Query 038079
Match_columns 144
No_of_seqs 102 out of 362
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 07:22:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038079.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038079hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4747 Two-component phosphor 100.0 4.6E-28 1E-32 179.1 13.1 136 3-141 5-140 (150)
2 COG2198 ArcB FOG: HPt domain [ 99.7 8.9E-16 1.9E-20 110.2 11.5 95 39-135 20-117 (122)
3 PF01627 Hpt: Hpt domain; Int 99.6 1.1E-15 2.3E-20 102.2 8.9 82 46-129 1-88 (90)
4 smart00073 HPT Histidine Phosp 99.5 1.9E-14 4.2E-19 96.6 5.3 85 46-133 2-86 (87)
5 cd00088 HPT Histidine Phosphot 99.4 4E-13 8.6E-18 91.8 5.6 64 45-110 2-69 (94)
6 TIGR02956 TMAO_torS TMAO reduc 99.4 2.4E-12 5.3E-17 117.4 10.1 93 39-135 876-968 (968)
7 PRK11091 aerobic respiration c 99.1 5.6E-10 1.2E-14 100.6 11.6 100 39-140 678-777 (779)
8 PRK10618 phosphotransfer inter 98.9 6.6E-09 1.4E-13 96.3 9.7 84 43-128 808-891 (894)
9 PRK11466 hybrid sensory histid 98.6 2.5E-07 5.4E-12 84.5 8.9 88 39-137 820-907 (914)
10 PRK11107 hybrid sensory histid 98.6 7.2E-07 1.6E-11 81.1 11.8 97 39-137 821-918 (919)
11 COG0643 CheA Chemotaxis protei 97.8 0.00015 3.3E-09 66.3 10.2 71 42-112 4-83 (716)
12 PRK10547 chemotaxis protein Ch 97.8 0.00018 3.9E-09 65.4 9.9 62 45-106 4-71 (670)
13 PRK09959 hybrid sensory histid 96.8 0.031 6.7E-07 53.0 13.1 95 40-136 1098-1193(1197)
14 PRK15347 two component system 96.4 0.01 2.3E-07 54.3 7.2 62 47-112 838-899 (921)
15 TIGR02302 aProt_lowcomp conser 76.3 24 0.00052 33.5 9.5 83 41-129 522-604 (851)
16 PF13779 DUF4175: Domain of un 68.0 31 0.00068 32.6 8.2 42 85-126 530-571 (820)
17 cd08323 CARD_APAF1 Caspase act 66.5 26 0.00057 23.7 5.7 66 10-81 16-82 (86)
18 TIGR00984 3a0801s03tim44 mitoc 61.7 70 0.0015 27.6 8.6 83 6-109 210-293 (378)
19 PF14276 DUF4363: Domain of un 60.4 15 0.00032 25.8 3.7 40 93-132 26-65 (121)
20 PRK03636 hypothetical protein; 60.3 29 0.00062 26.8 5.5 39 44-84 130-174 (179)
21 KOG4747 Two-component phosphor 59.6 74 0.0016 24.0 7.6 58 41-101 13-70 (150)
22 PRK03057 hypothetical protein; 56.9 34 0.00073 26.5 5.4 37 46-84 131-173 (180)
23 PF07743 HSCB_C: HSCB C-termin 51.8 62 0.0013 20.8 6.5 40 42-83 27-66 (78)
24 KOG2424 Protein involved in tr 51.5 24 0.00051 27.6 3.7 35 87-126 147-181 (195)
25 PF13326 PSII_Pbs27: Photosyst 48.0 1.1E+02 0.0024 22.7 7.8 86 46-132 44-145 (145)
26 PF08858 IDEAL: IDEAL domain; 47.9 43 0.00092 19.0 3.6 27 55-83 11-37 (37)
27 TIGR00714 hscB Fe-S protein as 47.3 1.2E+02 0.0025 22.6 7.2 77 40-135 76-152 (157)
28 PRK01356 hscB co-chaperone Hsc 46.0 1.3E+02 0.0028 22.7 7.3 51 72-131 107-157 (166)
29 TIGR03042 PS_II_psbQ_bact phot 44.2 1.3E+02 0.0029 22.4 8.4 73 55-139 48-141 (142)
30 PF03993 DUF349: Domain of Unk 44.1 52 0.0011 20.8 4.1 62 45-128 8-69 (77)
31 PF07304 SRA1: Steroid recepto 41.1 1.5E+02 0.0033 22.1 8.0 70 49-134 64-144 (157)
32 PF13446 RPT: A repeated domai 41.0 60 0.0013 20.0 3.9 36 33-68 11-46 (62)
33 PF04722 Ssu72: Ssu72-like pro 40.9 31 0.00067 27.1 2.9 38 87-125 145-183 (195)
34 COG2991 Uncharacterized protei 40.1 7.6 0.00016 25.9 -0.4 20 81-100 27-46 (77)
35 PF02845 CUE: CUE domain; Int 39.2 64 0.0014 18.3 3.5 34 27-62 5-38 (42)
36 PF03847 TFIID_20kDa: Transcri 39.1 88 0.0019 20.2 4.5 48 7-67 2-49 (68)
37 smart00188 IL10 Interleukin-10 39.0 1.6E+02 0.0035 21.8 8.6 32 22-57 29-60 (137)
38 TIGR03044 PS_II_psb27 photosys 39.0 1.6E+02 0.0035 21.8 7.2 89 45-134 31-134 (135)
39 PRK09591 celC cellobiose phosp 38.9 1.4E+02 0.0029 20.9 6.9 44 98-141 23-66 (104)
40 PF15079 DUF4546: Domain of un 38.8 47 0.001 25.7 3.6 25 119-143 50-74 (205)
41 PRK10698 phage shock protein P 38.5 2E+02 0.0042 22.7 8.3 24 45-68 26-49 (222)
42 KOG0796 Spliceosome subunit [R 38.0 2.5E+02 0.0054 23.8 11.0 73 42-123 83-159 (319)
43 PF03670 UPF0184: Uncharacteri 37.7 1.1E+02 0.0023 20.9 4.8 36 107-142 31-66 (83)
44 PF09403 FadA: Adhesion protei 36.6 99 0.0021 22.5 4.9 10 85-94 12-21 (126)
45 COG3027 zapA Cell division pro 35.3 1.6E+02 0.0034 20.7 7.0 78 50-137 15-100 (105)
46 KOG2580 Mitochondrial import i 35.1 1.4E+02 0.003 26.4 6.2 68 4-82 282-350 (459)
47 KOG1142 Transcription initiati 35.0 49 0.0011 27.1 3.4 48 8-68 158-205 (258)
48 PF11827 DUF3347: Protein of u 34.9 2E+02 0.0043 21.7 8.0 81 41-131 43-127 (174)
49 PF03858 Crust_neuro_H: Crusta 34.0 42 0.0009 19.8 2.1 22 72-93 5-26 (41)
50 PF08900 DUF1845: Domain of un 33.5 2.4E+02 0.0051 22.2 7.7 52 85-137 32-83 (217)
51 PRK13916 plasmid segregation p 33.1 75 0.0016 21.8 3.5 28 27-56 21-48 (97)
52 PF12854 PPR_1: PPR repeat 32.8 49 0.0011 17.9 2.2 22 100-121 12-33 (34)
53 PF13812 PPR_3: Pentatricopept 32.7 74 0.0016 16.1 3.2 23 101-123 7-29 (34)
54 PF04280 Tim44: Tim44-like dom 32.4 1.8E+02 0.0039 20.5 6.2 54 41-109 13-66 (147)
55 PF04840 Vps16_C: Vps16, C-ter 31.9 3E+02 0.0065 22.9 9.1 85 7-101 164-249 (319)
56 PF01535 PPR: PPR repeat; Int 31.9 72 0.0016 15.7 2.8 23 101-123 6-28 (31)
57 cd00215 PTS_IIA_lac PTS_IIA, P 31.6 1.7E+02 0.0038 20.1 6.9 43 98-140 18-60 (97)
58 COG1220 HslU ATP-dependent pro 31.0 64 0.0014 28.1 3.5 33 74-106 375-408 (444)
59 PF00435 Spectrin: Spectrin re 30.9 1.4E+02 0.0031 18.8 7.4 43 96-139 61-103 (105)
60 COG2178 Predicted RNA-binding 30.2 2.8E+02 0.006 22.0 6.9 47 92-138 26-72 (204)
61 PF08657 DASH_Spc34: DASH comp 29.6 2.5E+02 0.0054 22.9 6.6 63 74-136 134-200 (259)
62 TIGR00823 EIIA-LAC phosphotran 29.5 1.9E+02 0.0042 19.9 6.9 42 99-140 21-62 (99)
63 PLN02407 diphosphomevalonate d 29.5 90 0.0019 26.6 4.2 32 47-80 224-256 (343)
64 PRK10454 PTS system N,N'-diace 29.2 2.2E+02 0.0047 20.4 7.0 44 98-141 34-77 (115)
65 TIGR00756 PPR pentatricopeptid 29.1 84 0.0018 15.6 3.1 23 101-123 6-28 (35)
66 PRK10548 flagellar biosynthesi 28.7 2.2E+02 0.0048 20.4 5.7 21 94-114 13-33 (121)
67 smart00546 CUE Domain that may 28.5 1.2E+02 0.0026 17.2 3.5 35 26-62 5-39 (43)
68 cd07298 PX_RICS The phosphoino 28.0 64 0.0014 23.3 2.6 37 15-53 54-94 (115)
69 PF04012 PspA_IM30: PspA/IM30 27.7 2.8E+02 0.0061 21.2 12.9 47 6-68 2-48 (221)
70 PF09280 XPC-binding: XPC-bind 27.3 70 0.0015 20.1 2.5 36 26-64 9-44 (59)
71 PF05465 Halo_GVPC: Halobacter 27.2 1.2E+02 0.0026 16.7 3.7 24 114-137 4-27 (32)
72 PRK03578 hscB co-chaperone Hsc 27.1 2.8E+02 0.0061 21.0 7.3 75 40-133 93-168 (176)
73 COG2603 Predicted ATPase [Gene 26.7 2.1E+02 0.0046 24.2 5.8 81 43-127 242-326 (334)
74 smart00388 HisKA His Kinase A 26.6 1.3E+02 0.0028 16.9 7.1 58 75-140 5-62 (66)
75 COG0497 RecN ATPase involved i 26.0 5.1E+02 0.011 23.7 12.6 63 20-84 187-255 (557)
76 PF08581 Tup_N: Tup N-terminal 25.9 1.5E+02 0.0032 19.8 4.0 22 114-135 2-23 (79)
77 TIGR03761 ICE_PFL4669 integrat 25.8 3.4E+02 0.0074 21.5 7.2 49 87-136 32-80 (216)
78 PF02631 RecX: RecX family; I 25.8 2.3E+02 0.005 19.6 5.8 61 15-77 3-63 (121)
79 PF05957 DUF883: Bacterial pro 25.5 2.1E+02 0.0046 19.0 5.9 58 81-139 15-72 (94)
80 PF04136 Sec34: Sec34-like fam 25.3 2.9E+02 0.0062 20.5 8.5 96 42-137 38-143 (157)
81 PLN00061 photosystem II protei 24.8 1.8E+02 0.0038 22.0 4.6 60 17-82 27-87 (150)
82 PF05218 DUF713: Protein of un 24.2 3.1E+02 0.0067 21.0 6.0 92 6-100 72-167 (182)
83 PF07587 PSD1: Protein of unkn 24.1 83 0.0018 25.4 3.0 43 10-54 23-65 (266)
84 COG3046 Uncharacterized protei 21.9 1.9E+02 0.0041 25.8 4.8 76 40-121 226-303 (505)
85 PHA02666 hypothetical protein; 21.8 1E+02 0.0022 24.9 3.0 53 39-95 202-258 (287)
86 PRK01773 hscB co-chaperone Hsc 21.4 3.7E+02 0.008 20.4 7.6 75 40-133 90-164 (173)
87 PF02847 MA3: MA3 domain; Int 21.1 2.5E+02 0.0055 18.7 4.6 47 7-54 2-48 (113)
88 PF01044 Vinculin: Vinculin fa 21.0 7.7E+02 0.017 23.9 10.4 27 111-137 579-605 (968)
89 PF04049 APC8: Anaphase promot 21.0 3.4E+02 0.0074 19.8 5.6 82 3-90 6-104 (142)
90 KOG2833 Mevalonate pyrophospha 20.9 1.7E+02 0.0037 25.1 4.2 28 50-79 226-254 (395)
91 PRK10987 regulatory protein Am 20.1 2.7E+02 0.0058 22.7 5.2 35 87-121 79-113 (284)
No 1
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=99.96 E-value=4.6e-28 Score=179.10 Aligned_cols=136 Identities=33% Similarity=0.550 Sum_probs=132.5
Q ss_pred chhHHHHHHHHHhcccchhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhh
Q 038079 3 SNPLHQQIASMRQHLLDEEILDEQFVELEGLALASDEDPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHR 82 (144)
Q Consensus 3 ~~~l~~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~ 82 (144)
+..++.+...+-+|++++|++|++|.+|++| +|++.|+||.+++..|++||++.+..|+.|+..+ .|+.+++.+-|.
T Consensus 5 i~~~q~~~~d~~~sl~~qgild~qF~qlq~l--qD~~~p~fv~ev~~~fF~~s~~~i~~~r~ald~~-~d~k~~~~~~hq 81 (150)
T KOG4747|consen 5 IISMQRDVSDYTKSLFDQGILDSQFLQLQEL--QDDSSPDFVEEVVGLFFEDSERLINNLRLALDCE-RDFKKLGSHVHQ 81 (150)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHH--hcccCccHHHHHHHHHHHHHHHHHHHHHHHHhhH-hHHHHHHHHHHH
Confidence 4578999999999999999999999999999 9999999999999999999999999999999986 499999999999
Q ss_pred hcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038079 83 FKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYFELVKQ 141 (144)
Q Consensus 83 LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~~~~~ 141 (144)
|||||++|||.++...|..+..+|+.++.++|...+.+++.||..++++|++|.+++||
T Consensus 82 lkgssssIGa~kvk~~c~~~~~~~~~~n~egcvr~l~~v~ie~~~lkkkL~~~f~L~rq 140 (150)
T KOG4747|consen 82 LKGSSSSIGALKVKKVCVGFNEFCEAGNIEGCVRCLQQVKIEYSLLKKKLETLFQLERQ 140 (150)
T ss_pred ccCchhhhhHHHHHHHHHHHHHHHhhccchhHhhchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999998
No 2
>COG2198 ArcB FOG: HPt domain [Signal transduction mechanisms]
Probab=99.67 E-value=8.9e-16 Score=110.23 Aligned_cols=95 Identities=24% Similarity=0.423 Sum_probs=85.9
Q ss_pred CChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhc-CCHHHHHHH
Q 038079 39 EDPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRN-GDIEGAKAA 117 (144)
Q Consensus 39 ~~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~-~~~~~~~~~ 117 (144)
+.|+++.+++..|+++++..+..++.++..+ |+..+.+.||+||||++|+|+.+++.+|.++|..++. ...+....+
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 5699999999999999999999999999986 8899999999999999999999999999999999988 689999999
Q ss_pred HHHHHHH--HHHHHHHHHHH
Q 038079 118 FEQVKTE--QGNLKAKLDSY 135 (144)
Q Consensus 118 l~~l~~e--f~~~~~aL~~~ 135 (144)
+..++.+ ...+...+.++
T Consensus 98 i~~l~~~~~~~~~~~~~~~~ 117 (122)
T COG2198 98 IAELKDELQLDVLALELLTY 117 (122)
T ss_pred HHHHHHHhcchHHHHHHHHH
Confidence 9999999 54544444444
No 3
>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=99.65 E-value=1.1e-15 Score=102.20 Aligned_cols=82 Identities=22% Similarity=0.425 Sum_probs=71.3
Q ss_pred HHHHHHHHhHHHHHHHHHHHh---ccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHH---HHHHHH
Q 038079 46 VTINVYFEESNELLPMIEDLL---GKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEG---AKAAFE 119 (144)
Q Consensus 46 ~Li~~f~~ds~~~l~~l~~al---~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~---~~~~l~ 119 (144)
+|++.|+++++..+..|+.++ ..+ |++.+++.+|+|||+++++|+.+++.+|..+|..++.++.+. +.+.+.
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 654 899999999999999999999999999999999999998888 555555
Q ss_pred HHHHHHHHHH
Q 038079 120 QVKTEQGNLK 129 (144)
Q Consensus 120 ~l~~ef~~~~ 129 (144)
.+...+.++.
T Consensus 79 ~l~~~l~~l~ 88 (90)
T PF01627_consen 79 ELEAMLEQLR 88 (90)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHh
Confidence 5555555444
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=99.52 E-value=1.9e-14 Score=96.55 Aligned_cols=85 Identities=18% Similarity=0.183 Sum_probs=74.1
Q ss_pred HHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHH
Q 038079 46 VTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQ 125 (144)
Q Consensus 46 ~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef 125 (144)
+++..|+++.+..+..|..++..+ |+..+++.+|+||||++++|+..|..+|..+|...+... ++...+...+...|
T Consensus 2 e~~~~f~~~~~~~l~~l~~~~~~~--~~~~l~~~~H~LKG~a~~~g~~~l~~~~~~lE~~~~~~~-~~~~~~~~~l~~~~ 78 (87)
T smart00073 2 EELAEFLQSLEEGLLELEKALDAQ--DVNEIFRAAHTLKGSAGSLGLQQLAQLCHQLENLLDAAR-SGEVELTPDLLDLL 78 (87)
T ss_pred hHHHHHHHHHHHHHHHHHhCcCHh--HHHHHHHHHHhhhhhHHhcCHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHH
Confidence 678999999999999999999754 899999999999999999999999999999999888643 44456788888888
Q ss_pred HHHHHHHH
Q 038079 126 GNLKAKLD 133 (144)
Q Consensus 126 ~~~~~aL~ 133 (144)
..+...|.
T Consensus 79 ~~~~~~l~ 86 (87)
T smart00073 79 LELVDVLK 86 (87)
T ss_pred HHHHHHHc
Confidence 88877664
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=99.41 E-value=4e-13 Score=91.82 Aligned_cols=64 Identities=27% Similarity=0.343 Sum_probs=59.7
Q ss_pred HHHHHHHHHhHHHHHHHHHHHhc----cCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCC
Q 038079 45 EVTINVYFEESNELLPMIEDLLG----KNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGD 110 (144)
Q Consensus 45 ~~Li~~f~~ds~~~l~~l~~al~----~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~ 110 (144)
.+++..|+++.+..+..|..++. .+ |+..+++.+|+||||++++|+.+|..+|..+|..++.+.
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 57899999999999999999998 44 899999999999999999999999999999999998753
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=99.37 E-value=2.4e-12 Score=117.44 Aligned_cols=93 Identities=16% Similarity=0.293 Sum_probs=87.4
Q ss_pred CChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHH
Q 038079 39 EDPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAF 118 (144)
Q Consensus 39 ~~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l 118 (144)
.+++.+.+++..|+++++..+..|..++..+ |+..+++.+|.|||+++++||.+++.+|..||..++.|+. ....+
T Consensus 876 ~~~~~~~~~~~~f~~~~~~~~~~l~~~~~~~--d~~~~~~~~H~lkg~~~~~g~~~l~~~~~~le~~~~~~~~--~~~~~ 951 (968)
T TIGR02956 876 LGVEKVRQLVALFKTSSAEQLEELSAARAVD--DDAQIKKLAHKLKGSAGSLGLTQLTQLCQQLEKQGKTGAL--ELSDI 951 (968)
T ss_pred cCcHHHHHHHHHHHHhhHHHHHHHHHHHhCC--CHHHHHHHHHHHHHHHHHhCHHHHHHHHHHHHHhcccCCc--chhHH
Confidence 5688999999999999999999999999976 9999999999999999999999999999999999999988 45789
Q ss_pred HHHHHHHHHHHHHHHHH
Q 038079 119 EQVKTEQGNLKAKLDSY 135 (144)
Q Consensus 119 ~~l~~ef~~~~~aL~~~ 135 (144)
+.++..|..+..+|++|
T Consensus 952 ~~l~~~~~~~~~~l~~~ 968 (968)
T TIGR02956 952 DEIKQAWQASKTALDQW 968 (968)
T ss_pred HHHHHHHHHHHHHHHhC
Confidence 99999999999999875
No 7
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=99.12 E-value=5.6e-10 Score=100.59 Aligned_cols=100 Identities=14% Similarity=0.204 Sum_probs=93.8
Q ss_pred CChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHH
Q 038079 39 EDPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAF 118 (144)
Q Consensus 39 ~~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l 118 (144)
.++..+.+.+..|.+..+..+..|..++..+ |+..+...||.|||+++++|+..++.+|..+|.....+.++...+++
T Consensus 678 ~g~~~~~~~l~~~~~~~~~~~~~l~~~l~~~--d~~~~~~~ah~l~g~~~~~g~~~l~~~~~~le~~~~~~~~~~~~~~~ 755 (779)
T PRK11091 678 VGPKLITDSLAVFEKMMPGYLSVLDSNLTAR--DQKGIVEEAHKIKGAAGSVGLRHLQQLAQQIQSPDLPAWWDNVQDWV 755 (779)
T ss_pred cCHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhCcCccccHHHHHHHH
Confidence 4567788999999999999999999999976 89999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 038079 119 EQVKTEQGNLKAKLDSYFELVK 140 (144)
Q Consensus 119 ~~l~~ef~~~~~aL~~~l~~~~ 140 (144)
++++.+|.....+|+.|+...+
T Consensus 756 ~~l~~~~~~~~~~~~~~~~~~~ 777 (779)
T PRK11091 756 EELKNEWRHDVEVLKAWLAQAE 777 (779)
T ss_pred HHHHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999998654
No 8
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=98.90 E-value=6.6e-09 Score=96.31 Aligned_cols=84 Identities=12% Similarity=0.120 Sum_probs=77.5
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHH
Q 038079 43 FVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVK 122 (144)
Q Consensus 43 fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~ 122 (144)
+...++..|++..|.-+..|..++.++ |+..+++.||.|||+++++|...++.+|.+||..++.++..++...+.+|.
T Consensus 808 ~~s~~~~lF~~t~~~di~~L~~~~~~~--D~~~l~~~aHrLKG~~aml~l~~l~~~~~~LE~~i~~~~~~~i~~~i~~id 885 (894)
T PRK10618 808 HASDYYALFVDTVPDDVKRLYTEAATS--DFASLAQTAHRLKGVFAMLNLVPGKQLCETLEHLIREKDEPGIENYISDID 885 (894)
T ss_pred hhhhHHHHHHHhhHHHHHHHHHHHhcc--CHHHHHHHHHHHHHHHHHcChHHHHHHHHHHHHHHhhCChHHHHHHHHHHH
Confidence 344567899999999999999999986 999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHH
Q 038079 123 TEQGNL 128 (144)
Q Consensus 123 ~ef~~~ 128 (144)
..+.++
T Consensus 886 ~~v~~l 891 (894)
T PRK10618 886 SFVKSL 891 (894)
T ss_pred HHHHHH
Confidence 877654
No 9
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=98.57 E-value=2.5e-07 Score=84.50 Aligned_cols=88 Identities=15% Similarity=0.220 Sum_probs=72.2
Q ss_pred CChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHH
Q 038079 39 EDPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAF 118 (144)
Q Consensus 39 ~~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l 118 (144)
.+++.+.+++..|.++++..+..++.+...+ |+..+++.||.|||+++++|+..++.+|.++|..+...
T Consensus 820 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~ah~lkg~~~~lg~~~l~~~~~~le~~~~~~--------- 888 (914)
T PRK11466 820 MGTEKIHEWLALFKQHALPLLDEIDIARASQ--DSEKIKRAAHQLKSSCSSLGMRQASQACAQLEQQPLSA--------- 888 (914)
T ss_pred cCHHHHHHHHHHHHHhhHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhCCCCCc---------
Confidence 4566788999999999999999999999976 89999999999999999999999999999999975422
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 038079 119 EQVKTEQGNLKAKLDSYFE 137 (144)
Q Consensus 119 ~~l~~ef~~~~~aL~~~l~ 137 (144)
..+..++.+...+|..|+.
T Consensus 889 ~~~~~~~~~~~~~~~~~~~ 907 (914)
T PRK11466 889 PLPHEEITRSVAALEAWLA 907 (914)
T ss_pred hhHHHHHHHHHHHHHHHHH
Confidence 2234455555666666654
No 10
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=98.57 E-value=7.2e-07 Score=81.13 Aligned_cols=97 Identities=15% Similarity=0.337 Sum_probs=83.8
Q ss_pred CChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcC-CHHHHHHH
Q 038079 39 EDPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNG-DIEGAKAA 117 (144)
Q Consensus 39 ~~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~-~~~~~~~~ 117 (144)
+.++...+++..|.++.+..+..|..++... |...+...+|++||+++++|+.++..+|..+|...+.+ ..+.....
T Consensus 821 ~~~~~~~~~l~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~h~l~g~~~~~g~~~l~~~~~~le~~~~~~~~~~~~~~~ 898 (919)
T PRK11107 821 GKPDLARDMLQMLLDFLPEVRNKVEEALAGE--DPEGLLDLIHKLHGSCSYSGVPRLKKLCQLIEQQLRSGTSVEDLEPE 898 (919)
T ss_pred CCHHHHHHHHHHHHHhHHHHHHHHHHHHHCC--CHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHcCCChhhHHHH
Confidence 4567888999999999999999999999975 78999999999999999999999999999999999876 45666777
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 038079 118 FEQVKTEQGNLKAKLDSYFE 137 (144)
Q Consensus 118 l~~l~~ef~~~~~aL~~~l~ 137 (144)
+..+..++.++...+.++++
T Consensus 899 ~~~~~~~~~~~~~~~~~~~~ 918 (919)
T PRK11107 899 LLELLDEMENVARAAKKVLS 918 (919)
T ss_pred HHHHHHHHHHHHHHHHHHhh
Confidence 77777777777777776653
No 11
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=97.82 E-value=0.00015 Score=66.27 Aligned_cols=71 Identities=25% Similarity=0.404 Sum_probs=57.3
Q ss_pred hHHHHHHHHHHHhHHHHHHHHHHHhcc---CCCCH---HHHHHHHhhhcccccccChHHHHHHHHHHHHH---hhcCCHH
Q 038079 42 NFVEVTINVYFEESNELLPMIEDLLGK---NPIEG---SEMERILHRFKGSCASVGANKVKNEVNVVIAC---CRNGDIE 112 (144)
Q Consensus 42 ~fv~~Li~~f~~ds~~~l~~l~~al~~---~~~D~---~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~---~~~~~~~ 112 (144)
+-..++...|++++++++..|..++-. .+.|. .++.+.||+|||+++.+|-..++++|-.+|.. .++|...
T Consensus 4 ~~~~~~~~~F~~Ea~e~l~~l~~~Ll~LE~~~~d~~~ln~ifRaaHTlKG~a~~~g~~~l~~l~H~~E~~ld~~r~g~~~ 83 (716)
T COG0643 4 MDMEEILEDFLEEAEELLQALEQALLALEPDPEDLDLLNAIFRAAHTLKGGAGTLGLTTLAELAHAMEDLLDALRNGELE 83 (716)
T ss_pred hHHHHHHHHHHHhhHHHHHHHHHhHhhccCCCCCHHHHHHHHHHHHhhhhhhhhcChhHHHHHHHHHHHHHHHHhcCCcc
Confidence 445788999999999999999986543 23343 46789999999999999999999999999974 4566433
No 12
>PRK10547 chemotaxis protein CheA; Provisional
Probab=97.78 E-value=0.00018 Score=65.36 Aligned_cols=62 Identities=19% Similarity=0.288 Sum_probs=52.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHHhcc---CCCC---HHHHHHHHhhhcccccccChHHHHHHHHHHHHHh
Q 038079 45 EVTINVYFEESNELLPMIEDLLGK---NPIE---GSEMERILHRFKGSCASVGANKVKNEVNVVIACC 106 (144)
Q Consensus 45 ~~Li~~f~~ds~~~l~~l~~al~~---~~~D---~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~ 106 (144)
.+++..|++++.++|+.|+..+-. .+.| ...+-+.+|+|||+|+.+|-..+..+|-.+|..-
T Consensus 4 ~~~l~~F~~Ea~E~l~~le~~Ll~LE~~p~d~e~in~lFRa~HTiKG~a~~~g~~~i~~l~H~~E~ll 71 (670)
T PRK10547 4 SDFYQTFFDEADELLADMEQHLLVLDPEAPDAEQLNAIFRAAHSIKGGAGTFGFTVLQETTHLMENLL 71 (670)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHhhhhHHhhcCchHHHHHHHHHHHHH
Confidence 478999999999999999987654 3334 3467889999999999999999999999999765
No 13
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=96.77 E-value=0.031 Score=53.03 Aligned_cols=95 Identities=15% Similarity=0.226 Sum_probs=74.3
Q ss_pred ChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCC-HHHHHHHH
Q 038079 40 DPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGD-IEGAKAAF 118 (144)
Q Consensus 40 ~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~-~~~~~~~l 118 (144)
......+++..+...+...+..+..+...+ |...++..+|.+||++..+|+..+...|.++|......+ .+.....+
T Consensus 1098 ~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~h~~~g~~~~l~~~~l~~~~~~~e~~~~~~~~~~~l~~~~ 1175 (1197)
T PRK09959 1098 DLQLMQEILMTFQHETHKDLPAAFHALEAG--DNRTFHQCIHRIHGAANILNLQKLINISHQLEITPVSDDSKPEILQLL 1175 (1197)
T ss_pred CHHHHHHHHHHHHHhhHHHHHHHHHHHHcC--CHHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhhcCCchHHHHHHH
Confidence 446778888999999999898888888876 779999999999999999999999999999998876543 34455556
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 038079 119 EQVKTEQGNLKAKLDSYF 136 (144)
Q Consensus 119 ~~l~~ef~~~~~aL~~~l 136 (144)
+.+..........++.++
T Consensus 1176 ~~~~~~~~~~~~~~~~~~ 1193 (1197)
T PRK09959 1176 NSVKEHIAELDQEIAVFC 1193 (1197)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 655555555555555443
No 14
>PRK15347 two component system sensor kinase SsrA; Provisional
Probab=96.41 E-value=0.01 Score=54.27 Aligned_cols=62 Identities=21% Similarity=0.318 Sum_probs=51.8
Q ss_pred HHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHH
Q 038079 47 TINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIE 112 (144)
Q Consensus 47 Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~ 112 (144)
+-..+.+.....+..+..++..+ | .+++.+|.+||+++++|+.++...|.++|...+.+...
T Consensus 838 l~~~~~~~l~~~~~~~~~~~~~~--~--~l~~~~h~i~~~~~~~g~~~l~~~~~~~e~~~~~~~~~ 899 (921)
T PRK15347 838 LNSKLYQSLLLLLAQIEQAVENQ--E--VLSQLLHTLKGCAGQAGLTELQCAVIDLENALETGEIL 899 (921)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCH--H--HHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHhcCCCC
Confidence 44555566678888888888865 3 89999999999999999999999999999998876543
No 15
>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=76.26 E-value=24 Score=33.54 Aligned_cols=83 Identities=14% Similarity=0.218 Sum_probs=54.3
Q ss_pred hhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHH
Q 038079 41 PNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQ 120 (144)
Q Consensus 41 ~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~ 120 (144)
++=+.+|++.+-+=....+.+|.+...+++ +-.. -..-+.+.+++-.-|...-..||++.++|+.+.+.++|++
T Consensus 522 deEI~~Lm~eLR~Am~~ym~~LAeq~~~~~-~~~~-----~~~~~~~~~l~~~dLq~Mmd~ieela~~G~~~~A~qlL~q 595 (851)
T TIGR02302 522 DEEIKQLTDKLRAAMQTYMRQLAQQLRNNP-QQLA-----RPLDPNTKVLRQQDLQNMMDQIENLARSGDRDQAKQLLSQ 595 (851)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhCc-cccc-----ccCCccccccCHHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 334455555555555555555555444321 1000 0112335779999999999999999999999999999999
Q ss_pred HHHHHHHHH
Q 038079 121 VKTEQGNLK 129 (144)
Q Consensus 121 l~~ef~~~~ 129 (144)
+++-.+..+
T Consensus 596 lq~mmenlq 604 (851)
T TIGR02302 596 LQQMMNNLQ 604 (851)
T ss_pred HHHHHHHHh
Confidence 887665544
No 16
>PF13779 DUF4175: Domain of unknown function (DUF4175)
Probab=67.97 E-value=31 Score=32.64 Aligned_cols=42 Identities=14% Similarity=0.316 Sum_probs=37.3
Q ss_pred ccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 038079 85 GSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQG 126 (144)
Q Consensus 85 GSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~ 126 (144)
+.+.+++..-|...-..||++.++|+.+.+.++|+++++-.+
T Consensus 530 ~~~~~~~~~dL~~mmd~ie~la~~G~~~~A~q~L~qlq~mme 571 (820)
T PF13779_consen 530 GNSQMMSQQDLQRMMDRIEELARSGRMDEARQLLEQLQQMME 571 (820)
T ss_pred hhhhccCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHH
Confidence 456689999999999999999999999999999998876554
No 17
>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=66.55 E-value=26 Score=23.70 Aligned_cols=66 Identities=12% Similarity=0.184 Sum_probs=48.6
Q ss_pred HHHHHhcccchhhhHHH-HHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHh
Q 038079 10 IASMRQHLLDEEILDEQ-FVELEGLALASDEDPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILH 81 (144)
Q Consensus 10 ~~~~~~~~~~~~~lD~~-~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH 81 (144)
...++..+..+|+++.. .+.|+.- ....+=...||++-..-++.-......+|... .|+.+.++.|
T Consensus 16 v~~ild~L~~~gvlt~~~~e~I~~~----~t~~~qa~~Lld~L~trG~~Af~~F~~aL~~~--~~~~La~lL~ 82 (86)
T cd08323 16 TSYIMDHMISDGVLTLDEEEKVKSK----ATQKEKAVMLINMILTKDNHAYVSFYNALLHE--GYKDLALLLH 82 (86)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHcC----CChHHHHHHHHHHHHhcCHHHHHHHHHHHHhc--CChHHHHHHh
Confidence 45567778888999886 7777765 23356667888888888888888888888752 4777776655
No 18
>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=61.74 E-value=70 Score=27.63 Aligned_cols=83 Identities=16% Similarity=0.210 Sum_probs=57.6
Q ss_pred HHHHHHHHHhcccchhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHhHHHH-HHHHHHHhccCCCCHHHHHHHHhhhc
Q 038079 6 LHQQIASMRQHLLDEEILDEQFVELEGLALASDEDPNFVEVTINVYFEESNEL-LPMIEDLLGKNPIEGSEMERILHRFK 84 (144)
Q Consensus 6 l~~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~-l~~l~~al~~~~~D~~~l~~~aH~LK 84 (144)
+..++...+.++|.+.=+-..+.+++.+ . |.|- +..|+..+... +..|-.|...+ |.+.|+.+++
T Consensus 210 itdkv~~~~~~lF~ete~a~~l~eIk~~--D----PsFd---~~~Fl~gar~aI~p~ILeAf~kG--D~e~LK~~ls--- 275 (378)
T TIGR00984 210 VTDKIGGVFSGMFSETEVSEVLTEFKKI--D----PTFD---KEHFLRFLREYIVPEILEAYVKG--DLEVLKSWCS--- 275 (378)
T ss_pred hhhhhhhhhhcccCCCHHHHHHHHHHHh--C----CCCC---HHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHhhC---
Confidence 3344555566677777777667788877 3 4554 45678888888 68899999987 8899998844
Q ss_pred ccccccChHHHHHHHHHHHHHhhcC
Q 038079 85 GSCASVGANKVKNEVNVVIACCRNG 109 (144)
Q Consensus 85 GSSaslGA~~l~~~c~~lE~~~~~~ 109 (144)
-......|..+......|
T Consensus 276 -------e~vy~~f~a~I~qr~~~G 293 (378)
T TIGR00984 276 -------EAPFSVYATVVKEYKKMG 293 (378)
T ss_pred -------HHHHHHHHHHHHHHHHCC
Confidence 345556666677666655
No 19
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=60.43 E-value=15 Score=25.83 Aligned_cols=40 Identities=18% Similarity=0.241 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHH
Q 038079 93 NKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKL 132 (144)
Q Consensus 93 ~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL 132 (144)
..+...+..++....+++++.+...++.+...|.+.+..+
T Consensus 26 ~~i~~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~~~ 65 (121)
T PF14276_consen 26 DSIEEQLEQIEEAIENEDWEKAYKETEELEKEWDKNKKRW 65 (121)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhchhe
Confidence 4455566777777777777777777777777777665543
No 20
>PRK03636 hypothetical protein; Provisional
Probab=60.29 E-value=29 Score=26.82 Aligned_cols=39 Identities=15% Similarity=0.389 Sum_probs=30.1
Q ss_pred HHHHHHHHHHh------HHHHHHHHHHHhccCCCCHHHHHHHHhhhc
Q 038079 44 VEVTINVYFEE------SNELLPMIEDLLGKNPIEGSEMERILHRFK 84 (144)
Q Consensus 44 v~~Li~~f~~d------s~~~l~~l~~al~~~~~D~~~l~~~aH~LK 84 (144)
...+++.+++. -.+++..|..||+++ |.+.+.++...||
T Consensus 130 ~~~~ae~~L~~~~~~~r~~~L~~~ID~ALd~~--D~e~F~~Ls~~l~ 174 (179)
T PRK03636 130 DRLLAEQFLEQSVFQFRREKLLKQIDEALDRR--DKEAFHRLSDELN 174 (179)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC--CHHHHHHHHHHHH
Confidence 34555666665 467889999999987 8889998887776
No 21
>KOG4747 consensus Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms]
Probab=59.60 E-value=74 Score=23.99 Aligned_cols=58 Identities=7% Similarity=0.048 Sum_probs=47.2
Q ss_pred hhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHH
Q 038079 41 PNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNV 101 (144)
Q Consensus 41 ~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~ 101 (144)
.+|-..++..++.| ....+|.+......+|+ -..-..|.||+|+..+|-.+.+--|..
T Consensus 13 ~d~~~sl~~qgild--~qF~qlq~lqD~~~p~f-v~ev~~~fF~~s~~~i~~~r~ald~~~ 70 (150)
T KOG4747|consen 13 SDYTKSLFDQGILD--SQFLQLQELQDDSSPDF-VEEVVGLFFEDSERLINNLRLALDCER 70 (150)
T ss_pred HHHHHHHHHHHhhH--HHHHHHHHHhcccCccH-HHHHHHHHHHHHHHHHHHHHHHHhhHh
Confidence 46888888888888 67888888887754554 456678999999999999999999884
No 22
>PRK03057 hypothetical protein; Provisional
Probab=56.92 E-value=34 Score=26.49 Aligned_cols=37 Identities=19% Similarity=0.341 Sum_probs=28.9
Q ss_pred HHHHHHHHh------HHHHHHHHHHHhccCCCCHHHHHHHHhhhc
Q 038079 46 VTINVYFEE------SNELLPMIEDLLGKNPIEGSEMERILHRFK 84 (144)
Q Consensus 46 ~Li~~f~~d------s~~~l~~l~~al~~~~~D~~~l~~~aH~LK 84 (144)
..++.|++. -.+++..|..||+.+ |.+.+.++.+.||
T Consensus 131 ~~ae~~L~~~~~~~~~~~L~~~ID~ALd~~--D~e~F~~Lt~~L~ 173 (180)
T PRK03057 131 KETEQVLDEVLKRNEVSRLRMQIDQALDRK--DMEEFQRLTEKLK 173 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CHHHHHHHHHHHH
Confidence 456666666 567788999999987 8888888887765
No 23
>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=51.82 E-value=62 Score=20.76 Aligned_cols=40 Identities=15% Similarity=0.166 Sum_probs=19.4
Q ss_pred hHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhh
Q 038079 42 NFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRF 83 (144)
Q Consensus 42 ~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~L 83 (144)
+=+..+....-.....++..|..++..+ ||.......+.|
T Consensus 27 ~~L~~l~~~~~~~~~~~~~~l~~~f~~~--d~~~A~~~~~kL 66 (78)
T PF07743_consen 27 AELEELKKEIEERIKELIKELAEAFDAK--DWEEAKEALRKL 66 (78)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHccC--cHHHHHHHHHHH
Confidence 3344444444444555555555555433 555555555444
No 24
>KOG2424 consensus Protein involved in transcription start site selection [Transcription]
Probab=51.52 E-value=24 Score=27.63 Aligned_cols=35 Identities=17% Similarity=0.195 Sum_probs=24.3
Q ss_pred ccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHH
Q 038079 87 CASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQG 126 (144)
Q Consensus 87 SaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~ 126 (144)
-|++||..+.++|..|+. ++.+ ....++.|-.+|+
T Consensus 147 dA~~Gaf~I~elcq~l~~--~s~d---~Ed~ideil~~~e 181 (195)
T KOG2424|consen 147 DATLGAFLILELCQCLQA--QSDD---LEDNIDEILLEFE 181 (195)
T ss_pred hhhhhHHHHHHHHHHHHh--cccc---HHHHHHHHHHHHH
Confidence 478999999999999997 3333 3444555555444
No 25
>PF13326 PSII_Pbs27: Photosystem II Pbs27; PDB: 2KND_A 2KMF_A 2Y6X_A.
Probab=48.04 E-value=1.1e+02 Score=22.66 Aligned_cols=86 Identities=9% Similarity=0.084 Sum_probs=54.6
Q ss_pred HHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcc-----------cccccChHHHHHHHHHHHHHh----hcCC
Q 038079 46 VTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKG-----------SCASVGANKVKNEVNVVIACC----RNGD 110 (144)
Q Consensus 46 ~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKG-----------SSaslGA~~l~~~c~~lE~~~----~~~~ 110 (144)
.+-..|.+|+-..+..|+.+++.+ .|.+..++.+-.+|- ...--|=.-...+-..|...+ ..|+
T Consensus 44 ~l~~~Y~~dt~~vv~~lr~~l~l~-~d~~~~~~~~~~ar~~in~~vs~YRr~~~v~g~~Sf~~m~tAln~LaghY~s~g~ 122 (145)
T PF13326_consen 44 GLTGDYVKDTRAVVKTLREALELD-KDDPNRAEAAAEARELINDYVSRYRRGPSVSGLPSFTTMYTALNALAGHYSSYGN 122 (145)
T ss_dssp S--S-CHHHHHHHHHHHHHHHCS--TT-TTHHHHHHHHHHHHHHHHCCCCCCHHCCTSHHHHHHHHHHHHHHHHCHHHTT
T ss_pred cccchHHHHHHHHHHHHHHHHcCC-CCCccHHHHHHHHHHHHHHHHHHhCCCCCcCCcchHHHHHHHHHHHHHHHHhCCC
Confidence 344669999999999999999874 466777666666653 333344344444444454443 4466
Q ss_pred H-HHHHHHHHHHHHHHHHHHHHH
Q 038079 111 I-EGAKAAFEQVKTEQGNLKAKL 132 (144)
Q Consensus 111 ~-~~~~~~l~~l~~ef~~~~~aL 132 (144)
. +--....+.|.+||.++..+|
T Consensus 123 raPlP~k~k~rll~el~~Ae~aL 145 (145)
T PF13326_consen 123 RAPLPEKLKERLLKELDQAEKAL 145 (145)
T ss_dssp S-S--HHHHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHhcC
Confidence 5 666778889999998888765
No 26
>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=47.85 E-value=43 Score=19.03 Aligned_cols=27 Identities=15% Similarity=0.331 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhccCCCCHHHHHHHHhhh
Q 038079 55 SNELLPMIEDLLGKNPIEGSEMERILHRF 83 (144)
Q Consensus 55 s~~~l~~l~~al~~~~~D~~~l~~~aH~L 83 (144)
-+++...|..||.++ |-..+.+++..|
T Consensus 11 ~~~L~~~ID~ALd~~--D~e~F~~Ls~eL 37 (37)
T PF08858_consen 11 KEQLLELIDEALDNR--DKEWFYELSEEL 37 (37)
T ss_dssp HHHHHHHHHHHHHTT---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcC--CHHHHHHHHhhC
Confidence 357888999999987 888888876543
No 27
>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=47.31 E-value=1.2e+02 Score=22.63 Aligned_cols=77 Identities=10% Similarity=0.239 Sum_probs=46.7
Q ss_pred ChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHH
Q 038079 40 DPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFE 119 (144)
Q Consensus 40 ~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~ 119 (144)
+|+|+.++++. -..++.+-..+ |...+..+.+.++ .++..+...++.+-..++++.+...+.
T Consensus 76 d~~fLme~Me~--------rE~lee~~~~~--d~~~L~~l~~~~~--------~~~~~~~~~l~~~~~~~d~~~A~~~~~ 137 (157)
T TIGR00714 76 DTAFLMEQLEL--------REELDEIEQAK--DEARLESFIKRVK--------KMFQTRHQLLVEQLDNQTWAAAADYTR 137 (157)
T ss_pred CHHHHHHHHHH--------HHHHHHHHhCC--CHHHHHHHHHHHH--------HHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 46777666543 22222222222 5566766666655 466777777777777888888887777
Q ss_pred HHHHHHHHHHHHHHHH
Q 038079 120 QVKTEQGNLKAKLDSY 135 (144)
Q Consensus 120 ~l~~ef~~~~~aL~~~ 135 (144)
+++= |.++...+.++
T Consensus 138 kLky-~~kl~~~i~~~ 152 (157)
T TIGR00714 138 KLRF-LDKLRSSAEQL 152 (157)
T ss_pred HHHH-HHHHHHHHHHH
Confidence 7664 45555555443
No 28
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=45.98 E-value=1.3e+02 Score=22.69 Aligned_cols=51 Identities=22% Similarity=0.294 Sum_probs=32.3
Q ss_pred CHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHH
Q 038079 72 EGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAK 131 (144)
Q Consensus 72 D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~a 131 (144)
|...+..+...++. ++..+...|+.+-..++++.+...+.+|+= |.++...
T Consensus 107 ~~~~L~~l~~~~~~--------~~~~~~~~l~~~f~~~d~~~A~~~~~~L~y-~~kl~~~ 157 (166)
T PRK01356 107 LFSDLEKIKNKYEL--------MYKNEIDSLKQAFEEQNLSDATIKTSKLKY-IGTLLNK 157 (166)
T ss_pred CHHHHHHHHHHHHH--------HHHHHHHHHHHHHhcCCHHHHHHHHHHHHH-HHHHHHH
Confidence 34556666666653 445666777777777888888877777654 3333333
No 29
>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=44.24 E-value=1.3e+02 Score=22.37 Aligned_cols=73 Identities=21% Similarity=0.361 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHH---------------------HHHHHHHHHHHhhcCCHHH
Q 038079 55 SNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANK---------------------VKNEVNVVIACCRNGDIEG 113 (144)
Q Consensus 55 s~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~---------------------l~~~c~~lE~~~~~~~~~~ 113 (144)
+..++.++...++++ ||..++...| |+.+.++-.- |.+--..|-.+++.+|
T Consensus 48 ~~~r~~eLk~lI~kk--~W~~vrn~ir---gp~g~Lr~dl~~l~~sl~p~dqk~a~~L~~~Lf~~L~~LD~AA~~kd--- 119 (142)
T TIGR03042 48 AKDRLPELASLVAKE--DWVFTRNLIH---GPMGEVRREMTYLNQSLLPKDQKEALALAKELKDDLEKLDEAARLQD--- 119 (142)
T ss_pred HHHhhHHHHHHHhhc--chHHHHHHHh---ccHHHHHHHHHHHHHccCHHhHHHHHHHHHHHHHHHHHHHHHHHhcC---
Confidence 566777777777765 7777775544 5555544321 1112223333334333
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 114 AKAAFEQVKTEQGNLKAKLDSYFELV 139 (144)
Q Consensus 114 ~~~~l~~l~~ef~~~~~aL~~~l~~~ 139 (144)
-.+.++.|.++.+.|+.|+++.
T Consensus 120 ----~~~a~k~Y~~av~~~dafl~~~ 141 (142)
T TIGR03042 120 ----GPQAQKAYQKAAADFDAYLDLL 141 (142)
T ss_pred ----HHHHHHHHHHHHHHHHHHHhhC
Confidence 3456778999999999998763
No 30
>PF03993 DUF349: Domain of Unknown Function (DUF349); InterPro: IPR007139 This motif is found singly or as up to five tandem repeats in a small set of bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand.
Probab=44.13 E-value=52 Score=20.77 Aligned_cols=62 Identities=11% Similarity=0.178 Sum_probs=40.6
Q ss_pred HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHH
Q 038079 45 EVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTE 124 (144)
Q Consensus 45 ~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~e 124 (144)
..+.+.|..-.......+...... ++. .=..+|.+++.+....++......+..|..+
T Consensus 8 ~~a~~~~~~~~~~~~~~~~~~~~~---n~~-------------------~K~~Li~~~~~l~~~~d~~~~~~~~k~l~~~ 65 (77)
T PF03993_consen 8 RAACDAFFDRRKEFFEEQDAEREE---NLE-------------------KKEALIEEAEALAESEDWKEAAEEIKELQQE 65 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH---HHH-------------------HHHHHHHHHHHhcccccHHHHHHHHHHHHHH
Confidence 466667776666666666655553 111 1235778888888887877777777777777
Q ss_pred HHHH
Q 038079 125 QGNL 128 (144)
Q Consensus 125 f~~~ 128 (144)
|..+
T Consensus 66 Wk~i 69 (77)
T PF03993_consen 66 WKEI 69 (77)
T ss_pred HHHc
Confidence 7643
No 31
>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=41.13 E-value=1.5e+02 Score=22.12 Aligned_cols=70 Identities=10% Similarity=0.072 Sum_probs=39.6
Q ss_pred HHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHH-----------HhhcCCHHHHHHH
Q 038079 49 NVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIA-----------CCRNGDIEGAKAA 117 (144)
Q Consensus 49 ~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~-----------~~~~~~~~~~~~~ 117 (144)
...++|+.++|.-|...++++++.-... .+|..+|..|+. .--..+.+.|..|
T Consensus 64 kr~~~D~~KRL~iLfd~ln~g~Ls~~v~----------------~~L~~L~~aL~~~d~~~A~~Ih~~L~t~h~~E~~~W 127 (157)
T PF07304_consen 64 KRVVDDIEKRLNILFDHLNNGKLSKPVV----------------DKLHQLAQALQARDYDAADEIHVDLMTDHVDECGNW 127 (157)
T ss_dssp HHHHHHHHHHHHHHHHHHHHT-S-HHHH----------------HHHHHHHHHHHHT-HHHHHHHHHHHHHSSHHHHTTT
T ss_pred hhHHHHHHHHHHHHHHHHhcCCCCHHHH----------------HHHHHHHHHHHcCCHHHHHHHHHHHHhccHHHhhhH
Confidence 3446899999999999999875433322 234445544432 1123455666666
Q ss_pred HHHHHHHHHHHHHHHHH
Q 038079 118 FEQVKTEQGNLKAKLDS 134 (144)
Q Consensus 118 l~~l~~ef~~~~~aL~~ 134 (144)
+-.+++-...+++.-..
T Consensus 128 mvGVKRLI~~~r~~~~~ 144 (157)
T PF07304_consen 128 MVGVKRLIAMARNLPPE 144 (157)
T ss_dssp HHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHhcCcc
Confidence 66666666555554333
No 32
>PF13446 RPT: A repeated domain in UCH-protein
Probab=40.97 E-value=60 Score=19.99 Aligned_cols=36 Identities=14% Similarity=0.262 Sum_probs=28.3
Q ss_pred ChhcCCCChhHHHHHHHHHHHhHHHHHHHHHHHhcc
Q 038079 33 LALASDEDPNFVEVTINVYFEESNELLPMIEDLLGK 68 (144)
Q Consensus 33 L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l~~al~~ 68 (144)
||+.+.-..+++.......+.+.|.....++.||..
T Consensus 11 Lgi~~~~~Dd~Ii~~f~~~~~~~P~~~~~~r~AL~~ 46 (62)
T PF13446_consen 11 LGIDEDTDDDFIISAFQSKVNDDPSQKDTLREALRV 46 (62)
T ss_pred hCcCCCCCHHHHHHHHHHHHHcChHhHHHHHHHHHH
Confidence 444566667888889899999999888888888764
No 33
>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=40.88 E-value=31 Score=27.12 Aligned_cols=38 Identities=13% Similarity=0.204 Sum_probs=24.1
Q ss_pred ccccChHHHHHHHHHHHHHhhcCCHH-HHHHHHHHHHHHH
Q 038079 87 CASVGANKVKNEVNVVIACCRNGDIE-GAKAAFEQVKTEQ 125 (144)
Q Consensus 87 SaslGA~~l~~~c~~lE~~~~~~~~~-~~~~~l~~l~~ef 125 (144)
.|.+||..+.++|..|+.. ...+++ .+..++...+...
T Consensus 145 eA~~Ga~~ileLc~~l~~~-~~~d~e~~i~~il~~fe~k~ 183 (195)
T PF04722_consen 145 EATIGAFLILELCQMLEEE-ASEDLEDEIDEILQEFEEKH 183 (195)
T ss_dssp HHHHHHHHHHHHHHHHH---TSSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhh-ccccHHHHHHHHHHHHHHHc
Confidence 3569999999999999973 333443 3445555555543
No 34
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.14 E-value=7.6 Score=25.86 Aligned_cols=20 Identities=25% Similarity=0.552 Sum_probs=17.8
Q ss_pred hhhcccccccChHHHHHHHH
Q 038079 81 HRFKGSCASVGANKVKNEVN 100 (144)
Q Consensus 81 H~LKGSSaslGA~~l~~~c~ 100 (144)
-++|||++-|+|..+...|.
T Consensus 27 k~I~GSCGGi~alGi~K~Cd 46 (77)
T COG2991 27 KSIKGSCGGIAALGIEKVCD 46 (77)
T ss_pred cccccccccHHhhccchhcC
Confidence 47899999999999988887
No 35
>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=39.18 E-value=64 Score=18.32 Aligned_cols=34 Identities=12% Similarity=0.232 Sum_probs=25.0
Q ss_pred HHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHH
Q 038079 27 FVELEGLALASDEDPNFVEVTINVYFEESNELLPMI 62 (144)
Q Consensus 27 ~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l 62 (144)
+..|++| .+.-+++++..++..+-.|.+..+..|
T Consensus 5 v~~L~~m--FP~~~~~~I~~~L~~~~~~ve~ai~~L 38 (42)
T PF02845_consen 5 VQQLQEM--FPDLDREVIEAVLQANNGDVEAAIDAL 38 (42)
T ss_dssp HHHHHHH--SSSS-HHHHHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHH--CCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 6688888 888888888888877777766666554
No 36
>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=39.10 E-value=88 Score=20.19 Aligned_cols=48 Identities=6% Similarity=0.106 Sum_probs=29.4
Q ss_pred HHHHHHHHhcccchhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHHHHHhc
Q 038079 7 HQQIASMRQHLLDEEILDEQFVELEGLALASDEDPNFVEVTINVYFEESNELLPMIEDLLG 67 (144)
Q Consensus 7 ~~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l~~al~ 67 (144)
+.++.++++.+.-...+|+. -.+++.++.+.|++++-..--.+..-=.
T Consensus 2 K~~l~~Lv~~iDp~~~ld~~-------------vee~Ll~laddFv~~v~~~ac~lAKhR~ 49 (68)
T PF03847_consen 2 KRKLQELVKQIDPNEKLDPD-------------VEELLLELADDFVDDVVSFACRLAKHRK 49 (68)
T ss_dssp HHHHHHHHHCC-SS----HH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred hHHHHHHHHHcCCCCCCCHH-------------HHHHHHHHHHHHHHHHHHHHHHHHhccC
Confidence 35778888888666666652 2456778888888888776666655433
No 37
>smart00188 IL10 Interleukin-10 family. Interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells.
Probab=39.04 E-value=1.6e+02 Score=21.82 Aligned_cols=32 Identities=25% Similarity=0.249 Sum_probs=25.2
Q ss_pred hhHHHHHHHHcChhcCCCChhHHHHHHHHHHHhHHH
Q 038079 22 ILDEQFVELEGLALASDEDPNFVEVTINVYFEESNE 57 (144)
Q Consensus 22 ~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~ 57 (144)
.|++ +-|+.+ +++.+.-|+.+||.-|++++=.
T Consensus 29 ll~~--~ll~~~--k~~~gC~~l~ell~FYLd~V~p 60 (137)
T smart00188 29 LLTE--SLLEDF--KGYLGCQALSEMIQFYLEEVMP 60 (137)
T ss_pred hhhH--HHHHHh--CCCcchHHHHHHHHHHHHHHHH
Confidence 3454 356677 7889999999999999998754
No 38
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=38.97 E-value=1.6e+02 Score=21.82 Aligned_cols=89 Identities=7% Similarity=0.050 Sum_probs=58.5
Q ss_pred HHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhh-----------hcccccccChHHHHHHHHHHHHHhh----cC
Q 038079 45 EVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHR-----------FKGSCASVGANKVKNEVNVVIACCR----NG 109 (144)
Q Consensus 45 ~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~-----------LKGSSaslGA~~l~~~c~~lE~~~~----~~ 109 (144)
..|-..|.+|+-..+..|+.+++-+ .|-+...+.... -.+-....|-.-...+-..|+..+- .+
T Consensus 31 ~~Ltg~Y~~DT~~Vi~tlr~~i~lp-kd~p~~~~a~~~ar~~indyvsrYRr~~~v~g~~SFttm~TALNsLAGHY~sy~ 109 (135)
T TIGR03044 31 TRLTGDYVEDTLAVIQTLREAIDLP-DDDPNKSEAQAEARQLINDYISRYRRRPRVNGLSSFTTMQTALNSLAGHYKSYA 109 (135)
T ss_pred ccccchHHHHHHHHHHHHHHHHcCC-CCCccHHHHHHHHHHHHHHHHHHhcCCCCcCCcccHHHHHHHHHHHHHHhccCC
Confidence 4577899999999999999999973 344433333332 3344444555555555555554442 34
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 110 DIEGAKAAFEQVKTEQGNLKAKLDS 134 (144)
Q Consensus 110 ~~~~~~~~l~~l~~ef~~~~~aL~~ 134 (144)
+.+--..+-++|.+||.++..+|.+
T Consensus 110 ~rPlPeklk~Rl~~El~~AE~al~R 134 (135)
T TIGR03044 110 NRPLPEKLKERLEKELKKAEKALLR 134 (135)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHhc
Confidence 5555567888899999998887753
No 39
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=38.85 E-value=1.4e+02 Score=20.95 Aligned_cols=44 Identities=18% Similarity=0.200 Sum_probs=35.2
Q ss_pred HHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038079 98 EVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYFELVKQ 141 (144)
Q Consensus 98 ~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~~~~~ 141 (144)
.|.+-=..+++|+++.+..++.+-+.+|..+...=..+++.+-+
T Consensus 23 ~~~eAl~~ak~gdf~~A~~~l~eA~~~l~~AH~~qt~liq~Ea~ 66 (104)
T PRK09591 23 EVHEAFAAMREGNFDLAEQKLNQSNEELLEAHHAQTKLLQEYAS 66 (104)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 44555566899999999999999999999998887777766543
No 40
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=38.82 E-value=47 Score=25.72 Aligned_cols=25 Identities=28% Similarity=0.440 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc
Q 038079 119 EQVKTEQGNLKAKLDSYFELVKQAK 143 (144)
Q Consensus 119 ~~l~~ef~~~~~aL~~~l~~~~~~~ 143 (144)
..|++|..+|+..|..-|+-.+||+
T Consensus 50 ~eLkNeLREVREELkEKmeEIKQIK 74 (205)
T PF15079_consen 50 QELKNELREVREELKEKMEEIKQIK 74 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456666666666666666555553
No 41
>PRK10698 phage shock protein PspA; Provisional
Probab=38.48 E-value=2e+02 Score=22.69 Aligned_cols=24 Identities=8% Similarity=0.209 Sum_probs=19.2
Q ss_pred HHHHHHHHHhHHHHHHHHHHHhcc
Q 038079 45 EVTINVYFEESNELLPMIEDLLGK 68 (144)
Q Consensus 45 ~~Li~~f~~ds~~~l~~l~~al~~ 68 (144)
..+|+.|+.+....+..++.+++.
T Consensus 26 ~k~l~q~i~em~~~l~~~r~alA~ 49 (222)
T PRK10698 26 QKLVRLMIQEMEDTLVEVRSTSAR 49 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367888888888888888888775
No 42
>KOG0796 consensus Spliceosome subunit [RNA processing and modification]
Probab=37.96 E-value=2.5e+02 Score=23.76 Aligned_cols=73 Identities=12% Similarity=0.260 Sum_probs=47.6
Q ss_pred hHHHHHHHHHHHhHHHHHHHHHHHhccC---CCCHHHHH-HHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHH
Q 038079 42 NFVEVTINVYFEESNELLPMIEDLLGKN---PIEGSEME-RILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAA 117 (144)
Q Consensus 42 ~fv~~Li~~f~~ds~~~l~~l~~al~~~---~~D~~~l~-~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~ 117 (144)
+|+ +.|..|+.|+...+..+++-++.. ..+..+.. +..|.|- ..+..+-.++|.++.+|+.+.+..+
T Consensus 83 d~~-~~l~~~v~d~~rri~~~kerL~e~~ee~~~e~~~k~~~v~~l~--------e~I~~~l~~~E~LG~eG~Veeaq~~ 153 (319)
T KOG0796|consen 83 DAL-EILERFVADVDRRIEKAKERLAETVEERSEEAARKAEKVHELE--------EKIGKLLEKAEELGEEGNVEEAQKA 153 (319)
T ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHH--------HHHHHHHHHHHHHhhcCCHHHHHHH
Confidence 455 788889999999888887777642 11111100 1122221 4556667788999999999998887
Q ss_pred HHHHHH
Q 038079 118 FEQVKT 123 (144)
Q Consensus 118 l~~l~~ 123 (144)
+..++.
T Consensus 154 ~~e~E~ 159 (319)
T KOG0796|consen 154 MKEVEE 159 (319)
T ss_pred HHHHHH
Confidence 776665
No 43
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=37.66 E-value=1.1e+02 Score=20.86 Aligned_cols=36 Identities=17% Similarity=0.328 Sum_probs=30.7
Q ss_pred hcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 038079 107 RNGDIEGAKAAFEQVKTEQGNLKAKLDSYFELVKQA 142 (144)
Q Consensus 107 ~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~~~~~~ 142 (144)
-+..++.+..+|+.|+.--..+...|..+++..||+
T Consensus 31 ins~LD~Lns~LD~LE~rnD~l~~~L~~LLesnrq~ 66 (83)
T PF03670_consen 31 INSMLDQLNSCLDHLEQRNDHLHAQLQELLESNRQI 66 (83)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Confidence 345678888999999999999999999999988775
No 44
>PF09403 FadA: Adhesion protein FadA; InterPro: IPR018543 FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices. ; PDB: 3ETZ_B 3ETY_A 2GL2_B 3ETX_C 3ETW_A.
Probab=36.61 E-value=99 Score=22.51 Aligned_cols=10 Identities=30% Similarity=0.082 Sum_probs=0.0
Q ss_pred ccccccChHH
Q 038079 85 GSCASVGANK 94 (144)
Q Consensus 85 GSSaslGA~~ 94 (144)
-||.+++|..
T Consensus 12 lss~sfaA~~ 21 (126)
T PF09403_consen 12 LSSISFAATA 21 (126)
T ss_dssp ----------
T ss_pred HHHHHHHccc
Confidence 4677777776
No 45
>COG3027 zapA Cell division protein ZapA (stimulator of FtsZ polymerization and Z-ring component) [Cell cycle control, cell division, chromosome partitioning]
Probab=35.29 E-value=1.6e+02 Score=20.68 Aligned_cols=78 Identities=15% Similarity=0.140 Sum_probs=43.7
Q ss_pred HHH-HhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHH---HHHhhcCCHH----HHHHHHHHH
Q 038079 50 VYF-EESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVV---IACCRNGDIE----GAKAAFEQV 121 (144)
Q Consensus 50 ~f~-~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~l---E~~~~~~~~~----~~~~~l~~l 121 (144)
+|+ .+.+..|..+...++ ...+-||.++..+|-.+|.-++.-. |-....+... ...+-+..+
T Consensus 15 v~c~~~qee~L~~~A~~lD----------~kv~eik~~~~~~~~~rl~vmaAlNv~~eL~~l~~k~~~~~~~~~q~i~~~ 84 (105)
T COG3027 15 VNCPEEQEEHLRQAARLLD----------DKVRELKESNGVLDTERLAVMAALNVMHELLKLKEKLRDIEASLEQRIRKL 84 (105)
T ss_pred ecCCCCcHHHHHHHHHHHH----------HHHHHHHhcCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445 556666666655554 3445789999999999998766521 1111111111 344455555
Q ss_pred HHHHHHHHHHHHHHHH
Q 038079 122 KTEQGNLKAKLDSYFE 137 (144)
Q Consensus 122 ~~ef~~~~~aL~~~l~ 137 (144)
.+.+..+......+++
T Consensus 85 ~~~~~~Al~~~a~~~e 100 (105)
T COG3027 85 DQALENALTTLAQRLE 100 (105)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5555555555544443
No 46
>KOG2580 consensus Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.08 E-value=1.4e+02 Score=26.41 Aligned_cols=68 Identities=12% Similarity=0.279 Sum_probs=46.9
Q ss_pred hhHHHHHHHHHhcccchhhhHHHHHHHHcChhcC-CCChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhh
Q 038079 4 NPLHQQIASMRQHLLDEEILDEQFVELEGLALAS-DEDPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHR 82 (144)
Q Consensus 4 ~~l~~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~-~~~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~ 82 (144)
..+++.+.+.+.++++.-=..+.+.++..+ ++ -+.|+|+..+ +.| ++.++=+|.-.+ |.+-|...||.
T Consensus 282 rdvtdki~~~~~g~fsktE~Sev~tei~~i--DPsF~~~~Flr~~-ee~------IiPnVLeAyvkG--D~evLK~wcse 350 (459)
T KOG2580|consen 282 RDVTDKITDVDGGLFSKTEMSEVLTEIKKI--DPSFDKEDFLREC-EEY------IIPNVLEAYVKG--DLEVLKKWCSE 350 (459)
T ss_pred HHHHHhhhhcccccchhhHHHHHHHHHHhc--CCCCCcHHHHHHH-HHh------hhHHHHHHHHhc--cHHHHHHHHhh
Confidence 346678888888888876666668899988 66 3456776432 332 445566666766 88999998874
No 47
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=35.00 E-value=49 Score=27.08 Aligned_cols=48 Identities=6% Similarity=0.045 Sum_probs=33.0
Q ss_pred HHHHHHHhcccchhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHHHHHhcc
Q 038079 8 QQIASMRQHLLDEEILDEQFVELEGLALASDEDPNFVEVTINVYFEESNELLPMIEDLLGK 68 (144)
Q Consensus 8 ~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l~~al~~ 68 (144)
.+|.++++.+.-++.||+. -.||+.+|.+.|+++....--.|..-=..
T Consensus 158 ~kl~dLvqqId~~~~LD~d-------------VedlLleiADdFV~sii~~sC~LAKHRKs 205 (258)
T KOG1142|consen 158 RKLDDLVQQIDGTTKLDDD-------------VEDLLLEIADDFVSSIIHRSCKLAKHRKS 205 (258)
T ss_pred cchhHHHHhhcCcccccHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 4677777777777777752 24667788888888877766666554443
No 48
>PF11827 DUF3347: Protein of unknown function (DUF3347); InterPro: IPR021782 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 169 to 570 amino acids in length.
Probab=34.89 E-value=2e+02 Score=21.74 Aligned_cols=81 Identities=15% Similarity=0.247 Sum_probs=53.3
Q ss_pred hhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHH-HHHHHHHHHHhh---cCCHHHHHH
Q 038079 41 PNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKV-KNEVNVVIACCR---NGDIEGAKA 116 (144)
Q Consensus 41 ~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l-~~~c~~lE~~~~---~~~~~~~~~ 116 (144)
.+.+..|+.-|+ .|..||..+ |.......|=.|..+-..+....+ ......+..... ..+++..+.
T Consensus 43 ~~~l~~v~~~Yl--------~lk~ALv~d--d~~~a~~aA~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~di~~qR~ 112 (174)
T PF11827_consen 43 DDSLQQVLNAYL--------ALKDALVAD--DLKAAKAAAKALLAALKAVDMAELSASLAKALMEAAEDAKEHDIEHQRE 112 (174)
T ss_pred HHHHHHHHHHHH--------HHHHHHHhc--CHHHHHHHHHHHHHHHHhcccccccHHHHHHHHHHHHhhhhCCHHHHHH
Confidence 355667777776 688899986 888998888888888777776633 333444444332 227777777
Q ss_pred HHHHHHHHHHHHHHH
Q 038079 117 AFEQVKTEQGNLKAK 131 (144)
Q Consensus 117 ~l~~l~~ef~~~~~a 131 (144)
.|..|-..+-.+...
T Consensus 113 ~F~~lS~~~~~l~~~ 127 (174)
T PF11827_consen 113 AFESLSEAMIDLVKA 127 (174)
T ss_pred HHHHHHHHHHHHHHh
Confidence 777777665554433
No 49
>PF03858 Crust_neuro_H: Crustacean neurohormone H; InterPro: IPR005558 Arthropod express a family of neuropeptides [] which so far consist of the following types of neurohormones: Crustacean hyperglycemic hormone (CHH). CHH is primarily involved in blood sugar regulation, but also plays a role in the control of molting and reproduction. Molt-inhibiting hormone (MIH). MIH inhibits Y-organs where molting hormone (ecdysteroid) is secreted. A molting cycle is initiated when MIH secretion diminishes or stops. Gonad-inhibiting hormone (GIH), also known as vitellogenesis-inhibiting hormone (VIH) because of its role in inhibiting vitellogenesis in female animals. Mandibular organ-inhibiting hormone (MOIH). MOIH represses the synthesis of methyl farnesoate, the precursor of insect juvenile hormone III in the mandibular organ. Ion transport peptide (ITP) from locust. ITP stimulates salt and water reabsorption and inhibits acid secretion in the ileum of the locust. Caenorhabditis elegans hypothetical protein ZC168.2. These neurohormones are peptides of 70 to 80 residues which are processed from larger size precursors. They contain six conserved cysteines that are involved in disulphide bonds, as shown in the following schematic representation. Crustacean neurohormone H proteins are referred to as precursor-related peptides as they are typically co-transcribed and translated with the CHH neurohormone (IPR001166 from INTERPRO). However, in some species this neuropeptide is synthesized as a separate protein. Furthermore, neurohormone H can undergo proteolysis to give rise to 5 different neuropeptides [].
Probab=34.05 E-value=42 Score=19.82 Aligned_cols=22 Identities=32% Similarity=0.369 Sum_probs=18.6
Q ss_pred CHHHHHHHHhhhcccccccChH
Q 038079 72 EGSEMERILHRFKGSCASVGAN 93 (144)
Q Consensus 72 D~~~l~~~aH~LKGSSaslGA~ 93 (144)
-|.++.++.-+||||+.+.++.
T Consensus 5 G~GRMerLLaSlrg~~~s~~pl 26 (41)
T PF03858_consen 5 GFGRMERLLASLRGSADSSTPL 26 (41)
T ss_pred chhhHHHHHHHHhccCCCCcch
Confidence 3788999999999999887765
No 50
>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=33.50 E-value=2.4e+02 Score=22.19 Aligned_cols=52 Identities=15% Similarity=0.190 Sum_probs=34.2
Q ss_pred ccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 85 GSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYFE 137 (144)
Q Consensus 85 GSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~ 137 (144)
+..+=+|...+...+..+...+...| +-+..++-++++....+...|++..+
T Consensus 32 ~~~~I~Gm~~~~~~~~~i~~~a~~Dd-PyAD~~L~~iEe~i~~~~~~l~~~~~ 83 (217)
T PF08900_consen 32 GKPAIIGMPGFASRLNRIWRDARQDD-PYADWWLLRIEEKINEARQELQELIA 83 (217)
T ss_pred CCCCCcCHHHHHHHHHHHHHHHhcCC-cHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44477999999999999999887765 22344555555555555555544443
No 51
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=33.11 E-value=75 Score=21.85 Aligned_cols=28 Identities=21% Similarity=0.337 Sum_probs=23.6
Q ss_pred HHHHHcChhcCCCChhHHHHHHHHHHHhHH
Q 038079 27 FVELEGLALASDEDPNFVEVTINVYFEESN 56 (144)
Q Consensus 27 ~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~ 56 (144)
|+-|..+ -+..-|.||.++++.|+++..
T Consensus 21 F~FL~~~--P~GT~~~~iR~~L~rYI~~~G 48 (97)
T PRK13916 21 FDFLENV--PRGTKTAHIREALRRYIEEIG 48 (97)
T ss_pred HHHHHHC--CCCCccHHHHHHHHHHHHhcC
Confidence 7788888 776678999999999998753
No 52
>PF12854 PPR_1: PPR repeat
Probab=32.76 E-value=49 Score=17.89 Aligned_cols=22 Identities=18% Similarity=0.572 Sum_probs=17.8
Q ss_pred HHHHHHhhcCCHHHHHHHHHHH
Q 038079 100 NVVIACCRNGDIEGAKAAFEQV 121 (144)
Q Consensus 100 ~~lE~~~~~~~~~~~~~~l~~l 121 (144)
.-+..+|+.|..+.+..+|+..
T Consensus 12 ~lI~~~Ck~G~~~~A~~l~~~M 33 (34)
T PF12854_consen 12 TLIDGYCKAGRVDEAFELFDEM 33 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHhC
Confidence 4466789999999999988764
No 53
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=32.69 E-value=74 Score=16.11 Aligned_cols=23 Identities=30% Similarity=0.651 Sum_probs=17.7
Q ss_pred HHHHHhhcCCHHHHHHHHHHHHH
Q 038079 101 VVIACCRNGDIEGAKAAFEQVKT 123 (144)
Q Consensus 101 ~lE~~~~~~~~~~~~~~l~~l~~ 123 (144)
-+..+++.|+.+.+...++.++.
T Consensus 7 ll~a~~~~g~~~~a~~~~~~M~~ 29 (34)
T PF13812_consen 7 LLRACAKAGDPDAALQLFDEMKE 29 (34)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 35567788899988888887765
No 54
>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=32.42 E-value=1.8e+02 Score=20.50 Aligned_cols=54 Identities=17% Similarity=0.239 Sum_probs=38.9
Q ss_pred hhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcC
Q 038079 41 PNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNG 109 (144)
Q Consensus 41 ~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~ 109 (144)
|+|- ...|+..+.+.+..|..|..++ |...++.+ ++-.-...++.++......|
T Consensus 13 p~Fd---~~~F~~~ak~~f~~i~~A~~~~--D~~~l~~~----------~t~~~~~~~~~~i~~~~~~g 66 (147)
T PF04280_consen 13 PGFD---PAAFLEEAKEAFLPIQEAWAKG--DLEALRPL----------LTEELYERLQAEIKARRSRG 66 (147)
T ss_dssp TT-----HHHHHHHHHHTHHHHHHHHHHT---HHHHHHH----------B-HHHHHHHHHHHHHHHHTT
T ss_pred CCCC---HHHHHHHHHHHHHHHHHHHHcC--CHHHHHHH----------hCHHHHHHHHHHHHHHHHcC
Confidence 4554 5678888999999999999987 88999877 56667777777777764443
No 55
>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=31.88 E-value=3e+02 Score=22.87 Aligned_cols=85 Identities=11% Similarity=0.071 Sum_probs=53.7
Q ss_pred HHHHHHHHhcccchhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHh-HHHHHHHHHHHhccCCCCHHHHHHHHhhhcc
Q 038079 7 HQQIASMRQHLLDEEILDEQFVELEGLALASDEDPNFVEVTINVYFEE-SNELLPMIEDLLGKNPIEGSEMERILHRFKG 85 (144)
Q Consensus 7 ~~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~d-s~~~l~~l~~al~~~~~D~~~l~~~aH~LKG 85 (144)
+.+|.+-.+.-|-.--|+..+..|..+ |...-+..|...|-=. -.=..-.|+.....+ ||+.+.+.+.+=|+
T Consensus 164 Q~~Le~~~~~~f~~~Sl~~Ti~~li~~-----~~~k~A~kl~k~Fkv~dkrfw~lki~aLa~~~--~w~eL~~fa~skKs 236 (319)
T PF04840_consen 164 QKELEEKYNTNFVGLSLNDTIRKLIEM-----GQEKQAEKLKKEFKVPDKRFWWLKIKALAENK--DWDELEKFAKSKKS 236 (319)
T ss_pred HHHHHHHhccchhcCCHHHHHHHHHHC-----CCHHHHHHHHHHcCCcHHHHHHHHHHHHHhcC--CHHHHHHHHhCCCC
Confidence 444444444333333466666677777 4445677888887432 222334555666655 89999999987554
Q ss_pred cccccChHHHHHHHHH
Q 038079 86 SCASVGANKVKNEVNV 101 (144)
Q Consensus 86 SSaslGA~~l~~~c~~ 101 (144)
-||-..+.+.|..
T Consensus 237 ---PIGyepFv~~~~~ 249 (319)
T PF04840_consen 237 ---PIGYEPFVEACLK 249 (319)
T ss_pred ---CCChHHHHHHHHH
Confidence 4999999999964
No 56
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=31.86 E-value=72 Score=15.70 Aligned_cols=23 Identities=22% Similarity=0.615 Sum_probs=17.8
Q ss_pred HHHHHhhcCCHHHHHHHHHHHHH
Q 038079 101 VVIACCRNGDIEGAKAAFEQVKT 123 (144)
Q Consensus 101 ~lE~~~~~~~~~~~~~~l~~l~~ 123 (144)
-+..+++.|+.+.+...+.++..
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~ 28 (31)
T PF01535_consen 6 LISGYCKMGQFEEALEVFDEMRE 28 (31)
T ss_pred HHHHHHccchHHHHHHHHHHHhH
Confidence 46677888888888888887754
No 57
>cd00215 PTS_IIA_lac PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation.
Probab=31.61 E-value=1.7e+02 Score=20.08 Aligned_cols=43 Identities=9% Similarity=0.173 Sum_probs=34.8
Q ss_pred HHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 98 EVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYFELVK 140 (144)
Q Consensus 98 ~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~~~~ 140 (144)
.|.+-=..+++|+++.+..++.+-+.+|..+...=..+++.+-
T Consensus 18 ~~~eAl~~a~~g~fe~A~~~l~ea~~~l~~AH~~qt~liq~ea 60 (97)
T cd00215 18 KALEALKAAKEGDFAEAEELLEEANDSLNEAHHAQTKLLQQEA 60 (97)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444445689999999999999999999999888777776654
No 58
>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=31.01 E-value=64 Score=28.06 Aligned_cols=33 Identities=9% Similarity=0.211 Sum_probs=26.9
Q ss_pred HHHHHHHhhhcccccccChHHHHHHHHHH-HHHh
Q 038079 74 SEMERILHRFKGSCASVGANKVKNEVNVV-IACC 106 (144)
Q Consensus 74 ~~l~~~aH~LKGSSaslGA~~l~~~c~~l-E~~~ 106 (144)
+++.+.|..+-.++-||||.||..+-..+ |..+
T Consensus 375 ~~iAeiA~~vN~~~ENIGARRLhTvlErlLediS 408 (444)
T COG1220 375 KRIAEIAYQVNEKTENIGARRLHTVLERLLEDIS 408 (444)
T ss_pred HHHHHHHHHhcccccchhHHHHHHHHHHHHHHhC
Confidence 47788889999999999999999988763 4443
No 59
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=30.88 E-value=1.4e+02 Score=18.78 Aligned_cols=43 Identities=7% Similarity=0.078 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 96 KNEVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYFELV 139 (144)
Q Consensus 96 ~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~~~ 139 (144)
...|..| ......+.+.+...+..|...|..++..+..+.+..
T Consensus 61 ~~~~~~L-~~~~~~~~~~i~~~~~~l~~~w~~l~~~~~~r~~~L 103 (105)
T PF00435_consen 61 NEQAQQL-IDSGPEDSDEIQEKLEELNQRWEALCELVEERRQKL 103 (105)
T ss_dssp HHHHHHH-HHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHH-HHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 3445555 223355678888999999999999998888766543
No 60
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=30.20 E-value=2.8e+02 Score=21.98 Aligned_cols=47 Identities=21% Similarity=0.267 Sum_probs=36.7
Q ss_pred hHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 92 ANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYFEL 138 (144)
Q Consensus 92 A~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~~ 138 (144)
+..+...|...-...+.|+++.+...+..+......++..|..|-.+
T Consensus 26 sRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk~~l~~~pel 72 (204)
T COG2178 26 SREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLKRLLAGFPEL 72 (204)
T ss_pred HHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHhhhHHH
Confidence 45677888888888889999988888888888777777777665443
No 61
>PF08657 DASH_Spc34: DASH complex subunit Spc34 ; InterPro: IPR013966 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=29.56 E-value=2.5e+02 Score=22.88 Aligned_cols=63 Identities=10% Similarity=0.045 Sum_probs=48.9
Q ss_pred HHHHHHHhhhcccccc----cChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 74 SEMERILHRFKGSCAS----VGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYF 136 (144)
Q Consensus 74 ~~l~~~aH~LKGSSas----lGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l 136 (144)
...++.+|++..++-- +|=.-+-.+|+.++..|.-=...++...+..+.+.|..+...+..|=
T Consensus 134 ~~~~~~avA~vlG~~m~~e~~~d~dvevLL~~ae~L~~vYP~~ga~eki~~Lr~~y~~l~~~i~~lE 200 (259)
T PF08657_consen 134 KQRRNTAVALVLGGVMHEEIVEDVDVEVLLRGAEKLCNVYPLPGAREKIAALRQRYNQLSNSIAYLE 200 (259)
T ss_pred HHHHHHHHHHhccCcccccccccCCHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566667666665522 46667788999999999776777999999999999999998887653
No 62
>TIGR00823 EIIA-LAC phosphotransferase system enzyme II, lactose-specific, factor III. operon. While the Lac permeases consist of two polypeptide chains (IIA and IICB), the Chb permease of E. coli consists of three (IIA, IIB and IIC). In B. subtilis, a PTS permease similar to the Chb permease of E. coli is believed to transport lichenan (a b-1,3;1,4 glucan) degradation products, oligosaccharides of 2-4 glucose units. This model is specific for the IIA subunit of the Lac PTS family.
Probab=29.49 E-value=1.9e+02 Score=19.93 Aligned_cols=42 Identities=17% Similarity=0.134 Sum_probs=34.2
Q ss_pred HHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 99 VNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYFELVK 140 (144)
Q Consensus 99 c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~~~~ 140 (144)
|.+-=..+++|+++.+..++..-+.+|..+...=..+++.+-
T Consensus 21 ~~eAl~~a~~gdfe~A~~~l~eA~~~l~~AH~~qt~liq~ea 62 (99)
T TIGR00823 21 ALEALKAAKAGDFAKARALVEQAGMCLNEAHLAQTSLLAQEA 62 (99)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344445689999999999999999999999888777776654
No 63
>PLN02407 diphosphomevalonate decarboxylase
Probab=29.48 E-value=90 Score=26.60 Aligned_cols=32 Identities=6% Similarity=0.132 Sum_probs=27.0
Q ss_pred HHHHHHHh-HHHHHHHHHHHhccCCCCHHHHHHHH
Q 038079 47 TINVYFEE-SNELLPMIEDLLGKNPIEGSEMERIL 80 (144)
Q Consensus 47 Li~~f~~d-s~~~l~~l~~al~~~~~D~~~l~~~a 80 (144)
+....++. +++.+..|++|+.++ ||.++.+++
T Consensus 224 ~~~~w~~~~~~~~~~~~~~Ai~~~--Df~~~gei~ 256 (343)
T PLN02407 224 LLQHRAKEVVPKRILQMEEAIKNR--DFASFAKLT 256 (343)
T ss_pred hHHHHHHhhhHHHHHHHHHHHHhc--CHHHHHHHH
Confidence 46677887 899999999999987 999887664
No 64
>PRK10454 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIA; Provisional
Probab=29.24 E-value=2.2e+02 Score=20.38 Aligned_cols=44 Identities=16% Similarity=0.159 Sum_probs=35.5
Q ss_pred HHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 038079 98 EVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYFELVKQ 141 (144)
Q Consensus 98 ~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~~~~~ 141 (144)
.|.+-=..+++|+++.+..++.+-+..|..+...=..+++.+-+
T Consensus 34 ~~~eAl~~Ak~gdfe~A~~~l~eA~e~l~~AH~~qt~Liq~Ea~ 77 (115)
T PRK10454 34 LAYAALKQAKQGDFAAAKAMMDQSRMALNEAHLVQTKLIEGDQG 77 (115)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34455566899999999999999999999999887777766543
No 65
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=29.06 E-value=84 Score=15.62 Aligned_cols=23 Identities=22% Similarity=0.502 Sum_probs=18.0
Q ss_pred HHHHHhhcCCHHHHHHHHHHHHH
Q 038079 101 VVIACCRNGDIEGAKAAFEQVKT 123 (144)
Q Consensus 101 ~lE~~~~~~~~~~~~~~l~~l~~ 123 (144)
-+..+++.|+.+.+..++..++.
T Consensus 6 li~~~~~~~~~~~a~~~~~~M~~ 28 (35)
T TIGR00756 6 LIDGLCKAGRVEEALELFKEMLE 28 (35)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 35667888999998888887764
No 66
>PRK10548 flagellar biosynthesis protein FliT; Provisional
Probab=28.70 E-value=2.2e+02 Score=20.39 Aligned_cols=21 Identities=5% Similarity=0.142 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHhhcCCHHHH
Q 038079 94 KVKNEVNVVIACCRNGDIEGA 114 (144)
Q Consensus 94 ~l~~~c~~lE~~~~~~~~~~~ 114 (144)
.+..+..++=.+++.|+||..
T Consensus 13 ~I~~lS~~ML~aA~~g~Wd~L 33 (121)
T PRK10548 13 QILTLSQSMLRLATEGQWDEL 33 (121)
T ss_pred HHHHHHHHHHHHHHHCCHHHH
Confidence 456677888888889988874
No 67
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=28.45 E-value=1.2e+02 Score=17.16 Aligned_cols=35 Identities=6% Similarity=0.175 Sum_probs=25.0
Q ss_pred HHHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHH
Q 038079 26 QFVELEGLALASDEDPNFVEVTINVYFEESNELLPMI 62 (144)
Q Consensus 26 ~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l 62 (144)
.+..|+.| .+.-+++.+...+..+-.+.+..+..|
T Consensus 5 ~v~~L~~m--FP~l~~~~I~~~L~~~~g~ve~~i~~L 39 (43)
T smart00546 5 ALHDLKDM--FPNLDEEVIKAVLEANNGNVEATINNL 39 (43)
T ss_pred HHHHHHHH--CCCCCHHHHHHHHHHcCCCHHHHHHHH
Confidence 46788888 888888888777777666666655544
No 68
>cd07298 PX_RICS The phosphoinositide binding Phox Homology domain of PX-RICS. 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. RICS is a Rho GTPase-activating protein for cdc42 and Rac1. It is implicated in the regulation of postsynaptic signaling and neurite outgrowth. An N-terminal splicing variant of RICS containing additional PX and Src Homology 3 (SH3) domains, also called PX-RICS, is the main isoform expressed during neural development. PX-RICS is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and
Probab=27.99 E-value=64 Score=23.25 Aligned_cols=37 Identities=24% Similarity=0.403 Sum_probs=26.2
Q ss_pred hcccchhhhHHHHHHHHcChhcCC----CChhHHHHHHHHHHH
Q 038079 15 QHLLDEEILDEQFVELEGLALASD----EDPNFVEVTINVYFE 53 (144)
Q Consensus 15 ~~~~~~~~lD~~~~~L~~L~~~~~----~~~~fv~~Li~~f~~ 53 (144)
..+.+.=+-|..|++|.+| .+. .+|++|..++..|+.
T Consensus 54 D~~LHrCvyDRrfS~L~eL--p~~~~l~~~~~~v~~~l~~YL~ 94 (115)
T cd07298 54 DKHLHLCIYDRRFSQLPEL--PRSDSLKDSPESVTQMLMAYLS 94 (115)
T ss_pred HHHHHHHHHhhhhhccccC--CCcccccccHHHHHHHHHHHHH
Confidence 3445556778888888888 552 246788888888875
No 69
>PF04012 PspA_IM30: PspA/IM30 family; InterPro: IPR007157 This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma54-containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator [].
Probab=27.71 E-value=2.8e+02 Score=21.23 Aligned_cols=47 Identities=21% Similarity=0.410 Sum_probs=33.6
Q ss_pred HHHHHHHHHhcccchhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHHHHHhcc
Q 038079 6 LHQQIASMRQHLLDEEILDEQFVELEGLALASDEDPNFVEVTINVYFEESNELLPMIEDLLGK 68 (144)
Q Consensus 6 l~~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l~~al~~ 68 (144)
|+.++.+.+++-+. .+||. + .+|+ .+++.|+.|....|..++.++..
T Consensus 2 lf~Rl~~~~~a~~~-~~ld~-------~-----EDP~---~~l~q~ird~e~~l~~a~~~~a~ 48 (221)
T PF04012_consen 2 LFKRLKTLVKANIN-ELLDK-------A-----EDPE---KMLEQAIRDMEEQLRKARQALAR 48 (221)
T ss_pred HHHHHHHHHHHHHH-HHHHh-------h-----cCHH---HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555566655444 34442 4 4575 89999999999999999999885
No 70
>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=27.26 E-value=70 Score=20.11 Aligned_cols=36 Identities=22% Similarity=0.442 Sum_probs=26.0
Q ss_pred HHHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHHHH
Q 038079 26 QFVELEGLALASDEDPNFVEVTINVYFEESNELLPMIED 64 (144)
Q Consensus 26 ~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l~~ 64 (144)
+|.++|.+. . .+|+.+..++..--..-|.++..|.+
T Consensus 9 qf~~lR~~v--q-~NP~lL~~lLqql~~~nP~l~q~I~~ 44 (59)
T PF09280_consen 9 QFQQLRQLV--Q-QNPQLLPPLLQQLGQSNPQLLQLIQQ 44 (59)
T ss_dssp HHHHHHHHH--H-C-GGGHHHHHHHHHCCSHHHHHHHHH
T ss_pred HHHHHHHHH--H-HCHHHHHHHHHHHhccCHHHHHHHHH
Confidence 578888872 2 56888888888888888887776654
No 71
>PF05465 Halo_GVPC: Halobacterial gas vesicle protein C (GVPC) repeat; InterPro: IPR008639 This family consists of Halobacterium gas vesicle protein C sequences which are thought to confer stability to the gas vesicle membranes [,].; GO: 0031412 gas vesicle organization, 0031411 gas vesicle
Probab=27.19 E-value=1.2e+02 Score=16.73 Aligned_cols=24 Identities=17% Similarity=0.331 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 114 AKAAFEQVKTEQGNLKAKLDSYFE 137 (144)
Q Consensus 114 ~~~~l~~l~~ef~~~~~aL~~~l~ 137 (144)
....+...+.+|..+..++..|-+
T Consensus 4 l~a~I~~~r~~f~~~~~aF~aY~~ 27 (32)
T PF05465_consen 4 LLAAIAEFREEFDDTQDAFEAYAD 27 (32)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345677888999999999998853
No 72
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=27.13 E-value=2.8e+02 Score=21.04 Aligned_cols=75 Identities=15% Similarity=0.216 Sum_probs=44.8
Q ss_pred ChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhc-CCHHHHHHHH
Q 038079 40 DPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRN-GDIEGAKAAF 118 (144)
Q Consensus 40 ~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~-~~~~~~~~~l 118 (144)
+|+|+.++++. .+.|.+ +-..+ |...+..+...++ .++..+...+..+-.. ++++.+...+
T Consensus 93 d~~fLme~mE~-----rE~lee---~~~~~--d~~~L~~l~~e~~--------~~~~~~~~~l~~~~~~~~d~~~A~~~~ 154 (176)
T PRK03578 93 PPAFLMQQMEW-----REAIED---ARAAR--DVDALDALLAELR--------DERRERYAELGALLDSRGDDQAAAEAV 154 (176)
T ss_pred CHHHHHHHHHH-----HHHHHH---hhccC--CHHHHHHHHHHHH--------HHHHHHHHHHHHHHHccccHHHHHHHH
Confidence 58888777763 222222 22222 5667777777663 4666777777766655 8888887766
Q ss_pred HHHHHHHHHHHHHHH
Q 038079 119 EQVKTEQGNLKAKLD 133 (144)
Q Consensus 119 ~~l~~ef~~~~~aL~ 133 (144)
..++= |.++...+.
T Consensus 155 ~kL~y-~~kl~~ei~ 168 (176)
T PRK03578 155 RQLMF-IEKLAQEIG 168 (176)
T ss_pred HHHHH-HHHHHHHHH
Confidence 66653 334444333
No 73
>COG2603 Predicted ATPase [General function prediction only]
Probab=26.72 E-value=2.1e+02 Score=24.21 Aligned_cols=81 Identities=15% Similarity=0.165 Sum_probs=57.5
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHH----HHHhhcCCHHHHHHHH
Q 038079 43 FVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVV----IACCRNGDIEGAKAAF 118 (144)
Q Consensus 43 fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~l----E~~~~~~~~~~~~~~l 118 (144)
=|.++++.|+..-.+. +-..++... .-|.++. +=|.|-++---+|-.++..++..+ .+....|+.++-..++
T Consensus 242 rv~RIi~ey~~kkh~~--df~~~~~~~-~~~~~~~-l~~~l~~~~~r~~~qr~~~l~~~~~~~~~~q~~~~~~d~~~~~i 317 (334)
T COG2603 242 RVERIIEEYFKKKHKH--DFTHAVGDE-QGWQAYS-LHHGLSAIKRRLGLQRYNELAARLDAALTEQLTTGSTDGHLAWI 317 (334)
T ss_pred HHHHHHHHHHHHhhhh--hhhhhhccc-hhHHHHH-HhhhHHHHHHHHhHHHHHHHHHHHHHHHHhcCCcCCccchHHHH
Confidence 4678888888765422 223334332 2366666 779999999999999998888765 4445677899988998
Q ss_pred HHHHHHHHH
Q 038079 119 EQVKTEQGN 127 (144)
Q Consensus 119 ~~l~~ef~~ 127 (144)
.-+..||-.
T Consensus 318 ~~~~~e~~d 326 (334)
T COG2603 318 VPLLEEYYD 326 (334)
T ss_pred HHHHHHHHH
Confidence 888888755
No 74
>smart00388 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases.
Probab=26.65 E-value=1.3e+02 Score=16.89 Aligned_cols=58 Identities=9% Similarity=0.206 Sum_probs=33.5
Q ss_pred HHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 75 EMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYFELVK 140 (144)
Q Consensus 75 ~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~~~~ 140 (144)
-+...+|.+|.+=+++ ...|..+.. ...+.+. ...+..++.+..+...-++.++...+
T Consensus 5 ~~~~i~Hel~~pl~~i-----~~~~~~l~~--~~~~~~~-~~~~~~~~~~~~~~~~~v~~l~~~~~ 62 (66)
T smart00388 5 FLANLSHELRTPLTAI-----RGYLELLED--TELSEEQ-REYLETILRSAERLLRLINDLLDLSR 62 (66)
T ss_pred HHHHHHHhccCcHHHH-----HHHHHHHHh--CCCChHH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556789999665433 222333333 1222333 67777788777777777766665543
No 75
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=26.04 E-value=5.1e+02 Score=23.65 Aligned_cols=63 Identities=22% Similarity=0.230 Sum_probs=34.9
Q ss_pred hhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHHHHHhcc--CCCC----HHHHHHHHhhhc
Q 038079 20 EEILDEQFVELEGLALASDEDPNFVEVTINVYFEESNELLPMIEDLLGK--NPIE----GSEMERILHRFK 84 (144)
Q Consensus 20 ~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l~~al~~--~~~D----~~~l~~~aH~LK 84 (144)
..+|.+|+.+|..+.+++ |..+-+ .--..=+.+++++...+..|+.. ++.| +..+.+.-|.|.
T Consensus 187 ~d~L~fq~~Ele~~~l~~-gE~e~L-~~e~~rLsn~ekl~~~~~~a~~~L~ge~~~~~~~~~l~~a~~~l~ 255 (557)
T COG0497 187 ADLLQFQLEELEELNLQP-GEDEEL-EEERKRLSNSEKLAEAIQNALELLSGEDDTVSALSLLGRALEALE 255 (557)
T ss_pred HHHHHHHHHHHHhcCCCC-chHHHH-HHHHHHHhhHHHHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHH
Confidence 367788899999994333 222222 12223356777777777776654 1111 344555555555
No 76
>PF08581 Tup_N: Tup N-terminal; InterPro: IPR013890 The N-terminal region of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor []. ; PDB: 3VP9_B 3VP8_B.
Probab=25.90 E-value=1.5e+02 Score=19.82 Aligned_cols=22 Identities=23% Similarity=0.437 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 038079 114 AKAAFEQVKTEQGNLKAKLDSY 135 (144)
Q Consensus 114 ~~~~l~~l~~ef~~~~~aL~~~ 135 (144)
...+|+.|+.||..+...+..+
T Consensus 2 l~elLd~ir~Ef~~~~~e~~~~ 23 (79)
T PF08581_consen 2 LNELLDAIRQEFENLSQEANSY 23 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4578888999998887755544
No 77
>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=25.85 E-value=3.4e+02 Score=21.54 Aligned_cols=49 Identities=10% Similarity=0.135 Sum_probs=31.2
Q ss_pred ccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 87 CASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYF 136 (144)
Q Consensus 87 SaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l 136 (144)
.+=+|..++...+..|...+.+.| +=+..+|-++++....+...|++..
T Consensus 32 ~~IiGl~~f~s~~~~i~~~a~~Dd-PyAD~~Ll~~E~~l~~~~~~l~~~~ 80 (216)
T TIGR03761 32 PGIIGMPGFISRLNRINQASEQDD-PYADWALLRIEEKLLSARQEMQALL 80 (216)
T ss_pred CCCcCcHHHHHHHHHHHHHHHcCC-cHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345999999999999999887765 2223444444444444444444433
No 78
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=25.82 E-value=2.3e+02 Score=19.55 Aligned_cols=61 Identities=18% Similarity=0.225 Sum_probs=36.3
Q ss_pred hcccchhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHH
Q 038079 15 QHLLDEEILDEQFVELEGLALASDEDPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEME 77 (144)
Q Consensus 15 ~~~~~~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~ 77 (144)
..-+++..++..++.|...| =-++..|....|...+.....--..|+..|.+..+|-..+.
T Consensus 3 ~kg~~~e~I~~vi~~l~~~g--yidD~~ya~~~v~~~~~~~~~G~~~I~~~L~~kGi~~~~i~ 63 (121)
T PF02631_consen 3 RKGFSEEAIEEVIDRLKELG--YIDDERYAESYVRSRLRRKGKGPRRIRQKLKQKGIDREIIE 63 (121)
T ss_dssp HTT--HHHHHHHHHHHHHTT--SS-HHHHHHHHHHHHHHHTT--HHHHHHHHHHTT--HHHHH
T ss_pred ccCCCHHHHHHHHHHHHHcC--CCCHHHHHHHHHHHhcccccccHHHHHHHHHHHCCChHHHH
Confidence 34567788888888888884 33557888888888886444444556666666545544333
No 79
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=25.50 E-value=2.1e+02 Score=19.01 Aligned_cols=58 Identities=12% Similarity=0.164 Sum_probs=28.8
Q ss_pred hhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 81 HRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQVKTEQGNLKAKLDSYFELV 139 (144)
Q Consensus 81 H~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l~~ef~~~~~aL~~~l~~~ 139 (144)
..|..+.++.+......+-..++..... -.+.+......++..+.++....+.|++-+
T Consensus 15 ~~l~~~~~~~~~~~~~~~r~~~~~~~~~-a~~~~~~~~~~~~~~~~~~~~~~~~~V~e~ 72 (94)
T PF05957_consen 15 EDLARSAADLAGEKADEARDRAEEALDD-ARDRAEDAADQAREQAREAAEQTEDYVREN 72 (94)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence 3333333444444444444444332221 123345555666667777777777776643
No 80
>PF04136 Sec34: Sec34-like family ; InterPro: IPR007265 Sec34 and Sec35 form a sub-complex in a seven-protein complex that includes Dor1. This complex is thought to be important for tethering vesicles to the Golgi [].; GO: 0006886 intracellular protein transport, 0005801 cis-Golgi network, 0016020 membrane
Probab=25.34 E-value=2.9e+02 Score=20.52 Aligned_cols=96 Identities=16% Similarity=0.206 Sum_probs=68.0
Q ss_pred hHHHHHHHHHHHhHHHHH------HHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHh----hcCCH
Q 038079 42 NFVEVTINVYFEESNELL------PMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACC----RNGDI 111 (144)
Q Consensus 42 ~fv~~Li~~f~~ds~~~l------~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~----~~~~~ 111 (144)
..|..=-..|-+.|++++ ..+.+.+...=-=|..+......|.++..+|--.....+-..|..+- .+.+.
T Consensus 38 ~~Vs~kT~~l~~~ce~Ll~eq~~L~~~ae~I~~~L~yF~~Ld~itr~Ln~p~~sV~~~~F~~~L~~LD~cl~Fl~~h~~f 117 (157)
T PF04136_consen 38 NSVSEKTNSLHEACEQLLEEQTRLEELAEEISEKLQYFEELDPITRRLNSPGSSVNSDSFKPMLSRLDECLEFLEEHPNF 117 (157)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHhhHHHHHHHHcCCCCcccchHHHHHHHHHHHHHHHHHHhhhh
Confidence 344444555556665544 44555555422246788888999999999988777776666666543 45678
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 112 EGAKAAFEQVKTEQGNLKAKLDSYFE 137 (144)
Q Consensus 112 ~~~~~~l~~l~~ef~~~~~aL~~~l~ 137 (144)
.++...+.+.++...++.+.+..|+-
T Consensus 118 kea~~Y~~rf~q~ltRAl~lIk~y~~ 143 (157)
T PF04136_consen 118 KEAEVYLIRFRQCLTRALTLIKNYVV 143 (157)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88899999999999999999888764
No 81
>PLN00061 photosystem II protein Psb27; Provisional
Probab=24.84 E-value=1.8e+02 Score=21.97 Aligned_cols=60 Identities=12% Similarity=0.253 Sum_probs=41.9
Q ss_pred ccchhhhHHHHHHHHcChhcCCCChh-HHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhh
Q 038079 17 LLDEEILDEQFVELEGLALASDEDPN-FVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHR 82 (144)
Q Consensus 17 ~~~~~~lD~~~~~L~~L~~~~~~~~~-fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~ 82 (144)
-.++|+|+ -|..| .|++..- -=..|=..|.+|+-..+..|+.+|+.++.|-..+++.+..
T Consensus 27 ~~~~~~~~----~~~~~--fdp~e~tksg~~Lpg~Y~kdtr~VV~tLresl~l~p~D~~~~~~aa~~ 87 (150)
T PLN00061 27 EEGEGVVG----AIKSL--FDPNEKTKSGKKLPKAYLKSAREVVKTLRESLKEDPKDEAKFRRTADA 87 (150)
T ss_pred cccccHHH----HHHHh--cCccccccccccCchHHHHHHHHHHHHHHHHHccCCcchHHHHHHHHH
Confidence 34566776 66667 6655421 1235668899999999999999999866677776655443
No 82
>PF05218 DUF713: Protein of unknown function (DUF713); InterPro: IPR007883 This family contains proteins of unknown function from Caenorhabditis species.
Probab=24.15 E-value=3.1e+02 Score=21.03 Aligned_cols=92 Identities=12% Similarity=0.175 Sum_probs=57.2
Q ss_pred HHHHHHHHHhccc-chhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHhHHHHHHHHHHHhcc---CCCCHHHHHHHHh
Q 038079 6 LHQQIASMRQHLL-DEEILDEQFVELEGLALASDEDPNFVEVTINVYFEESNELLPMIEDLLGK---NPIEGSEMERILH 81 (144)
Q Consensus 6 l~~~~~~~~~~~~-~~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~ds~~~l~~l~~al~~---~~~D~~~l~~~aH 81 (144)
++.++..+.+++. ....|-..|..|..| .+.-......+|+...+.|....|-.+-..+.. +..+|..++..-=
T Consensus 72 ~~~E~~~l~~~v~~a~~~l~~~f~~L~~L--~~~~~D~iFlkvLqK~i~~va~~L~~il~~l~~~~~~~~~~~~L~~~~s 149 (182)
T PF05218_consen 72 LQSEISNLHKSVMSAYNMLENAFENLKKL--SEKFPDKIFLKVLQKCISDVANKLLEILESLDELENDKDWFQKLREAFS 149 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHH
Confidence 5556666666643 335566678889888 543333344488888888888888888777743 2335777777777
Q ss_pred hhcccccccChHHHHHHHH
Q 038079 82 RFKGSCASVGANKVKNEVN 100 (144)
Q Consensus 82 ~LKGSSaslGA~~l~~~c~ 100 (144)
.|+.|+ =-.-.+|..+|.
T Consensus 150 ~l~~~~-IptT~~Lr~ic~ 167 (182)
T PF05218_consen 150 RLDPSD-IPTTSQLRRICK 167 (182)
T ss_pred cCCccc-CCCHHHHHHHhc
Confidence 777644 123334444443
No 83
>PF07587 PSD1: Protein of unknown function (DUF1553); InterPro: IPR022655 The function is not known. It is found associated with IPR011444 from INTERPRO It is also found associated with the Planctomycete cytochrome C domain IPR011429 from INTERPRO.
Probab=24.07 E-value=83 Score=25.35 Aligned_cols=43 Identities=12% Similarity=0.308 Sum_probs=34.0
Q ss_pred HHHHHhcccchhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHh
Q 038079 10 IASMRQHLLDEEILDEQFVELEGLALASDEDPNFVEVTINVYFEE 54 (144)
Q Consensus 10 ~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~d 54 (144)
.+.+|+.++=.||++. .+++..+| ..+..|+++.-|-..|++.
T Consensus 23 VNRvW~~~fGrGlV~p-~dD~g~~~-~~PshPeLLd~La~~F~~~ 65 (266)
T PF07587_consen 23 VNRVWQHLFGRGLVEP-VDDFGPQG-NPPSHPELLDWLAAEFVEH 65 (266)
T ss_pred HHHHHHHHcCCcCcCC-HhhccCCC-CCCCCHHHHHHHHHHHHHc
Confidence 5788999999999886 23555543 5678899999999999986
No 84
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=21.88 E-value=1.9e+02 Score=25.76 Aligned_cols=76 Identities=9% Similarity=0.183 Sum_probs=59.5
Q ss_pred ChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCC--HHHHHHH
Q 038079 40 DPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGD--IEGAKAA 117 (144)
Q Consensus 40 ~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~--~~~~~~~ 117 (144)
++.=....+.-|++|.-.....-+.|+-.++. - +=|||=|++-|+|-..=-++|+..+.+-+.|+ +..++-.
T Consensus 226 tr~~A~~~L~~Fi~~~L~nFG~yQDam~~d~~---~---L~HSllS~alNigLL~PleVi~Aa~~Ay~~g~ipLN~VEGF 299 (505)
T COG3046 226 TRTQALRALKHFIADRLPNFGSYQDAMSADDP---H---LWHSLLSFALNIGLLTPLEVIRAALKAYREGDIPLNSVEGF 299 (505)
T ss_pred CHHHHHHHHHHHHHHhhhcCCcHHHHHhcCCc---h---hHHHHHHHHhhccCCCHHHHHHHHHHhhccCCCchHHHHHH
Confidence 34445688899999999999999999987532 3 55999999999999999999999999888875 3344444
Q ss_pred HHHH
Q 038079 118 FEQV 121 (144)
Q Consensus 118 l~~l 121 (144)
+.||
T Consensus 300 vRQi 303 (505)
T COG3046 300 VRQI 303 (505)
T ss_pred HHHH
Confidence 4444
No 85
>PHA02666 hypothetical protein; Provisional
Probab=21.76 E-value=1e+02 Score=24.91 Aligned_cols=53 Identities=21% Similarity=0.313 Sum_probs=39.5
Q ss_pred CChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcc----cccccChHHH
Q 038079 39 EDPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKG----SCASVGANKV 95 (144)
Q Consensus 39 ~~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKG----SSaslGA~~l 95 (144)
|.|++ +.=|.+.+.|-+.+|..|++.|+. .+.-.++..|.-|+ -++|||-..|
T Consensus 202 gkpNL-Q~DIcTLC~DIEtQLSALEKSLES---ElnFYrrYIqDTKsLLatRAANIgsKAL 258 (287)
T PHA02666 202 GKPNL-QSDICTLCHDIETQLSALEKSLES---ELNFYRRYIQDTKSLLATRAANIGSKAL 258 (287)
T ss_pred CCCch-hhHHHHhhhhHHHHHHHHHHHHHH---HHHHHHHHHHhHHHHHHHHhhcccccee
Confidence 34554 466788899999999999999997 46677888887775 4667765543
No 86
>PRK01773 hscB co-chaperone HscB; Provisional
Probab=21.37 E-value=3.7e+02 Score=20.37 Aligned_cols=75 Identities=9% Similarity=0.174 Sum_probs=45.0
Q ss_pred ChhHHHHHHHHHHHhHHHHHHHHHHHhccCCCCHHHHHHHHhhhcccccccChHHHHHHHHHHHHHhhcCCHHHHHHHHH
Q 038079 40 DPNFVEVTINVYFEESNELLPMIEDLLGKNPIEGSEMERILHRFKGSCASVGANKVKNEVNVVIACCRNGDIEGAKAAFE 119 (144)
Q Consensus 40 ~~~fv~~Li~~f~~ds~~~l~~l~~al~~~~~D~~~l~~~aH~LKGSSaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~ 119 (144)
+|+|+.++++. .+. |..+-..+ |...+..+...++ .++..+...++.+-..++++.+...+.
T Consensus 90 d~~fLme~ME~-----rE~---lee~~~~~--d~~~L~~l~~~v~--------~~~~~~~~~l~~~~~~~d~~~A~~~~~ 151 (173)
T PRK01773 90 DMAFLMQQMEW-----REQ---LEEIEQQQ--DEDALTAFSKEIK--------QEQQAILTELSTALNSQQWQQASQIND 151 (173)
T ss_pred CHHHHHHHHHH-----HHH---HHhhcccC--CHHHHHHHHHHHH--------HHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 57788777663 222 22222222 5667777766654 466777788888788889988877665
Q ss_pred HHHHHHHHHHHHHH
Q 038079 120 QVKTEQGNLKAKLD 133 (144)
Q Consensus 120 ~l~~ef~~~~~aL~ 133 (144)
+++= |.++...+.
T Consensus 152 rL~y-~~kl~~ei~ 164 (173)
T PRK01773 152 RLRF-IKKLIIEIE 164 (173)
T ss_pred HHHH-HHHHHHHHH
Confidence 5543 334444433
No 87
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=21.10 E-value=2.5e+02 Score=18.72 Aligned_cols=47 Identities=23% Similarity=0.309 Sum_probs=27.1
Q ss_pred HHHHHHHHhcccchhhhHHHHHHHHcChhcCCCChhHHHHHHHHHHHh
Q 038079 7 HQQIASMRQHLLDEEILDEQFVELEGLALASDEDPNFVEVTINVYFEE 54 (144)
Q Consensus 7 ~~~~~~~~~~~~~~~~lD~~~~~L~~L~~~~~~~~~fv~~Li~~f~~d 54 (144)
+.+....+..-+..+=.++.+..|.+|+.. ...++||..+|..-++.
T Consensus 2 rk~i~~~l~ey~~~~d~~ea~~~l~el~~~-~~~~~vv~~~l~~~le~ 48 (113)
T PF02847_consen 2 RKKIFSILMEYFSSGDVDEAVECLKELKLP-SQHHEVVKVILECALEE 48 (113)
T ss_dssp HHHHHHHHHHHHHHT-HHHHHHHHHHTT-G-GGHHHHHHHHHHHHHTS
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHhCCC-ccHHHHHHHHHHHHhhc
Confidence 445555666656556666667788888322 34455666666655554
No 88
>PF01044 Vinculin: Vinculin family; InterPro: IPR006077 Vinculin is a eukaryotic protein that seems to be involved in the attachment of the actin-based microfilaments to the plasma membrane. Vinculin is located at the cytoplasmic side of focal contacts or adhesion plaques []. In addition to actin, vinculin interacts with other structural proteins such as talin and alpha-actinins. Vinculin is a large protein of 116 kDa (about a 1000 residues). Structurally the protein consists of an acidic N-terminal domain of about 90 kDa separated from a basic C-terminal domain of about 25 kDa by a proline-rich region of about 50 residues. The central part of the N-terminal domain consists of a variable number (3 in vertebrates, 2 in Caenorhabditis elegans) of repeats of a 110 amino acids domain. Alpha-catenins are evolutionary related to vinculin IPR001033 from INTERPRO []. Catenins are proteins that associate with the cytoplasmic domain of a variety of cadherins. The association of catenins to cadherins produces a complex which is linked to the actin filament network, and which seems to be of primary importance for cadherins cell-adhesion properties. Three different types of catenins seem to exist: alpha, beta, and gamma. Alpha-catenins are proteins of about 100 kDa which are evolutionary related to vinculin. In terms of their structure the most significant differences are the absence, in alpha-catenin, of the repeated domain and of the proline-rich segment.; GO: 0005198 structural molecule activity, 0007155 cell adhesion, 0015629 actin cytoskeleton; PDB: 3S90_B 1TR2_B 2IBF_A 1RKC_A 3TJ5_A 3RF3_B 4DJ9_A 2GWW_A 2HSQ_A 3TJ6_A ....
Probab=21.04 E-value=7.7e+02 Score=23.90 Aligned_cols=27 Identities=15% Similarity=0.158 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 038079 111 IEGAKAAFEQVKTEQGNLKAKLDSYFE 137 (144)
Q Consensus 111 ~~~~~~~l~~l~~ef~~~~~aL~~~l~ 137 (144)
...+.+.|+.+.++|......|...+.
T Consensus 579 sk~A~e~le~~~~~W~~~v~~L~~~vd 605 (968)
T PF01044_consen 579 SKAAKEHLEVFREAWEDAVEDLTEAVD 605 (968)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455678899999999888888776653
No 89
>PF04049 APC8: Anaphase promoting complex subunit 8 / Cdc23 ; InterPro: IPR007192 The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8). This entry is for CDC23.; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0005680 anaphase-promoting complex
Probab=20.97 E-value=3.4e+02 Score=19.77 Aligned_cols=82 Identities=10% Similarity=0.099 Sum_probs=47.1
Q ss_pred chhHHHHHHHHHhcccchhhhHHH-HH--HHHcChhcCCCC-------------hhHHHH-HHHHHHHhHHHHHHHHHHH
Q 038079 3 SNPLHQQIASMRQHLLDEEILDEQ-FV--ELEGLALASDED-------------PNFVEV-TINVYFEESNELLPMIEDL 65 (144)
Q Consensus 3 ~~~l~~~~~~~~~~~~~~~~lD~~-~~--~L~~L~~~~~~~-------------~~fv~~-Li~~f~~ds~~~l~~l~~a 65 (144)
+..++.+|..-++-..+.|+++.. |. .|-.| .+... +.+-.. ......+..+.-.=-+...
T Consensus 6 ~~~ir~~L~~a~~~~s~RgL~~saKWaaElL~gL--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~d~yllAks 83 (142)
T PF04049_consen 6 LKEIRSELRQAIRECSERGLYQSAKWAAELLNGL--PPPWRDDTPDDPSSSPSSSQLSPSSPSEDQLESKEYDKYLLAKS 83 (142)
T ss_pred HHHHHHHHHHHHHHHHHhcHHHHHHHHHHHHHcC--CCCcccccccccccCCCccccCCCChhhhhhhhhHHHHHHHHHH
Confidence 456778888888888899999985 44 34445 52111 111111 1111111122222234455
Q ss_pred hccCCCCHHHHHHHHhhhccccccc
Q 038079 66 LGKNPIEGSEMERILHRFKGSCASV 90 (144)
Q Consensus 66 l~~~~~D~~~l~~~aH~LKGSSasl 90 (144)
+= |...+++.||.||++.+..
T Consensus 84 yF----D~kEy~RaA~~L~~~~s~~ 104 (142)
T PF04049_consen 84 YF----DCKEYDRAAHVLKDCKSPK 104 (142)
T ss_pred Hh----chhHHHHHHHHHccCCCch
Confidence 44 7789999999999988443
No 90
>KOG2833 consensus Mevalonate pyrophosphate decarboxylase [Lipid transport and metabolism]
Probab=20.91 E-value=1.7e+02 Score=25.13 Aligned_cols=28 Identities=4% Similarity=0.156 Sum_probs=23.0
Q ss_pred HHHHh-HHHHHHHHHHHhccCCCCHHHHHHH
Q 038079 50 VYFEE-SNELLPMIEDLLGKNPIEGSEMERI 79 (144)
Q Consensus 50 ~f~~d-s~~~l~~l~~al~~~~~D~~~l~~~ 79 (144)
-=++. .|+++.+|++|+.++ ||+.+.++
T Consensus 226 hRi~~vVP~Ri~~m~eaI~~r--DF~~FA~l 254 (395)
T KOG2833|consen 226 HRIESVVPQRIQQMREAIRER--DFESFAKL 254 (395)
T ss_pred HHHHhhhHHHHHHHHHHHHhc--CHHHHHHH
Confidence 33444 799999999999987 99998876
No 91
>PRK10987 regulatory protein AmpE; Provisional
Probab=20.14 E-value=2.7e+02 Score=22.70 Aligned_cols=35 Identities=17% Similarity=0.245 Sum_probs=28.6
Q ss_pred ccccChHHHHHHHHHHHHHhhcCCHHHHHHHHHHH
Q 038079 87 CASVGANKVKNEVNVVIACCRNGDIEGAKAAFEQV 121 (144)
Q Consensus 87 SaslGA~~l~~~c~~lE~~~~~~~~~~~~~~l~~l 121 (144)
..++|...+.+..+.+.+..++||.+.+...+.++
T Consensus 79 ~~~lg~r~L~~~~~~v~~AL~~gDl~aAR~~l~~l 113 (284)
T PRK10987 79 LLCIGAGKQRLHYKAYLQAACRGDSQACYHMAEEL 113 (284)
T ss_pred HHHhCCchHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence 45688888888888888888888888888876666
Done!