQGSMGLNC-PGGLSSMGSKLAYSMGF------ALNCPVVEYVTPEKY 58 (123)
Q Consensus 12 ~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~------a~~lTIGQYLqPSk~ 58 (123)
++||=| |--+.|+-| ||-=|.-||-+||.+|. .++|-+--+|-|.+.
T Consensus 276 IV~D~i~~Ar~~gI~vGpGRGSAAGSLVaY~LgIT~VDPl~~~LlFERFLNpeR~ 330 (971)
T PRK05898 276 IVYDFINFAKSNGIIIGPGRGSAAGSLIAYLLHITDIDPIKYNLIFERFLNPTRK 330 (971)
T ss_pred HHHHHHHHHHHCCceeCCCCccHHHHHHHHHhcCCccCccccCCcHHHhcCCCCC
Confidence 357766 888899988 99999999999999997 567778888888765
No 23
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=31.46 E-value=32 Score=33.95 Aligned_cols=46 Identities=30% Similarity=0.645 Sum_probs=36.5
Q ss_pred hhHhh-hhccccccC-CCCccccchhhhhhhccc------cccccccccCCCCC
Q psy6796 13 LWDEV-WQGSMGLNC-PGGLSSMGSKLAYSMGFA------LNCPVVEYVTPEKY 58 (123)
Q Consensus 13 ~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~a------~~lTIGQYLqPSk~ 58 (123)
+||=| |--..|+-| ||==|.-||-+||.+|.. ++|-+--+|-|.+.
T Consensus 341 V~D~i~~Ak~~gI~vGpGRGSaAGSLVaY~LgIT~VDPl~y~LlFERFLNpeR~ 394 (1151)
T PRK06826 341 VWDFIRFARENGIMVGPGRGSAAGSLVAYTLGITKIDPIKYNLLFERFLNPERV 394 (1151)
T ss_pred HHHHHHHHHHCCCeeCCCcccHHHHHHHHHhCCCccCccccCCCeeeecCCCCC
Confidence 46766 888889988 999999999999999974 46666667777654
No 24
>PF11243 DUF3045: Protein of unknown function (DUF3045); InterPro: IPR021405 This entry is represented by Bacteriophage T4, Gp30.1; it is a family of uncharacterised viral proteins.
Probab=30.51 E-value=94 Score=22.84 Aligned_cols=40 Identities=25% Similarity=0.325 Sum_probs=29.6
Q ss_pred HHHHhcCCcee----eeccccc-cchhhhH-HHHHHHHHHHHHHHH
Q psy6796 78 KVGNSMGFLYT----ASGPLVR-SSYKAGE-FFIGSVLRNRKAAAE 117 (123)
Q Consensus 78 ~~a~~mGF~~V----aSGPLVR-SSY~A~e-~~~~~~l~~~~~~~~ 117 (123)
+.+.+-||-|| .-|-.+| .|||-.- .++..+..||.....
T Consensus 40 ~eCVeqGFiYVs~~~~~g~~kri~tYhk~L~~LldevaYNR~~~~~ 85 (89)
T PF11243_consen 40 KECVEQGFIYVSKYWMDGNDKRITTYHKTLDELLDEVAYNRAVQQI 85 (89)
T ss_pred HHHHhcceEEEEeeeecCCceEEEeHHhHHHHHHHHHHHHHhhhhh
Confidence 47889999999 5688899 8998753 455666777766543
No 25
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=29.46 E-value=34 Score=23.42 Aligned_cols=14 Identities=14% Similarity=0.565 Sum_probs=12.1
Q ss_pred HHHHHHHhcCCcee
Q psy6796 75 HWEKVGNSMGFLYT 88 (123)
Q Consensus 75 ~~k~~a~~mGF~~V 88 (123)
.|+++|.+|||...
T Consensus 17 dWk~LAr~Lg~se~ 30 (84)
T cd08804 17 SWTELARELDFTEE 30 (84)
T ss_pred hHHHHHHHcCCCHH
Confidence 49999999999764
No 26
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=29.20 E-value=42 Score=23.61 Aligned_cols=16 Identities=13% Similarity=0.590 Sum_probs=13.8
Q ss_pred HHHHHHHHHhcCCcee
Q psy6796 73 YAHWEKVGNSMGFLYT 88 (123)
Q Consensus 73 F~~~k~~a~~mGF~~V 88 (123)
|+.|+++|+++||...
T Consensus 19 ~~~Wk~laR~LGLse~ 34 (96)
T cd08315 19 FDSWNRLMRQLGLSEN 34 (96)
T ss_pred HHHHHHHHHHcCCCHH
Confidence 6889999999999753
No 27
>PRK09121 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional
Probab=28.78 E-value=33 Score=28.60 Aligned_cols=52 Identities=12% Similarity=0.117 Sum_probs=38.6
Q ss_pred cccccccCCCCCCCcccccee----cChHHHHHHHHHH--------HhcCCceeeeccccccchhh
Q psy6796 47 CPVVEYVTPEKYAHWEKVVEY----VTPEKYAHWEKVG--------NSMGFLYTASGPLVRSSYKA 100 (123)
Q Consensus 47 lTIGQYLqPSk~~~HlpV~rY----VtPEeF~~~k~~a--------~~mGF~~VaSGPLVRSSY~A 100 (123)
-++|-|+||-.- .-....| +++++++...+.| ++.|...|.-|=+-|++|+.
T Consensus 6 t~VGS~prp~~l--~~~~~~~~~g~i~~~~l~~~~~~ai~~~V~~Q~~aGldiitDGE~rR~~~~~ 69 (339)
T PRK09121 6 STAGSLPKPSWL--AEPETLWSPWKLQGEELIEGKQDALRLSLQEQEDAGIDIVSDGEQTRQHFVT 69 (339)
T ss_pred ceecCCCCCHHH--HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCceeCCccccchHHH
Confidence 368999999654 2222233 7888887665554 47899999999999999876
No 28
>PF10728 DUF2520: Domain of unknown function (DUF2520); InterPro: IPR018931 This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. ; PDB: 3D1L_A 2I76_A 3DFU_A.
Probab=28.59 E-value=1.1e+02 Score=22.55 Aligned_cols=41 Identities=17% Similarity=0.197 Sum_probs=34.2
Q ss_pred ChHHHHHHHHHHHhcCCceeeeccccccchhhhHHHHHHHH
Q psy6796 69 TPEKYAHWEKVGNSMGFLYTASGPLVRSSYKAGEFFIGSVL 109 (123)
Q Consensus 69 tPEeF~~~k~~a~~mGF~~VaSGPLVRSSY~A~e~~~~~~l 109 (123)
.++-.+.+++++.++|-+.+..-+--|..|||.-.|..|.+
T Consensus 9 d~~~~~~l~~l~~~lg~~~~~i~~~~r~~yHaAav~asNf~ 49 (132)
T PF10728_consen 9 DEEALEVLQELAKELGGRPFEIDSEQRALYHAAAVFASNFL 49 (132)
T ss_dssp SHHHHHHHHHHHHHTTSEEEE--GGGHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHhCCceEEeCHHhHHHHHHHHHHHHhhH
Confidence 56778899999999999999999999999999987766643
No 29
>TIGR02021 BchM-ChlM magnesium protoporphyrin O-methyltransferase. This model represents the S-adenosylmethionine-dependent O-methyltransferase responsible for methylation of magnesium protoporphyrin IX. This step is essentiasl for the biosynthesis of both chlorophyll and bacteriochlorophyll. This model encompasses two closely related clades, from cyanobacteria (and plants) where it is called ChlM and other photosynthetic bacteria where it is known as BchM.
Probab=28.53 E-value=75 Score=23.66 Aligned_cols=37 Identities=11% Similarity=0.126 Sum_probs=27.8
Q ss_pred cccceecChHHHHHHHHHHHhcCCceeeeccccccchhhh
Q psy6796 62 EKVVEYVTPEKYAHWEKVGNSMGFLYTASGPLVRSSYKAG 101 (123)
Q Consensus 62 lpV~rYVtPEeF~~~k~~a~~mGF~~VaSGPLVRSSY~A~ 101 (123)
.+-..+++|+++ +++.++.||..+....+....|++.
T Consensus 179 ~~~~~~~~~~~~---~~~l~~~Gf~v~~~~~~~~~~~~~~ 215 (219)
T TIGR02021 179 ATSAYLHPMTDL---ERALGELGWKIVREGLVSTGFYNSM 215 (219)
T ss_pred ccceEEecHHHH---HHHHHHcCceeeeeecccccchhhH
Confidence 344566777755 4667899999999998888888763
No 30
>COG0482 TrmU Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]
Probab=28.43 E-value=26 Score=30.59 Aligned_cols=33 Identities=21% Similarity=0.308 Sum_probs=29.0
Q ss_pred ChHHHHHHHHHHHhcCCceeeeccccccchhhh
Q psy6796 69 TPEKYAHWEKVGNSMGFLYTASGPLVRSSYKAG 101 (123)
Q Consensus 69 tPEeF~~~k~~a~~mGF~~VaSGPLVRSSY~A~ 101 (123)
..-+|..+-++|+++|+.++++|=.+|.....+
T Consensus 101 ~~iKF~~~l~~a~~lgad~iATGHYar~~~~~~ 133 (356)
T COG0482 101 KEIKFKALLDYAKELGADYIATGHYARQREDEG 133 (356)
T ss_pred HHHHHHHHHHHHHHcCCCeEEEeeeEeeecCCc
Confidence 445799999999999999999999999988554
No 31
>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]
Probab=28.25 E-value=43 Score=29.09 Aligned_cols=29 Identities=24% Similarity=0.421 Sum_probs=26.9
Q ss_pred cChHHHHHHHHHHHhcCCceeeecccccc
Q psy6796 68 VTPEKYAHWEKVGNSMGFLYTASGPLVRS 96 (123)
Q Consensus 68 VtPEeF~~~k~~a~~mGF~~VaSGPLVRS 96 (123)
++||.-+...+.-+++||....+||.||.
T Consensus 75 i~~e~~~~v~~~L~~iG~~~G~~G~~vr~ 103 (317)
T COG2221 75 ISPEDADDVVEELREIGLPVGSTGPAVRA 103 (317)
T ss_pred CCHHHHHHHHHHHHHcCCCCCCcchhhhh
Confidence 77899999999999999999999999994
No 32
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=28.02 E-value=40 Score=33.57 Aligned_cols=50 Identities=30% Similarity=0.561 Sum_probs=35.3
Q ss_pred hhHhh-hhccccccCC-CCccccchhhhhhhccccccccccccCCCCCCCccccceecChH
Q psy6796 13 LWDEV-WQGSMGLNCP-GGLSSMGSKLAYSMGFALNCPVVEYVTPEKYAHWEKVVEYVTPE 71 (123)
Q Consensus 13 ~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~~~a~~lTIGQYLqPSk~~~HlpV~rYVtPE 71 (123)
+||=+ |--+.|+-|- |-=|.-||-.||.+|..- +-|-+. .|.-.||+.||
T Consensus 343 V~D~I~~Ak~~gI~vGPGRGSaAGSLVaY~L~IT~-------IDPl~~--~LLFERFLNpe 394 (1139)
T COG0587 343 VWDFIKFARDNGIPVGPGRGSAAGSLVAYALGITD-------IDPLKY--DLLFERFLNPE 394 (1139)
T ss_pred HHHHHHHHHHCCCccCCCCcchHHHHHHHHhcCCC-------cCcccc--CcchhhccCCC
Confidence 56655 8889999996 778889999999988632 345554 45555555554
No 33
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=27.82 E-value=42 Score=22.85 Aligned_cols=15 Identities=7% Similarity=0.355 Sum_probs=12.6
Q ss_pred HHHHHHHHhcCCcee
Q psy6796 74 AHWEKVGNSMGFLYT 88 (123)
Q Consensus 74 ~~~k~~a~~mGF~~V 88 (123)
..|+++|.+|||+..
T Consensus 19 ~~Wk~Lar~LGls~~ 33 (86)
T cd08318 19 EDWKTLAPHLEMKDK 33 (86)
T ss_pred hhHHHHHHHcCCCHH
Confidence 579999999999743
No 34
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=26.96 E-value=49 Score=18.68 Aligned_cols=19 Identities=16% Similarity=0.387 Sum_probs=16.7
Q ss_pred ecChHHHHHHHHHHHhcCC
Q psy6796 67 YVTPEKYAHWEKVGNSMGF 85 (123)
Q Consensus 67 YVtPEeF~~~k~~a~~mGF 85 (123)
.++++..+.+++.|.+.|-
T Consensus 5 ~l~~~~~~~l~~~a~~~g~ 23 (39)
T PF01402_consen 5 RLPDELYERLDELAKELGR 23 (39)
T ss_dssp EEEHHHHHHHHHHHHHHTS
T ss_pred EeCHHHHHHHHHHHHHHCc
Confidence 4789999999999999884
No 35
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=26.37 E-value=65 Score=20.05 Aligned_cols=21 Identities=14% Similarity=0.243 Sum_probs=18.6
Q ss_pred eecChHHHHHHHHHHHhcCCc
Q psy6796 66 EYVTPEKYAHWEKVGNSMGFL 86 (123)
Q Consensus 66 rYVtPEeF~~~k~~a~~mGF~ 86 (123)
..|+|+.-++..+.++++||.
T Consensus 24 ~~vs~~tr~rI~~~a~~lgY~ 44 (46)
T PF00356_consen 24 PRVSEETRERILEAAEELGYR 44 (46)
T ss_dssp SSSTHHHHHHHHHHHHHHTB-
T ss_pred CCCCHHHHHHHHHHHHHHCCC
Confidence 459999999999999999995
No 36
>cd02742 GH20_hexosaminidase Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself.
Probab=24.91 E-value=67 Score=26.02 Aligned_cols=25 Identities=8% Similarity=-0.033 Sum_probs=22.4
Q ss_pred cceecChHHHHHHHHHHHhcCCcee
Q psy6796 64 VVEYVTPEKYAHWEKVGNSMGFLYT 88 (123)
Q Consensus 64 V~rYVtPEeF~~~k~~a~~mGF~~V 88 (123)
-..++|++++.++-++|++.|...|
T Consensus 65 ~~~~yT~~di~elv~yA~~rgI~vi 89 (303)
T cd02742 65 PGGFYTYAQLKDIIEYAAARGIEVI 89 (303)
T ss_pred CCCeECHHHHHHHHHHHHHcCCEEE
Confidence 4569999999999999999999766
No 37
>PF02679 ComA: (2R)-phospho-3-sulfolactate synthase (ComA); InterPro: IPR003830 Methanogenic archaea produce methane via the anaerobic reduction of acetate or single carbon compounds []. Coenzyme M (CoM; 2-mercaptoethanesulphonic acid) serves as the terminal methyl carrier for this process. Previously thought to be unique to methanogenic archaea, CoM has also been found in methylotrophic bacteria. Biosynthesis of CoM begins with the Michael addition of sulphite to phosphoenolpyruvate, forming 2-phospho-3-sulpholactate (PSL). This reaction is catalyzed by members of this family, PSL synthase (ComA) []. Subsequently, PSL is dephosphorylated by phosphosulpholactate phosphatase (ComB) to form 3-sulpholactate [], which is then converted to 3-sulphopyruvate by L-sulpholactate dehydrogenase (ComC; 1.1.1.272 from EC) []. Sulphopyruvate decarboxylase (ComDE; 4.1.1.79 from EC) converts 3-sulphopyruvate to sulphoacetaldehyde []. Reductive thiolation of sulphoacetaldehyde is the final step.; GO: 0019295 coenzyme M biosynthetic process; PDB: 1U83_A 1QWG_A.
Probab=24.84 E-value=60 Score=26.88 Aligned_cols=24 Identities=13% Similarity=0.198 Sum_probs=18.6
Q ss_pred cChHHHHHHHHHHHhcCCceeeec
Q psy6796 68 VTPEKYAHWEKVGNSMGFLYTASG 91 (123)
Q Consensus 68 VtPEeF~~~k~~a~~mGF~~VaSG 91 (123)
+.+..|++|-+.++++||..|.-.
T Consensus 81 ~~q~~~~~yl~~~k~lGf~~IEiS 104 (244)
T PF02679_consen 81 YQQGKFDEYLEECKELGFDAIEIS 104 (244)
T ss_dssp HHTT-HHHHHHHHHHCT-SEEEE-
T ss_pred HhcChHHHHHHHHHHcCCCEEEec
Confidence 348899999999999999999764
No 38
>PF00220 Hormone_4: Neurohypophysial hormones, N-terminal Domain; InterPro: IPR022423 Oxytocin (or ocytocin) and vasopressin [] are small (nine amino acid residues), structurally and functionally related neurohypophysial peptide hormones. Oxytocin causes contraction of the smooth muscle of the uterus and of the mammary gland while vasopressin has a direct antidiuretic action on the kidney and also causes vasoconstriction of the peripheral vessels. Like the majority of active peptides, both hormones are synthesized as larger protein precursors that are enzymatically converted to their mature forms. Peptides belonging to this family are also found in birds, fish, reptiles and amphibians (mesotocin, isotocin, valitocin, glumitocin, aspargtocin, vasotocin, seritocin, asvatocin, phasvatocin), in worms (annetocin), octopi (cephalotocin), locust (locupressin or neuropeptide F1/F2) and in molluscs (conopressins G and S) []. The pattern developed to detect this category of peptides spans their entire sequence and includes four invariant amino acid residues. .; GO: 0005185 neurohypophyseal hormone activity, 0005576 extracellular region
Probab=24.74 E-value=35 Score=15.91 Aligned_cols=6 Identities=67% Similarity=1.265 Sum_probs=4.2
Q ss_pred ccCCCC
Q psy6796 24 LNCPGG 29 (123)
Q Consensus 24 ~~~~~~ 29 (123)
-|||-|
T Consensus 4 ~nCP~G 9 (9)
T PF00220_consen 4 RNCPIG 9 (9)
T ss_pred ccCCCC
Confidence 389865
No 39
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=24.59 E-value=63 Score=18.59 Aligned_cols=12 Identities=25% Similarity=0.805 Sum_probs=9.2
Q ss_pred cChHHHHHHHHH
Q psy6796 68 VTPEKYAHWEKV 79 (123)
Q Consensus 68 VtPEeF~~~k~~ 79 (123)
++||+|+++++.
T Consensus 10 MSPddy~~l~~~ 21 (23)
T PF12162_consen 10 MSPDDYDELERM 21 (23)
T ss_dssp S-HHHHHHHHHH
T ss_pred CCHHHHHHHHHh
Confidence 579999998875
No 40
>smart00258 SAND SAND domain.
Probab=24.36 E-value=40 Score=23.52 Aligned_cols=20 Identities=20% Similarity=0.415 Sum_probs=15.1
Q ss_pred eecChHHHHHHHHHHHhcCC
Q psy6796 66 EYVTPEKYAHWEKVGNSMGF 85 (123)
Q Consensus 66 rYVtPEeF~~~k~~a~~mGF 85 (123)
+|+||.||+.....+.+.-.
T Consensus 33 ~~~TP~eFe~~~g~~~~K~W 52 (73)
T smart00258 33 KWFTPKEFEIEGGKGKSKDW 52 (73)
T ss_pred EEEChHHHHhhcCCcccCCc
Confidence 89999999987765554443
No 41
>PRK03482 phosphoglycerate mutase; Provisional
Probab=24.24 E-value=73 Score=23.79 Aligned_cols=18 Identities=28% Similarity=0.276 Sum_probs=12.0
Q ss_pred cCCceeeeccccccchhh
Q psy6796 83 MGFLYTASGPLVRSSYKA 100 (123)
Q Consensus 83 mGF~~VaSGPLVRSSY~A 100 (123)
.+|..|.|+||.|+-=-|
T Consensus 46 ~~~~~I~sSpl~Ra~qTA 63 (215)
T PRK03482 46 LGITHIISSDLGRTRRTA 63 (215)
T ss_pred CCCCEEEECCcHHHHHHH
Confidence 457777888887765433
No 42
>TIGR03849 arch_ComA phosphosulfolactate synthase. This model finds the ComA (Coenzyme M biosynthesis A) protein, phosphosulfolactate synthase, in methanogenic archaea. The ComABC pathway is one of at least two pathways to the intermediate sulfopyruvate. Coenzyme M occurs rarely and sporadically outside of the archaea, as for expoxide metabolism in Xanthobacter autotrophicus Py2, but candidate phosphosulfolactate synthases from that and other species occur fall below the cutoff and outside the scope of this model. This model deliberately is narrower in scope than pfam02679.
Probab=23.77 E-value=61 Score=26.81 Aligned_cols=24 Identities=13% Similarity=0.239 Sum_probs=20.5
Q ss_pred cChHHHHHHHHHHHhcCCceeeec
Q psy6796 68 VTPEKYAHWEKVGNSMGFLYTASG 91 (123)
Q Consensus 68 VtPEeF~~~k~~a~~mGF~~VaSG 91 (123)
+....|++|-+.++++||..|.-.
T Consensus 68 ~~q~~~~~Yl~~~k~lGf~~IEiS 91 (237)
T TIGR03849 68 HSKGKFDEYLNECDELGFEAVEIS 91 (237)
T ss_pred HHhhhHHHHHHHHHHcCCCEEEEc
Confidence 344789999999999999999754
No 43
>cd06563 GH20_chitobiase-like The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This GH20 domain family includes an N-acetylglucosamidase (GlcNAcase A) from Pseudoalteromonas piscicida and an N-acetylhexosaminidase (SpHex) from Streptomyces plicatus. SpHex lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=23.61 E-value=98 Score=25.72 Aligned_cols=28 Identities=11% Similarity=-0.016 Sum_probs=24.3
Q ss_pred ccccceecChHHHHHHHHHHHhcCCcee
Q psy6796 61 WEKVVEYVTPEKYAHWEKVGNSMGFLYT 88 (123)
Q Consensus 61 HlpV~rYVtPEeF~~~k~~a~~mGF~~V 88 (123)
..+...|+|.++++++-++|.+.|...|
T Consensus 76 ~~~~~~~YT~~di~eiv~yA~~rgI~VI 103 (357)
T cd06563 76 GTPYGGFYTQEEIREIVAYAAERGITVI 103 (357)
T ss_pred CCccCceECHHHHHHHHHHHHHcCCEEE
Confidence 4566789999999999999999999755
No 44
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=23.61 E-value=86 Score=23.11 Aligned_cols=37 Identities=16% Similarity=0.159 Sum_probs=28.1
Q ss_pred ccccceecChHHHHHHHHHHHhcCCc------eeeeccccccc
Q psy6796 61 WEKVVEYVTPEKYAHWEKVGNSMGFL------YTASGPLVRSS 97 (123)
Q Consensus 61 HlpV~rYVtPEeF~~~k~~a~~mGF~------~VaSGPLVRSS 97 (123)
-.++.=+++|||.+.+++-|.+.|-. .++-|.-|+|-
T Consensus 10 ~~~I~vrvt~eE~~~I~~kA~~AGlS~SeYLR~~aLg~~I~s~ 52 (114)
T PRK13877 10 GRHLRVPVLPDEKAEIEANAAAAGLSVARYLRDVGQGYQIKGV 52 (114)
T ss_pred CceeEEEeCHHHHHHHHHHHHHhCCCHHHHHHHHHcCCCcccc
Confidence 46678899999999999999999973 23446666543
No 45
>COG1809 (2R)-phospho-3-sulfolactate synthase (PSL synthase, CoM biosynthesis) [Coenzyme transport and metabolism]
Probab=23.54 E-value=60 Score=27.77 Aligned_cols=27 Identities=11% Similarity=0.118 Sum_probs=23.1
Q ss_pred ceecChHHHHHHHHHHHhcCCceeeec
Q psy6796 65 VEYVTPEKYAHWEKVGNSMGFLYTASG 91 (123)
Q Consensus 65 ~rYVtPEeF~~~k~~a~~mGF~~VaSG 91 (123)
.-++..+.|++|-+.|+++||.++.-.
T Consensus 84 e~a~~~~kvdeyl~e~~~lGfe~iEIS 110 (258)
T COG1809 84 EIAYSQDKVDEYLNEAKELGFEAIEIS 110 (258)
T ss_pred EeehhcccHHHHHHHHHHcCccEEEec
Confidence 346778899999999999999998754
No 46
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=23.43 E-value=63 Score=22.38 Aligned_cols=15 Identities=13% Similarity=0.377 Sum_probs=12.8
Q ss_pred HHHHHHHHHhcCCce
Q psy6796 73 YAHWEKVGNSMGFLY 87 (123)
Q Consensus 73 F~~~k~~a~~mGF~~ 87 (123)
|..|+++|+++|+.-
T Consensus 11 ~~~wk~~~R~LGlse 25 (80)
T cd08313 11 PRRWKEFVRRLGLSD 25 (80)
T ss_pred HHHHHHHHHHcCCCH
Confidence 568999999999864
No 47
>PF02222 ATP-grasp: ATP-grasp domain; InterPro: IPR003135 The ATP-grasp domain has an unusual nucleotide-binding fold, also referred to as palmate, and is found in a superfamily of enzymes including D-alanine-D-alanine ligase, glutathione synthetase, biotin carboxylase, and carbamoyl phosphate synthetase, the ribosomal protein S6 modification enzyme (RimK), urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis. This family does not contain all known ATP-grasp domain members. All the enzymes of this family possess ATP-dependent carboxylate-amine ligase activity, and their catalytic mechanisms are likely to include acylphosphate intermediates.; PDB: 3K5H_C 3K5I_C 3AX6_A 3Q2O_B 3QFF_B 3R5H_A 3ORQ_B 3ORR_B 4E4T_B 2Z04_A ....
Probab=23.29 E-value=49 Score=25.31 Aligned_cols=30 Identities=20% Similarity=0.242 Sum_probs=25.0
Q ss_pred ccccceecChHHHHHHHHHHHhcCCceeee
Q psy6796 61 WEKVVEYVTPEKYAHWEKVGNSMGFLYTAS 90 (123)
Q Consensus 61 HlpV~rYVtPEeF~~~k~~a~~mGF~~VaS 90 (123)
-+||..|++-+..+.+++.+.++||..|.=
T Consensus 5 gip~~~~~~i~~~~~l~~a~~~iG~P~vlK 34 (172)
T PF02222_consen 5 GIPTAPYATIDSLEDLEEAAESIGFPAVLK 34 (172)
T ss_dssp T--B-EEEEESSHHHHHHHHHHHTSSEEEE
T ss_pred CCCCCCeEEECCHHHHHHHHHHcCCCEEEE
Confidence 489999999999999999999999999876
No 48
>PRK06520 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional
Probab=23.01 E-value=41 Score=28.40 Aligned_cols=54 Identities=11% Similarity=0.194 Sum_probs=38.9
Q ss_pred cccccccccCCCCCCCcccccee----cChHHHHHHHHHH--------HhcCCceeeeccccccchhh
Q psy6796 45 LNCPVVEYVTPEKYAHWEKVVEY----VTPEKYAHWEKVG--------NSMGFLYTASGPLVRSSYKA 100 (123)
Q Consensus 45 ~~lTIGQYLqPSk~~~HlpV~rY----VtPEeF~~~k~~a--------~~mGF~~VaSGPLVRSSY~A 100 (123)
..-++|-|+||-.- .-....| ++++++....+.| ++.|+..|.-|=+-|++|+-
T Consensus 9 ~tt~VGS~prP~~L--~~a~~~~~~g~i~~~~l~~~~~~ai~~~V~~Q~~aGldvitDGE~rR~~w~~ 74 (368)
T PRK06520 9 RADVVGSFLRPAAI--KQARQQFAAGEIDAAALRKIEDMEIRKVVEKQRACGLKVVTDGEFRRAWWHF 74 (368)
T ss_pred CcceeccCCCCHHH--HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCeeecCCccccceee
Confidence 34578999999654 2222233 7888887665544 47899999999999997764
No 49
>PF08108 Antimicrobial13: Halocidin family; InterPro: IPR012516 This family consists of the halocidin family of antimicrobial peptides. Halocidins are isolated from the haemocytes of the tunicate, Halocynthia aurantium (Sea peach). They are dimeric in structures, which are found via a disulphide linkage between cysteines of two different- sized monomers. Halocidins have been shown to have strong antimicrobial activities against a wide variety of pathogenic bacteria and could be ideal candidates as peptide antibiotics against multidrug-resistant bacteria [].; GO: 0042742 defense response to bacterium
Probab=22.83 E-value=31 Score=18.07 Aligned_cols=9 Identities=56% Similarity=1.191 Sum_probs=6.9
Q ss_pred ccccCCCCc
Q psy6796 22 MGLNCPGGL 30 (123)
Q Consensus 22 ~~~~~~~~~ 30 (123)
-||||.-|.
T Consensus 5 hglncakgv 13 (15)
T PF08108_consen 5 HGLNCAKGV 13 (15)
T ss_pred cccchhhhc
Confidence 489998764
No 50
>KOG0840|consensus
Probab=22.82 E-value=26 Score=30.14 Aligned_cols=10 Identities=40% Similarity=0.773 Sum_probs=8.5
Q ss_pred ccccCCCCcc
Q psy6796 22 MGLNCPGGLS 31 (123)
Q Consensus 22 ~~~~~~~~~~ 31 (123)
|=+|||||--
T Consensus 127 lyINSPGG~v 136 (275)
T KOG0840|consen 127 LYINSPGGSV 136 (275)
T ss_pred EEEeCCCCcc
Confidence 6799999965
No 51
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=22.77 E-value=59 Score=20.90 Aligned_cols=15 Identities=13% Similarity=0.465 Sum_probs=13.0
Q ss_pred HHHHHHHHHHhcCCc
Q psy6796 72 KYAHWEKVGNSMGFL 86 (123)
Q Consensus 72 eF~~~k~~a~~mGF~ 86 (123)
-...|+++|.+|||.
T Consensus 16 ~g~~W~~la~~Lg~~ 30 (88)
T smart00005 16 LGLDWRELARKLGLS 30 (88)
T ss_pred cchHHHHHHHHcCCC
Confidence 467899999999995
No 52
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=22.73 E-value=41 Score=24.67 Aligned_cols=17 Identities=18% Similarity=0.690 Sum_probs=12.8
Q ss_pred cChHHHHHHHHHHHhcC
Q psy6796 68 VTPEKYAHWEKVGNSMG 84 (123)
Q Consensus 68 VtPEeF~~~k~~a~~mG 84 (123)
.++|||+.|.+...+-|
T Consensus 61 Ls~eEf~~W~~av~rhg 77 (90)
T PF06627_consen 61 LSEEEFESWQRAVDRHG 77 (90)
T ss_dssp SSHHHHHHHHHHCCT--
T ss_pred CCHHHHHHHHHHHHHHh
Confidence 68999999998766544
No 53
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=22.48 E-value=63 Score=20.25 Aligned_cols=14 Identities=21% Similarity=0.662 Sum_probs=11.9
Q ss_pred HHHHHHHHhcCCce
Q psy6796 74 AHWEKVGNSMGFLY 87 (123)
Q Consensus 74 ~~~k~~a~~mGF~~ 87 (123)
..|+++|.++||..
T Consensus 11 ~~W~~la~~Lgl~~ 24 (79)
T cd01670 11 KDWKKLARKLGLSD 24 (79)
T ss_pred hHHHHHHHHhCCCH
Confidence 67999999999753
No 54
>PF01342 SAND: SAND domain; InterPro: IPR000770 The SAND domain (named after Sp100, AIRE-1, NucP41/75, DEAF-1) is a conserved ~80 residue region found in a number of nuclear proteins, many of which function in chromatin-dependent transcriptional control. These include proteins linked to various human diseases, such as the Sp100 (Speckled protein 100 kDa), NUDR (Nuclear DEAF-1 related), GMEB (Glucocorticoid Modulatory Element Binding) proteins and AIRE-1 (Autoimmune regulator 1) proteins. Proteins containing the SAND domain have a modular structure; the SAND domain can be associated with a number of other modules, including the bromodomain, the PHD finger and the MYND finger. Because no SAND domain has been found in yeast, it is thought that the SAND domain could be restricted to animal phyla. Many SAND domain-containing proteins, including NUDR, DEAF-1 (Deformed epidermal autoregulatory factor-1) and GMEB, have been shown to bind DNA sequences specifically. The SAND domain has been proposed to mediate the DNA binding activity of these proteins [, ]. The resolution of the 3D structure of the SAND domain from Sp100b has revealed that it consists of a novel alpha/beta fold. The SAND domain adopts a compact fold consisting of a strongly twisted, five-stranded antiparallel beta-sheet with four alpha-helices packing against one side of the beta-sheet. The opposite side of the beta-sheet is solvent exposed. The beta-sheet and alpha-helical parts of the structure form two distinct regions. Multiple hydrophobic residues pack between these regions to form a structural core. A conserved KDWK sequence motif is found within the alpha-helical, positively charged surface patch. The DNA binding surface has been mapped to the alpha-helical region encompassing the KDWK motif [].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1OQJ_B 1UFN_A 1H5P_A.
Probab=22.29 E-value=51 Score=22.77 Aligned_cols=16 Identities=19% Similarity=0.432 Sum_probs=11.8
Q ss_pred ceecChHHHHHHHHHH
Q psy6796 65 VEYVTPEKYAHWEKVG 80 (123)
Q Consensus 65 ~rYVtPEeF~~~k~~a 80 (123)
-+++||.||+...-.+
T Consensus 41 g~~~TP~eFE~~~G~~ 56 (82)
T PF01342_consen 41 GRWFTPSEFERHGGKG 56 (82)
T ss_dssp TEEE-HHHHHHHHTTC
T ss_pred CcEECHHHHHhhcCcc
Confidence 7899999999876433
No 55
>TIGR03841 F420_Rv3093c probable F420-dependent oxidoreductase, Rv3093c family. This model describes a small family of enzymes in the bacterial luciferase-like monooxygenase family, which includes F420-dependent enzymes such as N5,N10-methylenetetrahydromethanopterin reductase as well as FMN-dependent enzymes. All members of this family are from species that produce coenzyme F420; SIMBAL analysis suggests that members of this family bind F420 rather than FMN.
Probab=22.11 E-value=1.1e+02 Score=24.42 Aligned_cols=29 Identities=10% Similarity=0.165 Sum_probs=23.9
Q ss_pred cceecChHHHHHHHHHHHhcCCceeeecc
Q psy6796 64 VVEYVTPEKYAHWEKVGNSMGFLYTASGP 92 (123)
Q Consensus 64 V~rYVtPEeF~~~k~~a~~mGF~~VaSGP 92 (123)
.....++++.-.+.+.|+++||..+..+-
T Consensus 3 ~~~~~~~~~~~~~a~~AE~~Gfd~~w~~e 31 (301)
T TIGR03841 3 LWQDRPLAEATRLARAADELGYTDVWSGE 31 (301)
T ss_pred CCCCCCHHHHHHHHHHHHHcCCCEEEecc
Confidence 34456688899999999999999999775
No 56
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=21.98 E-value=55 Score=22.31 Aligned_cols=23 Identities=26% Similarity=0.625 Sum_probs=14.5
Q ss_pred cCccchheehhhHhhhhccccccCC
Q psy6796 3 GPIHGTVEFLLWDEVWQGSMGLNCP 27 (123)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~ 27 (123)
=|+||-+-..-.+-.-.-++| ||
T Consensus 35 CP~HG~~~~s~~~~~~~sk~G--CP 57 (60)
T PF05265_consen 35 CPKHGNFTCSTFNSFIKSKHG--CP 57 (60)
T ss_pred CCCCCcEEeccHHhhhhhccC--CC
Confidence 388887776655555555555 66
No 57
>PRK06233 hypothetical protein; Provisional
Probab=21.93 E-value=59 Score=27.44 Aligned_cols=58 Identities=16% Similarity=0.251 Sum_probs=41.5
Q ss_pred ccccccccCCCCCCCcccccee----cChHHHHHHHHHH--------HhcCCceeeeccccccchhhhHHHHHH
Q psy6796 46 NCPVVEYVTPEKYAHWEKVVEY----VTPEKYAHWEKVG--------NSMGFLYTASGPLVRSSYKAGEFFIGS 107 (123)
Q Consensus 46 ~lTIGQYLqPSk~~~HlpV~rY----VtPEeF~~~k~~a--------~~mGF~~VaSGPLVRSSY~A~e~~~~~ 107 (123)
.-.+|-|+||-.- .-....| +++++++...+.+ ++.|+..|.-|=+-||.++- .|+..
T Consensus 11 ~~~VGS~prP~~L--~~a~~~~~~g~i~~~~l~~~~~~ai~~~V~~Q~~aGldiitDGE~rR~~~~~--~f~~~ 80 (372)
T PRK06233 11 FDIVGSFLRPERL--KEAREQFAIGEISQDQLLKIQHAEIKRLVKEQVELGLKAVTDGEFNRSWWHL--DFLWG 80 (372)
T ss_pred cceEeeCCCCHHH--HHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCeeeCCCcCCccHHH--HHHhh
Confidence 3468999999654 2222333 7888887766554 46899999999999999874 45554
No 58
>cd03311 CIMS_C_terminal_like CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the C-terminal barrel, and a few single-barrel sequences most similar to the C-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Sidechains from
Probab=21.77 E-value=46 Score=26.74 Aligned_cols=51 Identities=18% Similarity=0.212 Sum_probs=38.2
Q ss_pred ccccccCCCCCCCcccc----ceecChHHHHHHHHHH--------HhcCCceeeeccccccchhh
Q psy6796 48 PVVEYVTPEKYAHWEKV----VEYVTPEKYAHWEKVG--------NSMGFLYTASGPLVRSSYKA 100 (123)
Q Consensus 48 TIGQYLqPSk~~~HlpV----~rYVtPEeF~~~k~~a--------~~mGF~~VaSGPLVRSSY~A 100 (123)
++|-|+||..- .... ..-++.++|++..+.| ++.|+..|..|=+.|.+|+.
T Consensus 4 ~vGS~prp~~l--~~a~~~~~~g~~~~~~l~~~~~~ai~~~v~~Q~~~GldiitDGe~~r~~~~~ 66 (332)
T cd03311 4 TVGSFPRPKEL--REARAKFKKGEISAEELREAEDDAIADAVKDQEEAGLDVVTDGEFRRSDMVE 66 (332)
T ss_pred eecCCCCCHHH--HHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCccccCCcccccHHH
Confidence 58999999644 2222 2347889997776655 46899999999999999876
No 59
>COG1519 KdtA 3-deoxy-D-manno-octulosonic-acid transferase [Cell envelope biogenesis, outer membrane]
Probab=21.76 E-value=76 Score=28.55 Aligned_cols=23 Identities=22% Similarity=0.340 Sum_probs=20.8
Q ss_pred ChHHHHHHHHHHHhcCCceeeec
Q psy6796 69 TPEKYAHWEKVGNSMGFLYTASG 91 (123)
Q Consensus 69 tPEeF~~~k~~a~~mGF~~VaSG 91 (123)
+||.|+..++.++++||+++.-.
T Consensus 269 HpERf~~v~~l~~~~gl~~~~rS 291 (419)
T COG1519 269 HPERFKAVENLLKRKGLSVTRRS 291 (419)
T ss_pred ChhhHHHHHHHHHHcCCeEEeec
Confidence 79999999999999999998643
No 60
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.61 E-value=87 Score=20.66 Aligned_cols=56 Identities=14% Similarity=0.182 Sum_probs=40.1
Q ss_pred CCCccccchhhhhhhccccccccccccCCCCCCCccccc---eecC-hHHHHHHHHHHHhcCCceee
Q psy6796 27 PGGLSSMGSKLAYSMGFALNCPVVEYVTPEKYAHWEKVV---EYVT-PEKYAHWEKVGNSMGFLYTA 89 (123)
Q Consensus 27 ~~~~~~~~~~~~~~~~~a~~lTIGQYLqPSk~~~HlpV~---rYVt-PEeF~~~k~~a~~mGF~~Va 89 (123)
||+|..+-+.|+ ..||+.-.|-+.+.. .-.|. +--. ++..+...+.-++.||++..
T Consensus 12 PG~L~~ll~~l~-----~anI~~~~y~~~~~~--~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~ 71 (85)
T cd04906 12 PGSFKKFCELIG-----PRNITEFNYRYADEK--DAHIFVGVSVANGAEELAELLEDLKSAGYEVVD 71 (85)
T ss_pred CcHHHHHHHHhC-----CCceeEEEEEccCCC--eeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEE
Confidence 788877666555 358887778776654 43333 4444 89999999999999998764
No 61
>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....
Probab=21.51 E-value=43 Score=23.45 Aligned_cols=25 Identities=20% Similarity=0.465 Sum_probs=21.2
Q ss_pred HHHHHhcCCceeeeccccccchhhh
Q psy6796 77 EKVGNSMGFLYTASGPLVRSSYKAG 101 (123)
Q Consensus 77 k~~a~~mGF~~VaSGPLVRSSY~A~ 101 (123)
+.+|.+.||.++..|-+.|..-..+
T Consensus 14 ~~la~~~~~~~is~~~llr~~~~~~ 38 (151)
T PF00406_consen 14 KRLAKRYGLVHISVGDLLREEIKSD 38 (151)
T ss_dssp HHHHHHHTSEEEEHHHHHHHHHHTT
T ss_pred HHHHHhcCcceechHHHHHHHHhhh
Confidence 4688899999999999999877554
No 62
>PF02775 TPP_enzyme_C: Thiamine pyrophosphate enzyme, C-terminal TPP binding domain; InterPro: IPR011766 A number of enzymes require thiamine pyrophosphate (TPP) (vitamin B1) as a cofactor. It has been shown [] that some of these enzymes are structurally related. This represents the C-terminal TPP binding domain of TPP enzymes.; GO: 0003824 catalytic activity, 0030976 thiamine pyrophosphate binding; PDB: 2WVA_V 1ZPD_F 2WVG_B 2WVH_B 3OE1_D 2NXW_A 2Q5L_B 2Q5Q_B 2Q5J_A 2Q5O_A ....
Probab=21.07 E-value=36 Score=24.06 Aligned_cols=23 Identities=39% Similarity=0.600 Sum_probs=18.3
Q ss_pred ccCCCCccccchhhhhhhccccc
Q psy6796 24 LNCPGGLSSMGSKLAYSMGFALN 46 (123)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~a~~ 46 (123)
.-++++.++||.-++..+|.+..
T Consensus 21 ~~~~~~~g~mG~~~~~aiGa~~a 43 (153)
T PF02775_consen 21 FLTSGGFGSMGYALPAAIGAALA 43 (153)
T ss_dssp EEESTTTT-TTTHHHHHHHHHHH
T ss_pred EEcCCCccccCCHHHhhhHHHhh
Confidence 34588999999999999998875
No 63
>cd02002 TPP_BFDC Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of benzoylformate to benzaldehyde and carbon dioxide. This enzyme is dependent on TPP and a divalent metal cation as cofactors.
Probab=21.07 E-value=57 Score=23.49 Aligned_cols=32 Identities=19% Similarity=0.172 Sum_probs=22.7
Q ss_pred hHhhhh--ccccccCCCCccccchhhhhhhccccc
Q psy6796 14 WDEVWQ--GSMGLNCPGGLSSMGSKLAYSMGFALN 46 (123)
Q Consensus 14 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~a~~ 46 (123)
+-..|. .....-|++| ++||.-+..++|.++.
T Consensus 31 ~~~~~~~~~~~~~~~~~~-g~mG~~lp~aiGaala 64 (178)
T cd02002 31 LRDQLPLTRPGSYFTLRG-GGLGWGLPAAVGAALA 64 (178)
T ss_pred HHHhcccCCCCCeeccCC-ccccchHHHHHHHHhc
Confidence 344554 3445668888 9999988888887654
No 64
>cd01986 Alpha_ANH_like Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group..
Probab=21.05 E-value=58 Score=21.68 Aligned_cols=65 Identities=18% Similarity=0.273 Sum_probs=43.2
Q ss_pred ccCCCCccccch-hhhhhhcc-ccccccccccCCCCCCCccccceecChHHHHHHHHHHHhcCCceeeecc
Q psy6796 24 LNCPGGLSSMGS-KLAYSMGF-ALNCPVVEYVTPEKYAHWEKVVEYVTPEKYAHWEKVGNSMGFLYTASGP 92 (123)
Q Consensus 24 ~~~~~~~~~~~~-~~~~~~~~-a~~lTIGQYLqPSk~~~HlpV~rYVtPEeF~~~k~~a~~mGF~~VaSGP 92 (123)
+-+-||..|+-. .++...+. ...+++-...+| + .....++..-..++.+.+.|.+.|+.+++.|.
T Consensus 3 v~~SGG~DS~~ll~~l~~~~~~~~~~~~~~~~~~--~--~~~~~~~~~~~r~~~~~~~a~~~g~~~i~~g~ 69 (103)
T cd01986 3 VAFSGGKDSSVAAALLKKLGYQVIAVTVDHGISP--R--LEDAKEIAKEAREEAAKRIAKEKGAETIATGT 69 (103)
T ss_pred EEEeCcHHHHHHHHHHHHhCCCEEEEEEcCCCcc--c--HHHHHHHHHHHHHHHHHHHHHHcCCCEEEEcC
Confidence 446677776542 33333332 345566666666 2 34556666668889999999999999999986
No 65
>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=20.99 E-value=1e+02 Score=23.09 Aligned_cols=25 Identities=24% Similarity=0.207 Sum_probs=20.9
Q ss_pred cChHHHHHHHHHHHhcCCceeeecc
Q psy6796 68 VTPEKYAHWEKVGNSMGFLYTASGP 92 (123)
Q Consensus 68 VtPEeF~~~k~~a~~mGF~~VaSGP 92 (123)
++++.|+..++..+++||..|....
T Consensus 94 i~~~d~~~~~~~l~~~Gv~~vF~pg 118 (134)
T TIGR01501 94 VGKQDFPDVEKRFKEMGFDRVFAPG 118 (134)
T ss_pred cChhhhHHHHHHHHHcCCCEEECcC
Confidence 5788899888889999999888643
No 66
>TIGR01915 npdG NADPH-dependent F420 reductase. This model represents a subset of a parent family described by Pfam model pfam03807. Unlike the parent family, members of this family are found only in species with evidence of coenzyme F420. All members of this family are believed to act as NADPH-dependent F420 reductase.
Probab=20.96 E-value=60 Score=24.61 Aligned_cols=47 Identities=11% Similarity=0.068 Sum_probs=31.0
Q ss_pred cccCCCCCCCccccceecChH--H-HHHHHHHHHhc-CCceeeeccccccchh
Q psy6796 51 EYVTPEKYAHWEKVVEYVTPE--K-YAHWEKVGNSM-GFLYTASGPLVRSSYK 99 (123)
Q Consensus 51 QYLqPSk~~~HlpV~rYVtPE--e-F~~~k~~a~~m-GF~~VaSGPLVRSSY~ 99 (123)
+.+++... +.+...||.=+ + =+.-.++..++ ||.-|-.|||-+|-+-
T Consensus 146 ~~~~~~~~--~~~~~~~v~Gdd~~ak~~v~~L~~~~~G~~~vd~G~l~~a~~~ 196 (219)
T TIGR01915 146 VLLQDVDD--EVDCDVLVCGDDEEAKEVVAELAGRIDGLRALDAGPLENAAIV 196 (219)
T ss_pred HHhcCCCC--CCCCCEEEECCCHHHHHHHHHHHHhcCCCCcccCCchhhHHHH
Confidence 44444333 44555666433 2 33456788899 9999999999888653
No 67
>TIGR03848 MSMEG_4193 probable phosphomutase, MSMEG_4193 family. A three-gene system broadly conserved among the Actinobacteria includes MSMEG_4193 and homologs, a subgroup among the larger phosphoglycerate mutase family protein (pfam00300). Another member of the trio is a probable kinase, related to phosphatidylinositol kinases; that context supports the hypothesis that this protein acts as a phosphomutase.
Probab=20.42 E-value=87 Score=23.18 Aligned_cols=18 Identities=28% Similarity=0.279 Sum_probs=11.6
Q ss_pred cCCceeeeccccccchhh
Q psy6796 83 MGFLYTASGPLVRSSYKA 100 (123)
Q Consensus 83 mGF~~VaSGPLVRSSY~A 100 (123)
+.|..|.|+||.|.-=-|
T Consensus 45 ~~~~~i~sSpl~Ra~qTA 62 (204)
T TIGR03848 45 LPIAAIVSSPLERCRETA 62 (204)
T ss_pred CCCCEEEeCcHHHHHHHH
Confidence 356777777777764444
No 68
>cd06564 GH20_DspB_LnbB-like Glycosyl hydrolase family 20 (GH20) catalytic domain of dispersin B (DspB), lacto-N-biosidase (LnbB) and related proteins. Dispersin B is a soluble beta-N-acetylglucosamidase found in bacteria that hydrolyzes the beta-1,6-linkages of PGA (poly-beta-(1,6)-N-acetylglucosamine), a major component of the extracellular polysaccharide matrix. Lacto-N-biosidase hydrolyzes lacto-N-biose (LNB) type I oligosaccharides at the nonreducing terminus to produce lacto-N-biose as part of the GNB/LNB (galacto-N-biose/lacto-N-biose I) degradation pathway. The lacto-N-biosidase from Bifidobacterium bifidum has this GH20 domain, a carbohydrate binding module 32, and a bacterial immunoglobulin-like domain 2, as well as a YSIRK signal peptide and a G5 membrane anchor at the N and C termini, respectively. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself.
Probab=20.28 E-value=93 Score=25.40 Aligned_cols=26 Identities=15% Similarity=0.128 Sum_probs=22.9
Q ss_pred ccceecChHHHHHHHHHHHhcCCcee
Q psy6796 63 KVVEYVTPEKYAHWEKVGNSMGFLYT 88 (123)
Q Consensus 63 pV~rYVtPEeF~~~k~~a~~mGF~~V 88 (123)
+-..|+|.++++++-++|.+.|...|
T Consensus 74 ~~~~~YT~~di~eiv~yA~~rgI~vI 99 (326)
T cd06564 74 ANDGYYTKEEFKELIAYAKDRGVNII 99 (326)
T ss_pred CCCCcccHHHHHHHHHHHHHcCCeEe
Confidence 34679999999999999999999766
No 69
>PF07733 DNA_pol3_alpha: Bacterial DNA polymerase III alpha subunit; InterPro: IPR011708 This is a conserved region found in the the DNA polymerase III alpha subunit, (2.7.7.7 from EC). DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity. The alpha chain is the DNA polymerase.; GO: 0008408 3'-5' exonuclease activity, 0006260 DNA replication, 0005737 cytoplasm; PDB: 3F2C_A 3F2B_A 3F2D_A 2HPM_A 2HPI_A 3E0D_A 2HQA_A 2HNH_A.
Probab=20.11 E-value=50 Score=28.94 Aligned_cols=41 Identities=29% Similarity=0.588 Sum_probs=23.4
Q ss_pred hhccccc-cCCCCccccchhhhhhhccc------cccccccccCCCCC
Q psy6796 18 WQGSMGL-NCPGGLSSMGSKLAYSMGFA------LNCPVVEYVTPEKY 58 (123)
Q Consensus 18 ~~~~~~~-~~~~~~~~~~~~~~~~~~~a------~~lTIGQYLqPSk~ 58 (123)
|--+.|+ -|||-=|.-||-+||.+|+. ++|-+=-+|-|.+.
T Consensus 52 ~a~~~~i~~g~GRGS~~gSlv~y~lgIT~vdPl~~~L~FERFlnp~R~ 99 (426)
T PF07733_consen 52 WARKNGILVGPGRGSAAGSLVAYLLGITEVDPLKYDLLFERFLNPERV 99 (426)
T ss_dssp HHHHTT--BES-EGGGGG-HHHHHTTSSSS-TTTTT--CHHHSTTTS-
T ss_pred HHHhcCCccccCCCchHHHHHHHHhcCcccCCcccccchheecCccCc
Confidence 4445666 46887899999999999975 34444444444443
Done!