Query 031712
Match_columns 154
No_of_seqs 145 out of 1063
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 04:19:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031712.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031712hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4747 Two-component phosphor 99.9 1.3E-22 2.9E-27 146.7 15.9 145 3-148 5-150 (150)
2 PF01627 Hpt: Hpt domain; Int 99.6 4.4E-15 9.5E-20 98.7 10.0 81 44-126 1-87 (90)
3 COG2198 ArcB FOG: HPt domain [ 99.6 1.2E-14 2.5E-19 103.4 12.7 95 37-133 20-117 (122)
4 smart00073 HPT Histidine Phosp 99.5 8.5E-14 1.8E-18 92.7 6.6 85 44-131 2-86 (87)
5 cd00088 HPT Histidine Phosphot 99.4 2.4E-12 5.3E-17 87.1 8.4 64 43-108 2-69 (94)
6 TIGR02956 TMAO_torS TMAO reduc 99.3 4.6E-11 1E-15 108.9 12.1 94 36-133 875-968 (968)
7 PRK11091 aerobic respiration c 99.1 1.7E-09 3.6E-14 97.2 13.2 107 30-138 671-777 (779)
8 PRK10618 phosphotransfer inter 99.1 7.1E-10 1.5E-14 101.6 10.8 82 44-127 811-892 (894)
9 PRK11107 hybrid sensory histid 98.7 5.3E-07 1.2E-11 81.9 14.6 98 36-135 820-918 (919)
10 PRK11466 hybrid sensory histid 98.6 2.7E-07 5.9E-12 84.1 11.3 89 37-136 820-908 (914)
11 COG0643 CheA Chemotaxis protei 98.1 1.8E-05 3.8E-10 71.4 9.6 94 39-132 3-105 (716)
12 PRK10547 chemotaxis protein Ch 98.1 2.2E-05 4.8E-10 70.3 9.6 63 43-105 4-72 (670)
13 PRK09959 hybrid sensory histid 97.5 0.002 4.4E-08 60.7 12.6 97 36-134 1096-1193(1197)
14 PRK15347 two component system 96.9 0.0057 1.2E-07 55.9 9.0 78 45-127 838-915 (921)
15 PF07743 HSCB_C: HSCB C-termin 92.1 1.6 3.6E-05 28.0 7.6 45 37-83 24-68 (78)
16 TIGR03042 PS_II_psbQ_bact phot 88.9 7.1 0.00015 28.6 9.2 73 51-135 46-139 (142)
17 PLN02956 PSII-Q subunit 88.7 6.8 0.00015 29.9 9.2 76 47-127 86-182 (185)
18 TIGR00714 hscB Fe-S protein as 88.3 4 8.7E-05 30.2 7.8 74 49-133 79-152 (157)
19 PRK01356 hscB co-chaperone Hsc 87.0 5.2 0.00011 29.9 7.8 42 70-119 107-148 (166)
20 cd08323 CARD_APAF1 Caspase act 86.6 4.6 0.0001 26.9 6.6 67 10-80 16-83 (86)
21 PF13779 DUF4175: Domain of un 81.3 10 0.00022 35.4 8.5 85 36-125 488-572 (820)
22 PRK01773 hscB co-chaperone Hsc 79.0 15 0.00033 27.6 7.6 60 49-118 93-152 (173)
23 TIGR02302 aProt_lowcomp conser 77.8 21 0.00046 33.5 9.4 89 33-127 516-604 (851)
24 PF08900 DUF1845: Domain of un 74.2 25 0.00053 27.4 7.7 57 84-141 33-89 (217)
25 PF05396 Phage_T7_Capsid: Phag 73.7 28 0.0006 24.9 7.1 47 36-84 43-89 (123)
26 TIGR02719 repress_PhaQ poly-be 73.4 8.7 0.00019 27.9 4.7 63 87-149 54-132 (138)
27 TIGR03761 ICE_PFL4669 integrat 72.1 30 0.00066 27.1 7.8 58 84-142 31-88 (216)
28 PRK03578 hscB co-chaperone Hsc 72.0 27 0.00058 26.3 7.3 50 59-118 106-156 (176)
29 COG3046 Uncharacterized protei 71.1 28 0.0006 30.2 7.8 67 38-110 226-292 (505)
30 PF04840 Vps16_C: Vps16, C-ter 69.5 63 0.0014 26.6 10.7 103 5-121 162-265 (319)
31 PF05757 PsbQ: Oxygen evolving 68.1 27 0.00058 27.1 6.6 75 50-126 105-197 (202)
32 cd08326 CARD_CASP9 Caspase act 65.5 35 0.00075 22.5 6.0 57 9-67 17-74 (84)
33 TIGR00984 3a0801s03tim44 mitoc 62.3 18 0.00039 30.7 5.1 81 8-107 212-293 (378)
34 PRK05014 hscB co-chaperone Hsc 61.7 64 0.0014 24.1 7.5 62 48-119 90-152 (171)
35 PRK03170 dihydrodipicolinate s 56.2 46 0.001 26.6 6.4 73 81-153 196-274 (292)
36 PF07304 SRA1: Steroid recepto 55.7 81 0.0018 23.2 8.5 79 46-129 63-141 (157)
37 PHA01929 putative scaffolding 55.5 59 0.0013 26.4 6.6 54 36-91 198-252 (306)
38 PF09537 DUF2383: Domain of un 53.2 67 0.0015 21.6 6.4 48 100-147 20-67 (111)
39 PF06367 Drf_FH3: Diaphanous F 52.1 91 0.002 23.2 7.1 47 14-65 65-111 (197)
40 PF14615 Rsa3: Ribosome-assemb 51.0 43 0.00094 19.7 4.0 39 46-87 7-45 (47)
41 PF11553 DUF3231: Protein of u 48.3 97 0.0021 22.6 6.6 73 70-151 15-87 (166)
42 KOG1142 Transcription initiati 48.0 27 0.00058 28.1 3.6 49 7-66 157-205 (258)
43 KOG2280 Vacuolar assembly/sort 46.2 1.5E+02 0.0032 27.7 8.4 83 29-122 690-773 (829)
44 PF07014 Hs1pro-1_C: Hs1pro-1 44.9 1.6E+02 0.0034 23.4 9.5 65 40-115 53-117 (261)
45 cd01671 CARD Caspase activatio 44.7 77 0.0017 19.8 6.3 58 8-67 13-71 (80)
46 PF06248 Zw10: Centromere/kine 44.5 2.3E+02 0.005 25.2 11.4 20 114-133 150-169 (593)
47 PRK15178 Vi polysaccharide exp 40.2 1.5E+02 0.0032 25.8 7.2 57 8-66 184-241 (434)
48 PF09280 XPC-binding: XPC-bind 37.9 94 0.002 19.1 4.3 37 25-62 8-44 (59)
49 PRK03057 hypothetical protein; 37.9 1.2E+02 0.0027 23.0 5.7 36 46-83 133-174 (180)
50 PRK03636 hypothetical protein; 37.7 1.3E+02 0.0029 22.7 5.9 29 53-83 147-175 (179)
51 TIGR02284 conserved hypothetic 37.6 1.2E+02 0.0027 21.6 5.6 38 110-147 29-66 (139)
52 PF11563 Protoglobin: Protoglo 36.9 1.5E+02 0.0032 20.9 6.7 54 2-55 59-117 (158)
53 PF08637 NCA2: ATP synthase re 36.8 2.3E+02 0.005 23.0 9.7 64 5-74 30-111 (290)
54 PF08858 IDEAL: IDEAL domain; 36.5 78 0.0017 17.5 5.5 24 55-80 13-36 (37)
55 KOG2424 Protein involved in tr 35.7 77 0.0017 24.3 4.3 34 86-124 148-181 (195)
56 PF03670 UPF0184: Uncharacteri 35.6 1.3E+02 0.0029 19.9 5.1 36 106-141 32-67 (83)
57 PF03847 TFIID_20kDa: Transcri 34.8 1.2E+02 0.0026 19.2 5.0 49 7-66 2-50 (68)
58 KOG3192 Mitochondrial J-type c 34.4 2E+02 0.0043 21.6 7.3 35 42-78 117-151 (168)
59 cd08332 CARD_CASP2 Caspase act 33.0 1.5E+02 0.0032 19.6 6.7 55 10-66 22-77 (90)
60 PF04722 Ssu72: Ssu72-like pro 32.7 82 0.0018 24.3 4.1 35 86-124 146-180 (195)
61 cd00408 DHDPS-like Dihydrodipi 30.8 1.6E+02 0.0034 23.2 5.7 70 82-153 193-270 (281)
62 COG2991 Uncharacterized protei 30.5 12 0.00025 24.3 -0.7 20 79-98 27-46 (77)
63 TIGR01220 Pmev_kin_Gr_pos phos 30.4 2.8E+02 0.0061 23.0 7.3 56 45-102 246-309 (358)
64 cd00950 DHDPS Dihydrodipicolin 29.4 2.2E+02 0.0047 22.5 6.3 70 82-153 196-273 (284)
65 smart00388 HisKA His Kinase A 29.3 1.1E+02 0.0024 17.0 6.8 56 73-136 5-60 (66)
66 PRK13916 plasmid segregation p 29.3 87 0.0019 21.0 3.2 28 26-53 20-47 (97)
67 COG5582 Uncharacterized conser 28.8 1.9E+02 0.0041 21.9 5.3 65 12-81 110-174 (182)
68 PLN02999 photosystem II oxygen 26.6 2.5E+02 0.0054 21.5 5.7 39 91-129 150-188 (190)
69 PHA00435 capsid assembly prote 26.0 3.7E+02 0.008 22.1 7.1 42 36-79 196-237 (306)
70 PRK08818 prephenate dehydrogen 25.8 2.9E+02 0.0062 23.3 6.6 34 50-85 233-266 (370)
71 cd08810 CARD_BCL10 Caspase act 25.3 2.1E+02 0.0045 18.9 5.1 52 10-64 18-70 (84)
72 PF01322 Cytochrom_C_2: Cytoch 24.6 2.2E+02 0.0047 19.5 4.9 30 54-85 85-114 (122)
73 PLN02407 diphosphomevalonate d 24.5 1.3E+02 0.0028 25.3 4.2 33 45-79 224-257 (343)
74 TIGR00674 dapA dihydrodipicoli 23.4 2.2E+02 0.0048 22.6 5.3 71 80-152 192-270 (285)
75 PF04280 Tim44: Tim44-like dom 22.7 85 0.0018 22.0 2.5 51 38-103 12-62 (147)
76 PF00701 DHDPS: Dihydrodipicol 22.6 1.7E+02 0.0037 23.2 4.5 60 93-153 210-274 (289)
77 TIGR00465 ilvC ketol-acid redu 22.3 2E+02 0.0044 23.5 4.9 59 36-109 187-246 (314)
78 COG0783 Dps DNA-binding ferrit 22.2 3.3E+02 0.0071 20.1 6.0 51 85-135 71-123 (156)
79 cd08819 CARD_MDA5_2 Caspase ac 22.1 2.6E+02 0.0055 18.8 5.2 15 11-25 22-36 (88)
80 PF15565 Imm16: Immunity prote 21.7 2.8E+02 0.0061 19.2 5.4 56 29-100 21-76 (106)
81 cd07299 PX_TCGAP The phosphoin 21.6 2.4E+02 0.0052 19.8 4.4 40 15-54 52-95 (113)
82 TIGR03687 pupylate_cterm ubiqu 21.4 1.1E+02 0.0023 16.7 2.1 22 24-45 6-27 (33)
83 PF02845 CUE: CUE domain; Int 21.3 1.6E+02 0.0035 16.2 3.8 34 27-60 5-38 (42)
84 KOG2580 Mitochondrial import i 21.0 2.1E+02 0.0045 24.9 4.8 63 9-80 287-350 (459)
85 PF06920 Ded_cyto: Dedicator o 21.0 3.5E+02 0.0076 20.0 6.9 89 50-143 68-156 (178)
86 TIGR00601 rad23 UV excision re 20.9 2.9E+02 0.0062 23.5 5.6 45 25-77 255-299 (378)
87 PRK14718 ribonuclease III; Pro 20.8 5.3E+02 0.011 22.7 7.2 73 1-81 1-85 (467)
88 PRK11199 tyrA bifunctional cho 20.6 5E+02 0.011 21.6 9.2 48 36-85 297-350 (374)
89 PF05549 Allexi_40kDa: Allexiv 20.6 4.7E+02 0.01 21.2 9.4 106 23-140 36-144 (271)
90 PRK00396 rnpA ribonuclease P; 20.6 1.1E+02 0.0023 21.9 2.6 26 125-150 101-129 (130)
91 PF07361 Cytochrom_B562: Cytoc 20.4 2.9E+02 0.0063 18.7 5.7 35 86-120 58-92 (103)
No 1
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=99.90 E-value=1.3e-22 Score=146.69 Aligned_cols=145 Identities=65% Similarity=1.026 Sum_probs=136.8
Q ss_pred hhHHHHHHHHHHHhhhhhhchHHHHHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Q 031712 3 VGQMQRRLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLK 82 (154)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~ild~~~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LK 82 (154)
|-+|++.+.+|.++++++||+|++|.+|++|.++..|.|+.+++..|++++.+.+..++.|+..+. |+..+....|.+|
T Consensus 5 i~~~q~~~~d~~~sl~~qgild~qF~qlq~lqD~~~p~fv~ev~~~fF~~s~~~i~~~r~ald~~~-d~k~~~~~~hqlk 83 (150)
T KOG4747|consen 5 IISMQRDVSDYTKSLFDQGILDSQFLQLQELQDDSSPDFVEEVVGLFFEDSERLINNLRLALDCER-DFKKLGSHVHQLK 83 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhcccCccHHHHHHHHHHHHHHHHHHHHHHHHhhHh-HHHHHHHHHHHcc
Confidence 568999999999999999999999999999999999999999999999999999999999998764 9999999999999
Q ss_pred hhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHh-hcCCCC
Q 031712 83 GSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVKNKLETLFRMEQQIVA-AGGSIP 148 (154)
Q Consensus 83 Gss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~~-~~~~~~ 148 (154)
|+|..+||.++...|..+-..|+.++.+.+...+++++.++..++..|+.++..+||..+ .|+..|
T Consensus 84 gssssIGa~kvk~~c~~~~~~~~~~n~egcvr~l~~v~ie~~~lkkkL~~~f~L~rq~i~~~~~~n~ 150 (150)
T KOG4747|consen 84 GSSSSIGALKVKKVCVGFNEFCEAGNIEGCVRCLQQVKIEYSLLKKKLETLFQLERQEILAAGGTNP 150 (150)
T ss_pred CchhhhhHHHHHHHHHHHHHHHhhccchhHhhchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCC
Confidence 999999999999999999999999999998899999999999999999999999999554 555544
No 2
>PF01627 Hpt: Hpt domain; InterPro: IPR008207 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represents a domain present at the N terminus in proteins which undergo autophosphorylation. The group includes, the gliding motility regulatory protein from Myxococcus xanthus and a number of bacterial chemotaxis proteins.; GO: 0004871 signal transducer activity, 0000160 two-component signal transduction system (phosphorelay); PDB: 3KYJ_A 3KYI_A 3IQT_A 1Y6D_A 2LD6_A 1TQG_A 2R25_A 1OXB_A 1QSP_B 1C03_B ....
Probab=99.63 E-value=4.4e-15 Score=98.73 Aligned_cols=81 Identities=21% Similarity=0.369 Sum_probs=68.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHh---cCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhh---HHHHHH
Q 031712 44 EVVSLFFADSERLLNDLTRAL---DQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEG---CMSCLQ 117 (154)
Q Consensus 44 ~ll~~Fl~~~~~~l~~L~~a~---~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~---~~~~~~ 117 (154)
++++.|+++.++.+..|..++ ..+ |+..+.+.+|+|||+++++|+.+++.+|..+|..++.++... +...++
T Consensus 1 ell~~f~~~~~~~~~~l~~~~~~~~~~--d~~~l~~~~H~lkG~a~~~g~~~l~~~~~~lE~~~~~~~~~~~~~~~~~~~ 78 (90)
T PF01627_consen 1 ELLDIFLEEAPEDLEQLEQALQALEQE--DWEELRRLAHRLKGSAGNLGAPRLAELAEQLEQALKSGDKPEAEELEQLLD 78 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHCSSHHC--HHHHHHHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHTTHHHHSHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhHh--hHHHHHHHHHHHhhhHHhcCHHHHHHHHHHHHHHHHcCCccchhHHHHHHH
Confidence 589999999999999999999 888 999999999999999999999999999999999999877665 333444
Q ss_pred HHHHHHHHH
Q 031712 118 QVKQEYCLV 126 (154)
Q Consensus 118 ~l~~~~~~l 126 (154)
.+...+.++
T Consensus 79 ~l~~~l~~l 87 (90)
T PF01627_consen 79 ELEAMLEQL 87 (90)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 444444333
No 3
>COG2198 ArcB FOG: HPt domain [Signal transduction mechanisms]
Probab=99.62 E-value=1.2e-14 Score=103.41 Aligned_cols=95 Identities=23% Similarity=0.414 Sum_probs=84.2
Q ss_pred CCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHh-cCHhhHHHH
Q 031712 37 SNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEE-QNIEGCMSC 115 (154)
Q Consensus 37 ~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~-~~~~~~~~~ 115 (154)
|+++++.+++..|+++.+..+..+..++..+ |+..+.+.+|+|||+|+++|+.+|..+|.+||..++. ...+....+
T Consensus 20 ~~~~~~~~ll~~f~~~~~~~l~~l~~~l~~~--d~~~~~~~aH~lkg~a~~lg~~~L~~~~~~lE~~~~~~~~~~~~~~~ 97 (122)
T COG2198 20 GDPDLLRELLAMFLEEAPAQLEQLESALAAE--DNDGLARLAHRLKGSAASLGLPALAQLCQQLEDALRSGASLEELEEL 97 (122)
T ss_pred CChHHHHHHHHHHHHHhHHHHHHHHHHHhcC--CcHHHHHHHHHHHhHHHhccHHHHHHHHHHHHHHHHcCCcHHHHHHH
Confidence 6799999999999999999999999999999 9999999999999999999999999999999999998 566678888
Q ss_pred HHHHHHH--HHHHHHHHHHH
Q 031712 116 LQQVKQE--YCLVKNKLETL 133 (154)
Q Consensus 116 ~~~l~~~--~~~l~~~L~~~ 133 (154)
+..++.+ +......+.++
T Consensus 98 i~~l~~~~~~~~~~~~~~~~ 117 (122)
T COG2198 98 IAELKDELQLDVLALELLTY 117 (122)
T ss_pred HHHHHHHhcchHHHHHHHHH
Confidence 8888888 44444444443
No 4
>smart00073 HPT Histidine Phosphotransfer domain. Contains an active histidine residue that mediates phosphotransfer reactions. Domain detected only in eubacteria. This alignment is an extension to that shown in the Cell structure paper.
Probab=99.49 E-value=8.5e-14 Score=92.67 Aligned_cols=85 Identities=22% Similarity=0.332 Sum_probs=72.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHH
Q 031712 44 EVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEY 123 (154)
Q Consensus 44 ~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~ 123 (154)
+++..|+++.+..+..|..++..+ |+..+.+.+|+|||+|+++|+..|..+|..+|..++...... ....+.+...+
T Consensus 2 e~~~~f~~~~~~~l~~l~~~~~~~--~~~~l~~~~H~LKG~a~~~g~~~l~~~~~~lE~~~~~~~~~~-~~~~~~l~~~~ 78 (87)
T smart00073 2 EELAEFLQSLEEGLLELEKALDAQ--DVNEIFRAAHTLKGSAGSLGLQQLAQLCHQLENLLDAARSGE-VELTPDLLDLL 78 (87)
T ss_pred hHHHHHHHHHHHHHHHHHhCcCHh--HHHHHHHHHHhhhhhHHhcCHHHHHHHHHHHHHHHHHHHcCC-CCCCHHHHHHH
Confidence 678999999999999999999988 999999999999999999999999999999999888644322 24667777777
Q ss_pred HHHHHHHH
Q 031712 124 CLVKNKLE 131 (154)
Q Consensus 124 ~~l~~~L~ 131 (154)
.++...|+
T Consensus 79 ~~~~~~l~ 86 (87)
T smart00073 79 LELVDVLK 86 (87)
T ss_pred HHHHHHHc
Confidence 77766553
No 5
>cd00088 HPT Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is modulated by phosphorylation and dephosphorylation of a conserved aspartic acid residue; two-component proteins are abundant in most eubacteria; In E. coli there are 62 two-component proteins involved in a variety of processes such as chemotaxis, osmoregulation, metabolism and transport 1; also present in both Gram positive and Gram negative pathogenic bacteria where they regulate basic housekeeping functions and control expression of toxins and other proteins important for pathogenesis; in archaea and eukaryotes, two-component pathways constitute a very small number of all signaling systems; in fungi they mediate environmental stress responses and, in pathogenic yeast, hyphal development. In Dictyostelium and in plants, they are i
Probab=99.39 E-value=2.4e-12 Score=87.10 Aligned_cols=64 Identities=30% Similarity=0.527 Sum_probs=60.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHHhc----CCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcC
Q 031712 43 AEVVSLFFADSERLLNDLTRALD----QPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQN 108 (154)
Q Consensus 43 ~~ll~~Fl~~~~~~l~~L~~a~~----~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~ 108 (154)
.+++..|+++.++.+..|..++. .+ |+..+...+|+|||+++++|+..|..+|..+|..++.+.
T Consensus 2 ~~l~~~f~~~~~~~l~~l~~~~~~~~~~~--d~~~l~~~~H~LkGsa~~~G~~~l~~~~~~lE~~~~~~~ 69 (94)
T cd00088 2 EELLELFLEEAEELLEELERALLELEDAE--DLNEIFRAAHTLKGSAASLGLQRLAQLAHQLEDLLDALR 69 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCHH--HHHHHHHHHHhhhhHHhcCChHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999 78 999999999999999999999999999999999999753
No 6
>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS. This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072).
Probab=99.27 E-value=4.6e-11 Score=108.91 Aligned_cols=94 Identities=24% Similarity=0.371 Sum_probs=87.0
Q ss_pred cCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHH
Q 031712 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSC 115 (154)
Q Consensus 36 ~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~ 115 (154)
..+++.+.+++..|+++.+..+..|..++..+ |+..++..+|+|||+++++|+.+|..+|..||+.++.++.. ...
T Consensus 875 ~~~~~~~~~~~~~f~~~~~~~~~~l~~~~~~~--d~~~~~~~~H~lkg~~~~~g~~~l~~~~~~le~~~~~~~~~--~~~ 950 (968)
T TIGR02956 875 VLGVEKVRQLVALFKTSSAEQLEELSAARAVD--DDAQIKKLAHKLKGSAGSLGLTQLTQLCQQLEKQGKTGALE--LSD 950 (968)
T ss_pred hcCcHHHHHHHHHHHHhhHHHHHHHHHHHhCC--CHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHhcccCCcc--hhH
Confidence 44678899999999999999999999999999 99999999999999999999999999999999999988763 467
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 031712 116 LQQVKQEYCLVKNKLETL 133 (154)
Q Consensus 116 ~~~l~~~~~~l~~~L~~~ 133 (154)
+..++..|..+..+|+.|
T Consensus 951 ~~~l~~~~~~~~~~l~~~ 968 (968)
T TIGR02956 951 IDEIKQAWQASKTALDQW 968 (968)
T ss_pred HHHHHHHHHHHHHHHHhC
Confidence 899999999999999865
No 7
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.09 E-value=1.7e-09 Score=97.18 Aligned_cols=107 Identities=16% Similarity=0.241 Sum_probs=96.3
Q ss_pred HHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCH
Q 031712 30 LQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNI 109 (154)
Q Consensus 30 L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~ 109 (154)
+..+.+..+...+...+..|.+..+..++.+..++..+ |+..+...+|+|||+++++|+..+.++|..+|.....+.+
T Consensus 671 l~~~~~~~g~~~~~~~l~~~~~~~~~~~~~l~~~l~~~--d~~~~~~~ah~l~g~~~~~g~~~l~~~~~~le~~~~~~~~ 748 (779)
T PRK11091 671 LEQYVELVGPKLITDSLAVFEKMMPGYLSVLDSNLTAR--DQKGIVEEAHKIKGAAGSVGLRHLQQLAQQIQSPDLPAWW 748 (779)
T ss_pred HHHHHHhcCHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCccccH
Confidence 33343434567788899999999999999999999999 9999999999999999999999999999999998888888
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 031712 110 EGCMSCLQQVKQEYCLVKNKLETLFRMEQ 138 (154)
Q Consensus 110 ~~~~~~~~~l~~~~~~l~~~L~~~l~~~~ 138 (154)
......+.++..+|......|+.|+...+
T Consensus 749 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~ 777 (779)
T PRK11091 749 DNVQDWVEELKNEWRHDVEVLKAWLAQAE 777 (779)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 88889999999999999999999998765
No 8
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=99.09 E-value=7.1e-10 Score=101.63 Aligned_cols=82 Identities=16% Similarity=0.231 Sum_probs=75.8
Q ss_pred HHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHH
Q 031712 44 EVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEY 123 (154)
Q Consensus 44 ~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~ 123 (154)
.++..|+++.+.++..|..++..+ |+..+++.+|+|||+++++|+..++++|..||+.++.++..++...+.+|...+
T Consensus 811 ~~~~lF~~t~~~di~~L~~~~~~~--D~~~l~~~aHrLKG~~aml~l~~l~~~~~~LE~~i~~~~~~~i~~~i~~id~~v 888 (894)
T PRK10618 811 DYYALFVDTVPDDVKRLYTEAATS--DFASLAQTAHRLKGVFAMLNLVPGKQLCETLEHLIREKDEPGIENYISDIDSFV 888 (894)
T ss_pred hHHHHHHHhhHHHHHHHHHHHhcc--CHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHHhhCChHHHHHHHHHHHHHH
Confidence 355889999999999999999999 999999999999999999999999999999999999999888888888888877
Q ss_pred HHHH
Q 031712 124 CLVK 127 (154)
Q Consensus 124 ~~l~ 127 (154)
.++.
T Consensus 889 ~~ll 892 (894)
T PRK10618 889 KSLL 892 (894)
T ss_pred HHHh
Confidence 6653
No 9
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.69 E-value=5.3e-07 Score=81.87 Aligned_cols=98 Identities=19% Similarity=0.282 Sum_probs=85.0
Q ss_pred cCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhc-CHhhHHH
Q 031712 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQ-NIEGCMS 114 (154)
Q Consensus 36 ~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~-~~~~~~~ 114 (154)
.+.+....+++..|.+..+.....|..++... |+..+...+|++||+++++|+.++..+|..+|..++.+ ..+.+..
T Consensus 820 ~~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~h~l~g~~~~~g~~~l~~~~~~le~~~~~~~~~~~~~~ 897 (919)
T PRK11107 820 AGKPDLARDMLQMLLDFLPEVRNKVEEALAGE--DPEGLLDLIHKLHGSCSYSGVPRLKKLCQLIEQQLRSGTSVEDLEP 897 (919)
T ss_pred CCCHHHHHHHHHHHHHhHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCCChhhHHH
Confidence 45678888999999999999999999999999 99999999999999999999999999999999999865 3456666
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 031712 115 CLQQVKQEYCLVKNKLETLFR 135 (154)
Q Consensus 115 ~~~~l~~~~~~l~~~L~~~l~ 135 (154)
.+..+..++.++...++.|+.
T Consensus 898 ~~~~~~~~~~~~~~~~~~~~~ 918 (919)
T PRK11107 898 ELLELLDEMENVARAAKKVLS 918 (919)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 777777777777777777654
No 10
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=98.64 E-value=2.7e-07 Score=84.07 Aligned_cols=89 Identities=22% Similarity=0.274 Sum_probs=72.4
Q ss_pred CCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHH
Q 031712 37 SNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCL 116 (154)
Q Consensus 37 ~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~ 116 (154)
.+.+.+.+++..|..+....+..+..+...+ |+..++..+|+|||+++++|+..+..+|..+|..+...
T Consensus 820 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~ah~lkg~~~~lg~~~l~~~~~~le~~~~~~--------- 888 (914)
T PRK11466 820 MGTEKIHEWLALFKQHALPLLDEIDIARASQ--DSEKIKRAAHQLKSSCSSLGMRQASQACAQLEQQPLSA--------- 888 (914)
T ss_pred cCHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCCCc---------
Confidence 3567778899999999999999999999999 99999999999999999999999999999999875421
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 031712 117 QQVKQEYCLVKNKLETLFRM 136 (154)
Q Consensus 117 ~~l~~~~~~l~~~L~~~l~~ 136 (154)
..+...+.+...+|..|++.
T Consensus 889 ~~~~~~~~~~~~~~~~~~~~ 908 (914)
T PRK11466 889 PLPHEEITRSVAALEAWLAK 908 (914)
T ss_pred hhHHHHHHHHHHHHHHHHHh
Confidence 22334445555566666544
No 11
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=98.12 E-value=1.8e-05 Score=71.38 Aligned_cols=94 Identities=19% Similarity=0.287 Sum_probs=66.7
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHhcCC---CCC---HHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHH---HhcCH
Q 031712 39 PDFVAEVVSLFFADSERLLNDLTRALDQP---TID---FKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFC---EEQNI 109 (154)
Q Consensus 39 ~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~---~~D---~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~---~~~~~ 109 (154)
.....+++..|+.+.++.+..|...+-.- +.| ...+.+.+|+|||+|+.+|+..+..+|..+|... +++..
T Consensus 3 ~~~~~~~~~~F~~Ea~e~l~~l~~~Ll~LE~~~~d~~~ln~ifRaaHTlKG~a~~~g~~~l~~l~H~~E~~ld~~r~g~~ 82 (716)
T COG0643 3 SMDMEEILEDFLEEAEELLQALEQALLALEPDPEDLDLLNAIFRAAHTLKGGAGTLGLTTLAELAHAMEDLLDALRNGEL 82 (716)
T ss_pred hhHHHHHHHHHHHhhHHHHHHHHHhHhhccCCCCCHHHHHHHHHHHHhhhhhhhhcChhHHHHHHHHHHHHHHHHhcCCc
Confidence 35567889999999999999999755221 113 4678999999999999999999999999999854 34443
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHH
Q 031712 110 EGCMSCLQQVKQEYCLVKNKLET 132 (154)
Q Consensus 110 ~~~~~~~~~l~~~~~~l~~~L~~ 132 (154)
.--.++++.+-.+...+...+..
T Consensus 83 ~~~~~l~d~~l~~~D~l~~~~~~ 105 (716)
T COG0643 83 ELTSELLDLLLEALDALEEMLDA 105 (716)
T ss_pred cCcHHHHHHHhhhhHHHHHHHHh
Confidence 32234455554444444444433
No 12
>PRK10547 chemotaxis protein CheA; Provisional
Probab=98.09 E-value=2.2e-05 Score=70.32 Aligned_cols=63 Identities=21% Similarity=0.451 Sum_probs=52.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHHh---cCCCCC---HHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHH
Q 031712 43 AEVVSLFFADSERLLNDLTRAL---DQPTID---FKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCE 105 (154)
Q Consensus 43 ~~ll~~Fl~~~~~~l~~L~~a~---~~~~~D---~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~ 105 (154)
.+++..|++++.+.++.|...+ +..+.| ...+.+.+|+|||+|+.+|+..+..+|..+|....
T Consensus 4 ~~~l~~F~~Ea~E~l~~le~~Ll~LE~~p~d~e~in~lFRa~HTiKG~a~~~g~~~i~~l~H~~E~lld 72 (670)
T PRK10547 4 SDFYQTFFDEADELLADMEQHLLVLDPEAPDAEQLNAIFRAAHSIKGGAGTFGFTVLQETTHLMENLLD 72 (670)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhhhhHHhhcCchHHHHHHHHHHHHHH
Confidence 4778899999999998888876 221113 46789999999999999999999999999998775
No 13
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=97.47 E-value=0.002 Score=60.69 Aligned_cols=97 Identities=12% Similarity=0.241 Sum_probs=76.5
Q ss_pred cCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcC-HhhHHH
Q 031712 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQN-IEGCMS 114 (154)
Q Consensus 36 ~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~-~~~~~~ 114 (154)
..+...+.+++..+.......+..+..+...+ |...+...+|++||++..+|+..+...|.++|......+ ...+..
T Consensus 1096 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~h~~~g~~~~l~~~~l~~~~~~~e~~~~~~~~~~~l~~ 1173 (1197)
T PRK09959 1096 ANDLQLMQEILMTFQHETHKDLPAAFHALEAG--DNRTFHQCIHRIHGAANILNLQKLINISHQLEITPVSDDSKPEILQ 1173 (1197)
T ss_pred CCCHHHHHHHHHHHHHhhHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhhcCCchHHHHH
Confidence 34567888999999999999999999999999 999999999999999999999999999999998887544 334444
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 031712 115 CLQQVKQEYCLVKNKLETLF 134 (154)
Q Consensus 115 ~~~~l~~~~~~l~~~L~~~l 134 (154)
.+..+..........+..|+
T Consensus 1174 ~~~~~~~~~~~~~~~~~~~~ 1193 (1197)
T PRK09959 1174 LLNSVKEHIAELDQEIAVFC 1193 (1197)
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 55555554444444444443
No 14
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=96.90 E-value=0.0057 Score=55.91 Aligned_cols=78 Identities=18% Similarity=0.291 Sum_probs=58.2
Q ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHH
Q 031712 45 VVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYC 124 (154)
Q Consensus 45 ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~ 124 (154)
+...+.+.....+..+..++..+ | .+...+|++||+++.+|+..+...|..+|..++.+..... ..+..++..+.
T Consensus 838 l~~~~~~~l~~~~~~~~~~~~~~--~--~l~~~~h~i~~~~~~~g~~~l~~~~~~~e~~~~~~~~~~~-~~~~~~~~~~~ 912 (921)
T PRK15347 838 LNSKLYQSLLLLLAQIEQAVENQ--E--VLSQLLHTLKGCAGQAGLTELQCAVIDLENALETGEILSL-EELTDLRELIH 912 (921)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCH--H--HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHhcCCCCCH-HHHHHHHHHHH
Confidence 34455555667788888888887 5 8999999999999999999999999999999987654322 23444554444
Q ss_pred HHH
Q 031712 125 LVK 127 (154)
Q Consensus 125 ~l~ 127 (154)
.+.
T Consensus 913 ~~~ 915 (921)
T PRK15347 913 ALF 915 (921)
T ss_pred HHh
Confidence 433
No 15
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=92.07 E-value=1.6 Score=28.03 Aligned_cols=45 Identities=18% Similarity=0.265 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhh
Q 031712 37 SNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKG 83 (154)
Q Consensus 37 ~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKG 83 (154)
++.+-+..+....-......+..|..++..+ ||..+...+++||=
T Consensus 24 ~~~~~L~~l~~~~~~~~~~~~~~l~~~f~~~--d~~~A~~~~~kLky 68 (78)
T PF07743_consen 24 DDEAELEELKKEIEERIKELIKELAEAFDAK--DWEEAKEALRKLKY 68 (78)
T ss_dssp TSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHccC--cHHHHHHHHHHHHH
Confidence 5667888888888888888899999999998 99999999999863
No 16
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=88.88 E-value=7.1 Score=28.61 Aligned_cols=73 Identities=11% Similarity=0.219 Sum_probs=45.0
Q ss_pred HhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcH---------------------HHHHHHHHHHHHHHHhcCH
Q 031712 51 ADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGA---------------------ERIKNACVAFRNFCEEQNI 109 (154)
Q Consensus 51 ~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa---------------------~~L~~~~~~lE~~~~~~~~ 109 (154)
+...+.+.+++..++.+ ||..++...|. .++.++- ..|.+-...|-.+++.++
T Consensus 46 ~~~~~r~~eLk~lI~kk--~W~~vrn~irg---p~g~Lr~dl~~l~~sl~p~dqk~a~~L~~~Lf~~L~~LD~AA~~kd- 119 (142)
T TIGR03042 46 EAAKDRLPELASLVAKE--DWVFTRNLIHG---PMGEVRREMTYLNQSLLPKDQKEALALAKELKDDLEKLDEAARLQD- 119 (142)
T ss_pred HHHHHhhHHHHHHHhhc--chHHHHHHHhc---cHHHHHHHHHHHHHccCHHhHHHHHHHHHHHHHHHHHHHHHHHhcC-
Confidence 34667888899999999 99999998885 3333332 222333333444444443
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHH
Q 031712 110 EGCMSCLQQVKQEYCLVKNKLETLFR 135 (154)
Q Consensus 110 ~~~~~~~~~l~~~~~~l~~~L~~~l~ 135 (154)
..+..+.|.++...++.|++
T Consensus 120 ------~~~a~k~Y~~av~~~dafl~ 139 (142)
T TIGR03042 120 ------GPQAQKAYQKAAADFDAYLD 139 (142)
T ss_pred ------HHHHHHHHHHHHHHHHHHHh
Confidence 24455566666667777654
No 17
>PLN02956 PSII-Q subunit
Probab=88.67 E-value=6.8 Score=29.92 Aligned_cols=76 Identities=7% Similarity=0.042 Sum_probs=48.7
Q ss_pred HHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhc---------------------HHHHHHHHHHHHHHHH
Q 031712 47 SLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIG---------------------AERIKNACVAFRNFCE 105 (154)
Q Consensus 47 ~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lG---------------------a~~L~~~~~~lE~~~~ 105 (154)
..=+.++.+.+-.|+..++.+ +|..++...| |.+++++ +..|.+-...|..+++
T Consensus 86 ~ar~k~~A~~l~~LK~LI~k~--~W~yvrn~LR---gp~s~Lr~DL~~Ii~slpp~Drk~a~~La~~LFd~l~~LD~AAR 160 (185)
T PLN02956 86 ESGVRGHAENLLRVKALIESE--SWKEAQKALR---RSASNLKQDLYAIIQAKPGKDRPQLRRLYSDLFNSVTKLDYAAR 160 (185)
T ss_pred HHHHHHHHHHHHHHHHHhhhc--cHHHHHHHHH---ccHHHHHHHHHHHHHhcCHhHhHHHHHHHHHHHHHHHHHHHHHh
Confidence 334566777788888889988 8888888776 4444444 2445555666667777
Q ss_pred hcCHhhHHHHHHHHHHHHHHHH
Q 031712 106 EQNIEGCMSCLQQVKQEYCLVK 127 (154)
Q Consensus 106 ~~~~~~~~~~~~~l~~~~~~l~ 127 (154)
..+..++...+......+..+.
T Consensus 161 ~kd~~~a~k~Y~~tva~lD~Vl 182 (185)
T PLN02956 161 DKDETRVWEYYENIVASLDDIF 182 (185)
T ss_pred cCCHHHHHHHHHHHHHHHHHHH
Confidence 6666555555555555444443
No 18
>TIGR00714 hscB Fe-S protein assembly co-chaperone HscB. This model describes the small subunit, Hsc20 (20K heat shock cognate protein) of a pair of proteins Hsc66-Hsc20, related to the DnaK-DnaJ heat shock proteins, which also serve as molecular chaperones. Hsc20, unlike DnaJ, appears not to have chaperone activity on its own, but to act solely as a regulatory subunit for Hsc66 (i.e., to be a co-chaperone). The gene for Hsc20 in E. coli, hscB, is not induced by heat shock.
Probab=88.34 E-value=4 Score=30.17 Aligned_cols=74 Identities=12% Similarity=0.180 Sum_probs=37.7
Q ss_pred HHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHHH
Q 031712 49 FFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVKN 128 (154)
Q Consensus 49 Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~ 128 (154)
|+-+.-+.-+.+..+-..+ |...+..+.+.++ .++..+...++.+...++++.+...+..++ -|..+..
T Consensus 79 fLme~Me~rE~lee~~~~~--d~~~L~~l~~~~~--------~~~~~~~~~l~~~~~~~d~~~A~~~~~kLk-y~~kl~~ 147 (157)
T TIGR00714 79 FLMEQLELREELDEIEQAK--DEARLESFIKRVK--------KMFQTRHQLLVEQLDNQTWAAAADYTRKLR-FLDKLRS 147 (157)
T ss_pred HHHHHHHHHHHHHHHHhCC--CHHHHHHHHHHHH--------HHHHHHHHHHHHHHhcCCHHHHHHHHHHHH-HHHHHHH
Confidence 4444334444444444445 6666666665544 244555555665666666665555444443 3444444
Q ss_pred HHHHH
Q 031712 129 KLETL 133 (154)
Q Consensus 129 ~L~~~ 133 (154)
.++.+
T Consensus 148 ~i~~~ 152 (157)
T TIGR00714 148 SAEQL 152 (157)
T ss_pred HHHHH
Confidence 44443
No 19
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=86.98 E-value=5.2 Score=29.89 Aligned_cols=42 Identities=17% Similarity=0.152 Sum_probs=20.7
Q ss_pred CHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHH
Q 031712 70 DFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQV 119 (154)
Q Consensus 70 D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l 119 (154)
+...+..+.+.++.. +..+...++.+...++++.+...+..+
T Consensus 107 ~~~~L~~l~~~~~~~--------~~~~~~~l~~~f~~~d~~~A~~~~~~L 148 (166)
T PRK01356 107 LFSDLEKIKNKYELM--------YKNEIDSLKQAFEEQNLSDATIKTSKL 148 (166)
T ss_pred CHHHHHHHHHHHHHH--------HHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 344455555554432 234445555555555665555444443
No 20
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. 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 PYRIN and DED (Death Effect
Probab=86.58 E-value=4.6 Score=26.93 Aligned_cols=67 Identities=10% Similarity=0.162 Sum_probs=52.0
Q ss_pred HHHHHHhhhhhhchHHH-HHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Q 031712 10 LLEYTKSLFMEGVLDNQ-FLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQ 80 (154)
Q Consensus 10 ~~~~~~~~~~~~ild~~-~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~ 80 (154)
+...|..++.+||++.. .+.|..- ....+-...+++....-.+.-+.....++... .+..++.+.|.
T Consensus 16 v~~ild~L~~~gvlt~~~~e~I~~~--~t~~~qa~~Lld~L~trG~~Af~~F~~aL~~~--~~~~La~lL~~ 83 (86)
T cd08323 16 TSYIMDHMISDGVLTLDEEEKVKSK--ATQKEKAVMLINMILTKDNHAYVSFYNALLHE--GYKDLALLLHD 83 (86)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHcC--CChHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--CChHHHHHHhc
Confidence 67789999999999964 4444442 45578888999999999999999988888765 57777777664
No 21
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=81.33 E-value=10 Score=35.39 Aligned_cols=85 Identities=8% Similarity=0.120 Sum_probs=56.4
Q ss_pred cCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHH
Q 031712 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSC 115 (154)
Q Consensus 36 ~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~ 115 (154)
+-+.+=+.++++.+-+-..+.+.+|.+-.... .-.. ..+.--+.+.+++-..|......||+.+++|+.+++...
T Consensus 488 gAs~eEI~rLm~eLR~A~~~ym~~LAeq~~~~--~~~~---~~p~~~~~~~~~~~~dL~~mmd~ie~la~~G~~~~A~q~ 562 (820)
T PF13779_consen 488 GASDEEIARLMQELREAMQDYMQALAEQAQRN--PQQQ---DQPPDQGNSQMMSQQDLQRMMDRIEELARSGRMDEARQL 562 (820)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHhHhC--cccc---cCcccchhhhccCHHHHHHHHHHHHHHHHcCCHHHHHHH
Confidence 33555566666666666666666665554443 1110 111124667789999999999999999999999988887
Q ss_pred HHHHHHHHHH
Q 031712 116 LQQVKQEYCL 125 (154)
Q Consensus 116 ~~~l~~~~~~ 125 (154)
++++..-++.
T Consensus 563 L~qlq~mmen 572 (820)
T PF13779_consen 563 LEQLQQMMEN 572 (820)
T ss_pred HHHHHHHHHh
Confidence 7777665554
No 22
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=79.02 E-value=15 Score=27.60 Aligned_cols=60 Identities=10% Similarity=0.114 Sum_probs=35.9
Q ss_pred HHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHH
Q 031712 49 FFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQ 118 (154)
Q Consensus 49 Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~ 118 (154)
|+-+.-+.-+.|..+-..+ |...+..+...++ ..+..+...++.+...++++.+...+..
T Consensus 93 fLme~ME~rE~lee~~~~~--d~~~L~~l~~~v~--------~~~~~~~~~l~~~~~~~d~~~A~~~~~r 152 (173)
T PRK01773 93 FLMQQMEWREQLEEIEQQQ--DEDALTAFSKEIK--------QEQQAILTELSTALNSQQWQQASQINDR 152 (173)
T ss_pred HHHHHHHHHHHHHhhcccC--CHHHHHHHHHHHH--------HHHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 3333334444555555556 7777777777654 3456666777777777777766554433
No 23
>TIGR02302 aProt_lowcomp conserved hypothetical protein TIGR02302. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model.
Probab=77.84 E-value=21 Score=33.52 Aligned_cols=89 Identities=11% Similarity=0.197 Sum_probs=60.2
Q ss_pred hhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhH
Q 031712 33 LQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGC 112 (154)
Q Consensus 33 L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~ 112 (154)
|..+-+.+=+.++++.+-+-..+.+.+|.+-..++ . ..-. -..-+.+.+++-..|-+....||+.+++|+.+++
T Consensus 516 L~~gAsdeEI~~Lm~eLR~Am~~ym~~LAeq~~~~--~-~~~~---~~~~~~~~~l~~~dLq~Mmd~ieela~~G~~~~A 589 (851)
T TIGR02302 516 LERGASDEEIKQLTDKLRAAMQTYMRQLAQQLRNN--P-QQLA---RPLDPNTKVLRQQDLQNMMDQIENLARSGDRDQA 589 (851)
T ss_pred HHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHhhhC--c-cccc---ccCCccccccCHHHHHHHHHHHHHHHHcCCHHHH
Confidence 33344566667777777777777777776655432 1 0000 1112345779999999999999999999999988
Q ss_pred HHHHHHHHHHHHHHH
Q 031712 113 MSCLQQVKQEYCLVK 127 (154)
Q Consensus 113 ~~~~~~l~~~~~~l~ 127 (154)
..++.+|..-++.++
T Consensus 590 ~qlL~qlq~mmenlq 604 (851)
T TIGR02302 590 KQLLSQLQQMMNNLQ 604 (851)
T ss_pred HHHHHHHHHHHHHHh
Confidence 888888777666555
No 24
>PF08900 DUF1845: Domain of unknown function (DUF1845); InterPro: IPR014996 Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=74.15 E-value=25 Score=27.43 Aligned_cols=57 Identities=9% Similarity=0.082 Sum_probs=41.1
Q ss_pred hhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Q 031712 84 SSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVKNKLETLFRMEQQIV 141 (154)
Q Consensus 84 ss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~ 141 (154)
..+.+|...+...+..|...+.+.|+ -+...+-.|+..+..+...+++..+...+..
T Consensus 33 ~~~I~Gm~~~~~~~~~i~~~a~~DdP-yAD~~L~~iEe~i~~~~~~l~~~~~~l~~~l 89 (217)
T PF08900_consen 33 KPAIIGMPGFASRLNRIWRDARQDDP-YADWWLLRIEEKINEARQELQELIARLDALL 89 (217)
T ss_pred CCCCcCHHHHHHHHHHHHHHHhcCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34899999999999999999987664 2344566666666666666666666555544
No 25
>PF05396 Phage_T7_Capsid: Phage T7 capsid assembly protein; InterPro: IPR008768 This family contains the capsid assembly protein (scaffolding protein) of bacteriophage T7.; GO: 0019069 viral capsid assembly
Probab=73.66 E-value=28 Score=24.85 Aligned_cols=47 Identities=19% Similarity=0.184 Sum_probs=37.6
Q ss_pred cCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhh
Q 031712 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGS 84 (154)
Q Consensus 36 ~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGs 84 (154)
.|+++-+..++...-..++..++.+..+++++ |...++.+.-.+.++
T Consensus 43 AGG~e~f~~i~~~~~~~~~~~~ea~~~Ai~~~--dla~vk~~vn~~~~s 89 (123)
T PF05396_consen 43 AGGEEGFAAIMSHAEANSPAAAEAFNEAIESG--DLATVKAAVNLAGAS 89 (123)
T ss_pred hcCHHHHHHHHHHHHhCCHHHHHHHHHHHHhC--CHHHHHHHHHHHHHH
Confidence 57888888888777777899999999999999 988887776555443
No 26
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=73.40 E-value=8.7 Score=27.95 Aligned_cols=63 Identities=11% Similarity=0.079 Sum_probs=46.1
Q ss_pred hhcHHHHHHHHHHHHHHHHh-------c-CH--------hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHhhcCCCCc
Q 031712 87 SIGAERIKNACVAFRNFCEE-------Q-NI--------EGCMSCLQQVKQEYCLVKNKLETLFRMEQQIVAAGGSIPM 149 (154)
Q Consensus 87 ~lGa~~L~~~~~~lE~~~~~-------~-~~--------~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~~~~~~~~~ 149 (154)
.+.-..|+-+...||...-- + .. +.-...+......|..+...+..++...+...|.||+.|-
T Consensus 54 ~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~~~~~~l~~ll~~~~~~~~~~~~~~~ 132 (138)
T TIGR02719 54 SVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFEHYQNMLDSFFHLYTDAFFPFSSSPE 132 (138)
T ss_pred CCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCC
Confidence 34555677777777765310 0 00 1123578888899999999999999999999999999984
No 27
>TIGR03761 ICE_PFL4669 integrating conjugative element protein, PFL_4669 family. Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens.
Probab=72.11 E-value=30 Score=27.07 Aligned_cols=58 Identities=10% Similarity=0.169 Sum_probs=43.2
Q ss_pred hhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHh
Q 031712 84 SSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVKNKLETLFRMEQQIVA 142 (154)
Q Consensus 84 ss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~~ 142 (154)
-.+.+|+..+...+..|...+.+.|+= +...+-+++..+..+...+++..++..+...
T Consensus 31 ~~~IiGl~~f~s~~~~i~~~a~~DdPy-AD~~Ll~~E~~l~~~~~~l~~~~~~l~~~l~ 88 (216)
T TIGR03761 31 KPGIIGMPGFISRLNRINQASEQDDPY-ADWALLRIEEKLLSARQEMQALLQRLDDLLA 88 (216)
T ss_pred CCCCcCcHHHHHHHHHHHHHHHcCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345899999999999999999876642 3446677777777777777777666666543
No 28
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=71.99 E-value=27 Score=26.33 Aligned_cols=50 Identities=10% Similarity=0.212 Sum_probs=24.2
Q ss_pred HHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHh-cCHhhHHHHHHH
Q 031712 59 DLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEE-QNIEGCMSCLQQ 118 (154)
Q Consensus 59 ~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~-~~~~~~~~~~~~ 118 (154)
.|..+-..+ |...+..+...++. ++..+...++.+... ++++.+...+..
T Consensus 106 ~lee~~~~~--d~~~L~~l~~e~~~--------~~~~~~~~l~~~~~~~~d~~~A~~~~~k 156 (176)
T PRK03578 106 AIEDARAAR--DVDALDALLAELRD--------ERRERYAELGALLDSRGDDQAAAEAVRQ 156 (176)
T ss_pred HHHHhhccC--CHHHHHHHHHHHHH--------HHHHHHHHHHHHHHccccHHHHHHHHHH
Confidence 333343445 66666666666543 334444444444443 555544443333
No 29
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=71.10 E-value=28 Score=30.20 Aligned_cols=67 Identities=18% Similarity=0.096 Sum_probs=56.1
Q ss_pred CHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHh
Q 031712 38 NPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIE 110 (154)
Q Consensus 38 ~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~ 110 (154)
+++-....++.|+++.-..+..-+.|+... |+- +-|++-+.+-|+|+..=.++|+..+.+-+.++..
T Consensus 226 tr~~A~~~L~~Fi~~~L~nFG~yQDam~~d--~~~----L~HSllS~alNigLL~PleVi~Aa~~Ay~~g~ip 292 (505)
T COG3046 226 TRTQALRALKHFIADRLPNFGSYQDAMSAD--DPH----LWHSLLSFALNIGLLTPLEVIRAALKAYREGDIP 292 (505)
T ss_pred CHHHHHHHHHHHHHHhhhcCCcHHHHHhcC--Cch----hHHHHHHHHhhccCCCHHHHHHHHHHhhccCCCc
Confidence 556667889999999877777777888777 544 8999999999999999999999999998886543
No 30
>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm
Probab=69.52 E-value=63 Score=26.64 Aligned_cols=103 Identities=16% Similarity=0.236 Sum_probs=65.4
Q ss_pred HHHHHHHHHHHhhhhhhchHHHHHHHHhhhccCCHHHHHHHHHHHH-HhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhh
Q 031712 5 QMQRRLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFF-ADSERLLNDLTRALDQPTIDFKMVDSHVHQLKG 83 (154)
Q Consensus 5 ~~~~~~~~~~~~~~~~~ild~~~~~L~~L~~~~~~~~~~~ll~~Fl-~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKG 83 (154)
.+|.+|.+-+..-+-..-|++++..+..+ |......++...|- .+-.-..-.++..+..+ +|+++...+.+=|+
T Consensus 162 ~~Q~~Le~~~~~~f~~~Sl~~Ti~~li~~---~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~--~w~eL~~fa~skKs 236 (319)
T PF04840_consen 162 EYQKELEEKYNTNFVGLSLNDTIRKLIEM---GQEKQAEKLKKEFKVPDKRFWWLKIKALAENK--DWDELEKFAKSKKS 236 (319)
T ss_pred HHHHHHHHHhccchhcCCHHHHHHHHHHC---CCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcC--CHHHHHHHHhCCCC
Confidence 34555554444333334455555555444 55677778887772 33333566788889999 99999999987554
Q ss_pred hhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHH
Q 031712 84 SSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQ 121 (154)
Q Consensus 84 ss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~ 121 (154)
-+|..++++.|-. .++...+...++.+..
T Consensus 237 ---PIGyepFv~~~~~------~~~~~eA~~yI~k~~~ 265 (319)
T PF04840_consen 237 ---PIGYEPFVEACLK------YGNKKEASKYIPKIPD 265 (319)
T ss_pred ---CCChHHHHHHHHH------CCCHHHHHHHHHhCCh
Confidence 5999999999964 2334445555555443
No 31
>PF05757 PsbQ: Oxygen evolving enhancer protein 3 (PsbQ); InterPro: IPR008797 Oxygenic photosynthesis uses two multi-subunit photosystems (I and II) located in the cell membranes of cyanobacteria and in the thylakoid membranes of chloroplasts in plants and algae. Photosystem II (PSII) has a P680 reaction centre containing chlorophyll 'a' that uses light energy to carry out the oxidation (splitting) of water molecules, and to produce ATP via a proton pump. Photosystem I (PSI) has a P700 reaction centre containing chlorophyll that takes the electron and associated hydrogen donated from PSII to reduce NADP+ to NADPH. Both ATP and NADPH are subsequently used in the light-independent reactions to convert carbon dioxide to glucose using the hydrogen atom extracted from water by PSII, releasing oxygen as a by-product. PSII is a multisubunit protein-pigment complex containing polypeptides both intrinsic and extrinsic to the photosynthetic membrane [, ]. Within the core of the complex, the chlorophyll and beta-carotene pigments are mainly bound to the antenna proteins CP43 (PsbC) and CP47 (PsbB), which pass the excitation energy on to the reaction centre proteins D1 (Qb, PsbA) and D2 (Qa, PsbD) that bind all the redox-active cofactors involved in the energy conversion process. The PSII oxygen-evolving complex (OEC) oxidises water to provide protons for use by PSI, and consists of OEE1 (PsbO), OEE2 (PsbP) and OEE3 (PsbQ). The remaining subunits in PSII are of low molecular weight (less than 10 kDa), and are involved in PSII assembly, stabilisation, dimerisation, and photo-protection []. In PSII, the oxygen-evolving complex (OEC) is responsible for catalysing the splitting of water to O(2) and 4H+. The OEC is composed of a cluster of manganese, calcium and chloride ions bound to extrinsic proteins. In cyanobacteria there are five extrinsic proteins in OEC (PsbO, PsbP-like, PsbQ-like, PsbU and PsbV), while in plants there are only three (PsbO, PsbP and PsbQ), PsbU and PsbV having been lost during the evolution of green plants []. This family represents the PSII OEC protein PsbQ. Both PsbQ and PsbP (IPR002683 from INTERPRO) are regulators that are necessary for the biogenesis of optically active PSII. The crystal structure of PsbQ from spinach revealed a 4-helical bundle polypeptide. The distribution of positive and negative charges on the protein surface might explain the ability of PsbQ to increase the binding of chloride and calcium ions and make them available to PSII [].; GO: 0005509 calcium ion binding, 0015979 photosynthesis, 0009523 photosystem II, 0009654 oxygen evolving complex, 0019898 extrinsic to membrane; PDB: 1VYK_A 1NZE_A 3LS1_A 3LS0_A.
Probab=68.05 E-value=27 Score=27.09 Aligned_cols=75 Identities=13% Similarity=0.138 Sum_probs=47.3
Q ss_pred HHhHHHHHHHHHHHhcCCCCCHHHHHHHHHH--------hhhhhhhhc----------HHHHHHHHHHHHHHHHhcCHhh
Q 031712 50 FADSERLLNDLTRALDQPTIDFKMVDSHVHQ--------LKGSSSSIG----------AERIKNACVAFRNFCEEQNIEG 111 (154)
Q Consensus 50 l~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~--------LKGss~~lG----------a~~L~~~~~~lE~~~~~~~~~~ 111 (154)
+.++.+.|..++..++.. .|..+....|. |+......+ +..|+.-..+|..+++..+...
T Consensus 105 ik~sa~~L~~lk~lIdk~--sW~~v~~~LRlka~~Lr~DL~~liss~p~~~kk~l~~La~~lf~~ie~LD~Aar~K~~~~ 182 (202)
T PF05757_consen 105 IKESAKRLLSLKELIDKK--SWPYVRNYLRLKAGYLRYDLNTLISSKPKDEKKALTDLANKLFDNIEELDYAARSKDVPE 182 (202)
T ss_dssp HHHHHHHHCCCHHHHHTT---HHHHHHHHHCCCCCHHHHHHHHHCCS-HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHH
T ss_pred HHHHHHHHHHHHHHHhhc--cHHHHHHHHHHHHhHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH
Confidence 466777888888999998 99999888875 222222222 2556777777778888777665
Q ss_pred HHHHHHHHHHHHHHH
Q 031712 112 CMSCLQQVKQEYCLV 126 (154)
Q Consensus 112 ~~~~~~~l~~~~~~l 126 (154)
+..++......++.+
T Consensus 183 a~~~Y~~t~~~Ldev 197 (202)
T PF05757_consen 183 AEKYYADTVKALDEV 197 (202)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 555555444444443
No 32
>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt
Probab=65.52 E-value=35 Score=22.50 Aligned_cols=57 Identities=14% Similarity=0.177 Sum_probs=38.0
Q ss_pred HHHHHHHhhhhhhchHHHHHHHHhhhc-cCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCC
Q 031712 9 RLLEYTKSLFMEGVLDNQFLQLQQLQD-ESNPDFVAEVVSLFFADSERLLNDLTRALDQP 67 (154)
Q Consensus 9 ~~~~~~~~~~~~~ild~~~~~L~~L~~-~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~ 67 (154)
++.+.|..++.+||+... ....+.. ....+-..++++...+-.+.-+...-.++...
T Consensus 17 ~~~~v~~~L~~~~Vlt~~--~~e~I~~~~tr~~q~~~LLd~L~~RG~~AF~~F~~aL~~~ 74 (84)
T cd08326 17 QPKYLWDHLLSRGVFTPD--MIEEIQAAGSRRDQARQLLIDLETRGKQAFPAFLSALRET 74 (84)
T ss_pred CHHHHHHHHHhcCCCCHH--HHHHHHcCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHhc
Confidence 356778888888888853 3333333 45566677777777777777777776666544
No 33
>TIGR00984 3a0801s03tim44 mitochondrial import inner membrane, translocase subunit. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tim proteins.
Probab=62.35 E-value=18 Score=30.70 Aligned_cols=81 Identities=10% Similarity=0.213 Sum_probs=55.7
Q ss_pred HHHHHHHHhhhhhhchHHHHHHHHhhhccCCHHHHHHHHHHHHHhHHHH-HHHHHHHhcCCCCCHHHHHHHHHHhhhhhh
Q 031712 8 RRLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERL-LNDLTRALDQPTIDFKMVDSHVHQLKGSSS 86 (154)
Q Consensus 8 ~~~~~~~~~~~~~~ild~~~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~-l~~L~~a~~~~~~D~~~l~~~aH~LKGss~ 86 (154)
.++....-+++.+.=+...+.+|..+ ||.|- +..|+...... +..+-.|+..+ |.+.|+.+++.
T Consensus 212 dkv~~~~~~lF~ete~a~~l~eIk~~----DPsFd---~~~Fl~gar~aI~p~ILeAf~kG--D~e~LK~~lse------ 276 (378)
T TIGR00984 212 DKIGGVFSGMFSETEVSEVLTEFKKI----DPTFD---KEHFLRFLREYIVPEILEAYVKG--DLEVLKSWCSE------ 276 (378)
T ss_pred hhhhhhhhcccCCCHHHHHHHHHHHh----CCCCC---HHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHhhCH------
Confidence 34444455566666666656666554 56665 67899999888 79999999999 99999988765
Q ss_pred hhcHHHHHHHHHHHHHHHHhc
Q 031712 87 SIGAERIKNACVAFRNFCEEQ 107 (154)
Q Consensus 87 ~lGa~~L~~~~~~lE~~~~~~ 107 (154)
......|..|+....+|
T Consensus 277 ----~vy~~f~a~I~qr~~~G 293 (378)
T TIGR00984 277 ----APFSVYATVVKEYKKMG 293 (378)
T ss_pred ----HHHHHHHHHHHHHHHCC
Confidence 33444556666555544
No 34
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=61.68 E-value=64 Score=24.07 Aligned_cols=62 Identities=11% Similarity=0.207 Sum_probs=29.9
Q ss_pred HHHHhHHHHHHHHHHHhcCCCCCH-HHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHH
Q 031712 48 LFFADSERLLNDLTRALDQPTIDF-KMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQV 119 (154)
Q Consensus 48 ~Fl~~~~~~l~~L~~a~~~~~~D~-~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l 119 (154)
.|+-+.-+.-++|..+-... |. ..+..+...++. .+..+...++.....++++.+...+..+
T Consensus 90 efLme~me~rE~le~~~~~~--d~~~~l~~l~~~~~~--------~~~~~~~~l~~~~~~~d~~~A~~~~~~L 152 (171)
T PRK05014 90 AFLMEQMELREELEDIEQSK--DPEAALESFIKRVKK--------MFKTRLQQMVEQLDNEAWDAAADTVRKL 152 (171)
T ss_pred HHHHHHHHHHHHHHhhcccc--CHHHHHHHHHHHHHH--------HHHHHHHHHHHHHhhCCHHHHHHHHHHH
Confidence 33333334445555554444 52 335566655543 3344445555555555666555444333
No 35
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=56.16 E-value=46 Score=26.61 Aligned_cols=73 Identities=7% Similarity=-0.042 Sum_probs=42.5
Q ss_pred hhhhhhhhcHHH--HHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHHH----HHHHHHHhhhhHHhhcCCCCccccC
Q 031712 81 LKGSSSSIGAER--IKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVKN----KLETLFRMEQQIVAAGGSIPMMELS 153 (154)
Q Consensus 81 LKGss~~lGa~~--L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~----~L~~~l~~~~~~~~~~~~~~~~~~~ 153 (154)
.-|+.|.++... +-+.+.++=++.++++.+.+..+...+......... ..-+++...+++..-.++.|...++
T Consensus 196 ~~G~~G~is~~~n~~P~~~~~l~~~~~~gd~~~a~~l~~~l~~~~~~~~~~~~~~~~K~~l~~~G~~~g~~R~P~~~l~ 274 (292)
T PRK03170 196 ALGGVGVISVAANVAPKEMAEMCDAALAGDFAEAREIHRRLLPLHKALFIEPNPIPVKAALNLLGLIEGELRLPLVPLS 274 (292)
T ss_pred HcCCCEEEEhHHhhhHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhccCCcHHHHHHHHHcCCCCCCCCCCCCCCC
Confidence 346666665533 668888888888999888766655555443322211 1123333445554433777887664
No 36
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=55.71 E-value=81 Score=23.24 Aligned_cols=79 Identities=18% Similarity=0.184 Sum_probs=38.0
Q ss_pred HHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHH
Q 031712 46 VSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCL 125 (154)
Q Consensus 46 l~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~ 125 (154)
-...++|..++|.-|...+.++ ++..- ...+|.--+..|-... +..+.+|-......+.+++..++-.++..+..
T Consensus 63 ~kr~~~D~~KRL~iLfd~ln~g--~Ls~~--v~~~L~~L~~aL~~~d-~~~A~~Ih~~L~t~h~~E~~~WmvGVKRLI~~ 137 (157)
T PF07304_consen 63 KKRVVDDIEKRLNILFDHLNNG--KLSKP--VVDKLHQLAQALQARD-YDAADEIHVDLMTDHVDECGNWMVGVKRLIAM 137 (157)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHT---S-HH--HHHHHHHHHHHHHHT--HHHHHHHHHHHHHSSHHHHTTTHHHHHHHHHH
T ss_pred chhHHHHHHHHHHHHHHHHhcC--CCCHH--HHHHHHHHHHHHHcCC-HHHHHHHHHHHHhccHHHhhhHHHHHHHHHHH
Confidence 3445678888888888888877 43221 1222222233333333 33333444334444444555555555554444
Q ss_pred HHHH
Q 031712 126 VKNK 129 (154)
Q Consensus 126 l~~~ 129 (154)
++..
T Consensus 138 ~r~~ 141 (157)
T PF07304_consen 138 ARNL 141 (157)
T ss_dssp HHHH
T ss_pred HHhc
Confidence 4443
No 37
>PHA01929 putative scaffolding protein
Probab=55.47 E-value=59 Score=26.41 Aligned_cols=54 Identities=13% Similarity=0.167 Sum_probs=39.3
Q ss_pred cCCHHHHHHHHHHHHHhHHHHH-HHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHH
Q 031712 36 ESNPDFVAEVVSLFFADSERLL-NDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAE 91 (154)
Q Consensus 36 ~~~~~~~~~ll~~Fl~~~~~~l-~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~ 91 (154)
.|+.+.+..-.+.|-+..+... ..+...++++ |...+...+-.+-+-+...|+.
T Consensus 198 ~GGee~w~qAa~vFn~kAd~~~r~ai~~L~nSG--d~~~mk~AAk~V~~FA~~sG~v 252 (306)
T PHA01929 198 VGGEAVWKQAAGLFNQKADPATRAAIGRLMNSG--DAQAMQYAAKQVAAFAQGSGAV 252 (306)
T ss_pred cccHHHHHHHHHHHHhcCCHHHHHHHHHHHccc--hHHHHHHHHHHHHHHHHhcCce
Confidence 5678888888888888876644 4567777888 8888887777776666665554
No 38
>PF09537 DUF2383: Domain of unknown function (DUF2383); InterPro: IPR019052 This entry represents a functionally uncharacterised ferritin like domain.; PDB: 3FSE_B.
Probab=53.25 E-value=67 Score=21.59 Aligned_cols=48 Identities=17% Similarity=0.099 Sum_probs=30.6
Q ss_pred HHHHHHhcCHhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHhhcCCC
Q 031712 100 FRNFCEEQNIEGCMSCLQQVKQEYCLVKNKLETLFRMEQQIVAAGGSI 147 (154)
Q Consensus 100 lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~~~~~~~ 147 (154)
.+.++..-....+...+..+.....+....|+.++...+..++.+++.
T Consensus 20 Y~~a~~~~~~~~lk~~f~~~~~~~~~~~~~L~~~i~~~Gg~p~~~gs~ 67 (111)
T PF09537_consen 20 YEKAAEKAEDPELKSLFQEFAQERQQHAEELQAEIQELGGEPEESGSF 67 (111)
T ss_dssp HHHHHHH--SHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--H----HH
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcccCH
Confidence 334444333356788899999999999999999999998888766543
No 39
>PF06367 Drf_FH3: Diaphanous FH3 Domain; InterPro: IPR010472 Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of the cell cortex including motility, adhesion, and cytokinesis []. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain (IPR003104 from INTERPRO) is required to inhibit actin polymerisation. The FH3 domain is less well conserved and is required for directing formins to the correct intracellular location, such the mitotic spindle [], or the projection tip during conjugation []. In addition, some formins can contain a GTPase-binding domain (GBD) (IPR010473 from INTERPRO) required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD). This entry represents the FH3 domain.; GO: 0003779 actin binding, 0016043 cellular component organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=52.11 E-value=91 Score=23.17 Aligned_cols=47 Identities=23% Similarity=0.382 Sum_probs=30.6
Q ss_pred HHhhhhhhchHHHHHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhc
Q 031712 14 TKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALD 65 (154)
Q Consensus 14 ~~~~~~~~ild~~~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~ 65 (154)
..-+...|+.+ .+..|..-.++. +..-++.|.+...++...+....+
T Consensus 65 r~e~~~~GL~~----il~~l~~~~~~~-L~~Qi~~f~~~~~~D~~el~~~~~ 111 (197)
T PF06367_consen 65 RNEFERLGLLD----ILEKLRNLEDDD-LQEQIDIFEENEEEDEEELLERFD 111 (197)
T ss_dssp HHHHHHTTHHH----HHHHHTTS--HH-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHCCcHH----HHHHHHhcchHH-HHHHHHHHHHHHHhhHHHHHHhhc
Confidence 34455666665 555555554444 445599999999888888877554
No 40
>PF14615 Rsa3: Ribosome-assembly protein 3
Probab=51.03 E-value=43 Score=19.73 Aligned_cols=39 Identities=15% Similarity=0.129 Sum_probs=25.9
Q ss_pred HHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhh
Q 031712 46 VSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSS 87 (154)
Q Consensus 46 l~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~ 87 (154)
+....++-.+++++|+.+-.- .-..+.-++|.||+++..
T Consensus 7 l~~~t~efgdDLd~lR~~~dF---~~~sl~~Li~aL~~G~~~ 45 (47)
T PF14615_consen 7 LQRLTDEFGDDLDELRKAPDF---TDKSLPLLIDALQQGTDM 45 (47)
T ss_pred HHHHHHHHHHHHHHHhcCCCC---CchhHHHHHHHHHhcccc
Confidence 444445555667778754333 347799999999987654
No 41
>PF11553 DUF3231: Protein of unknown function (DUF3231); InterPro: IPR021617 This bacterial family of proteins has no known function. ; PDB: 2RBD_B.
Probab=48.31 E-value=97 Score=22.59 Aligned_cols=73 Identities=15% Similarity=0.020 Sum_probs=36.0
Q ss_pred CHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHhhcCCCCc
Q 031712 70 DFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVKNKLETLFRMEQQIVAAGGSIPM 149 (154)
Q Consensus 70 D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~~~~~~~~~ 149 (154)
+..++..+-+.+....-++. .+...-+.++ ..+++.++....+....-...|+..+..++-+.|.||..+-
T Consensus 15 ~~~Ei~~Lw~~~~~~~~~~~------~~~~f~~~~~---D~dik~~l~~~~~~~~~~i~~l~~ll~~e~ip~P~~~~~~~ 85 (166)
T PF11553_consen 15 NASEIGNLWNNYMANYMSIC------LLQYFLQVAE---DKDIKKLLKKGLDLSQKQIEQLEKLLKEEGIPVPPGFPESD 85 (166)
T ss_dssp BHHHHHHHHHHHHHHHHHHH------HHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-----------
T ss_pred CHHHHHHHHHHHHHHHHHHH------HHHHHHHHcC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCcccc
Confidence 44556666665544433322 2222233333 34577777777788888888899999999999999997655
Q ss_pred cc
Q 031712 150 ME 151 (154)
Q Consensus 150 ~~ 151 (154)
|.
T Consensus 86 v~ 87 (166)
T PF11553_consen 86 VT 87 (166)
T ss_dssp --
T ss_pred cC
Confidence 54
No 42
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=47.95 E-value=27 Score=28.12 Aligned_cols=49 Identities=16% Similarity=0.197 Sum_probs=37.7
Q ss_pred HHHHHHHHHhhhhhhchHHHHHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhcC
Q 031712 7 QRRLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQ 66 (154)
Q Consensus 7 ~~~~~~~~~~~~~~~ild~~~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~ 66 (154)
++++.+..+-+..++.||+ +-.+++.++.+.|+++.-.....|...=..
T Consensus 157 k~kl~dLvqqId~~~~LD~-----------dVedlLleiADdFV~sii~~sC~LAKHRKs 205 (258)
T KOG1142|consen 157 KRKLDDLVQQIDGTTKLDD-----------DVEDLLLEIADDFVSSIIHRSCKLAKHRKS 205 (258)
T ss_pred ccchhHHHHhhcCcccccH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 5678888888888888885 124778899999999998877777665444
No 43
>KOG2280 consensus Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport]
Probab=46.17 E-value=1.5e+02 Score=27.72 Aligned_cols=83 Identities=17% Similarity=0.163 Sum_probs=56.4
Q ss_pred HHHhhhccCCHHHHHHHHHHHH-HhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhc
Q 031712 29 QLQQLQDESNPDFVAEVVSLFF-ADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQ 107 (154)
Q Consensus 29 ~L~~L~~~~~~~~~~~ll~~Fl-~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~ 107 (154)
.+.+|...|...-+.++-..|- .+-.-..-.+......+ ||+++...|-+-|+ -+|...+.+.|-. .+
T Consensus 690 Tv~~li~~g~~k~a~ql~~~FkipdKr~~wLk~~aLa~~~--kweeLekfAkskks---PIGy~PFVe~c~~------~~ 758 (829)
T KOG2280|consen 690 TVTTLILIGQNKRAEQLKSDFKIPDKRLWWLKLTALADIK--KWEELEKFAKSKKS---PIGYLPFVEACLK------QG 758 (829)
T ss_pred HHHHHHHccchHHHHHHHHhcCCcchhhHHHHHHHHHhhh--hHHHHHHHHhccCC---CCCchhHHHHHHh------cc
Confidence 4445555566677778777774 33333445667777888 99999999988776 7999999998864 44
Q ss_pred CHhhHHHHHHHHHHH
Q 031712 108 NIEGCMSCLQQVKQE 122 (154)
Q Consensus 108 ~~~~~~~~~~~l~~~ 122 (154)
+.+++...++.+...
T Consensus 759 n~~EA~KYiprv~~l 773 (829)
T KOG2280|consen 759 NKDEAKKYIPRVGGL 773 (829)
T ss_pred cHHHHhhhhhccCCh
Confidence 555555555554443
No 44
>PF07014 Hs1pro-1_C: Hs1pro-1 protein C-terminus; InterPro: IPR009743 This entry represents the C terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance [].
Probab=44.88 E-value=1.6e+02 Score=23.44 Aligned_cols=65 Identities=12% Similarity=0.223 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHH
Q 031712 40 DFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSC 115 (154)
Q Consensus 40 ~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~ 115 (154)
-...++++..+.-+.+.+..+...++++ +++..+.-++.+ .++-++..++|..-.--|.+++..+
T Consensus 53 ~t~hQIlEsWi~~a~~LL~ri~~~i~~~--~~ekAa~dc~~v---------ERiWKLL~eieDlhllMDPdDFlrL 117 (261)
T PF07014_consen 53 HTTHQILESWIHVARKLLERIEERIEAR--DFEKAASDCWIV---------ERIWKLLAEIEDLHLLMDPDDFLRL 117 (261)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcc--cHHHHHhHHHHH---------HHHHHHHHHHHHHHHhcCHHHHHHH
Confidence 3467889999999999999999999999 999999999874 6888999999988877777765443
No 45
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. 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 PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=44.74 E-value=77 Score=19.80 Aligned_cols=58 Identities=12% Similarity=0.320 Sum_probs=38.0
Q ss_pred HHHHHHHHhhhhhhchHHHHHHHHhhhc-cCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCC
Q 031712 8 RRLLEYTKSLFMEGVLDNQFLQLQQLQD-ESNPDFVAEVVSLFFADSERLLNDLTRALDQP 67 (154)
Q Consensus 8 ~~~~~~~~~~~~~~ild~~~~~L~~L~~-~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~ 67 (154)
..+..++..+...+++... ....+.. ....+-..++++......+.....+-.++...
T Consensus 13 ~~~~~il~~L~~~~vlt~~--e~~~i~~~~~~~~k~~~Lld~l~~kg~~af~~F~~~L~~~ 71 (80)
T cd01671 13 LDVEDVLDHLLSDGVLTEE--EYEKIRSESTRQDKARKLLDILPRKGPKAFQSFLQALQET 71 (80)
T ss_pred ccHHHHHHHHHHcCCCCHH--HHHHHHcCCChHHHHHHHHHHHHhcChHHHHHHHHHHHhc
Confidence 3556677778888888853 3334433 33566777777777777777777777777655
No 46
>PF06248 Zw10: Centromere/kinetochore Zw10; InterPro: IPR009361 Zeste white 10 (ZW10) was initially identified as a mitotic checkpoint protein involved in chromosome segregation, and then implicated in targeting cytoplasmic dynein and dynactin to mitotic kinetochores, but it is also important in non-dividing cells. These include cytoplasmic dynein targeting to Golgi and other membranes, and SNARE-mediated ER-Golgi trafficking [, ]. Dominant-negative ZW10, anti-ZW10 antibody, and ZW10 RNA interference (RNAi) cause Golgi dispersal. ZW10 RNAi also disperse endosomes and lysosomes []. Drosophila kinetochore components Rough deal (Rod) and Zw10 are required for the proper functioning of the metaphase checkpoint in flies []. The eukaryotic spindle assembly checkpoint (SAC) monitors microtubule attachment to kinetochores and prevents anaphase onset until all kinetochores are aligned on the metaphase plate. It is an essential surveillance mechanism that ensures high fidelity chromosome segregation during mitosis. In higher eukaryotes, cytoplasmic dynein is involved in silencing the SAC by removing the checkpoint proteins Mad2 and the Rod-Zw10-Zwilch complex (RZZ) from aligned kinetochores [, , ].; GO: 0007067 mitosis, 0000775 chromosome, centromeric region, 0005634 nucleus
Probab=44.45 E-value=2.3e+02 Score=25.21 Aligned_cols=20 Identities=25% Similarity=0.433 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 031712 114 SCLQQVKQEYCLVKNKLETL 133 (154)
Q Consensus 114 ~~~~~l~~~~~~l~~~L~~~ 133 (154)
..+..|+.+|...+..|...
T Consensus 150 ~i~~~Lk~e~~~lr~~L~~~ 169 (593)
T PF06248_consen 150 KILKLLKDEYSELRENLQYQ 169 (593)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 45666666666555554433
No 47
>PRK15178 Vi polysaccharide export inner membrane protein VexD; Provisional
Probab=40.23 E-value=1.5e+02 Score=25.81 Aligned_cols=57 Identities=11% Similarity=0.043 Sum_probs=43.3
Q ss_pred HHHHHHHHhhhhhhchHHHHHHHHhhhc-cCCHHHHHHHHHHHHHhHHHHHHHHHHHhcC
Q 031712 8 RRLLEYTKSLFMEGVLDNQFLQLQQLQD-ESNPDFVAEVVSLFFADSERLLNDLTRALDQ 66 (154)
Q Consensus 8 ~~~~~~~~~~~~~~ild~~~~~L~~L~~-~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~ 66 (154)
+.+.+||+..++-.+... +.|..|.. .-+|+.-..+-...+..+++.++.|..-...
T Consensus 184 E~l~~Yy~~~V~V~~D~~--sGIi~l~V~AF~PedA~~ia~aLL~~sE~~VN~Ls~rar~ 241 (434)
T PRK15178 184 DDPYRYYLSKVSVAVDIQ--QGMLRLNVKARSAKQAEFFAQRILSFAEQHVNTVSARMQK 241 (434)
T ss_pred HHHHHHHHhceEEeecCC--CCeEEEEEEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467788888887777664 24555555 5689999999999999999999998776644
No 48
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=37.92 E-value=94 Score=19.09 Aligned_cols=37 Identities=27% Similarity=0.445 Sum_probs=27.9
Q ss_pred HHHHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHH
Q 031712 25 NQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTR 62 (154)
Q Consensus 25 ~~~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~ 62 (154)
++|.+++++-.. +|+.+..++...-.+.|..+..|..
T Consensus 8 Pqf~~lR~~vq~-NP~lL~~lLqql~~~nP~l~q~I~~ 44 (59)
T PF09280_consen 8 PQFQQLRQLVQQ-NPQLLPPLLQQLGQSNPQLLQLIQQ 44 (59)
T ss_dssp HHHHHHHHHHHC--GGGHHHHHHHHHCCSHHHHHHHHH
T ss_pred hHHHHHHHHHHH-CHHHHHHHHHHHhccCHHHHHHHHH
Confidence 456677776544 7899999999988888888877766
No 49
>PRK03057 hypothetical protein; Provisional
Probab=37.88 E-value=1.2e+02 Score=23.00 Aligned_cols=36 Identities=22% Similarity=0.337 Sum_probs=26.9
Q ss_pred HHHHHHh------HHHHHHHHHHHhcCCCCCHHHHHHHHHHhhh
Q 031712 46 VSLFFAD------SERLLNDLTRALDQPTIDFKMVDSHVHQLKG 83 (154)
Q Consensus 46 l~~Fl~~------~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKG 83 (154)
++.|++. -.....+|..|++.+ |.+...++++.|+-
T Consensus 133 ae~~L~~~~~~~~~~~L~~~ID~ALd~~--D~e~F~~Lt~~L~~ 174 (180)
T PRK03057 133 TEQVLDEVLKRNEVSRLRMQIDQALDRK--DMEEFQRLTEKLKK 174 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHHH
Confidence 4455554 455778899999999 99888888877753
No 50
>PRK03636 hypothetical protein; Provisional
Probab=37.73 E-value=1.3e+02 Score=22.74 Aligned_cols=29 Identities=28% Similarity=0.414 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHhhh
Q 031712 53 SERLLNDLTRALDQPTIDFKMVDSHVHQLKG 83 (154)
Q Consensus 53 ~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKG 83 (154)
-.+.+.+|..|++.+ |.+...+++..||-
T Consensus 147 ~~~L~~~ID~ALd~~--D~e~F~~Ls~~l~~ 175 (179)
T PRK03636 147 REKLLKQIDEALDRR--DKEAFHRLSDELNQ 175 (179)
T ss_pred HHHHHHHHHHHHHcC--CHHHHHHHHHHHHH
Confidence 355788999999999 99998888887763
No 51
>TIGR02284 conserved hypothetical protein. Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.
Probab=37.56 E-value=1.2e+02 Score=21.59 Aligned_cols=38 Identities=11% Similarity=0.121 Sum_probs=30.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHhhcCCC
Q 031712 110 EGCMSCLQQVKQEYCLVKNKLETLFRMEQQIVAAGGSI 147 (154)
Q Consensus 110 ~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~~~~~~~ 147 (154)
..+...+..+...-.+....|+..+...++.++.+|+.
T Consensus 29 ~~lk~~f~~~~~~~~~~~~eL~~~v~~lGg~p~~~gs~ 66 (139)
T TIGR02284 29 PELATLFRRIAGEKSAIVSELQQVVASLGGKPEDHGSM 66 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCcH
Confidence 46778888888888888888888888888877776654
No 52
>PF11563 Protoglobin: Protoglobin; PDB: 2VEE_G 3QZZ_A 3R0G_A 3QZX_A 2VEB_A 1OR6_A 1OR4_B 2W31_B.
Probab=36.94 E-value=1.5e+02 Score=20.88 Aligned_cols=54 Identities=7% Similarity=0.049 Sum_probs=35.3
Q ss_pred chhHHHHHHHHHHHhhhhhhchHHHHHHHHhhhc-----cCCHHHHHHHHHHHHHhHHH
Q 031712 2 EVGQMQRRLLEYTKSLFMEGVLDNQFLQLQQLQD-----ESNPDFVAEVVSLFFADSER 55 (154)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~ild~~~~~L~~L~~-----~~~~~~~~~ll~~Fl~~~~~ 55 (154)
.+..|+....+||..+++.++.++-+.....+.. +-++.++......+.+...+
T Consensus 59 ~~~~lk~~q~~~~~~l~s~~~d~~y~~~~~~iG~~H~~igl~~~~~~~~~~~~~~~l~~ 117 (158)
T PF11563_consen 59 TIERLKATQRRHWRELFSGDFDEEYVERRRRIGQVHARIGLPPRWYIGAYSFLREFLLE 117 (158)
T ss_dssp CHHHHHHHHHHHHHHCTSS-CSHHHHHHHHHHHHHHHHCT--HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHHhHcCCCHHHHHHHHHHHHHHHHH
Confidence 4678999999999999888876665666555544 55667776665555555433
No 53
>PF08637 NCA2: ATP synthase regulation protein NCA2; InterPro: IPR013946 NCA2 (Nuclear Control of ATPase), is one of the two nuclear genes involved in the control of mitochondrial expression of subunits 6 and 8 of the Fo-F1 ATP synthase in Saccharomyces cerevisiae (Baker's yeast). Mutations in either NCA2 or NCA3 (IPR005556 from INTERPRO) dramatically lower the level of the co-transcript encoding subunits 6 and 8 [, ].
Probab=36.76 E-value=2.3e+02 Score=23.05 Aligned_cols=64 Identities=17% Similarity=0.223 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHhhhhhhchHHHHHHHHhhhcc--------------CCHHHHHHHHHHHHHhHH----HHHHHHHHHhcC
Q 031712 5 QMQRRLLEYTKSLFMEGVLDNQFLQLQQLQDE--------------SNPDFVAEVVSLFFADSE----RLLNDLTRALDQ 66 (154)
Q Consensus 5 ~~~~~~~~~~~~~~~~~ild~~~~~L~~L~~~--------------~~~~~~~~ll~~Fl~~~~----~~l~~L~~a~~~ 66 (154)
+..+-+..||.+-+=+|+-+ .+.+|..+ .+.+-+.+|+..|..|+. ..++.|...+..
T Consensus 30 ~~~~t~~~f~~nwV~~Pl~~----I~~tlr~d~~s~~~i~s~~sL~~d~~SLeRMv~dF~~d~~~~~~~~~~~l~~~v~~ 105 (290)
T PF08637_consen 30 NAVETVRGFWKNWVWEPLKS----IWDTLRHDEKSEIAIMSKESLQSDMESLERMVVDFAKDNSPNMPADLEELRQQVRE 105 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHH----HHHHHhCCCCCCcccccHHHHHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHc
Confidence 44455556666555555444 44444432 255678899999999986 468899999999
Q ss_pred CCCCHHHH
Q 031712 67 PTIDFKMV 74 (154)
Q Consensus 67 ~~~D~~~l 74 (154)
| |...+
T Consensus 106 G--dlt~V 111 (290)
T PF08637_consen 106 G--DLTPV 111 (290)
T ss_pred C--CcHHH
Confidence 9 87553
No 54
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=36.50 E-value=78 Score=17.48 Aligned_cols=24 Identities=25% Similarity=0.263 Sum_probs=18.2
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHH
Q 031712 55 RLLNDLTRALDQPTIDFKMVDSHVHQ 80 (154)
Q Consensus 55 ~~l~~L~~a~~~~~~D~~~l~~~aH~ 80 (154)
.....|..|++.+ |.+....++..
T Consensus 13 ~L~~~ID~ALd~~--D~e~F~~Ls~e 36 (37)
T PF08858_consen 13 QLLELIDEALDNR--DKEWFYELSEE 36 (37)
T ss_dssp HHHHHHHHHHHTT---HHHHHHHHHH
T ss_pred HHHHHHHHHHHcC--CHHHHHHHHhh
Confidence 4778889999999 98888777654
No 55
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=35.70 E-value=77 Score=24.31 Aligned_cols=34 Identities=15% Similarity=0.317 Sum_probs=23.0
Q ss_pred hhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHH
Q 031712 86 SSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYC 124 (154)
Q Consensus 86 ~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~ 124 (154)
+++||..+.++|..|+. ++. .+...++.|-..|.
T Consensus 148 A~~Gaf~I~elcq~l~~--~s~---d~Ed~ideil~~~e 181 (195)
T KOG2424|consen 148 ATLGAFLILELCQCLQA--QSD---DLEDNIDEILLEFE 181 (195)
T ss_pred hhhhHHHHHHHHHHHHh--ccc---cHHHHHHHHHHHHH
Confidence 56999999999999986 232 34444555554443
No 56
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=35.59 E-value=1.3e+02 Score=19.93 Aligned_cols=36 Identities=22% Similarity=0.375 Sum_probs=23.9
Q ss_pred hcCHhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhHH
Q 031712 106 EQNIEGCMSCLQQVKQEYCLVKNKLETLFRMEQQIV 141 (154)
Q Consensus 106 ~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~~ 141 (154)
+...+.+..+++.|++--..+...|+.+++..||+-
T Consensus 32 ns~LD~Lns~LD~LE~rnD~l~~~L~~LLesnrq~R 67 (83)
T PF03670_consen 32 NSMLDQLNSCLDHLEQRNDHLHAQLQELLESNRQIR 67 (83)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence 344456666777777777777777777777666653
No 57
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=34.82 E-value=1.2e+02 Score=19.15 Aligned_cols=49 Identities=20% Similarity=0.260 Sum_probs=31.5
Q ss_pred HHHHHHHHHhhhhhhchHHHHHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhcC
Q 031712 7 QRRLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQ 66 (154)
Q Consensus 7 ~~~~~~~~~~~~~~~ild~~~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~ 66 (154)
++++.++.+.+.....+|+. -.+++.++.+.|+++.-.....|...=.+
T Consensus 2 K~~l~~Lv~~iDp~~~ld~~-----------vee~Ll~laddFv~~v~~~ac~lAKhR~s 50 (68)
T PF03847_consen 2 KRKLQELVKQIDPNEKLDPD-----------VEELLLELADDFVDDVVSFACRLAKHRKS 50 (68)
T ss_dssp HHHHHHHHHCC-SS----HH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred hHHHHHHHHHcCCCCCCCHH-----------HHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 56788888888777777752 13677788999999987777777665433
No 58
>KOG3192 consensus Mitochondrial J-type chaperone [Posttranslational modification, protein turnover, chaperones]
Probab=34.42 E-value=2e+02 Score=21.59 Aligned_cols=35 Identities=9% Similarity=0.093 Sum_probs=15.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 031712 42 VAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHV 78 (154)
Q Consensus 42 ~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~a 78 (154)
+..+=..--+...+..++|.+++++. +|.+.....
T Consensus 117 l~~lk~q~q~ri~q~~~qlge~~esk--~~~~Al~~i 151 (168)
T KOG3192|consen 117 LKQLKSQNQERIAQCKQQLGEAFESK--KYDEALKKI 151 (168)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc--cHHHHHHHH
Confidence 43433333334444444555555555 554444433
No 59
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. 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 PYRIN and
Probab=32.99 E-value=1.5e+02 Score=19.63 Aligned_cols=55 Identities=15% Similarity=0.159 Sum_probs=26.8
Q ss_pred HHHHHHhhhhhhchHHH-HHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhcC
Q 031712 10 LLEYTKSLFMEGVLDNQ-FLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQ 66 (154)
Q Consensus 10 ~~~~~~~~~~~~ild~~-~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~ 66 (154)
+.+-+..++.+||+.+. .+.|... ....+-...+++...+-++.-...+-.++..
T Consensus 22 ~~~v~~~L~~~gvlt~~~~~~I~~~--~t~~~k~~~Lld~L~~RG~~AF~~F~~aL~~ 77 (90)
T cd08332 22 LDELLIHLLQKDILTDSMAESIMAK--PTSFSQNVALLNLLPKRGPRAFSAFCEALRE 77 (90)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHcC--CCcHHHHHHHHHHHHHhChhHHHHHHHHHHh
Confidence 34445556666666642 3333322 2334455555555555555555555555544
No 60
>PF04722 Ssu72: Ssu72-like protein; InterPro: IPR006811 The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB []. It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs [].; GO: 0004721 phosphoprotein phosphatase activity, 0006397 mRNA processing, 0005634 nucleus; PDB: 3O2S_B 3O2Q_E 3FMV_H 3OMW_D 3P9Y_B 3FDF_A 3OMX_A.
Probab=32.72 E-value=82 Score=24.31 Aligned_cols=35 Identities=20% Similarity=0.354 Sum_probs=21.4
Q ss_pred hhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHH
Q 031712 86 SSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYC 124 (154)
Q Consensus 86 ~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~ 124 (154)
+.+|+..+.++|..||.. ...++ ...++.|-..|+
T Consensus 146 A~~Ga~~ileLc~~l~~~-~~~d~---e~~i~~il~~fe 180 (195)
T PF04722_consen 146 ATIGAFLILELCQMLEEE-ASEDL---EDEIDEILQEFE 180 (195)
T ss_dssp HHHHHHHHHHHHHHHH---TSSSH---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhh-ccccH---HHHHHHHHHHHH
Confidence 458999999999999962 22333 334444444443
No 61
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=30.82 E-value=1.6e+02 Score=23.22 Aligned_cols=70 Identities=14% Similarity=0.209 Sum_probs=41.1
Q ss_pred hhhhhhhcH--HHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHH-----HHHHHHHHhhhhHHhhc-CCCCccccC
Q 031712 82 KGSSSSIGA--ERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVK-----NKLETLFRMEQQIVAAG-GSIPMMELS 153 (154)
Q Consensus 82 KGss~~lGa--~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~-----~~L~~~l~~~~~~~~~~-~~~~~~~~~ 153 (154)
-|+.|.++. .-+.+.+..+-.+.++++.+.+..+...+.....-+. ..++..+.. +++ +.| ++.|...++
T Consensus 193 ~G~~G~i~~~~n~~p~~~~~~~~~~~~g~~~~a~~~~~~~~~~~~~~~~~~~~~~~K~~l~~-~G~-~~g~~R~P~~~l~ 270 (281)
T cd00408 193 LGADGAISGAANVAPKLAVALYEAARAGDLEEARALQDRLLPLIEALFKEGNPAPVKAALAL-LGL-DAGPVRLPLVPLS 270 (281)
T ss_pred cCCCEEEehHHhhCHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHHHH-cCC-CCCCcCCCCCCCC
Confidence 355455555 5667888888888888888776665555554433322 224444443 443 344 566876553
No 62
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.53 E-value=12 Score=24.33 Aligned_cols=20 Identities=35% Similarity=0.572 Sum_probs=17.0
Q ss_pred HHhhhhhhhhcHHHHHHHHH
Q 031712 79 HQLKGSSSSIGAERIKNACV 98 (154)
Q Consensus 79 H~LKGss~~lGa~~L~~~~~ 98 (154)
-++|||+|-+++-.+.+.|.
T Consensus 27 k~I~GSCGGi~alGi~K~Cd 46 (77)
T COG2991 27 KSIKGSCGGIAALGIEKVCD 46 (77)
T ss_pred cccccccccHHhhccchhcC
Confidence 36899999999988888876
No 63
>TIGR01220 Pmev_kin_Gr_pos phosphomevalonate kinase, ERG8-type, Gram-positive branch. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the animal type and this ERG8 type. This model represents the low GC Gram-positive organism forms of the ERG8 type of phosphomevalonate kinase.
Probab=30.37 E-value=2.8e+02 Score=22.98 Aligned_cols=56 Identities=16% Similarity=0.311 Sum_probs=38.2
Q ss_pred HHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhh------c--HHHHHHHHHHHHH
Q 031712 45 VVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSI------G--AERIKNACVAFRN 102 (154)
Q Consensus 45 ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~l------G--a~~L~~~~~~lE~ 102 (154)
..+.|++...+...++..++..+ |+..+.++.+.-.+.-..+ | -..+-+++...+.
T Consensus 246 ~~~~~l~~~~~i~~~~~~al~~~--d~~~lg~~~~~~~~lL~~l~~~~~~~vs~~~l~~li~~a~~ 309 (358)
T TIGR01220 246 SYQRFLETSTDCVESAITAFETG--DITSLQKEIRRNRQELARLDDEVGVGIETEKLKALCDAAEA 309 (358)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhC--CHHHHHHHHHHHHHHHHHhhcccCCCcCCHHHHHHHHHHhh
Confidence 35678888888999999999999 9988877666555544433 3 4455555544443
No 64
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=29.43 E-value=2.2e+02 Score=22.53 Aligned_cols=70 Identities=10% Similarity=0.078 Sum_probs=41.1
Q ss_pred hhhhhhhcHHH--HHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHH-----HHHHHHHHhhhhHHhhc-CCCCccccC
Q 031712 82 KGSSSSIGAER--IKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVK-----NKLETLFRMEQQIVAAG-GSIPMMELS 153 (154)
Q Consensus 82 KGss~~lGa~~--L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~-----~~L~~~l~~~~~~~~~~-~~~~~~~~~ 153 (154)
-|+.|.+.... +-+.+.++=.+..+++.+.+.++...+......+. ..++..+ ..+++ +.| ++.|...++
T Consensus 196 ~G~~G~~s~~~n~~p~~~~~~~~~~~~g~~~~a~~l~~~l~~~~~~~~~~~~~~~~K~~l-~~~G~-~~g~~R~P~~~l~ 273 (284)
T cd00950 196 LGGVGVISVAANVAPKLMAEMVRAALAGDLEKARELHRKLLPLIKALFAEPNPIPVKAAL-ALLGL-ISGELRLPLVPLS 273 (284)
T ss_pred CCCCEEEehHHHhhHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHH-HHcCC-CCCCCCCCCCCCC
Confidence 47666665444 66888888888888888776665555544332221 1233333 34454 455 466877654
No 65
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=29.33 E-value=1.1e+02 Score=17.04 Aligned_cols=56 Identities=13% Similarity=0.170 Sum_probs=28.0
Q ss_pred HHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHHHHHHHHHHh
Q 031712 73 MVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVKNKLETLFRM 136 (154)
Q Consensus 73 ~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~ 136 (154)
-+..++|.+|..-+.+. ..+..+.. ...+... ...+..+.....++...++..+..
T Consensus 5 ~~~~i~Hel~~pl~~i~-----~~~~~l~~--~~~~~~~-~~~~~~~~~~~~~~~~~v~~l~~~ 60 (66)
T smart00388 5 FLANLSHELRTPLTAIR-----GYLELLED--TELSEEQ-REYLETILRSAERLLRLINDLLDL 60 (66)
T ss_pred HHHHHHHhccCcHHHHH-----HHHHHHHh--CCCChHH-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35667899885544332 22222222 1112222 455666666666666666555443
No 66
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=29.27 E-value=87 Score=20.98 Aligned_cols=28 Identities=11% Similarity=0.240 Sum_probs=24.8
Q ss_pred HHHHHHhhhccCCHHHHHHHHHHHHHhH
Q 031712 26 QFLQLQQLQDESNPDFVAEVVSLFFADS 53 (154)
Q Consensus 26 ~~~~L~~L~~~~~~~~~~~ll~~Fl~~~ 53 (154)
.|+=|..+-++.-+.++++.+..|+++.
T Consensus 20 iF~FL~~~P~GT~~~~iR~~L~rYI~~~ 47 (97)
T PRK13916 20 IFDFLENVPRGTKTAHIREALRRYIEEI 47 (97)
T ss_pred HHHHHHHCCCCCccHHHHHHHHHHHHhc
Confidence 3778889998889999999999999875
No 67
>COG5582 Uncharacterized conserved protein [Function unknown]
Probab=28.79 E-value=1.9e+02 Score=21.90 Aligned_cols=65 Identities=22% Similarity=0.251 Sum_probs=40.0
Q ss_pred HHHHhhhhhhchHHHHHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Q 031712 12 EYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQL 81 (154)
Q Consensus 12 ~~~~~~~~~~ild~~~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~L 81 (154)
+|.+.+.+.+.+-+.++....+.+. ...++.+.+..|..+. .+.+|..|++.. |-+...+++-.|
T Consensus 110 qyl~vLe~np~~~~~~~~~~~~k~l-ad~~ie~~~~~f~~~~--LL~~IDeALd~~--Dk~~F~~L~q~L 174 (182)
T COG5582 110 QYLAVLESNPQLPENLSEQTKLKEL-ADALIERSVHAFERKK--LLQQIDEALDMR--DKERFYQLVQIL 174 (182)
T ss_pred HHHHHHhhChhcccCHHHHHHHHHH-HHHHHHHHHHHHHHHH--HHHHHHHHHhhh--hHHHHHHHHHHH
Confidence 3455566666665544454444432 2356666666666554 889999999998 877666655443
No 68
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=26.57 E-value=2.5e+02 Score=21.51 Aligned_cols=39 Identities=3% Similarity=0.008 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHHHH
Q 031712 91 ERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVKNK 129 (154)
Q Consensus 91 ~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~ 129 (154)
.+|.+-...|+.+++..+..+...++......+..+...
T Consensus 150 nkLFdnvt~LDyAAR~K~~~eae~yY~~Tv~slddVl~~ 188 (190)
T PLN02999 150 NELVENMSELDYYVRTPKVYESYLYYEKTLKSIDNVVEL 188 (190)
T ss_pred HHHhhhHHHHHHHHhcCChHHHHHHHHHHHHHHHHHHHH
Confidence 567888889999999888777777776666666655543
No 69
>PHA00435 capsid assembly protein
Probab=26.04 E-value=3.7e+02 Score=22.06 Aligned_cols=42 Identities=14% Similarity=0.201 Sum_probs=28.7
Q ss_pred cCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 031712 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVH 79 (154)
Q Consensus 36 ~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH 79 (154)
.|+++-+..|+...-.+.+...+.|..++.++ |...++.+.-
T Consensus 196 AGG~E~F~~i~shl~atnp~~~eal~~Ave~~--dl~t~K~ivn 237 (306)
T PHA00435 196 AGGRERFQAIYSHLEATNPSAAESLEAAIENR--DLATVKAIIN 237 (306)
T ss_pred hccHHHHHHHHHHHHhcChhHHHHHHHHHHcC--CHHHHHHHHH
Confidence 46777777765555556777777888888777 7766665443
No 70
>PRK08818 prephenate dehydrogenase; Provisional
Probab=25.83 E-value=2.9e+02 Score=23.34 Aligned_cols=34 Identities=15% Similarity=0.034 Sum_probs=23.7
Q ss_pred HHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhh
Q 031712 50 FADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSS 85 (154)
Q Consensus 50 l~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss 85 (154)
++...+.+..++.++.++ |.+.+.+..|++.-+-
T Consensus 233 l~~~~~~L~~l~~~i~~~--D~~~~~~~~~~f~~a~ 266 (370)
T PRK08818 233 LDRLLAQLQELRALVAQG--DDAARARFRAQFLHAN 266 (370)
T ss_pred HHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHH
Confidence 344445567888888889 9998888866655433
No 71
>cd08810 CARD_BCL10 Caspase activation and recruitment domain of B-cell lymphoma 10. Caspase activation and recruitment domain (CARD) similar to that found in BCL10 (B-cell lymphoma 10). BCL10 and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1) are the integral components of CBM signalosomes. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. Both CARMA1 and CARD9 associate with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. 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 asso
Probab=25.30 E-value=2.1e+02 Score=18.91 Aligned_cols=52 Identities=8% Similarity=0.147 Sum_probs=25.7
Q ss_pred HHHHHHhhhhhhchHHHHHHHHhhhc-cCCHHHHHHHHHHHHHhHHHHHHHHHHHh
Q 031712 10 LLEYTKSLFMEGVLDNQFLQLQQLQD-ESNPDFVAEVVSLFFADSERLLNDLTRAL 64 (154)
Q Consensus 10 ~~~~~~~~~~~~ild~~~~~L~~L~~-~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~ 64 (154)
.++.|.-+...+|+++. ..+++.. ..+.+-...+++... ..+.-+..+-.++
T Consensus 18 ~~~l~d~L~s~~ILt~~--d~EeI~~~~t~~~qa~~LLdiL~-rGp~Af~~F~esL 70 (84)
T cd08810 18 ADRHFDYLRSKRILTRD--DCEEISCRTTSRKQAGKLLDILA-ENPKGLDALIESI 70 (84)
T ss_pred HHHHHHHHHHcCCCCHH--HHHHHhccCCcHHHHHHHHHHHh-hCchHHHHHHHHH
Confidence 45667777777777752 2222222 334444445454444 4444444444443
No 72
>PF01322 Cytochrom_C_2: Cytochrome C'; InterPro: IPR002321 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class II includes the high-spin cytC' and a number of low-spin cytochromes, e.g. cyt c-556. The haem-attachment site is close to the C terminus. The cytC' are capable of binding such ligands as CO, NO or CN(-), albeit with rate and equilibrium constants 100 to 1,000,000-fold smaller than other high-spin haemoproteins []. This, coupled with its relatively low redox potential, makes it unlikely that cytC' is a terminal oxidase. Thus cytC' probably functions as an electron transfer protein []. The 3D structures of a number of cytC' have been determined. The molecule usually exists as a dimer, each monomer folding as a four-alpha-helix bundle incorporating a covalently-bound haem group at the core []. The Chromatium vinosum cytC' exhibits dimer dissociation upon ligand binding [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0005746 mitochondrial respiratory chain; PDB: 1BBH_A 2J9B_B 2J8W_A 1JAF_B 3ZTM_A 2XLD_A 2XL6_A 1E86_A 2YLD_A 2YKZ_A ....
Probab=24.63 E-value=2.2e+02 Score=19.46 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=15.8
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhh
Q 031712 54 ERLLNDLTRALDQPTIDFKMVDSHVHQLKGSS 85 (154)
Q Consensus 54 ~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss 85 (154)
......|..+..++ |...+......+.++|
T Consensus 85 ~~aa~~L~~aa~~~--d~~~~~~a~~~v~~~C 114 (122)
T PF01322_consen 85 QKAAAALAAAAKSG--DLAAIKAAFGEVGKSC 114 (122)
T ss_dssp HHHHHHHHHHHHHT--SHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcC--CHHHHHHHHHHHHHHH
Confidence 33445555555555 6665555555544444
No 73
>PLN02407 diphosphomevalonate decarboxylase
Probab=24.50 E-value=1.3e+02 Score=25.26 Aligned_cols=33 Identities=9% Similarity=0.139 Sum_probs=27.7
Q ss_pred HHHHHHHh-HHHHHHHHHHHhcCCCCCHHHHHHHHH
Q 031712 45 VVSLFFAD-SERLLNDLTRALDQPTIDFKMVDSHVH 79 (154)
Q Consensus 45 ll~~Fl~~-~~~~l~~L~~a~~~~~~D~~~l~~~aH 79 (154)
++..-++. +++++..|+.|+.++ ||..+.+++=
T Consensus 224 ~~~~w~~~~~~~~~~~~~~Ai~~~--Df~~~gei~e 257 (343)
T PLN02407 224 LLQHRAKEVVPKRILQMEEAIKNR--DFASFAKLTC 257 (343)
T ss_pred hHHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHHHH
Confidence 45566777 799999999999999 9999988764
No 74
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=23.42 E-value=2.2e+02 Score=22.63 Aligned_cols=71 Identities=14% Similarity=0.075 Sum_probs=41.1
Q ss_pred HhhhhhhhhcHHH--HHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHH-----HHHHHHHHhhhhHHhhc-CCCCccc
Q 031712 80 QLKGSSSSIGAER--IKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVK-----NKLETLFRMEQQIVAAG-GSIPMME 151 (154)
Q Consensus 80 ~LKGss~~lGa~~--L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~-----~~L~~~l~~~~~~~~~~-~~~~~~~ 151 (154)
..-|+.|.++... +-+.+.++=+++.+++.+.+..+...+.....-+. ..++..+ ..++. +.| ++.|...
T Consensus 192 ~~~G~~G~i~~~~~~~P~~~~~l~~a~~~gd~~~A~~lq~~l~~l~~~~~~~~~~~~~K~~l-~~~G~-~~g~~R~P~~~ 269 (285)
T TIGR00674 192 MALGGKGVISVTANVAPKLMKEMVNNALEGDFAEAREIHQKLMPLHKALFIETNPIPVKTAL-ALLGL-IEGELRLPLTE 269 (285)
T ss_pred HHcCCCEEEehHHHhhHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHhccCCcHHHHHHH-HHcCC-CCCCCCCCCCC
Confidence 3556777764444 55888999889999998877665555544332211 1133333 33444 344 5667765
Q ss_pred c
Q 031712 152 L 152 (154)
Q Consensus 152 ~ 152 (154)
+
T Consensus 270 l 270 (285)
T TIGR00674 270 L 270 (285)
T ss_pred C
Confidence 4
No 75
>PF04280 Tim44: Tim44-like domain; InterPro: IPR007379 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane []. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005744 mitochondrial inner membrane presequence translocase complex; PDB: 2CW9_A 2FXT_A 3QK9_A.
Probab=22.70 E-value=85 Score=22.04 Aligned_cols=51 Identities=12% Similarity=0.230 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHH
Q 031712 38 NPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNF 103 (154)
Q Consensus 38 ~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~ 103 (154)
+|.|- ...|+....+.+..+..|+.++ |+..++.++ +-.-+..++..+...
T Consensus 12 dp~Fd---~~~F~~~ak~~f~~i~~A~~~~--D~~~l~~~~----------t~~~~~~~~~~i~~~ 62 (147)
T PF04280_consen 12 DPGFD---PAAFLEEAKEAFLPIQEAWAKG--DLEALRPLL----------TEELYERLQAEIKAR 62 (147)
T ss_dssp -TT-----HHHHHHHHHHTHHHHHHHHHHT---HHHHHHHB-----------HHHHHHHHHHHHHH
T ss_pred CCCCC---HHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHh----------CHHHHHHHHHHHHHH
Confidence 34554 6788999999999999999999 988887764 334445556666554
No 76
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=22.62 E-value=1.7e+02 Score=23.20 Aligned_cols=60 Identities=12% Similarity=0.068 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHH-----HHHHHHHHhhhhHHhhcCCCCccccC
Q 031712 93 IKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVK-----NKLETLFRMEQQIVAAGGSIPMMELS 153 (154)
Q Consensus 93 L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~-----~~L~~~l~~~~~~~~~~~~~~~~~~~ 153 (154)
+-+.+.++-.++.+++.+.+..+.+.+......+. ..++..+ ..++...-.++.|...++
T Consensus 210 ~P~~~~~i~~~~~~Gd~~~A~~l~~~l~~~~~~~~~~~~~~~~K~~l-~~~G~~~g~~R~Pl~~l~ 274 (289)
T PF00701_consen 210 FPELIVEIYDAFQAGDWEEARELQQRLLPLREALFSGGNIAAIKYAL-ELRGLIAGPVRPPLLPLS 274 (289)
T ss_dssp HHHHHHHHHHHHHTTCHHHHHHHHHHHHHHHHHHTSSSTTHHHHHHH-HHTTSSSSB--TTS-SS-
T ss_pred ChHHHHHHHHHHHcCcHHHHHHHHHHHhHHHHHHHccCCHHHHHHHH-HHCCCCCCCCCCCCCCCC
Confidence 67888999999999998877666555555444432 2334333 334444444666766543
No 77
>TIGR00465 ilvC ketol-acid reductoisomerase. This is the second enzyme in the parallel isoleucine-valine biosynthetic pathway
Probab=22.26 E-value=2e+02 Score=23.55 Aligned_cols=59 Identities=14% Similarity=0.026 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHH-HHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCH
Q 031712 36 ESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFK-MVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNI 109 (154)
Q Consensus 36 ~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~-~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~ 109 (154)
+++|.++..+++.+ ++.+ ++.+ .....+|++||++..+.-..+..+...+=..++=|+.
T Consensus 187 Gs~pa~v~~~~eal--------------v~~G-~~~e~A~~~~~~~~~g~~~l~~e~g~~~l~~~Vsstaeyg~~ 246 (314)
T TIGR00465 187 GGLTALIKAGFDTL--------------VEAG-YQPELAYFETVHELKLIVDLIYEGGITGMRDRISNTAEYGAL 246 (314)
T ss_pred hHHHHHHHHHHHHH--------------HHcC-CCHHHHHHHHHHHHHHHHHHHHHhcHHHHHHHcCCHHHcCcc
Confidence 45666666655443 2332 2444 4556699999999999666555554444444444433
No 78
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=22.23 E-value=3.3e+02 Score=20.11 Aligned_cols=51 Identities=8% Similarity=0.098 Sum_probs=29.0
Q ss_pred hhhhcHHHHHHHHHHHHHHHHhcCH--hhHHHHHHHHHHHHHHHHHHHHHHHH
Q 031712 85 SSSIGAERIKNACVAFRNFCEEQNI--EGCMSCLQQVKQEYCLVKNKLETLFR 135 (154)
Q Consensus 85 s~~lGa~~L~~~~~~lE~~~~~~~~--~~~~~~~~~l~~~~~~l~~~L~~~l~ 135 (154)
...+|..++.....-++..+-.... ....+.+..+...|..+...++.-+.
T Consensus 71 i~~LGg~p~~t~~~~~~~s~ike~~~~~~~~~~l~~l~~~~~~l~~~~r~~~~ 123 (156)
T COG0783 71 IRALGGVPLGTLSEYLKLSSIKEEPGDYTAREMLKELVEDYEYLIKELRKGIE 123 (156)
T ss_pred HHHcCCCCcccHHHHHHhCCCcccCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446666666666666665543211 23556666666666666665555443
No 79
>cd08819 CARD_MDA5_2 Caspase activation and recruitment domain found in MDA5, second repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protei
Probab=22.11 E-value=2.6e+02 Score=18.79 Aligned_cols=15 Identities=13% Similarity=0.290 Sum_probs=7.0
Q ss_pred HHHHHhhhhhhchHH
Q 031712 11 LEYTKSLFMEGVLDN 25 (154)
Q Consensus 11 ~~~~~~~~~~~ild~ 25 (154)
.+-|-.++..||+..
T Consensus 22 ~~v~d~ll~~~ilT~ 36 (88)
T cd08819 22 RDVCDKCLEQGLLTE 36 (88)
T ss_pred HHHHHHHHhcCCCCH
Confidence 344444455555443
No 80
>PF15565 Imm16: Immunity protein 16
Probab=21.70 E-value=2.8e+02 Score=19.16 Aligned_cols=56 Identities=18% Similarity=0.215 Sum_probs=37.7
Q ss_pred HHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHH
Q 031712 29 QLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAF 100 (154)
Q Consensus 29 ~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~l 100 (154)
.|.++....+.+.+..+...|-.+. |.+-...+.|.+......-|+.+++...-.+
T Consensus 21 ~L~~l~~~~d~~~I~~L~~~F~D~~----------------d~eVmf~lvh~lE~~~~~~~l~~l~~~~p~m 76 (106)
T PF15565_consen 21 ALNELAKYPDNDVIDDLCLIFDDET----------------DHEVMFSLVHFLEHFDMEEYLPALAEAIPQM 76 (106)
T ss_pred HHHHHHhcCCHhHHHHHHHHhcCcc----------------chHHHHHHHHHHHHccHHHHHHHHHHHHHHH
Confidence 3445555556666666666665542 6788889999998877777777776665555
No 81
>cd07299 PX_TCGAP The phosphoinositide binding Phox Homology domain of Tc10/Cdc42 GTPase-activating protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. TCGAP (Tc10/Cdc42 GTPase-activating protein) contains N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal proline-rich regions. It is widely expressed in the brain where it is involved in regulating the outgrowth of axons and dendrites and is regulated by the protein tyrosine kinase Fyn. It interacts with cdc42 and TC10beta through its GAP domain and with phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] through its PX domain. It is translocated to the plasma membrane in adipocytes in response to insulin and may be involved in the regulation of insulin-stimulated glucose transport. TCGAP has also been named sorting nexins 26 (SNX26). SNXs
Probab=21.56 E-value=2.4e+02 Score=19.78 Aligned_cols=40 Identities=15% Similarity=0.285 Sum_probs=27.8
Q ss_pred HhhhhhhchHHHHHHHHhhhc----cCCHHHHHHHHHHHHHhHH
Q 031712 15 KSLFMEGVLDNQFLQLQQLQD----ESNPDFVAEVVSLFFADSE 54 (154)
Q Consensus 15 ~~~~~~~ild~~~~~L~~L~~----~~~~~~~~~ll~~Fl~~~~ 54 (154)
-..++.-|-|+.|++|.+|.. ....+.+..++..|++.-.
T Consensus 52 D~~LHrCiyDRr~S~L~eL~~~~~l~~~~~~~~~~l~~YL~RlS 95 (113)
T cd07299 52 DAHLHRCIFDRRFSQLLELPPLCEIGDRLQILTPLLSEYLNRLT 95 (113)
T ss_pred HHHHHHHHHhhhhhhhhccCccccccchHHHHHHHHHHHHHHHH
Confidence 345667788888999999887 2334567777777776543
No 82
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=21.36 E-value=1.1e+02 Score=16.69 Aligned_cols=22 Identities=14% Similarity=0.345 Sum_probs=10.6
Q ss_pred HHHHHHHHhhhccCCHHHHHHH
Q 031712 24 DNQFLQLQQLQDESNPDFVAEV 45 (154)
Q Consensus 24 d~~~~~L~~L~~~~~~~~~~~l 45 (154)
|..++.|..+...+-.+|++..
T Consensus 6 D~lLDeId~vLe~NAe~FV~~f 27 (33)
T TIGR03687 6 DDLLDEIDGVLESNAEEFVRGF 27 (33)
T ss_pred HHHHHHHHHHHHHhHHHHHHHH
Confidence 3334455555544444555443
No 83
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=21.33 E-value=1.6e+02 Score=16.21 Aligned_cols=34 Identities=21% Similarity=0.292 Sum_probs=20.8
Q ss_pred HHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHH
Q 031712 27 FLQLQQLQDESNPDFVAEVVSLFFADSERLLNDL 60 (154)
Q Consensus 27 ~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L 60 (154)
+.+|.++...-+++.+...+...-.+.+..+..|
T Consensus 5 v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~L 38 (42)
T PF02845_consen 5 VQQLQEMFPDLDREVIEAVLQANNGDVEAAIDAL 38 (42)
T ss_dssp HHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 4566666666677777776666665555555544
No 84
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.99 E-value=2.1e+02 Score=24.93 Aligned_cols=63 Identities=13% Similarity=0.374 Sum_probs=42.1
Q ss_pred HHHHHHHhhhhhhchHHHHHHHHhhhccCCHHHHHHHHHHHHHhHHH-HHHHHHHHhcCCCCCHHHHHHHHHH
Q 031712 9 RLLEYTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFADSER-LLNDLTRALDQPTIDFKMVDSHVHQ 80 (154)
Q Consensus 9 ~~~~~~~~~~~~~ild~~~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~-~l~~L~~a~~~~~~D~~~l~~~aH~ 80 (154)
+....|-.|+++.-..+++.++..+ ||.|- ...|+.+.++ .+.++-+|+-.+ |.+.|..-||.
T Consensus 287 ki~~~~~g~fsktE~Sev~tei~~i----DPsF~---~~~Flr~~ee~IiPnVLeAyvkG--D~evLK~wcse 350 (459)
T KOG2580|consen 287 KITDVDGGLFSKTEMSEVLTEIKKI----DPSFD---KEDFLRECEEYIIPNVLEAYVKG--DLEVLKKWCSE 350 (459)
T ss_pred hhhhcccccchhhHHHHHHHHHHhc----CCCCC---cHHHHHHHHHhhhHHHHHHHHhc--cHHHHHHHHhh
Confidence 4444556677777777777777765 44444 2344444444 455688888899 99999999986
No 85
>PF06920 Ded_cyto: Dedicator of cytokinesis; InterPro: IPR010703 This family represents a conserved region of approximately 200 residues within a number of eukaryotic dedicator of cytokinesis (DOCK) proteins. These proteins are potential guanine nucleotide exchange factors that activate some small GTPases, such as Rac, by exchanging bound GDP for free GTP []. DOCK proteins are required during several cellular processes, such as cell motility and phagocytosis. For instance, DOCK2 is specifically expressed in haemopoietic cells, and plays a critical role in lymphocyte migration [].; GO: 0005085 guanyl-nucleotide exchange factor activity, 0005525 GTP binding, 0051020 GTPase binding; PDB: 2WMO_A 2WM9_A 2WMN_A 3VHL_A 3B13_A 2YIN_B.
Probab=20.98 E-value=3.5e+02 Score=19.96 Aligned_cols=89 Identities=9% Similarity=0.129 Sum_probs=48.0
Q ss_pred HHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHHHHHHHHHHH
Q 031712 50 FADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVKQEYCLVKNK 129 (154)
Q Consensus 50 l~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~ 129 (154)
+++......+|..++.....|...+.......=.++.|=|.....+..-.-+.. +. .-...+..|+..+.+....
T Consensus 68 ie~i~~k~~eL~~~~~~~~~~~~~L~~~L~G~v~a~VngG~~~y~~~Fl~~~~~----~~-~~~~~~~~L~~~~~~~~~~ 142 (178)
T PF06920_consen 68 IEDIEKKNKELEELINSYKPNINPLQMLLQGSVDAAVNGGPSKYAEAFLSPEYL----HP-EDKELVEKLKEAFIDQLIV 142 (178)
T ss_dssp HHHHHHHHHHHHHHHHHSSS-HHHHHHHHHHHHS-SSS-TTHHHHHHHSSCHHC----SH-CCHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhhccchhHHHHHhcccccccccCchHHHHHHHcCcccc----Cc-ccHHHHHHHHHHHHHHHHH
Confidence 344444555555555443225566666555555555566666655544433332 11 1234677788888888888
Q ss_pred HHHHHHhhhhHHhh
Q 031712 130 LETLFRMEQQIVAA 143 (154)
Q Consensus 130 L~~~l~~~~~~~~~ 143 (154)
++.-+..++..++.
T Consensus 143 ~~~~L~~h~~~~~~ 156 (178)
T PF06920_consen 143 LERALELHKKLCSP 156 (178)
T ss_dssp HHHHHHHHHHC--G
T ss_pred HHHHHHHHHHHCCh
Confidence 88888777776654
No 86
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.91 E-value=2.9e+02 Score=23.51 Aligned_cols=45 Identities=20% Similarity=0.346 Sum_probs=32.7
Q ss_pred HHHHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHhcCCCCCHHHHHHH
Q 031712 25 NQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRALDQPTIDFKMVDSH 77 (154)
Q Consensus 25 ~~~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~ 77 (154)
++|.+|+++-.. +|+++..||...-.++++.+..|.. |.+.+.++
T Consensus 255 pqf~~lR~~vq~-NP~~L~~lLqql~~~nP~l~q~I~~-------n~e~Fl~l 299 (378)
T TIGR00601 255 PQFQQLRQVVQQ-NPQLLPPLLQQIGQENPQLLQQISQ-------HPEQFLQM 299 (378)
T ss_pred HHHHHHHHHHHH-CHHHHHHHHHHHHhhCHHHHHHHHH-------CHHHHHHH
Confidence 457777776544 7899999998888888888877765 55555544
No 87
>PRK14718 ribonuclease III; Provisional
Probab=20.80 E-value=5.3e+02 Score=22.70 Aligned_cols=73 Identities=16% Similarity=0.130 Sum_probs=39.5
Q ss_pred CchhHHHHHHHH-------HHHhhhhhhchHHHHHHHHhhhccCCHHHHHHHHHHHHH-----hHHHHHHHHHHHhcCCC
Q 031712 1 MEVGQMQRRLLE-------YTKSLFMEGVLDNQFLQLQQLQDESNPDFVAEVVSLFFA-----DSERLLNDLTRALDQPT 68 (154)
Q Consensus 1 ~~~~~~~~~~~~-------~~~~~~~~~ild~~~~~L~~L~~~~~~~~~~~ll~~Fl~-----~~~~~l~~L~~a~~~~~ 68 (154)
|++.+|+.++-- +.+.|.+..+..+..++|+-|. ..++.-++..|+- ..+..+..++..+-++
T Consensus 1 ~~l~~LEkrLGY~Fkn~~LL~eALTH~Sys~e~NERLEFLG----DAVL~liVse~Lf~~fPdl~EGeLT~LRS~LVSn- 75 (467)
T PRK14718 1 MPLSQLESRLRYEFRNAELLRQALTHRSHSATHNERLEFLG----DSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQ- 75 (467)
T ss_pred CCHHHHHHHhCCCcCCHHHHHHHHhccCcCcccHHHHHHHH----HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHhhh-
Confidence 566666665542 2233333333332245666663 3555555555444 3467888888888765
Q ss_pred CCHHHHHHHHHHh
Q 031712 69 IDFKMVDSHVHQL 81 (154)
Q Consensus 69 ~D~~~l~~~aH~L 81 (154)
..+..++..|
T Consensus 76 ---etLA~IAr~L 85 (467)
T PRK14718 76 ---QSLYEIAQAL 85 (467)
T ss_pred ---HHHHHHHHHc
Confidence 4555555443
No 88
>PRK11199 tyrA bifunctional chorismate mutase/prephenate dehydrogenase; Provisional
Probab=20.63 E-value=5e+02 Score=21.63 Aligned_cols=48 Identities=10% Similarity=0.160 Sum_probs=28.7
Q ss_pred cCCHHHHHHHHHH------HHHhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhh
Q 031712 36 ESNPDFVAEVVSL------FFADSERLLNDLTRALDQPTIDFKMVDSHVHQLKGSS 85 (154)
Q Consensus 36 ~~~~~~~~~ll~~------Fl~~~~~~l~~L~~a~~~~~~D~~~l~~~aH~LKGss 85 (154)
.++|+++..++.. -+++....+..+..+++++ |.+.+....-.-|..-
T Consensus 297 ~~~p~lw~dI~~~N~~~~~~l~~~~~~l~~l~~~l~~~--d~~~l~~~~~~a~~~~ 350 (374)
T PRK11199 297 AQDPQLYADIIMSSPENLALIKRYYQRFGEALELLEQG--DKQAFIDSFRKVEHWF 350 (374)
T ss_pred cCCHHHHHHHHHhChhHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHH
Confidence 3456666555421 1233445566777777888 8888777766654443
No 89
>PF05549 Allexi_40kDa: Allexivirus 40kDa protein; InterPro: IPR008398 This family of sequences contains the 40 kDa polypeptides from garlic viruses (Allexiviruses), which do not resemble any other plant virus gene products reported so far []. Rod-shaped flexuous viruses have been isolated from garlic plants, Allium sativum. Infection by this virus creates typical mosaic symptoms. The core-like sequence of a zinc finger protein preceded by a cluster of basic amino acid residues shows similarities to the corresponding 12K proteins of the potexviruses and carlaviruses []. Viral epidemics by allexiviruses are also known to be caused by aphids and eriophyid mites (Aceria tulipae) carrying Potyviruses, Carlaviruses, and Allexiviruses [].
Probab=20.59 E-value=4.7e+02 Score=21.21 Aligned_cols=106 Identities=12% Similarity=0.139 Sum_probs=61.2
Q ss_pred hHHHHHHHHhhhccCCHHHHHHHHHHHHHhHHHHHHHHHHHh---cCCCCCHHHHHHHHHHhhhhhhhhcHHHHHHHHHH
Q 031712 23 LDNQFLQLQQLQDESNPDFVAEVVSLFFADSERLLNDLTRAL---DQPTIDFKMVDSHVHQLKGSSSSIGAERIKNACVA 99 (154)
Q Consensus 23 ld~~~~~L~~L~~~~~~~~~~~ll~~Fl~~~~~~l~~L~~a~---~~~~~D~~~l~~~aH~LKGss~~lGa~~L~~~~~~ 99 (154)
+|+-|.+|.+|-.. .-++ +..--.+++..+..+.... +.. -...++...|+|.+.-. .+......
T Consensus 36 lDELyGqLHALHqN-sLEW----LTHI~h~~d~ii~~ln~~~~~s~~t--~ls~~r~~~~tL~~~~~-----~i~~~~~~ 103 (271)
T PF05549_consen 36 LDELYGQLHALHQN-SLEW----LTHINHNVDQIINMLNPINLTSQGT--PLSRIRDALRTLTRLLD-----SIHSVEQK 103 (271)
T ss_pred HHHHHHHHHHHHhh-hHHH----HHhcCccHHHHHHHhCcccchhhcc--hHHHHHHHHHHHHhhHH-----HHHHHHHH
Confidence 56777788777532 2222 2333333444444433321 333 56788888888876533 44555555
Q ss_pred HHHHHHhcCHhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhH
Q 031712 100 FRNFCEEQNIEGCMSCLQQVKQEYCLVKNKLETLFRMEQQI 140 (154)
Q Consensus 100 lE~~~~~~~~~~~~~~~~~l~~~~~~l~~~L~~~l~~~~~~ 140 (154)
++..+...........+..|+..++.+...|+......-.-
T Consensus 104 ~~~~~~~~~~~~~~~~l~~iet~L~~lh~kld~l~~~~~~~ 144 (271)
T PF05549_consen 104 SELSANTPSSSKLLKKLASIETSLESLHIKLDELISSLTSN 144 (271)
T ss_pred HhcccCCccchhHHHHHHHHHhHHHHHHHHHHHHHhccccC
Confidence 66555444444566778888888888887777665554443
No 90
>PRK00396 rnpA ribonuclease P; Reviewed
Probab=20.56 E-value=1.1e+02 Score=21.93 Aligned_cols=26 Identities=12% Similarity=0.222 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHh--hhhHHhhcCCC-Ccc
Q 031712 125 LVKNKLETLFRM--EQQIVAAGGSI-PMM 150 (154)
Q Consensus 125 ~l~~~L~~~l~~--~~~~~~~~~~~-~~~ 150 (154)
++...|...+.. .....|+||++ |-|
T Consensus 101 ~l~~~l~~ll~kl~~~~~~~~~~~~~~~~ 129 (130)
T PRK00396 101 ELHQQFGKLWKRLARNRPNPAASAESPGV 129 (130)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCcCCCCCC
Confidence 333344333333 33455899988 655
No 91
>PF07361 Cytochrom_B562: Cytochrome b562; InterPro: IPR009155 Cytochrome b562 is a haem-containing protein that is expressed in the periplasm of Escherichia coli. In b-type cytochromes, the haem atom is not covalently attached to the polypeptide. Cytochrome b562 has a four-helical bundle structure that is structurally similar to that found in members of the cytochrome c family (IPR002321 from INTERPRO). Cytochrome b562 has a reduction potential of 167 mV, which sets the energy yield possible in metabolism and is also a key determinant of the rate at which redox reactions proceed [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0042597 periplasmic space; PDB: 4ER9_A 3IQ6_G 2QLA_B 3FOO_A 3M79_C 256B_A 3NMI_F 3HNK_A 3NMK_D 2BC5_A ....
Probab=20.36 E-value=2.9e+02 Score=18.72 Aligned_cols=35 Identities=9% Similarity=0.222 Sum_probs=26.7
Q ss_pred hhhcHHHHHHHHHHHHHHHHhcCHhhHHHHHHHHH
Q 031712 86 SSIGAERIKNACVAFRNFCEEQNIEGCMSCLQQVK 120 (154)
Q Consensus 86 ~~lGa~~L~~~~~~lE~~~~~~~~~~~~~~~~~l~ 120 (154)
..=|+..|......++..+.+|+.+++...+..|.
T Consensus 58 Y~~Gl~~li~~id~a~~~~~~G~l~~AK~~l~~l~ 92 (103)
T PF07361_consen 58 YQEGLDKLIDQIDKAEALAEAGKLDEAKAALKKLD 92 (103)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34588899999999999999998877665544443
Done!