Query psy6193
Match_columns 122
No_of_seqs 120 out of 173
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 20:05:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6193.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6193hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3799|consensus 99.9 2.3E-25 5E-30 170.9 5.9 99 16-114 1-161 (169)
2 PF02318 FYVE_2: FYVE-type zin 99.9 3.2E-24 7E-29 154.9 4.9 63 23-85 1-117 (118)
3 PF04810 zf-Sec23_Sec24: Sec23 75.5 0.79 1.7E-05 27.6 -0.2 15 60-74 22-36 (40)
4 PF13945 NST1: Salt tolerance 71.2 6 0.00013 31.7 3.7 39 24-72 113-151 (190)
5 COG1997 RPL43A Ribosomal prote 59.6 6.8 0.00015 28.3 1.8 28 43-70 25-61 (89)
6 PRK10778 dksA RNA polymerase-b 58.7 30 0.00065 26.4 5.3 48 27-75 79-145 (151)
7 PF01780 Ribosomal_L37ae: Ribo 58.5 5.8 0.00012 28.5 1.3 40 43-86 25-73 (90)
8 PRK12495 hypothetical protein; 57.6 19 0.00041 29.8 4.3 48 24-72 4-68 (226)
9 PF04545 Sigma70_r4: Sigma-70, 53.2 9.4 0.0002 22.9 1.5 25 22-46 2-26 (50)
10 PF09776 Mitoc_L55: Mitochondr 52.3 12 0.00026 28.0 2.2 16 20-35 72-87 (116)
11 PF14156 AbbA_antirepres: Anti 51.7 14 0.0003 25.2 2.2 20 23-42 7-26 (63)
12 COG1150 HdrC Heterodisulfide r 47.5 17 0.00037 29.4 2.5 25 18-42 7-31 (195)
13 PLN03131 hypothetical protein; 47.5 15 0.00032 34.8 2.4 30 41-70 4-51 (705)
14 KOG1013|consensus 47.2 8.4 0.00018 33.8 0.8 23 62-87 185-207 (362)
15 PRK09458 pspB phage shock prot 44.2 43 0.00093 23.4 3.8 24 23-46 34-57 (75)
16 PLN03119 putative ADP-ribosyla 43.9 17 0.00038 34.0 2.3 30 41-70 4-51 (648)
17 PF13274 DUF4065: Protein of u 40.3 31 0.00068 22.9 2.6 28 20-47 66-93 (108)
18 PF09098 Dehyd-heme_bind: Quin 39.8 19 0.00042 28.5 1.7 36 24-59 50-104 (167)
19 TIGR02890 spore_yteA sporulati 39.8 76 0.0016 24.4 4.9 48 26-74 53-119 (159)
20 KOG1985|consensus 39.1 10 0.00022 36.8 -0.0 20 55-74 221-252 (887)
21 PF06667 PspB: Phage shock pro 38.2 61 0.0013 22.4 3.8 25 22-46 33-57 (75)
22 PRK14890 putative Zn-ribbon RN 36.8 13 0.00027 25.0 0.2 19 55-73 28-47 (59)
23 PF07295 DUF1451: Protein of u 36.6 72 0.0016 24.3 4.3 21 20-40 28-48 (146)
24 PF03754 DUF313: Domain of unk 36.5 16 0.00034 26.9 0.7 16 18-33 46-61 (114)
25 PHA02078 hypothetical protein 36.5 19 0.00041 23.9 1.0 28 21-48 26-53 (54)
26 TIGR00280 L37a ribosomal prote 36.3 24 0.00051 25.4 1.5 29 54-86 37-73 (91)
27 PF01586 Basic: Myogenic Basic 35.6 12 0.00026 26.7 -0.1 15 56-72 68-82 (86)
28 COG5028 Vesicle coat complex C 34.5 12 0.00027 36.0 -0.2 21 55-75 202-234 (861)
29 PLN00162 transport protein sec 34.0 12 0.00027 34.9 -0.2 20 55-74 56-87 (761)
30 COG1734 DksA DnaK suppressor p 33.7 1.2E+02 0.0026 22.5 5.0 57 19-76 41-115 (120)
31 PTZ00255 60S ribosomal protein 33.5 27 0.00058 25.1 1.5 40 43-86 26-74 (90)
32 PF08986 DUF1889: Domain of un 32.9 12 0.00025 28.0 -0.5 26 3-37 31-57 (119)
33 PF04829 PT-VENN: Pre-toxin do 32.7 32 0.0007 22.3 1.6 16 21-36 1-16 (55)
34 PRK03976 rpl37ae 50S ribosomal 32.2 30 0.00064 24.8 1.5 40 43-86 26-74 (90)
35 PF13442 Cytochrome_CBB3: Cyto 31.3 70 0.0015 19.7 3.0 19 19-37 48-67 (67)
36 PRK14810 formamidopyrimidine-D 31.3 72 0.0016 26.0 3.8 16 55-70 247-272 (272)
37 PF10335 DUF294_C: Putative nu 30.8 90 0.002 22.9 3.9 32 16-47 110-141 (145)
38 cd02406 CRS2 Chloroplast RNA s 28.8 84 0.0018 24.9 3.7 26 15-41 143-168 (191)
39 PF13936 HTH_38: Helix-turn-he 28.2 35 0.00077 20.4 1.2 17 23-39 3-19 (44)
40 PF01921 tRNA-synt_1f: tRNA sy 27.8 48 0.001 28.9 2.3 50 30-79 141-216 (360)
41 PF10910 DUF2744: Protein of u 27.7 41 0.00088 25.5 1.6 27 14-40 91-117 (125)
42 TIGR03045 PS_II_C550 cytochrom 27.6 78 0.0017 24.5 3.2 27 16-42 123-149 (159)
43 cd00729 rubredoxin_SM Rubredox 26.0 24 0.00052 20.5 0.1 10 62-71 2-11 (34)
44 PF07649 C1_3: C1-like domain; 25.7 25 0.00054 19.5 0.1 16 64-84 2-17 (30)
45 PF01935 DUF87: Domain of unkn 25.7 56 0.0012 24.7 2.1 22 18-39 206-227 (229)
46 PF04120 Iron_permease: Low af 25.6 93 0.002 23.5 3.3 26 17-42 87-112 (132)
47 PF09862 DUF2089: Protein of u 25.2 74 0.0016 23.5 2.6 33 18-50 27-59 (113)
48 PF04959 ARS2: Arsenite-resist 25.1 71 0.0015 25.9 2.7 24 60-83 75-106 (214)
49 KOG0860|consensus 24.5 68 0.0015 24.0 2.3 19 30-48 46-64 (116)
50 CHL00183 petJ cytochrome c553; 24.0 1.1E+02 0.0023 21.0 3.2 23 19-41 81-104 (108)
51 PF08432 Vfa1: AAA-ATPase Vps4 23.6 18 0.0004 27.9 -0.9 36 64-100 15-53 (182)
52 PF13864 Enkurin: Calmodulin-b 23.5 1.7E+02 0.0036 20.2 4.0 31 20-50 32-62 (98)
53 PF11161 DUF2944: Protein of u 23.4 30 0.00064 27.9 0.2 11 78-88 65-75 (187)
54 PF03107 C1_2: C1 domain; Int 23.3 29 0.00062 19.4 0.1 10 63-72 1-10 (30)
55 PF14445 Prok-RING_2: Prokaryo 23.2 41 0.00088 22.4 0.8 22 54-77 24-45 (57)
56 PF11686 DUF3283: Protein of u 23.1 64 0.0014 21.8 1.7 14 21-34 1-14 (61)
57 TIGR02420 dksA RNA polymerase- 23.1 2.2E+02 0.0048 20.0 4.7 43 27-70 48-109 (110)
58 PF09332 Mcm10: Mcm10 replicat 23.0 24 0.00051 30.6 -0.4 12 60-71 283-294 (344)
59 smart00520 BASIC Basic domain 21.9 26 0.00055 25.4 -0.4 15 56-72 68-82 (91)
60 KOG4275|consensus 21.8 46 0.001 29.1 1.1 22 19-40 240-264 (350)
61 TIGR00447 pth peptidyl-tRNA hy 21.4 1.6E+02 0.0034 23.2 3.9 27 15-42 142-168 (188)
62 PF04936 DUF658: Protein of un 20.9 1.4E+02 0.0031 24.0 3.6 35 17-54 134-169 (186)
63 cd08818 CARD_MDA5_1 Caspase ac 20.5 2.2E+02 0.0049 20.3 4.2 45 19-64 25-69 (88)
64 cd01277 HINT_subgroup HINT (hi 20.1 1.2E+02 0.0027 19.9 2.7 24 18-41 44-67 (103)
65 PRK13622 psbV cytochrome c-550 20.0 1.2E+02 0.0025 24.3 2.9 29 14-42 132-160 (180)
66 PF10955 DUF2757: Protein of u 20.0 54 0.0012 22.8 0.9 19 18-36 25-43 (76)
No 1
>KOG3799|consensus
Probab=99.92 E-value=2.3e-25 Score=170.90 Aligned_cols=99 Identities=43% Similarity=0.791 Sum_probs=87.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHhh----------------------------hhccc--------
Q psy6193 16 ADIIPDLSHLTLEERQIIESVMMRQKQEEERELEIMRSA----------------------------CQVYL-------- 59 (122)
Q Consensus 16 ~~e~pdLS~LTeeEreiIl~VL~Rdk~le~~E~eRirrL----------------------------C~~C~-------- 59 (122)
|.+||||||||+.||-.|.+|+.|++.++.++.+++++. |+||+
T Consensus 1 ~~~~~d~sh~T~he~~qik~vf~rqk~ee~kq~ei~~~~~~e~~el~~Qi~erkEqqKKaGv~ddatC~IC~KTKFADG~ 80 (169)
T KOG3799|consen 1 MDEMPDLSHLTPHERMQIKEVFIRQKIEEHKQFEIYKEQVKEMGELSQQIQERKEQQKKAGVGDDATCGICHKTKFADGC 80 (169)
T ss_pred CccccchhhcCccchHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCcCcchhhhhhccccccc
Confidence 578999999999999999999999999999887765433 66666
Q ss_pred ------------------------ccccccchhhhhhhHhhhcccccccCCCCCC-CCccc-cccccccCCCccccchhh
Q psy6193 60 ------------------------MVIWVCILCRKKQELLSKTGQWINKGMNSTP-QGDAI-MRKIEADMMFEDKRPKLE 113 (122)
Q Consensus 60 ------------------------k~~W~C~vC~k~~eL~~kSGeWFye~~~~~~-~~~~~-~r~~~~~~~~~dk~~kl~ 113 (122)
|++|+|++|+++++|+++||.|||++++.+| ++|.. +|+++.+..|+||+|||-
T Consensus 81 GH~C~YCq~r~CARCGGrv~lrsNKv~wvcnlc~k~q~il~ksg~wf~~sgs~~~~~pd~~v~~~~~~~~~p~~k~p~~~ 160 (169)
T KOG3799|consen 81 GHNCSYCQTRFCARCGGRVSLRSNKVMWVCNLCRKQQEILTKSGAWFYNSGSNTPQQPDQKVLRGLRNEEAPQEKKPKLH 160 (169)
T ss_pred CcccchhhhhHHHhcCCeeeeccCceEEeccCCcHHHHHHHhcchHHHhcCCCCCCCcccccccchhcccCCcccccchh
Confidence 6899999999999999999999999999877 55544 999999999999999985
Q ss_pred c
Q psy6193 114 R 114 (122)
Q Consensus 114 ~ 114 (122)
.
T Consensus 161 ~ 161 (169)
T KOG3799|consen 161 E 161 (169)
T ss_pred h
Confidence 4
No 2
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=99.90 E-value=3.2e-24 Score=154.90 Aligned_cols=63 Identities=40% Similarity=0.730 Sum_probs=56.6
Q ss_pred CCCCHHHHHHHHHHHHhHHHHHHHHHHHHHhh------------------------hhccc-------------------
Q psy6193 23 SHLTLEERQIIESVMMRQKQEEERELEIMRSA------------------------CQVYL------------------- 59 (122)
Q Consensus 23 S~LTeeEreiIl~VL~Rdk~le~~E~eRirrL------------------------C~~C~------------------- 59 (122)
||||++||++|++||+||++++++|++||++| |++|.
T Consensus 1 s~Lt~eE~~~I~~Vl~R~~~l~~~E~~Ri~kLk~~L~~e~~r~~~~~~~~~~~~~~C~~C~~~fg~l~~~~~~C~~C~~~ 80 (118)
T PF02318_consen 1 SHLTEEEREIILQVLQRDEELRKKEEERIRKLKQELQKEKMRREALGNSQKYGERHCARCGKPFGFLFNRGRVCVDCKHR 80 (118)
T ss_dssp TTS-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSCSTTHCCSB-TTTS-BCSCTSTTCEEETTTTEE
T ss_pred CCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccCCcchhhhCCcccccCCCCCcCCcCCcc
Confidence 89999999999999999999999999999887 55544
Q ss_pred -----------ccccccchhhhhhhHhhhcccccccC
Q psy6193 60 -----------MVIWVCILCRKKQELLSKTGQWINKG 85 (122)
Q Consensus 60 -----------k~~W~C~vC~k~~eL~~kSGeWFye~ 85 (122)
+..|+|++|++.++|+++||+|||++
T Consensus 81 VC~~C~~~~~~~~~WlC~vC~k~rel~~~sG~Wf~~~ 117 (118)
T PF02318_consen 81 VCKKCGVYSKKEPIWLCKVCQKQRELKKKSGEWFYEE 117 (118)
T ss_dssp EETTSEEETSSSCCEEEHHHHHHHHHHHHCSHHHHCC
T ss_pred ccCccCCcCCCCCCEEChhhHHHHHHHHHhhhHHhcc
Confidence 46999999999999999999999986
No 3
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=75.54 E-value=0.79 Score=27.57 Aligned_cols=15 Identities=33% Similarity=0.893 Sum_probs=9.4
Q ss_pred ccccccchhhhhhhH
Q psy6193 60 MVIWVCILCRKKQEL 74 (122)
Q Consensus 60 k~~W~C~vC~k~~eL 74 (122)
...|.|++|....+|
T Consensus 22 ~~~w~C~~C~~~N~l 36 (40)
T PF04810_consen 22 GKTWICNFCGTKNPL 36 (40)
T ss_dssp TTEEEETTT--EEE-
T ss_pred CCEEECcCCCCcCCC
Confidence 358999999876544
No 4
>PF13945 NST1: Salt tolerance down-regulator
Probab=71.20 E-value=6 Score=31.67 Aligned_cols=39 Identities=18% Similarity=0.335 Sum_probs=21.6
Q ss_pred CCCHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhcccccccccchhhhhh
Q psy6193 24 HLTLEERQIIESVMMRQKQEEERELEIMRSACQVYLMVIWVCILCRKKQ 72 (122)
Q Consensus 24 ~LTeeEreiIl~VL~Rdk~le~~E~eRirrLC~~C~k~~W~C~vC~k~~ 72 (122)
.|+|+||.-|+.| ..+.-|+.+-++- ++-|- |+||+..+
T Consensus 113 SL~eeERr~LVkI-EKe~VLkkmKeqq----~h~C~-----C~vCgr~~ 151 (190)
T PF13945_consen 113 SLSEEERRSLVKI-EKEAVLKKMKEQQ----KHSCS-----CSVCGRKR 151 (190)
T ss_pred ccCHHHHHHHHHh-hHHHHHHHHHHHh----ccCcc-----cHHHhchh
Confidence 4777777777775 3443333332211 33344 88888765
No 5
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=59.59 E-value=6.8 Score=28.26 Aligned_cols=28 Identities=25% Similarity=0.428 Sum_probs=19.1
Q ss_pred HHHHHHHHHHhh-hhccc--------ccccccchhhh
Q psy6193 43 EEERELEIMRSA-CQVYL--------MVIWVCILCRK 70 (122)
Q Consensus 43 le~~E~eRirrL-C~~C~--------k~~W~C~vC~k 70 (122)
..++|.++..+. |..|. ..+|.|.-|..
T Consensus 25 v~~ie~~~~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~ 61 (89)
T COG1997 25 VKEIEAQQRAKHVCPFCGRTTVKRIATGIWKCRKCGA 61 (89)
T ss_pred HHHHHHHHhcCCcCCCCCCcceeeeccCeEEcCCCCC
Confidence 344554444333 99998 36999999975
No 6
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=58.72 E-value=30 Score=26.41 Aligned_cols=48 Identities=19% Similarity=0.292 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhHHH-HHHHHHHHHHhh-------hhcccc-----------cccccchhhhhhhHh
Q psy6193 27 LEERQIIESVMMRQKQ-EEERELEIMRSA-------CQVYLM-----------VIWVCILCRKKQELL 75 (122)
Q Consensus 27 eeEreiIl~VL~Rdk~-le~~E~eRirrL-------C~~C~k-----------~~W~C~vC~k~~eL~ 75 (122)
+.++.+.+..+.|+++ +.+++ .-+.|+ |-.|.. ..-.|.-|+...|.+
T Consensus 79 ~~~~~~~l~~~~r~~~~L~~I~-~AL~Ri~~gtYG~Ce~CGe~I~~~RL~A~P~A~~CI~CQe~~E~~ 145 (151)
T PRK10778 79 EEEFSLELRNRDRERKLIKKIE-KTLKKVEDEDFGYCESCGVEIGIRRLEARPTADLCIDCKTLAEIR 145 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHHHhCCCCceeccCCCcccHHHHhcCCCccccHHHHHHHHHH
Confidence 3444455555666633 33333 333444 999982 466799999988754
No 7
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=58.55 E-value=5.8 Score=28.48 Aligned_cols=40 Identities=20% Similarity=0.353 Sum_probs=25.0
Q ss_pred HHHHHHHHH-Hhhhhccc--------ccccccchhhhhhhHhhhcccccccCC
Q psy6193 43 EEERELEIM-RSACQVYL--------MVIWVCILCRKKQELLSKTGQWINKGM 86 (122)
Q Consensus 43 le~~E~eRi-rrLC~~C~--------k~~W~C~vC~k~~eL~~kSGeWFye~~ 86 (122)
..++|...- +..|..|. ..+|.|.-|.+ .+..|+|-++..
T Consensus 25 vkkie~~q~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~----~~AGGAy~~~T~ 73 (90)
T PF01780_consen 25 VKKIEISQHAKYTCPFCGKTSVKRVATGIWKCKKCGK----KFAGGAYTPSTP 73 (90)
T ss_dssp HHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTE----EEE-BSSSSS-H
T ss_pred HHHHHHHHhCCCcCCCCCCceeEEeeeEEeecCCCCC----EEeCCCccccch
Confidence 344443332 23399998 36999999996 456788876653
No 8
>PRK12495 hypothetical protein; Provisional
Probab=57.65 E-value=19 Score=29.82 Aligned_cols=48 Identities=19% Similarity=0.203 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHhHHHHHHHHHHHHHhh-----------hhccc------ccccccchhhhhh
Q psy6193 24 HLTLEERQIIESVMMRQKQEEERELEIMRSA-----------CQVYL------MVIWVCILCRKKQ 72 (122)
Q Consensus 24 ~LTeeEreiIl~VL~Rdk~le~~E~eRirrL-----------C~~C~------k~~W~C~vC~k~~ 72 (122)
|=.|-||+.+-+-..+|++-++.- ++|-.| |..|. .+.-+|.+|++..
T Consensus 4 FDkEaEREkLREKye~d~~~R~~~-~~ma~lL~~gatmsa~hC~~CG~PIpa~pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 4 FDKEAEREKLREKYEQDEQKREAT-ERMSELLLQGATMTNAHCDECGDPIFRHDGQEFCPTCQQPV 68 (226)
T ss_pred hhHHHHHHHHHHHHhhhHHHHHHH-HHHHHHHHhhcccchhhcccccCcccCCCCeeECCCCCCcc
Confidence 446889999998887777655544 333222 99998 3466799999754
No 9
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=53.15 E-value=9.4 Score=22.86 Aligned_cols=25 Identities=28% Similarity=0.295 Sum_probs=18.2
Q ss_pred CCCCCHHHHHHHHHHHHhHHHHHHH
Q psy6193 22 LSHLTLEERQIIESVMMRQKQEEER 46 (122)
Q Consensus 22 LS~LTeeEreiIl~VL~Rdk~le~~ 46 (122)
|+.|++.||++|.-+...+..++++
T Consensus 2 l~~L~~~er~vi~~~y~~~~t~~eI 26 (50)
T PF04545_consen 2 LDQLPPREREVIRLRYFEGLTLEEI 26 (50)
T ss_dssp HCTS-HHHHHHHHHHHTST-SHHHH
T ss_pred hhhCCHHHHHHHHHHhcCCCCHHHH
Confidence 5789999999999987666555554
No 10
>PF09776 Mitoc_L55: Mitochondrial ribosomal protein L55; InterPro: IPR018615 Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Probab=52.33 E-value=12 Score=27.99 Aligned_cols=16 Identities=38% Similarity=0.345 Sum_probs=14.6
Q ss_pred CCCCCCCHHHHHHHHH
Q psy6193 20 PDLSHLTLEERQIIES 35 (122)
Q Consensus 20 pdLS~LTeeEreiIl~ 35 (122)
+||+.|||+||...+.
T Consensus 72 lDl~~LSeeERk~rl~ 87 (116)
T PF09776_consen 72 LDLDTLSEEERKARLR 87 (116)
T ss_pred cCcccCCHHHHHHHHH
Confidence 4999999999999887
No 11
>PF14156 AbbA_antirepres: Antirepressor AbbA
Probab=51.71 E-value=14 Score=25.16 Aligned_cols=20 Identities=25% Similarity=0.501 Sum_probs=17.6
Q ss_pred CCCCHHHHHHHHHHHHhHHH
Q psy6193 23 SHLTLEERQIIESVMMRQKQ 42 (122)
Q Consensus 23 S~LTeeEreiIl~VL~Rdk~ 42 (122)
..||+||++.+|.||.+|..
T Consensus 7 ~rlt~EE~~LLLdiLf~q~Y 26 (63)
T PF14156_consen 7 ERLTEEEKKLLLDILFQQNY 26 (63)
T ss_pred HHhhHHHHHHHHHHHHHHHH
Confidence 45899999999999999854
No 12
>COG1150 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]
Probab=47.53 E-value=17 Score=29.35 Aligned_cols=25 Identities=16% Similarity=0.037 Sum_probs=18.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhHHH
Q psy6193 18 IIPDLSHLTLEERQIIESVMMRQKQ 42 (122)
Q Consensus 18 e~pdLS~LTeeEreiIl~VL~Rdk~ 42 (122)
...|++.++.++++.+.++..-.+.
T Consensus 7 ~~~~~~~v~~e~~~~~ve~~~~~~~ 31 (195)
T COG1150 7 EVIDGEDVSPEEKEEAVERTEEVKG 31 (195)
T ss_pred hhhcccccChHHHHHHHHHHHHhcC
Confidence 3568889999999998887544433
No 13
>PLN03131 hypothetical protein; Provisional
Probab=47.46 E-value=15 Score=34.81 Aligned_cols=30 Identities=30% Similarity=0.634 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHhh--------hhccc--cc--------ccccchhhh
Q psy6193 41 KQEEERELEIMRSA--------CQVYL--MV--------IWVCILCRK 70 (122)
Q Consensus 41 k~le~~E~eRirrL--------C~~C~--k~--------~W~C~vC~k 70 (122)
++++++.+++|+.| |++|. .+ +.+|..|..
T Consensus 4 kkqqErnekiLreLlk~PgNk~CADCga~~P~WASiNlGIFICi~CSG 51 (705)
T PLN03131 4 RKEEERNEKIIRGLMKLPPNRRCINCNSLGPQFVCTNFWTFICMTCSG 51 (705)
T ss_pred hHHHHHHHHHHHHHhhCcCCCccccCCCCCCCeeEeccceEEchhchh
Confidence 44555666667666 99999 33 457888875
No 14
>KOG1013|consensus
Probab=47.17 E-value=8.4 Score=33.79 Aligned_cols=23 Identities=9% Similarity=0.040 Sum_probs=20.7
Q ss_pred ccccchhhhhhhHhhhcccccccCCC
Q psy6193 62 IWVCILCRKKQELLSKTGQWINKGMN 87 (122)
Q Consensus 62 ~W~C~vC~k~~eL~~kSGeWFye~~~ 87 (122)
.|+|++|-.+. ..++.|||.+.+
T Consensus 185 ~~lkKl~p~q~---k~f~~cl~~~lp 207 (362)
T KOG1013|consen 185 VSLKKLKPLQR---KSFNICLEKSLP 207 (362)
T ss_pred hhhhccChhhc---chhhhhhhccCC
Confidence 69999998887 789999999987
No 15
>PRK09458 pspB phage shock protein B; Provisional
Probab=44.19 E-value=43 Score=23.38 Aligned_cols=24 Identities=25% Similarity=0.360 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHHHHHHhHHHHHHH
Q psy6193 23 SHLTLEERQIIESVMMRQKQEEER 46 (122)
Q Consensus 23 S~LTeeEreiIl~VL~Rdk~le~~ 46 (122)
+.||++|.+.+.+...++++++++
T Consensus 34 ~~Ls~~d~~~L~~L~~~A~rm~~R 57 (75)
T PRK09458 34 QGLSQEEQQRLAQLTEKAERMRER 57 (75)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Confidence 579999999999999999998766
No 16
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=43.89 E-value=17 Score=34.03 Aligned_cols=30 Identities=37% Similarity=0.635 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHhh--------hhccc--c--------cccccchhhh
Q psy6193 41 KQEEERELEIMRSA--------CQVYL--M--------VIWVCILCRK 70 (122)
Q Consensus 41 k~le~~E~eRirrL--------C~~C~--k--------~~W~C~vC~k 70 (122)
++++++.+++|+.| |++|. . .+.+|..|..
T Consensus 4 KR~qERnekILreLlklPgNk~CADCgs~~P~WASiNlGIFICi~CSG 51 (648)
T PLN03119 4 KREEERNEKIIRGLMKLPPNRRCINCNSLGPQYVCTTFWTFVCMACSG 51 (648)
T ss_pred hHHHHHHHHHHHHHhhCcCCCccccCCCCCCCceeeccceEEeccchh
Confidence 44556666666666 99999 2 3557887765
No 17
>PF13274 DUF4065: Protein of unknown function (DUF4065)
Probab=40.32 E-value=31 Score=22.86 Aligned_cols=28 Identities=32% Similarity=0.461 Sum_probs=23.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhHHHHHHHH
Q psy6193 20 PDLSHLTLEERQIIESVMMRQKQEEERE 47 (122)
Q Consensus 20 pdLS~LTeeEreiIl~VL~Rdk~le~~E 47 (122)
.+...|+++|+++|-.|+.+-......+
T Consensus 66 ~~~~~l~~~~~~~i~~V~~~~~~~s~~~ 93 (108)
T PF13274_consen 66 FDLEELSEEEKEIIDEVINKYGDKSAWE 93 (108)
T ss_pred cccccCCHHHHHHHHHHHHHHcCCCHHH
Confidence 6889999999999999999886554433
No 18
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=39.82 E-value=19 Score=28.53 Aligned_cols=36 Identities=14% Similarity=0.167 Sum_probs=22.8
Q ss_pred CCCHHHHHHHHHHHHhHHHHH-------------------HHHHHHHHhhhhccc
Q psy6193 24 HLTLEERQIIESVMMRQKQEE-------------------ERELEIMRSACQVYL 59 (122)
Q Consensus 24 ~LTeeEreiIl~VL~Rdk~le-------------------~~E~eRirrLC~~C~ 59 (122)
.||++||..|...|....=+. ..+.+.|..+|++|+
T Consensus 50 ~Is~eer~avVkYLAd~~GLap~Et~~~ry~~er~~~~~e~~~~e~~~~~C~rCH 104 (167)
T PF09098_consen 50 PISPEERRAVVKYLADTQGLAPSETAPVRYALERRPNTVEQFPNEEITQMCARCH 104 (167)
T ss_dssp ---HHHHHHHHHHHHHHT---CGGCTT-CCCCCT-TT-----SCHHHHHHHSSSS
T ss_pred CCCHHHHHHHHHHHHHccCCCchhhcchhhhhhcCcchhhcccchHHHHHHHHhh
Confidence 589999999999998764333 223355677799999
No 19
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=39.80 E-value=76 Score=24.41 Aligned_cols=48 Identities=21% Similarity=0.358 Sum_probs=32.3
Q ss_pred CHHHHHHHHHHHHhHH-HHHHHHHHHHHhh-------hhccc-----------ccccccchhhhhhhH
Q psy6193 26 TLEERQIIESVMMRQK-QEEERELEIMRSA-------CQVYL-----------MVIWVCILCRKKQEL 74 (122)
Q Consensus 26 TeeEreiIl~VL~Rdk-~le~~E~eRirrL-------C~~C~-----------k~~W~C~vC~k~~eL 74 (122)
.+.|+++.+.++.|+. .+.+++.. +.|+ |-.|. -..-.|.-|+...+.
T Consensus 53 ~~~e~~~~~~l~~~~~~~L~~Ie~A-L~Ri~~G~YG~Ce~CGe~I~~~RL~a~P~a~~Ci~Cq~~~E~ 119 (159)
T TIGR02890 53 ELYEREKDIALREHEERELREIEHA-LQKIENGTYGICEVCGKPIPYERLEAIPTATTCVECQNRKEV 119 (159)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhCCCCCeecccCCcccHHHHhhCCCcchhHHHHHHhhh
Confidence 3557777777766653 35555533 3444 99999 247789999998877
No 20
>KOG1985|consensus
Probab=39.06 E-value=10 Score=36.75 Aligned_cols=20 Identities=25% Similarity=0.700 Sum_probs=17.2
Q ss_pred hhccc------------ccccccchhhhhhhH
Q psy6193 55 CQVYL------------MVIWVCILCRKKQEL 74 (122)
Q Consensus 55 C~~C~------------k~~W~C~vC~k~~eL 74 (122)
|.+|+ ...|.||+|....++
T Consensus 221 Cr~CRtYiNPFV~fid~gr~WrCNlC~~~Ndv 252 (887)
T KOG1985|consen 221 CRRCRTYINPFVEFIDQGRRWRCNLCGRVNDV 252 (887)
T ss_pred ehhhhhhcCCeEEecCCCceeeechhhhhcCC
Confidence 99999 249999999998776
No 21
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=38.20 E-value=61 Score=22.38 Aligned_cols=25 Identities=24% Similarity=0.330 Sum_probs=21.6
Q ss_pred CCCCCHHHHHHHHHHHHhHHHHHHH
Q psy6193 22 LSHLTLEERQIIESVMMRQKQEEER 46 (122)
Q Consensus 22 LS~LTeeEreiIl~VL~Rdk~le~~ 46 (122)
-+.||++|.+.+.+...+.+.++++
T Consensus 33 ~~gLs~~d~~~L~~L~~~a~rm~eR 57 (75)
T PF06667_consen 33 SQGLSEEDEQRLQELYEQAERMEER 57 (75)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3679999999999999999888765
No 22
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=36.79 E-value=13 Score=24.98 Aligned_cols=19 Identities=37% Similarity=0.709 Sum_probs=16.3
Q ss_pred hhccccc-ccccchhhhhhh
Q psy6193 55 CQVYLMV-IWVCILCRKKQE 73 (122)
Q Consensus 55 C~~C~k~-~W~C~vC~k~~e 73 (122)
|..|-.. +|.|..|+++..
T Consensus 28 CPnCG~~~I~RC~~CRk~~~ 47 (59)
T PRK14890 28 CPNCGEVIIYRCEKCRKQSN 47 (59)
T ss_pred CCCCCCeeEeechhHHhcCC
Confidence 8888876 999999999863
No 23
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=36.64 E-value=72 Score=24.33 Aligned_cols=21 Identities=24% Similarity=0.314 Sum_probs=19.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhH
Q psy6193 20 PDLSHLTLEERQIIESVMMRQ 40 (122)
Q Consensus 20 pdLS~LTeeEreiIl~VL~Rd 40 (122)
..++.||.+|-+.|...|+||
T Consensus 28 ~~~~elT~eEl~lv~~ylkRD 48 (146)
T PF07295_consen 28 VAAGELTREELALVSAYLKRD 48 (146)
T ss_pred HHHhhcCHHHHHHHHHHHHHH
Confidence 357889999999999999999
No 24
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=36.55 E-value=16 Score=26.94 Aligned_cols=16 Identities=50% Similarity=0.515 Sum_probs=13.9
Q ss_pred CCCCCCCCCHHHHHHH
Q psy6193 18 IIPDLSHLTLEERQII 33 (122)
Q Consensus 18 e~pdLS~LTeeEreiI 33 (122)
...+..|||++|.++|
T Consensus 46 qi~~~dFLt~eE~~~i 61 (114)
T PF03754_consen 46 QIIDNDFLTEEEKRII 61 (114)
T ss_pred HhcccccCCHHHHHHH
Confidence 3558899999999999
No 25
>PHA02078 hypothetical protein
Probab=36.48 E-value=19 Score=23.86 Aligned_cols=28 Identities=21% Similarity=0.401 Sum_probs=21.6
Q ss_pred CCCCCCHHHHHHHHHHHHhHHHHHHHHH
Q psy6193 21 DLSHLTLEERQIIESVMMRQKQEEEREL 48 (122)
Q Consensus 21 dLS~LTeeEreiIl~VL~Rdk~le~~E~ 48 (122)
|+-.+-+.||+|.+..|..+-+++.+++
T Consensus 26 ~ienMmP~ER~Iylsll~k~lkE~n~~q 53 (54)
T PHA02078 26 ELENMMPWEREIYAALLIQYIQEKNKKQ 53 (54)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHhc
Confidence 3445668999999999999977666554
No 26
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=36.28 E-value=24 Score=25.41 Aligned_cols=29 Identities=24% Similarity=0.469 Sum_probs=22.1
Q ss_pred hhhccc--------ccccccchhhhhhhHhhhcccccccCC
Q psy6193 54 ACQVYL--------MVIWVCILCRKKQELLSKTGQWINKGM 86 (122)
Q Consensus 54 LC~~C~--------k~~W~C~vC~k~~eL~~kSGeWFye~~ 86 (122)
.|..|. ..+|.|.-|.+. +..|+|-++..
T Consensus 37 ~CpfCgk~~vkR~a~GIW~C~~C~~~----~AGGAy~p~T~ 73 (91)
T TIGR00280 37 VCPFCGKKTVKRGSTGIWTCRKCGAK----FAGGAYTPVTP 73 (91)
T ss_pred cCCCCCCCceEEEeeEEEEcCCCCCE----EeCCccccccc
Confidence 399996 369999999985 45788886553
No 27
>PF01586 Basic: Myogenic Basic domain; InterPro: IPR002546 This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding []. With 12 residues of the basic domain involved in DNA binding []. The basic domain forms an extended alpha helix in the structure.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007517 muscle organ development, 0005634 nucleus; PDB: 1MDY_C.
Probab=35.65 E-value=12 Score=26.66 Aligned_cols=15 Identities=33% Similarity=1.030 Sum_probs=0.9
Q ss_pred hcccccccccchhhhhh
Q psy6193 56 QVYLMVIWVCILCRKKQ 72 (122)
Q Consensus 56 ~~C~k~~W~C~vC~k~~ 72 (122)
++|. .|-|++|.++.
T Consensus 68 G~CL--~WACKaCKRKt 82 (86)
T PF01586_consen 68 GQCL--LWACKACKRKT 82 (86)
T ss_dssp -------------S---
T ss_pred Ccch--HHHhHhhhccC
Confidence 4577 99999998753
No 28
>COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
Probab=34.49 E-value=12 Score=36.00 Aligned_cols=21 Identities=29% Similarity=0.743 Sum_probs=17.7
Q ss_pred hhccc------------ccccccchhhhhhhHh
Q psy6193 55 CQVYL------------MVIWVCILCRKKQELL 75 (122)
Q Consensus 55 C~~C~------------k~~W~C~vC~k~~eL~ 75 (122)
|.+|+ ...|.||+|+-..++-
T Consensus 202 CrrCrsYiNPfv~fi~~g~kw~CNiC~~kN~vp 234 (861)
T COG5028 202 CRRCRSYINPFVQFIEQGRKWRCNICRSKNDVP 234 (861)
T ss_pred hhhhHhhcCceEEEecCCcEEEEeeccccccCc
Confidence 99999 2389999999988764
No 29
>PLN00162 transport protein sec23; Provisional
Probab=33.97 E-value=12 Score=34.92 Aligned_cols=20 Identities=25% Similarity=0.928 Sum_probs=16.5
Q ss_pred hhccc------------ccccccchhhhhhhH
Q psy6193 55 CQVYL------------MVIWVCILCRKKQEL 74 (122)
Q Consensus 55 C~~C~------------k~~W~C~vC~k~~eL 74 (122)
|.+|+ ...|.|++|....++
T Consensus 56 C~~CraylNPf~~~d~~~~~W~C~~C~~~N~~ 87 (761)
T PLN00162 56 CRTCRAVLNPYCRVDFQAKIWICPFCFQRNHF 87 (761)
T ss_pred cCCCcCEECCceEEecCCCEEEccCCCCCCCC
Confidence 88898 358999999987765
No 30
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=33.66 E-value=1.2e+02 Score=22.53 Aligned_cols=57 Identities=18% Similarity=0.254 Sum_probs=34.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHhh-------hhcccc-----------cccccchhhhhhhHhh
Q psy6193 19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRSA-------CQVYLM-----------VIWVCILCRKKQELLS 76 (122)
Q Consensus 19 ~pdLS~LTeeEreiIl~VL~Rdk~le~~E~eRirrL-------C~~C~k-----------~~W~C~vC~k~~eL~~ 76 (122)
+.|..... .+++..+.+..|..++-.+=..-+.|+ |-.|.. +.-.|.-|+...+...
T Consensus 41 ~aD~a~~~-~~~~~~~~~~~r~r~~l~~i~~al~rIe~gtYG~Ce~cG~~Ip~~RL~A~P~A~~Ci~cQ~~~E~~~ 115 (120)
T COG1734 41 PADRATQE-EERELELRLRDRERKLLRKIESALDRIEEGTYGICEECGEPIPEARLEARPTARLCIECQERAERRE 115 (120)
T ss_pred hhhhhHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCccchhccCCcCCHHHHhhCcchHHHHHHHHHHHHHH
Confidence 44443333 778888888777755443322333443 988982 4667888888776654
No 31
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=33.51 E-value=27 Score=25.06 Aligned_cols=40 Identities=23% Similarity=0.449 Sum_probs=26.2
Q ss_pred HHHHHHHHH-Hhhhhccc--------ccccccchhhhhhhHhhhcccccccCC
Q psy6193 43 EEERELEIM-RSACQVYL--------MVIWVCILCRKKQELLSKTGQWINKGM 86 (122)
Q Consensus 43 le~~E~eRi-rrLC~~C~--------k~~W~C~vC~k~~eL~~kSGeWFye~~ 86 (122)
..++|...- ...|.-|. ..+|.|.-|.+. +..|+|-++..
T Consensus 26 v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~----~AGGAy~~~T~ 74 (90)
T PTZ00255 26 IKKIEISQHAKYFCPFCGKHAVKRQAVGIWRCKGCKKT----VAGGAWTLSTP 74 (90)
T ss_pred HHHHHHHHhCCccCCCCCCCceeeeeeEEEEcCCCCCE----EeCCccccccc
Confidence 344443332 23399995 369999999985 45788886554
No 32
>PF08986 DUF1889: Domain of unknown function (DUF1889); InterPro: IPR015079 This family consist of hypothetical bacterial proteins. ; PDB: 2JN8_A 2ES9_A.
Probab=32.89 E-value=12 Score=28.05 Aligned_cols=26 Identities=23% Similarity=0.166 Sum_probs=16.3
Q ss_pred ccCccccc-CCCCCCCCCCCCCCCCHHHHHHHHHHH
Q psy6193 3 LTEGMVTS-MAQTNADIIPDLSHLTLEERQIIESVM 37 (122)
Q Consensus 3 ~~~~~~~~-~~~~~~~e~pdLS~LTeeEreiIl~VL 37 (122)
|.|||-+| ++|.+|++ ...+.|+.-|
T Consensus 31 FIggMntSas~P~sMdE---------STAKGi~KyL 57 (119)
T PF08986_consen 31 FIGGMNTSASVPHSMDE---------STAKGIFKYL 57 (119)
T ss_dssp HHHTS-TT-SS--HCCC---------HHHHHHHHHH
T ss_pred HhcccccCCCCCCccch---------HHHHHHHHHH
Confidence 67999998 77777765 4566776654
No 33
>PF04829 PT-VENN: Pre-toxin domain with VENN motif; InterPro: IPR006914 This group of proteins, mainly from Neisseria meningitidis, may have haemagglutinin or haemolysin activity. A number of them have a second conserved domain, IPR006915 from INTERPRO, which is found in possible Pseudomonas aeruginosa haemagglutinins []. Filamentous haemagglutinin (FHA) is a major virulence attachment factor produced by certain bacterial species that functions as both a primary adhesin and an immunomodulator. Haemolysin is pore-forming toxin.
Probab=32.71 E-value=32 Score=22.31 Aligned_cols=16 Identities=44% Similarity=0.530 Sum_probs=13.3
Q ss_pred CCCCCCHHHHHHHHHH
Q psy6193 21 DLSHLTLEERQIIESV 36 (122)
Q Consensus 21 dLS~LTeeEreiIl~V 36 (122)
|-+.||++|++.|..+
T Consensus 1 d~~~Lte~eK~~v~~l 16 (55)
T PF04829_consen 1 DPSELTEEEKQKVSAL 16 (55)
T ss_pred ChHhcCHHHHHHHHHH
Confidence 4578999999998865
No 34
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=32.22 E-value=30 Score=24.84 Aligned_cols=40 Identities=23% Similarity=0.407 Sum_probs=26.1
Q ss_pred HHHHHHHHH-Hhhhhccc--------ccccccchhhhhhhHhhhcccccccCC
Q psy6193 43 EEERELEIM-RSACQVYL--------MVIWVCILCRKKQELLSKTGQWINKGM 86 (122)
Q Consensus 43 le~~E~eRi-rrLC~~C~--------k~~W~C~vC~k~~eL~~kSGeWFye~~ 86 (122)
..++|...- +..|..|. ..+|.|.-|.+. +..|+|-++..
T Consensus 26 v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~----~AGGAy~~~T~ 74 (90)
T PRK03976 26 VADIEEKMRAKHVCPVCGRPKVKRVGTGIWECRKCGAK----FAGGAYTPETP 74 (90)
T ss_pred HHHHHHHHhcCccCCCCCCCceEEEEEEEEEcCCCCCE----EeCCccccccc
Confidence 344443332 23399995 369999999874 45788876654
No 35
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=31.31 E-value=70 Score=19.75 Aligned_cols=19 Identities=21% Similarity=0.448 Sum_probs=14.1
Q ss_pred CCCCC-CCCHHHHHHHHHHH
Q psy6193 19 IPDLS-HLTLEERQIIESVM 37 (122)
Q Consensus 19 ~pdLS-~LTeeEreiIl~VL 37 (122)
||... .||++|++.|...|
T Consensus 48 Mp~~~~~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 48 MPPFGGQLSDEEIEALAAYI 67 (67)
T ss_dssp BSCTTTTSTHHHHHHHHHHH
T ss_pred CCCCCCCCCHHHHHHHHHHC
Confidence 44444 79999999987754
No 36
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=31.25 E-value=72 Score=26.05 Aligned_cols=16 Identities=25% Similarity=0.457 Sum_probs=13.9
Q ss_pred hhccc----------ccccccchhhh
Q psy6193 55 CQVYL----------MVIWVCILCRK 70 (122)
Q Consensus 55 C~~C~----------k~~W~C~vC~k 70 (122)
|.+|. +..|.|..||+
T Consensus 247 CprCG~~I~~~~~~gR~t~~CP~CQ~ 272 (272)
T PRK14810 247 CLNCKTPIRRVVVAGRSSHYCPHCQK 272 (272)
T ss_pred CCCCCCeeEEEEECCCccEECcCCcC
Confidence 99998 56899999985
No 37
>PF10335 DUF294_C: Putative nucleotidyltransferase substrate binding domain; InterPro: IPR018821 This entry is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding domains.
Probab=30.78 E-value=90 Score=22.86 Aligned_cols=32 Identities=19% Similarity=0.114 Sum_probs=27.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhHHHHHHHH
Q psy6193 16 ADIIPDLSHLTLEERQIIESVMMRQKQEEERE 47 (122)
Q Consensus 16 ~~e~pdLS~LTeeEreiIl~VL~Rdk~le~~E 47 (122)
++..+|++.|+..||+.+-..+..-+.+++.-
T Consensus 110 ~~n~i~~~~Ls~~er~~Lk~al~~i~~lq~~l 141 (145)
T PF10335_consen 110 PDNYIDPDELSKLERRRLKEALRVIKRLQRLL 141 (145)
T ss_pred CCCccCHHHCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999998888877653
No 38
>cd02406 CRS2 Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of group II introns in the chloroplast. CRS2 forms stable complexes with two CRS2-associated factors, CAF1 and CAF2, which are required for the splicing of distinct subsets of CRS2-dependent introns. CRS2 is closely related to bacterial peptidyl-tRNA hydrolases (PTH).
Probab=28.77 E-value=84 Score=24.94 Aligned_cols=26 Identities=19% Similarity=0.333 Sum_probs=21.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhHH
Q psy6193 15 NADIIPDLSHLTLEERQIIESVMMRQK 41 (122)
Q Consensus 15 ~~~e~pdLS~LTeeEreiIl~VL~Rdk 41 (122)
...+.+ ||.++++|++.|..++.+..
T Consensus 143 ~v~~yV-L~~f~~~E~~~l~~~~~~a~ 168 (191)
T cd02406 143 DPRAFL-LQKFSSEEREQIDTALEQGV 168 (191)
T ss_pred chhhhh-cCCCCHHHHHHHHHHHHHHH
Confidence 445677 99999999999999988764
No 39
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=28.24 E-value=35 Score=20.41 Aligned_cols=17 Identities=47% Similarity=0.663 Sum_probs=5.6
Q ss_pred CCCCHHHHHHHHHHHHh
Q psy6193 23 SHLTLEERQIIESVMMR 39 (122)
Q Consensus 23 S~LTeeEreiIl~VL~R 39 (122)
.|||.+||..|...+..
T Consensus 3 ~~Lt~~eR~~I~~l~~~ 19 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ 19 (44)
T ss_dssp ---------HHHHHHCS
T ss_pred cchhhhHHHHHHHHHHc
Confidence 68999999999976543
No 40
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=27.76 E-value=48 Score=28.92 Aligned_cols=50 Identities=18% Similarity=0.247 Sum_probs=31.9
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHhh-----------hhccc---------------ccccccchhhhhhhHhhhcc
Q psy6193 30 RQIIESVMMRQKQEEERELEIMRSA-----------CQVYL---------------MVIWVCILCRKKQELLSKTG 79 (122)
Q Consensus 30 reiIl~VL~Rdk~le~~E~eRirrL-----------C~~C~---------------k~~W~C~vC~k~~eL~~kSG 79 (122)
.+.|+.+|++..+..++-.+..++- |..|. .+.+.|..|+...++-...|
T Consensus 141 ~~~i~~aL~~~~~I~~Il~~~~~~~~~~~y~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~~g 216 (360)
T PF01921_consen 141 DEQIRTALENRDEIREILNEYRGRERPETYSPFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDITGG 216 (360)
T ss_dssp HHHHCHHHHTHHHHHHHHHHHHHHT--TT--SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETTTT
T ss_pred HHHHHHHHHhHHHHHHHHHHhcCcCCCCCeeeeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecCCC
Confidence 3567777777777776655554433 88888 35899999999988888775
No 41
>PF10910 DUF2744: Protein of unknown function (DUF2744); InterPro: IPR021226 This entry is represented by Mycobacteriophage D29, Gp29. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=27.65 E-value=41 Score=25.55 Aligned_cols=27 Identities=26% Similarity=0.342 Sum_probs=21.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhH
Q psy6193 14 TNADIIPDLSHLTLEERQIIESVMMRQ 40 (122)
Q Consensus 14 ~~~~e~pdLS~LTeeEreiIl~VL~Rd 40 (122)
|.....||.+.||..|+..+++-|++.
T Consensus 91 p~p~~~~d~~~lt~~E~~a~l~ql~~~ 117 (125)
T PF10910_consen 91 PEPVRIPDVSKLTQQEQRAMLEQLREL 117 (125)
T ss_pred CCCCCCcCHHHHhHHHHHHHHHHHHHc
Confidence 334568999999999999999866654
No 42
>TIGR03045 PS_II_C550 cytochrome c-550. Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself.
Probab=27.55 E-value=78 Score=24.54 Aligned_cols=27 Identities=33% Similarity=0.546 Sum_probs=22.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhHHH
Q psy6193 16 ADIIPDLSHLTLEERQIIESVMMRQKQ 42 (122)
Q Consensus 16 ~~e~pdLS~LTeeEreiIl~VL~Rdk~ 42 (122)
..-||.+..||++|.+.|-.-|-++.+
T Consensus 123 ~~~mP~~~~LsdeEL~avAaYIl~q~~ 149 (159)
T TIGR03045 123 ADIFPKMRNLTDEDLRLIAGHILVQPK 149 (159)
T ss_pred ccccCCcCCCCHHHHHHHHHHHHHhcc
Confidence 356899999999999999998877654
No 43
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=25.97 E-value=24 Score=20.53 Aligned_cols=10 Identities=40% Similarity=1.255 Sum_probs=8.1
Q ss_pred ccccchhhhh
Q psy6193 62 IWVCILCRKK 71 (122)
Q Consensus 62 ~W~C~vC~k~ 71 (122)
.|+|.+|+..
T Consensus 2 ~~~C~~CG~i 11 (34)
T cd00729 2 VWVCPVCGYI 11 (34)
T ss_pred eEECCCCCCE
Confidence 6999999754
No 44
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=25.71 E-value=25 Score=19.45 Aligned_cols=16 Identities=31% Similarity=0.787 Sum_probs=4.9
Q ss_pred ccchhhhhhhHhhhccccccc
Q psy6193 64 VCILCRKKQELLSKTGQWINK 84 (122)
Q Consensus 64 ~C~vC~k~~eL~~kSGeWFye 84 (122)
.|.+|++.. +|.|+|.
T Consensus 2 ~C~~C~~~~-----~~~~~Y~ 17 (30)
T PF07649_consen 2 RCDACGKPI-----DGGWFYR 17 (30)
T ss_dssp --TTTS---------S--EEE
T ss_pred cCCcCCCcC-----CCCceEE
Confidence 466676655 4456664
No 45
>PF01935 DUF87: Domain of unknown function DUF87; InterPro: IPR002789 The function of this domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.
Probab=25.66 E-value=56 Score=24.71 Aligned_cols=22 Identities=45% Similarity=0.588 Sum_probs=19.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHh
Q psy6193 18 IIPDLSHLTLEERQIIESVMMR 39 (122)
Q Consensus 18 e~pdLS~LTeeEreiIl~VL~R 39 (122)
-.+|||++.++.+.+|..+|-|
T Consensus 206 ~IiDLs~~~~~~~~~i~~~i~r 227 (229)
T PF01935_consen 206 VIIDLSGVDEEVQDIIVSVILR 227 (229)
T ss_pred EEEECCCCCHHHHHHHHHHHHh
Confidence 3569999999999999999876
No 46
>PF04120 Iron_permease: Low affinity iron permease ; InterPro: IPR007251 Although originally identified as a low-affinity iron(II) permease [, ], Fet4 has since been shown to import several other transition metal ions, including copper [, ] and zinc []. Copper, cobalt, and cadmium inhibit Fet4 [, ]. Fet4 is an integral protein of the plasma membrane [, ]. FET4 is not essential, not even in fet3 fet4 double mutants []. Over expression of FET4 improves growth under alkaline conditions []. Transcription of FET4 is induced by Aft1 in response to low levels of iron [, , ] or by Zap1 in response to low zinc [, ], but not in response to low copper []. When the high-affinity iron permease component Fet3 is deleted, FET4 is induced by the addition of copper, zinc, cobalt, or manganese []. It is also induced under anaerobic conditions [, , ] and repressed by Rox1 in aerobic conditions [, ]. Rox1 attenuates the activation of FET4 by Aft1 or Zap1 []. ; GO: 0055085 transmembrane transport
Probab=25.64 E-value=93 Score=23.51 Aligned_cols=26 Identities=27% Similarity=0.261 Sum_probs=20.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhHHH
Q psy6193 17 DIIPDLSHLTLEERQIIESVMMRQKQ 42 (122)
Q Consensus 17 ~e~pdLS~LTeeEreiIl~VL~Rdk~ 42 (122)
.+++|+.+|+++|.+.|..-+++...
T Consensus 87 n~li~iE~l~~~el~~~~~~~~~~~~ 112 (132)
T PF04120_consen 87 NELIDIEDLTEEELEEIRKRYERLAE 112 (132)
T ss_pred HHhCCcccCCHHHHHHHHHHHHHHHH
Confidence 46899999999999998886555443
No 47
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=25.20 E-value=74 Score=23.54 Aligned_cols=33 Identities=21% Similarity=0.296 Sum_probs=28.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhHHHHHHHHHHH
Q psy6193 18 IIPDLSHLTLEERQIIESVMMRQKQEEERELEI 50 (122)
Q Consensus 18 e~pdLS~LTeeEreiIl~VL~Rdk~le~~E~eR 50 (122)
+++.+..|++++.+.|..++.-...+.+.+.+.
T Consensus 27 ~l~~~~~L~~E~~~Fi~~Fi~~rGnlKe~e~~l 59 (113)
T PF09862_consen 27 ELPWFARLSPEQLEFIKLFIKNRGNLKEMEKEL 59 (113)
T ss_pred ccchhhcCCHHHHHHHHHHHHhcCCHHHHHHHH
Confidence 467799999999999999999998888887543
No 48
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=25.08 E-value=71 Score=25.90 Aligned_cols=24 Identities=25% Similarity=0.567 Sum_probs=14.2
Q ss_pred ccccccchhhhh--------hhHhhhcccccc
Q psy6193 60 MVIWVCILCRKK--------QELLSKTGQWIN 83 (122)
Q Consensus 60 k~~W~C~vC~k~--------~eL~~kSGeWFy 83 (122)
+-.|+|.+|.|. -.|..|=++|+-
T Consensus 75 ~~K~~C~lc~KlFkg~eFV~KHI~nKH~e~ve 106 (214)
T PF04959_consen 75 EDKWRCPLCGKLFKGPEFVRKHIFNKHPEKVE 106 (214)
T ss_dssp SEEEEE-SSS-EESSHHHHHHHHHHH-HHHHH
T ss_pred CCEECCCCCCcccCChHHHHHHHhhcCHHHHH
Confidence 458999999972 345566677754
No 49
>KOG0860|consensus
Probab=24.51 E-value=68 Score=24.05 Aligned_cols=19 Identities=26% Similarity=0.370 Sum_probs=15.0
Q ss_pred HHHHHHHHHhHHHHHHHHH
Q psy6193 30 RQIIESVMMRQKQEEEREL 48 (122)
Q Consensus 30 reiIl~VL~Rdk~le~~E~ 48 (122)
|+-|..||+|+++|.+.++
T Consensus 46 r~NV~KVlER~ekL~~L~d 64 (116)
T KOG0860|consen 46 RENVEKVLERGEKLDELDD 64 (116)
T ss_pred HHhHHHHHHhcchHHHHHH
Confidence 4557789999999888764
No 50
>CHL00183 petJ cytochrome c553; Provisional
Probab=24.02 E-value=1.1e+02 Score=20.96 Aligned_cols=23 Identities=17% Similarity=0.371 Sum_probs=18.2
Q ss_pred CCCC-CCCCHHHHHHHHHHHHhHH
Q psy6193 19 IPDL-SHLTLEERQIIESVMMRQK 41 (122)
Q Consensus 19 ~pdL-S~LTeeEreiIl~VL~Rdk 41 (122)
||-+ ..||++|++.|...|.-+.
T Consensus 81 MP~f~~~Ls~~ei~~i~aYi~~~~ 104 (108)
T CHL00183 81 MPAFGGRLSDEDIEDVANYVLSQA 104 (108)
T ss_pred cccccCCCCHHHHHHHHHHHHHhh
Confidence 6655 6899999999999876543
No 51
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=23.56 E-value=18 Score=27.92 Aligned_cols=36 Identities=14% Similarity=0.285 Sum_probs=17.1
Q ss_pred ccchhhhhhh-Hhhh--cccccccCCCCCCCCcccccccc
Q psy6193 64 VCILCRKKQE-LLSK--TGQWINKGMNSTPQGDAIMRKIE 100 (122)
Q Consensus 64 ~C~vC~k~~e-L~~k--SGeWFye~~~~~~~~~~~~r~~~ 100 (122)
-|.||.+-.- +++. ..+|||-=.+-- .+.....|+.
T Consensus 15 ~C~IC~KpsttVL~t~~~~DfFY~C~~HL-~D~~F~~p~~ 53 (182)
T PF08432_consen 15 ACFICYKPSTTVLITPDNKDFFYVCPSHL-KDRQFATPIY 53 (182)
T ss_pred ceeEecCCCceEEecCCCCCeEEeCcccc-cCcccCCCCC
Confidence 4556665332 2221 379999533110 3333355555
No 52
>PF13864 Enkurin: Calmodulin-binding
Probab=23.50 E-value=1.7e+02 Score=20.24 Aligned_cols=31 Identities=26% Similarity=0.321 Sum_probs=23.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhHHHHHHHHHHH
Q psy6193 20 PDLSHLTLEERQIIESVMMRQKQEEERELEI 50 (122)
Q Consensus 20 pdLS~LTeeEreiIl~VL~Rdk~le~~E~eR 50 (122)
+-..-|+++||..+|.-|...-..=..+.++
T Consensus 32 ~~~~~l~eeER~~lL~~Lk~~~~el~~ey~~ 62 (98)
T PF13864_consen 32 PGMRLLSEEERQELLEGLKKNWDELNKEYQK 62 (98)
T ss_pred cccccCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5567899999999999988765544445444
No 53
>PF11161 DUF2944: Protein of unknown function (DUF2946); InterPro: IPR021332 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=23.41 E-value=30 Score=27.89 Aligned_cols=11 Identities=18% Similarity=0.543 Sum_probs=10.0
Q ss_pred cccccccCCCC
Q psy6193 78 TGQWINKGMNS 88 (122)
Q Consensus 78 SGeWFye~~~~ 88 (122)
.|.|||.++|+
T Consensus 65 ~G~WfFQNGPQ 75 (187)
T PF11161_consen 65 DGRWFFQNGPQ 75 (187)
T ss_pred CccEEEecCCE
Confidence 59999999997
No 54
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=23.35 E-value=29 Score=19.41 Aligned_cols=10 Identities=40% Similarity=1.022 Sum_probs=7.5
Q ss_pred cccchhhhhh
Q psy6193 63 WVCILCRKKQ 72 (122)
Q Consensus 63 W~C~vC~k~~ 72 (122)
|.|.+|.+..
T Consensus 1 ~~C~~C~~~~ 10 (30)
T PF03107_consen 1 FWCDVCRRKI 10 (30)
T ss_pred CCCCCCCCCc
Confidence 6788887765
No 55
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=23.21 E-value=41 Score=22.38 Aligned_cols=22 Identities=23% Similarity=0.578 Sum_probs=16.2
Q ss_pred hhhcccccccccchhhhhhhHhhh
Q psy6193 54 ACQVYLMVIWVCILCRKKQELLSK 77 (122)
Q Consensus 54 LC~~C~k~~W~C~vC~k~~eL~~k 77 (122)
.|.+|. .|-|+.|.+.--...+
T Consensus 24 QCvlCG--RWaC~sCW~deYY~Ck 45 (57)
T PF14445_consen 24 QCVLCG--RWACNSCWQDEYYTCK 45 (57)
T ss_pred HHhhhc--hhhhhhhhhhhHhHHH
Confidence 388887 8999999987644443
No 56
>PF11686 DUF3283: Protein of unknown function (DUF3283); InterPro: IPR021700 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=23.13 E-value=64 Score=21.83 Aligned_cols=14 Identities=50% Similarity=0.581 Sum_probs=12.3
Q ss_pred CCCCCCHHHHHHHH
Q psy6193 21 DLSHLTLEERQIIE 34 (122)
Q Consensus 21 dLS~LTeeEreiIl 34 (122)
|||.|+.+|++.|.
T Consensus 1 NLslLp~~EKnkIE 14 (61)
T PF11686_consen 1 NLSLLPPEEKNKIE 14 (61)
T ss_pred CcccCCHHHHhHHH
Confidence 68999999999885
No 57
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=23.08 E-value=2.2e+02 Score=20.01 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHhHHH-HHHHHHHHHHhh-------hhcccc-----------cccccchhhh
Q psy6193 27 LEERQIIESVMMRQKQ-EEERELEIMRSA-------CQVYLM-----------VIWVCILCRK 70 (122)
Q Consensus 27 eeEreiIl~VL~Rdk~-le~~E~eRirrL-------C~~C~k-----------~~W~C~vC~k 70 (122)
+.++++-+..+.|+.. +.+++.. +.|+ |-.|.+ ..-.|.-|+.
T Consensus 48 ~~~~~~~~~~~~~~~~~l~~i~~A-L~ri~~g~yG~C~~Cge~I~~~RL~a~P~a~~Cv~Cq~ 109 (110)
T TIGR02420 48 EEERALELRTRDRERKLIKKIDEA-LKRIEDGEYGYCEECGEEIGLRRLEARPTATLCIDCKT 109 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-HHHHhCCCCCchhccCCcccHHHHhhCCCccccHHhHc
Confidence 4455555555555533 4455432 2233 888883 3455766654
No 58
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=22.99 E-value=24 Score=30.61 Aligned_cols=12 Identities=17% Similarity=0.526 Sum_probs=5.4
Q ss_pred ccccccchhhhh
Q psy6193 60 MVIWVCILCRKK 71 (122)
Q Consensus 60 k~~W~C~vC~k~ 71 (122)
+.-|.|.-|...
T Consensus 283 KRFFkC~~C~~R 294 (344)
T PF09332_consen 283 KRFFKCKDCGNR 294 (344)
T ss_dssp -EEEE-T-TS-E
T ss_pred eeeEECCCCCCe
Confidence 346777777765
No 59
>smart00520 BASIC Basic domain in HLH proteins of MYOD family.
Probab=21.90 E-value=26 Score=25.41 Aligned_cols=15 Identities=33% Similarity=0.915 Sum_probs=11.5
Q ss_pred hcccccccccchhhhhh
Q psy6193 56 QVYLMVIWVCILCRKKQ 72 (122)
Q Consensus 56 ~~C~k~~W~C~vC~k~~ 72 (122)
++|. .|-|++|.++.
T Consensus 68 g~CL--~WACk~CkrK~ 82 (91)
T smart00520 68 GQCL--PWACKACKRKS 82 (91)
T ss_pred CccH--HHHHHHhcccC
Confidence 4576 99999997643
No 60
>KOG4275|consensus
Probab=21.81 E-value=46 Score=29.11 Aligned_cols=22 Identities=23% Similarity=0.360 Sum_probs=14.5
Q ss_pred CCCCCCCCHHH---HHHHHHHHHhH
Q psy6193 19 IPDLSHLTLEE---RQIIESVMMRQ 40 (122)
Q Consensus 19 ~pdLS~LTeeE---reiIl~VL~Rd 40 (122)
++|++.|+++| +..+++++.++
T Consensus 240 lsd~edl~d~Eg~~v~qLke~l~~d 264 (350)
T KOG4275|consen 240 LSDLEDLLDEEGLTVRQLKEILDDD 264 (350)
T ss_pred cCccccccccccchHHHhhhhhhcc
Confidence 66777777766 45566666665
No 61
>TIGR00447 pth peptidyl-tRNA hydrolase. The natural substrate for this enzyme may be peptidyl-tRNAs that drop off the ribosome during protein synthesis. Peptidyl-tRNA hydrolase is a bacterial protein; YHR189W from Saccharomyces cerevisiae appears to be orthologous and likely has the same function.
Probab=21.38 E-value=1.6e+02 Score=23.18 Aligned_cols=27 Identities=19% Similarity=0.209 Sum_probs=21.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhHHH
Q psy6193 15 NADIIPDLSHLTLEERQIIESVMMRQKQ 42 (122)
Q Consensus 15 ~~~e~pdLS~LTeeEreiIl~VL~Rdk~ 42 (122)
...+.+ ||-++++|++.|..++.+..+
T Consensus 142 ~v~~yV-L~~f~~~e~~~l~~~i~~~~~ 168 (188)
T TIGR00447 142 KVVEFV-LSKFTKSELPLLEKALDKAVE 168 (188)
T ss_pred chhhhc-cCCCCHHHHHHHHHHHHHHHH
Confidence 345667 999999999999999888643
No 62
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=20.93 E-value=1.4e+02 Score=24.02 Aligned_cols=35 Identities=26% Similarity=0.331 Sum_probs=21.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhH-HHHHHHHHHHHHhh
Q psy6193 17 DIIPDLSHLTLEERQIIESVMMRQ-KQEEERELEIMRSA 54 (122)
Q Consensus 17 ~e~pdLS~LTeeEreiIl~VL~Rd-k~le~~E~eRirrL 54 (122)
..+|.||.|.|.|..-+-+ ++ ++-|.+|+.|++|.
T Consensus 134 kRfP~lst~~e~e~~E~k~---k~rrK~e~k~err~rr~ 169 (186)
T PF04936_consen 134 KRFPKLSTLSEEELIETKE---KYRRKHETKEERRLRRN 169 (186)
T ss_pred hcCccccccccHHHHHHhh---HHHhhhhHHHHHHHHHH
Confidence 3589999999999844333 22 23344566666553
No 63
>cd08818 CARD_MDA5_1 Caspase activation and recruitment domain found in MDA5, first repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), first repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-
Probab=20.49 E-value=2.2e+02 Score=20.32 Aligned_cols=45 Identities=13% Similarity=0.128 Sum_probs=26.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHhhhhcccccccc
Q psy6193 19 IPDLSHLTLEERQIIESVMMRQKQEEERELEIMRSACQVYLMVIWV 64 (122)
Q Consensus 19 ~pdLS~LTeeEreiIl~VL~Rdk~le~~E~eRirrLC~~C~k~~W~ 64 (122)
++.|.+|++++++.|+.=.......+..+ -.+..+|..++.+.|.
T Consensus 25 L~~l~~L~~e~ke~I~a~~~~~Gn~~AA~-~LL~~l~~~~~~~GWf 69 (88)
T cd08818 25 LDYLTFLEAEVKERIRAAAATRGNIAAAE-LLLSTLEKGTWDPGWF 69 (88)
T ss_pred hhhcccCCHHHHHHHHHHHHccCcHHHHH-HHHHHHHHhccCCchH
Confidence 45678999999999987544333333332 3344454434455554
No 64
>cd01277 HINT_subgroup HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life. Although the biochemical function has not been characterised for many of the members of this subgroup, the proteins from Yeast have been shown to be involved in secretion, peroxisome formation and gene expression.
Probab=20.10 E-value=1.2e+02 Score=19.87 Aligned_cols=24 Identities=17% Similarity=0.026 Sum_probs=19.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhHH
Q psy6193 18 IIPDLSHLTLEERQIIESVMMRQK 41 (122)
Q Consensus 18 e~pdLS~LTeeEreiIl~VL~Rdk 41 (122)
...+++.|+++|+..+..++.+-.
T Consensus 44 H~~~~~~l~~~e~~~l~~~~~~v~ 67 (103)
T cd01277 44 HYENLLDLDPEELAELILAAKKVA 67 (103)
T ss_pred ccCChhhCCHHHHHHHHHHHHHHH
Confidence 356899999999999999876653
No 65
>PRK13622 psbV cytochrome c-550; Provisional
Probab=20.04 E-value=1.2e+02 Score=24.26 Aligned_cols=29 Identities=24% Similarity=0.306 Sum_probs=23.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhHHH
Q psy6193 14 TNADIIPDLSHLTLEERQIIESVMMRQKQ 42 (122)
Q Consensus 14 ~~~~e~pdLS~LTeeEreiIl~VL~Rdk~ 42 (122)
..++.+|.+..|||+|.+.|-..+.++.+
T Consensus 132 ~~~~~~p~~~~LsdeEI~~VA~yIl~qa~ 160 (180)
T PRK13622 132 QLLSEYPRLRNLTDEDLKLIAGYILVQAK 160 (180)
T ss_pred hhccccccccCCCHHHHHHHHHHHHhCcc
Confidence 34667898889999999999998877754
No 66
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=20.03 E-value=54 Score=22.84 Aligned_cols=19 Identities=42% Similarity=0.298 Sum_probs=15.3
Q ss_pred CCCCCCCCCHHHHHHHHHH
Q psy6193 18 IIPDLSHLTLEERQIIESV 36 (122)
Q Consensus 18 e~pdLS~LTeeEreiIl~V 36 (122)
+..-|.+||++||+-|+.+
T Consensus 25 ~~LGf~~Lt~eEr~dmI~~ 43 (76)
T PF10955_consen 25 EQLGFHHLTPEERQDMISY 43 (76)
T ss_pred hhcCcccCCHHHHhhheEE
Confidence 4455899999999988874
Done!