Query psy18081
Match_columns 82
No_of_seqs 106 out of 158
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 22:08:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18081.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18081hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2916|consensus 99.9 4.3E-28 9.4E-33 186.9 7.6 74 1-74 210-283 (304)
2 PTZ00248 eukaryotic translatio 99.9 4E-22 8.6E-27 155.0 8.9 71 2-73 213-283 (319)
3 PRK03987 translation initiatio 99.6 1E-14 2.2E-19 110.3 8.4 56 2-57 205-260 (262)
4 COG1093 SUI2 Translation initi 99.3 9.4E-12 2E-16 95.8 8.3 63 2-64 207-269 (269)
5 cd01271 Fe65_C Fe65 C-terminal 90.7 0.44 9.6E-06 33.4 3.9 50 19-68 8-58 (124)
6 PF01106 NifU: NifU-like domai 71.9 4.8 0.0001 24.7 2.7 23 34-56 1-23 (68)
7 PF05763 DUF835: Protein of un 71.5 4 8.6E-05 28.3 2.5 46 28-73 90-135 (136)
8 PF07541 EIF_2_alpha: Eukaryot 70.6 9.7 0.00021 25.5 4.1 41 20-61 65-106 (114)
9 PF07045 DUF1330: Protein of u 59.8 34 0.00074 20.2 4.9 31 33-63 3-34 (65)
10 PRK01215 competence damage-ind 59.2 27 0.00059 26.5 5.1 41 13-53 219-261 (264)
11 PF14189 DUF4312: Domain of un 56.5 27 0.00059 23.1 4.2 52 20-74 8-62 (85)
12 cd01216 Fe65 Fe65 Phosphotyros 56.0 23 0.0005 24.0 3.9 48 20-67 9-57 (123)
13 PF08734 GYD: GYD domain; Int 51.1 34 0.00073 21.9 3.9 36 18-53 1-37 (91)
14 PF02391 MoaE: MoaE protein; 49.5 46 0.001 22.2 4.5 32 13-44 85-116 (117)
15 cd06926 RNAP_II_RPB11 RPB11 su 49.0 24 0.00053 23.0 3.0 36 17-52 58-93 (93)
16 COG5470 Uncharacterized conser 48.2 48 0.001 22.5 4.4 25 32-56 16-40 (96)
17 COG3100 Uncharacterized protei 47.6 58 0.0013 22.3 4.7 42 13-59 45-86 (103)
18 TIGR03341 YhgI_GntY IscR-regul 47.5 18 0.00039 26.3 2.4 29 28-56 104-133 (190)
19 TIGR02000 NifU_proper Fe-S clu 46.7 20 0.00043 27.8 2.7 30 27-56 217-246 (290)
20 PF10865 DUF2703: Domain of un 44.6 67 0.0015 22.1 4.8 46 31-81 22-67 (120)
21 PF13656 RNA_pol_L_2: RNA poly 44.5 24 0.00052 22.1 2.4 30 18-47 43-72 (77)
22 cd03799 GT1_amsK_like This is 41.4 89 0.0019 22.0 5.1 30 15-44 178-207 (355)
23 cd07029 RNAP_I_III_AC19 AC19 s 41.4 35 0.00076 21.9 2.8 31 18-48 51-81 (85)
24 COG2092 EFB1 Translation elong 41.1 22 0.00047 23.7 1.8 37 4-43 40-76 (88)
25 PRK11190 Fe/S biogenesis prote 39.8 25 0.00054 25.8 2.2 28 29-56 106-134 (192)
26 KOG1588|consensus 38.9 65 0.0014 25.2 4.4 32 14-45 158-189 (259)
27 CHL00123 rps6 ribosomal protei 38.9 51 0.0011 21.3 3.3 20 33-52 22-41 (97)
28 PF12224 Amidoligase_2: Putati 38.0 54 0.0012 23.4 3.7 46 8-61 76-124 (252)
29 PF01193 RNA_pol_L: RNA polyme 37.6 75 0.0016 18.8 3.7 29 17-45 37-65 (66)
30 PF00534 Glycos_transf_1: Glyc 37.0 1.1E+02 0.0025 19.6 5.5 30 15-44 14-43 (172)
31 COG4585 Signal transduction hi 35.4 40 0.00088 25.5 2.8 50 8-58 300-353 (365)
32 TIGR00166 S6 ribosomal protein 35.2 60 0.0013 20.5 3.2 20 34-53 17-36 (93)
33 PRK03987 translation initiatio 34.8 72 0.0016 24.3 4.1 42 19-61 179-222 (262)
34 PF12691 Minor_capsid_3: Minor 34.8 1.3E+02 0.0029 20.7 5.1 47 17-63 58-113 (135)
35 cd07302 CHD cyclase homology d 34.0 84 0.0018 20.0 3.8 31 24-54 18-48 (177)
36 PF05773 RWD: RWD domain; Int 33.5 1.1E+02 0.0025 18.6 4.2 31 14-44 64-94 (113)
37 cd03798 GT1_wlbH_like This fam 33.2 1.5E+02 0.0033 20.2 5.1 30 15-44 201-230 (377)
38 PF10719 ComFB: Late competenc 32.0 79 0.0017 19.6 3.3 10 15-24 42-51 (85)
39 TIGR02765 crypto_DASH cryptoch 31.3 83 0.0018 24.7 4.0 40 16-55 31-80 (429)
40 PF00828 Ribosomal_L18e: Ribos 30.9 45 0.00097 22.2 2.1 14 41-54 115-128 (129)
41 PRK06419 rpl15p 50S ribosomal 30.8 56 0.0012 23.0 2.7 18 39-56 129-146 (148)
42 COG3469 Chitinase [Carbohydrat 30.8 57 0.0012 26.3 3.0 27 33-59 155-181 (332)
43 COG0694 Thioredoxin-like prote 30.7 37 0.00081 22.5 1.7 27 30-56 10-37 (93)
44 cd00460 RNAP_RPB11_RPB3 RPB11 30.1 1.4E+02 0.0029 18.8 4.2 31 17-47 55-85 (86)
45 cd00756 MoaE MoaE family. Memb 29.7 1.3E+02 0.0028 20.4 4.3 33 13-45 77-109 (124)
46 KOG4513|consensus 29.5 1E+02 0.0022 26.2 4.4 48 7-55 407-455 (531)
47 PF00586 AIRS: AIR synthase re 29.5 83 0.0018 19.4 3.1 38 15-52 54-91 (96)
48 PF03197 FRD2: Bacteriophage F 29.3 44 0.00096 22.9 1.9 17 42-58 3-19 (102)
49 cd03817 GT1_UGDG_like This fam 28.6 2E+02 0.0043 19.8 5.5 30 15-44 201-230 (374)
50 COG4443 Uncharacterized protei 28.6 33 0.00071 22.2 1.1 32 14-45 35-69 (72)
51 COG0525 ValS Valyl-tRNA synthe 27.6 22 0.00047 32.0 0.2 56 14-69 799-858 (877)
52 PF01250 Ribosomal_S6: Ribosom 27.4 97 0.0021 19.2 3.1 21 33-53 17-37 (92)
53 cd07027 RNAP_RPB11_like RPB11 27.3 1.1E+02 0.0025 19.4 3.5 29 19-47 52-80 (83)
54 TIGR01046 S10_Arc_S20_Euk ribo 26.9 1.9E+02 0.004 19.1 4.5 29 20-52 5-33 (99)
55 cd00027 BRCT Breast Cancer Sup 26.8 66 0.0014 17.0 2.0 21 37-57 14-34 (72)
56 PF03147 FDX-ACB: Ferredoxin-f 26.7 1.7E+02 0.0036 18.3 4.2 36 17-52 57-93 (94)
57 cd03794 GT1_wbuB_like This fam 26.5 1.8E+02 0.0038 20.0 4.5 31 14-44 218-248 (394)
58 PF02120 Flg_hook: Flagellar h 26.3 1.5E+02 0.0033 17.6 5.1 46 8-53 27-72 (85)
59 cd01514 Elongation_Factor_C El 26.2 1.5E+02 0.0032 17.5 3.9 29 16-53 2-30 (79)
60 PF04455 Saccharop_dh_N: LOR/S 26.1 89 0.0019 21.0 2.9 19 33-55 17-35 (103)
61 PF04155 Ground-like: Ground-l 25.9 1.2E+02 0.0026 18.5 3.3 19 41-59 31-50 (76)
62 PF13601 HTH_34: Winged helix 25.9 1.6E+02 0.0034 18.3 3.9 24 16-45 55-80 (80)
63 COG1303 Uncharacterized protei 25.8 83 0.0018 23.5 2.9 21 36-56 44-64 (179)
64 KOG0005|consensus 25.7 1.7E+02 0.0037 18.7 4.0 34 8-51 3-36 (70)
65 PRK12271 rps10p 30S ribosomal 25.5 2E+02 0.0043 19.1 4.5 29 20-52 6-34 (102)
66 PF00533 BRCT: BRCA1 C Terminu 25.4 57 0.0012 18.4 1.7 14 39-52 22-35 (78)
67 cd03805 GT1_ALG2_like This fam 25.1 78 0.0017 23.1 2.7 32 14-45 209-240 (392)
68 smart00044 CYCc Adenylyl- / gu 24.8 1.7E+02 0.0036 19.8 4.2 30 24-53 53-82 (194)
69 PRK01146 DNA-directed RNA poly 24.5 1.3E+02 0.0029 19.1 3.4 29 19-47 54-82 (85)
70 smart00864 Tubulin Tubulin/Fts 23.5 1.6E+02 0.0034 20.7 3.9 27 26-52 61-87 (192)
71 cd03820 GT1_amsD_like This fam 23.2 2.5E+02 0.0053 19.0 4.7 29 15-43 177-205 (348)
72 PRK02255 putrescine carbamoylt 23.1 80 0.0017 24.9 2.6 39 6-57 177-215 (338)
73 PF05949 DUF881: Bacterial pro 22.9 2.7E+02 0.0058 19.3 5.1 45 11-61 86-133 (149)
74 PRK04005 50S ribosomal protein 22.3 88 0.0019 21.3 2.4 16 39-54 78-93 (111)
75 cd01479 Sec24-like Sec24-like: 22.3 2.3E+02 0.005 20.8 4.8 34 14-49 2-37 (244)
76 PF05166 YcgL: YcgL domain; I 22.1 46 0.001 21.3 0.9 41 13-58 33-73 (74)
77 PF12862 Apc5: Anaphase-promot 22.0 1.3E+02 0.0028 18.7 3.0 19 26-44 56-74 (94)
78 PLN02390 molybdopterin synthas 21.5 2.2E+02 0.0047 19.2 4.1 33 13-45 66-98 (111)
79 PF10087 DUF2325: Uncharacteri 21.5 1.4E+02 0.003 18.7 3.0 40 38-79 12-52 (97)
80 PF08651 DASH_Duo1: DASH compl 21.3 55 0.0012 20.9 1.1 24 29-52 8-31 (78)
81 TIGR00658 orni_carb_tr ornithi 21.3 1.5E+02 0.0031 22.9 3.6 36 6-54 171-206 (304)
82 PF08416 PTB: Phosphotyrosine- 21.2 98 0.0021 21.1 2.4 47 20-67 7-59 (131)
83 PF09702 Cas_Csa5: CRISPR-asso 21.2 1.5E+02 0.0032 20.4 3.3 40 23-62 16-55 (105)
84 cd02749 Macro Macro domain, a 21.1 1.5E+02 0.0034 19.1 3.3 41 16-57 73-118 (147)
85 PF02680 DUF211: Uncharacteriz 21.0 88 0.0019 21.1 2.1 16 38-53 60-75 (95)
86 PF04811 Sec23_trunk: Sec23/Se 21.0 2.1E+02 0.0045 20.6 4.2 36 14-49 2-37 (243)
87 KOG0177|consensus 20.8 1.7E+02 0.0036 22.3 3.8 32 24-55 150-181 (200)
88 PF02112 PDEase_II: cAMP phosp 20.6 41 0.00088 26.7 0.5 15 65-80 119-133 (335)
89 cd04893 ACT_GcvR_1 ACT domains 20.5 1.6E+02 0.0036 17.6 3.1 29 17-45 1-29 (77)
90 PF13250 DUF4041: Domain of un 20.5 1.9E+02 0.0041 17.3 3.3 29 30-58 22-50 (56)
91 smart00292 BRCT breast cancer 20.4 1.1E+02 0.0024 16.5 2.2 22 37-58 18-39 (80)
92 COG4274 Uncharacterized conser 20.3 1.4E+02 0.0029 20.6 2.9 37 18-56 11-50 (104)
93 COG0643 CheA Chemotaxis protei 20.1 1.1E+02 0.0023 26.9 2.9 21 38-58 541-561 (716)
94 TIGR03433 padR_acidobact trans 20.1 2E+02 0.0043 18.2 3.6 25 17-47 70-94 (100)
95 cd01569 PBEF_like pre-B-cell c 20.1 2.8E+02 0.006 22.9 5.2 38 15-55 253-290 (407)
No 1
>KOG2916|consensus
Probab=99.95 E-value=4.3e-28 Score=186.93 Aligned_cols=74 Identities=46% Similarity=0.673 Sum_probs=71.8
Q ss_pred CCCCCcceEEEEecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEEeceeEeeccccchhhhccc
Q psy18081 1 MSTEKMPIKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAVSILLMSMIQNSQTDLF 74 (82)
Q Consensus 1 ~ste~~~IkIkLIApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~PkvVse~d~~~l~~~~~ 74 (82)
+||++|||||+|||||+|||||+|+||++|+++|++||+.|.+.|+++||.|+|+|+||+||++|+++|++.|=
T Consensus 210 ~~te~~piki~LIApPlYVlTT~tldK~~g~e~l~~Ai~~i~~~I~~~~G~~~V~~~pk~vte~d~~~l~~~~e 283 (304)
T KOG2916|consen 210 LSTEECPIKIKLIAPPLYVLTTQTLDKTKGLEVLEEAIEVIISKIEEYGGTFTVIMEPKLVTETDEAELARRME 283 (304)
T ss_pred CCcccCceEEEEecCceEEEEEeeccccccHHHHHHHHHHHHHHHHhhCCEEEEEeCCeecccccHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999653
No 2
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=99.87 E-value=4e-22 Score=155.01 Aligned_cols=71 Identities=31% Similarity=0.481 Sum_probs=68.1
Q ss_pred CCCCcceEEEEecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEEeceeEeeccccchhhhcc
Q psy18081 2 STEKMPIKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAVSILLMSMIQNSQTDL 73 (82)
Q Consensus 2 ste~~~IkIkLIApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~PkvVse~d~~~l~~~~ 73 (82)
++++++|+|+|||||+|+|+++|+||..|+++|++|+++|++.|+++||+|+++++||+||++|+++ +.+|
T Consensus 213 ~~~~~~i~i~~igaP~Y~i~~~~~d~k~g~~~l~~a~~~i~~~i~~~gG~~~~~~~p~~v~~~~~~~-~~~~ 283 (319)
T PTZ00248 213 ATDECKITIKLIAPPQYVIVTTCSDKDKGMEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDL-EELL 283 (319)
T ss_pred CCCcCcEEEEEEcCCeEEEEEEeCCHHHHHHHHHHHHHHHHHHHHHcCCeEEEEECCEEecchhHHH-HHHH
Confidence 6778999999999999999999999999999999999999999999999999999999999999998 6665
No 3
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=99.57 E-value=1e-14 Score=110.27 Aligned_cols=56 Identities=21% Similarity=0.335 Sum_probs=53.8
Q ss_pred CCCCcceEEEEecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEEec
Q psy18081 2 STEKMPIKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMA 57 (82)
Q Consensus 2 ste~~~IkIkLIApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~ 57 (82)
++++++|+|+||+||+|+|+++|+|+..|+++|++|+++|.+.|+++||+|+++..
T Consensus 205 ~~~~~~v~i~~ig~P~Y~i~~~~~d~k~~~~~l~~~~~~~~~~i~~~gg~~~~~r~ 260 (262)
T PRK03987 205 KYEDVEVEIYYVGAPRYRIDVTAPDYKTAEKALKKIAERAIKVIKKLGGEGSFVRE 260 (262)
T ss_pred CCCCCcEEEEEECCCeEEEEEEeCCHHHHHHHHHHHHHHHHHHHHHhCCEEEEEEe
Confidence 67899999999999999999999999999999999999999999999999999854
No 4
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=99.31 E-value=9.4e-12 Score=95.79 Aligned_cols=63 Identities=17% Similarity=0.305 Sum_probs=59.7
Q ss_pred CCCCcceEEEEecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEEeceeEeecc
Q psy18081 2 STEKMPIKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAVSILLMS 64 (82)
Q Consensus 2 ste~~~IkIkLIApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~PkvVse~ 64 (82)
++++++++|.+|++|+|+++++.+|+.+|.+.|++|++.+.+.|+++||.+.+.++|+.+++.
T Consensus 207 ~~~~v~~kv~~VgaPrYri~v~a~dykkaee~l~~a~~~~~~~ikk~gg~~~~~r~~k~~~~~ 269 (269)
T COG1093 207 GEEEVELKVYYVGAPRYRIDVQAPDYKKAEEVLEKAAEAAIKTIKKLGGEGTFIREPKLVGEA 269 (269)
T ss_pred CccceeEEEEEecCCeEEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCeEEEEecccccccC
Confidence 456789999999999999999999999999999999999999999999999999999999863
No 5
>cd01271 Fe65_C Fe65 C-terminal Phosphotyrosine-binding (PTB) domain. Fe65 C-terminal Phosphotyrosine-binding (PTB) domain. Fe65 is an amyloid beta A4 precursor (APP) protein-binding. It contains an N-terminal WW domain followed by two PTB domains. The C-terminal PTB domain is responsible for APP binding. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=90.75 E-value=0.44 Score=33.44 Aligned_cols=50 Identities=20% Similarity=0.261 Sum_probs=36.1
Q ss_pred EEEeeeCCHHHHHHHHHHHHHHHHHHHhhcC-CeEEEEeceeEeeccccch
Q psy18081 19 VMTTVTPEKADGLKALQEAIDTIKAKIEQLG-GVFQVQMAVSILLMSMIQN 68 (82)
Q Consensus 19 vltt~tlDK~~Gi~~L~~Aie~I~~~I~~~g-G~~~Vk~~PkvVse~d~~~ 68 (82)
-+-.+.-+|-.|+++|++||+.+..+..... =...|.-+|--++..+...
T Consensus 8 yLG~~~V~~p~Gmdvln~AI~~l~~~~~~~~w~~V~vsvaps~v~v~~~~~ 58 (124)
T cd01271 8 YLGMLPVDKPTGMEILNSAIDNLMSSSNKEDWLSVNVNVAPSTITVISEKN 58 (124)
T ss_pred EeccEeecCCccHHHHHHHHHHHHhcCCcccCceEEEEeCCceEEEEccCc
Confidence 4556778899999999999999998775432 3455666777777655443
No 6
>PF01106 NifU: NifU-like domain; InterPro: IPR001075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents the C-terminal of NifU and homologous proteins. NifU contains two domains: an N-terminal (IPR002871 from INTERPRO) and a C-terminal domain []. These domains exist either together or on different polypeptides, both domains being found in organisms that do not fix nitrogen (e.g. yeast), so they have a broader significance in the cell than nitrogen fixation. ; GO: 0005506 iron ion binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly; PDB: 2JNV_A 2Z51_A 1TH5_A 1VEH_A 1XHJ_A.
Probab=71.94 E-value=4.8 Score=24.73 Aligned_cols=23 Identities=17% Similarity=0.401 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHhhcCCeEEEEe
Q psy18081 34 LQEAIDTIKAKIEQLGGVFQVQM 56 (82)
Q Consensus 34 L~~Aie~I~~~I~~~gG~~~Vk~ 56 (82)
++++|+.|+-.+..+||.+.+..
T Consensus 1 V~~~l~~IrP~L~~dGGdv~lv~ 23 (68)
T PF01106_consen 1 VEEVLEEIRPYLQSDGGDVELVD 23 (68)
T ss_dssp HHHHHHHCHHHHHHTTEEEEEEE
T ss_pred CHHHHHHhChHHHhcCCcEEEEE
Confidence 47899999999999999998763
No 7
>PF05763 DUF835: Protein of unknown function (DUF835); InterPro: IPR008553 The members of this archaebacterial protein entry are around 250-300 amino acid residues in length. The function of these proteins is not known.
Probab=71.48 E-value=4 Score=28.30 Aligned_cols=46 Identities=9% Similarity=0.094 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhcCCeEEEEeceeEeeccccchhhhcc
Q psy18081 28 ADGLKALQEAIDTIKAKIEQLGGVFQVQMAVSILLMSMIQNSQTDL 73 (82)
Q Consensus 28 ~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~PkvVse~d~~~l~~~~ 73 (82)
+-|++.+=+-+..+++.+-.+||.+-|.-.|.+.++++-+-|++.|
T Consensus 90 ~NgF~~v~KFL~~LkD~~~~~~~~lIl~~~~~al~ere~~lL~ref 135 (136)
T PF05763_consen 90 ENGFESVLKFLASLKDYALLNNGTLILVVDPEALDEREWALLRREF 135 (136)
T ss_pred HcCHHHHHHHHHHhHHHeeccCCEEEEEEChhhcCHHHHHHHHHHh
Confidence 4577888888999999999999999999999999999999888754
No 8
>PF07541 EIF_2_alpha: Eukaryotic translation initiation factor 2 alpha subunit; InterPro: IPR011488 In Eukaryota and Archaea, translation initiation factor 2 (eIF2/aIF2), which contains three subunits (alpha, beta and gamma), is pivotal for binding of charged initiator tRNA to the small ribosomal subunit. This entry represents the alpha subunit of both eukaryota and archaeal translation initiator factor 2.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0005850 eukaryotic translation initiation factor 2 complex; PDB: 2QN6_B 3CW2_C 2AHO_B 3QSY_B 3V11_B 2QMU_B 1YZ7_A 1YZ6_A 3AEV_A 1KL9_A ....
Probab=70.56 E-value=9.7 Score=25.52 Aligned_cols=41 Identities=15% Similarity=0.158 Sum_probs=31.1
Q ss_pred EEeeeCCHHHHHHHHHHHHHHHHHHH-hhcCCeEEEEeceeEe
Q psy18081 20 MTTVTPEKADGLKALQEAIDTIKAKI-EQLGGVFQVQMAVSIL 61 (82)
Q Consensus 20 ltt~tlDK~~Gi~~L~~Aie~I~~~I-~~~gG~~~Vk~~PkvV 61 (82)
+..+|... .||+.+++|+.+.++.. +...-+++...+|+=+
T Consensus 65 iel~c~~~-dGIe~IK~aL~~~~~~~~~~~~v~I~~igaP~Y~ 106 (114)
T PF07541_consen 65 IELTCFAP-DGIEAIKKALRAAEEASTEDVPVKIKLIGAPRYR 106 (114)
T ss_dssp EEEEE-ST-THHHHHHHHHHHHHHCCCTTCCEEEEEECTTEEE
T ss_pred EEEEeCCC-CHHHHHHHHHHHHHhcCCCCCeEEEEEECCCeEE
Confidence 44566665 79999999999988776 4466888888999743
No 9
>PF07045 DUF1330: Protein of unknown function (DUF1330); InterPro: IPR010753 This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown.; PDB: 2FIU_B 3HHL_A 3DCA_D 3LO3_I.
Probab=59.77 E-value=34 Score=20.22 Aligned_cols=31 Identities=23% Similarity=0.249 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHhhcCCeEEEE-eceeEeec
Q psy18081 33 ALQEAIDTIKAKIEQLGGVFQVQ-MAVSILLM 63 (82)
Q Consensus 33 ~L~~Aie~I~~~I~~~gG~~~Vk-~~PkvVse 63 (82)
.+++=.+.+...++++||++.+. ..|.++-.
T Consensus 3 ~~~~Y~~~~~~~l~~~GG~~l~~~~~~~~leG 34 (65)
T PF07045_consen 3 AYQEYREAVPPILEKYGGRVLARGGEPEVLEG 34 (65)
T ss_dssp HHHHHHHHHHHHHHHTT-EEEEECEEEEEEES
T ss_pred HHHHHHHHHHHHHHHcCCEEEEECCceeEEec
Confidence 34556677888999999999998 44444443
No 10
>PRK01215 competence damage-inducible protein A; Provisional
Probab=59.25 E-value=27 Score=26.49 Aligned_cols=41 Identities=15% Similarity=0.462 Sum_probs=32.9
Q ss_pred ecCCeEEEEee--eCCHHHHHHHHHHHHHHHHHHHhhcCCeEE
Q psy18081 13 IAPPLYVMTTV--TPEKADGLKALQEAIDTIKAKIEQLGGVFQ 53 (82)
Q Consensus 13 IApPlYvltt~--tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~ 53 (82)
...|.+.+..+ ..++++.-++++++.+.|++.+++.|+.|.
T Consensus 219 ~~~~~v~vrl~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~ 261 (264)
T PRK01215 219 VSKPILEIQIAGSGEREEEAKVKVEKVLEELKELIKKLGGIIR 261 (264)
T ss_pred cCCCeEEEEEEEecCCHHHHHHHHHHHHHHHHHHHHHhCCeee
Confidence 44555555554 478889999999999999999999999885
No 11
>PF14189 DUF4312: Domain of unknown function (DUF4312)
Probab=56.54 E-value=27 Score=23.06 Aligned_cols=52 Identities=12% Similarity=0.153 Sum_probs=36.9
Q ss_pred EEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEEecee---Eeeccccchhhhccc
Q psy18081 20 MTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAVS---ILLMSMIQNSQTDLF 74 (82)
Q Consensus 20 ltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~Pk---vVse~d~~~l~~~~~ 74 (82)
++....-|++ ++.+|+..|+..+.+.....-++++|. ++++++.---++-||
T Consensus 8 vsGkG~tKe~---Afa~als~vq~~v~~~~~~vlLrIEP~dV~vl~a~e~~~tEkFL~ 62 (85)
T PF14189_consen 8 VSGKGETKEE---AFAKALSQVQKTVLKETNGVLLRIEPVDVEVLKAKEKVYTEKFLF 62 (85)
T ss_pred EEcccccHHH---HHHHHHHHHHHHHHhcCCCcEEEEcCcEEEEEEeeeeeeehhhhe
Confidence 3444444554 567899999999999999999999995 556665555555544
No 12
>cd01216 Fe65 Fe65 Phosphotyrosine-binding (PTB) domain, phosphotyrosine-interaction (PI) domain. Fe65 Phosphotyrosine-binding (PTB) domain, phosphotyrosine-interaction (PI) domain. Fe65 is an amyloid beta A4 precursor (APP) protein-binding. It contains an N-terminal WW domain followed by two PTB domains. The C-terminal PTB domain is responsible for APP binding. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=56.00 E-value=23 Score=24.03 Aligned_cols=48 Identities=23% Similarity=0.190 Sum_probs=31.0
Q ss_pred EEeeeCCHHHHHHHHHHHHHHHHHHHhhcCC-eEEEEeceeEeeccccc
Q psy18081 20 MTTVTPEKADGLKALQEAIDTIKAKIEQLGG-VFQVQMAVSILLMSMIQ 67 (82)
Q Consensus 20 ltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG-~~~Vk~~PkvVse~d~~ 67 (82)
|-.+.-++..|.+++++||..+...-....| ...+.-.|.-++--|.+
T Consensus 9 LG~~eV~~~~g~~vv~~ai~~L~~~~~~~~~~~v~l~Vs~~~l~l~d~~ 57 (123)
T cd01216 9 LGWVEVAEEDGSEALNKAIDDLSSCSNWEDWKDLNMDLAPSTLSLIDPD 57 (123)
T ss_pred eeeEEECCCCCHHHHHHHHHHHHhccccccCeEEEEEEecCcEEEEcCC
Confidence 4455666777999999999999876554333 34444455555544443
No 13
>PF08734 GYD: GYD domain; InterPro: IPR014845 These proteins of unknown function are usually less than 100 amino acids in length. They may belong to the dimeric alpha/beta barrel superfamily.
Probab=51.08 E-value=34 Score=21.91 Aligned_cols=36 Identities=31% Similarity=0.569 Sum_probs=22.1
Q ss_pred EEEEeeeC-CHHHHHHHHHHHHHHHHHHHhhcCCeEE
Q psy18081 18 YVMTTVTP-EKADGLKALQEAIDTIKAKIEQLGGVFQ 53 (82)
Q Consensus 18 Yvltt~tl-DK~~Gi~~L~~Aie~I~~~I~~~gG~~~ 53 (82)
|++.++-+ +--+|+.-..+=.+++++.+++.||+++
T Consensus 1 yi~l~~~T~~g~~~~~~~~~R~~a~~~~~e~~Gg~l~ 37 (91)
T PF08734_consen 1 YIILARYTPEGAKGIKDSPDRAEAVRALIEALGGKLK 37 (91)
T ss_pred CEEEEEeCHHHHHHHhhcHHHHHHHHHHHHHcCCEEE
Confidence 33333333 3334444444556678899999999986
No 14
>PF02391 MoaE: MoaE protein; InterPro: IPR003448 This family contains the MoaE protein that is involved in biosynthesis of molybdopterin []. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulphurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins.; GO: 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 2WP4_B 2OMD_B 1NVJ_E 1FM0_E 3BII_E 1NVI_E 1FMA_E 2QIE_K 2Q5W_E 3RPF_A ....
Probab=49.46 E-value=46 Score=22.15 Aligned_cols=32 Identities=22% Similarity=0.504 Sum_probs=28.6
Q ss_pred ecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHH
Q psy18081 13 IAPPLYVMTTVTPEKADGLKALQEAIDTIKAK 44 (82)
Q Consensus 13 IApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~ 44 (82)
+.-|..++...+.-+.++++.++.+|+.|++.
T Consensus 85 vGe~~v~V~vsa~hR~eaf~A~~~~id~iK~~ 116 (117)
T PF02391_consen 85 VGEPIVLVAVSAPHRKEAFEACEYIIDRIKKE 116 (117)
T ss_dssp TTSEEEEEEEEESSHHHHHHHHHHHHHHHHHH
T ss_pred CCCeEEEEEEecCCHHHHHHHHHHHHHHHhhc
Confidence 56678889999999999999999999999875
No 15
>cd06926 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association.
Probab=49.03 E-value=24 Score=22.95 Aligned_cols=36 Identities=19% Similarity=0.191 Sum_probs=27.2
Q ss_pred eEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeE
Q psy18081 17 LYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVF 52 (82)
Q Consensus 17 lYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~ 52 (82)
.-+|+.+|.....-.++|++|++.+.+.+....+.|
T Consensus 58 ~~~l~i~t~~~~~p~~al~~a~~~l~~~~~~~~~~f 93 (93)
T cd06926 58 KIELRIQTDGSITPKEALKNAITDLISELSLLKEEF 93 (93)
T ss_pred ceEEEEEeCCCCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 346666776657789999999999999887765543
No 16
>COG5470 Uncharacterized conserved protein [Function unknown]
Probab=48.24 E-value=48 Score=22.46 Aligned_cols=25 Identities=24% Similarity=0.484 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHhhcCCeEEEEe
Q psy18081 32 KALQEAIDTIKAKIEQLGGVFQVQM 56 (82)
Q Consensus 32 ~~L~~Aie~I~~~I~~~gG~~~Vk~ 56 (82)
+..++=..++...|+++||+|-+..
T Consensus 16 e~y~~Y~~~~~~a~~~~Ggr~LvRG 40 (96)
T COG5470 16 EQYKDYVSKAKPAIEKFGGRYLVRG 40 (96)
T ss_pred HHHHHHHHHhHHHHHHhCCeeEeeC
Confidence 4455667788899999999998875
No 17
>COG3100 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.57 E-value=58 Score=22.35 Aligned_cols=42 Identities=24% Similarity=0.411 Sum_probs=31.7
Q ss_pred ecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEEecee
Q psy18081 13 IAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAVS 59 (82)
Q Consensus 13 IApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~Pk 59 (82)
..+|++||-..-..+. ++.+.-++++++.|++.| |-++++|-
T Consensus 45 FG~Pq~vm~l~L~~rk---~L~n~dv~kV~~~i~~QG--fyLQ~pp~ 86 (103)
T COG3100 45 FGKPQLVMMLNLDGRK---KLVNADVEKVKQAIEEQG--FYLQLPPP 86 (103)
T ss_pred cCCCeEEEEeccchhH---HHHHhhHHHHHHHHHhcc--eeEecCCC
Confidence 4689999987765442 356777899999999887 66788874
No 18
>TIGR03341 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization.
Probab=47.55 E-value=18 Score=26.34 Aligned_cols=29 Identities=14% Similarity=0.200 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHH-HHHHHHhhcCCeEEEEe
Q psy18081 28 ADGLKALQEAID-TIKAKIEQLGGVFQVQM 56 (82)
Q Consensus 28 ~~Gi~~L~~Aie-~I~~~I~~~gG~~~Vk~ 56 (82)
+.=.+.++++|+ .||-.+.++||.+.+..
T Consensus 104 ~~~~~~i~~~l~~~irP~l~~dGGdielv~ 133 (190)
T TIGR03341 104 APLEERINYVLQSEINPQLASHGGKVTLVE 133 (190)
T ss_pred hHHHHHHHHHHHhccCHHHHhcCCceEEEE
Confidence 335788999997 79999999999998875
No 19
>TIGR02000 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens.
Probab=46.65 E-value=20 Score=27.77 Aligned_cols=30 Identities=10% Similarity=0.335 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCeEEEEe
Q psy18081 27 KADGLKALQEAIDTIKAKIEQLGGVFQVQM 56 (82)
Q Consensus 27 K~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~ 56 (82)
-.+=++.++++|+.|+-.+..+||.+.+..
T Consensus 217 ~~~~~~~v~~~l~~irP~l~~dGGdv~lv~ 246 (290)
T TIGR02000 217 NVQRIQLIQKVLEEVRPVLQADGGDVELYD 246 (290)
T ss_pred hHHHHHHHHHHHHHhCchHhhcCCcEEEEE
Confidence 345578899999999999999999998875
No 20
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=44.65 E-value=67 Score=22.11 Aligned_cols=46 Identities=17% Similarity=0.154 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHhhcCCeEEEEeceeEeeccccchhhhccccCcceec
Q psy18081 31 LKALQEAIDTIKAKIEQLGGVFQVQMAVSILLMSMIQNSQTDLFNSDVIWQ 81 (82)
Q Consensus 31 i~~L~~Aie~I~~~I~~~gG~~~Vk~~PkvVse~d~~~l~~~~~~~~~~~~ 81 (82)
-+.|++|+..++...+..|=+.++..- .+ ++.++.++.+.|.-||-
T Consensus 22 g~~L~~av~~l~~~L~~~Giev~l~~~--~l---~~~~~~~~~~~S~~I~i 67 (120)
T PF10865_consen 22 GETLREAVKELAPVLAPLGIEVRLEEI--EL---DEEEFARQPLESPTIRI 67 (120)
T ss_pred HHHHHHHHHHHHHHHHhCCcEEEEEEE--EC---ChHHHhhcccCCCeeeE
Confidence 467999999999999999977766632 22 33467777789999885
No 21
>PF13656 RNA_pol_L_2: RNA polymerase Rpb3/Rpb11 dimerisation domain; PDB: 2Y0S_L 1I3Q_K 4A3D_K 2JA8_K 3GTP_K 1R9T_K 3PO2_K 4A3J_K 3HOX_K 2JA7_K ....
Probab=44.54 E-value=24 Score=22.14 Aligned_cols=30 Identities=17% Similarity=0.208 Sum_probs=23.2
Q ss_pred EEEEeeeCCHHHHHHHHHHHHHHHHHHHhh
Q psy18081 18 YVMTTVTPEKADGLKALQEAIDTIKAKIEQ 47 (82)
Q Consensus 18 Yvltt~tlDK~~Gi~~L~~Aie~I~~~I~~ 47 (82)
-.++.+|..+...+++|++|++.+.+..+.
T Consensus 43 i~l~Iqt~~~~~p~~~l~~a~~~l~~~~~~ 72 (77)
T PF13656_consen 43 INLRIQTKGGITPIEALKKALEDLIKICEE 72 (77)
T ss_dssp EEEEEEESTTS-HHHHHHHHHHHHHHHHHH
T ss_pred eEEEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence 456677777768999999999999887654
No 22
>cd03799 GT1_amsK_like This is a family of GT1 glycosyltransferases found specifically in certain bacteria. amsK in Erwinia amylovora, has been reported to be involved in the biosynthesis of amylovoran, a exopolysaccharide acting as a virulence factor.
Probab=41.44 E-value=89 Score=21.98 Aligned_cols=30 Identities=27% Similarity=0.414 Sum_probs=23.7
Q ss_pred CCeEEEEeeeCCHHHHHHHHHHHHHHHHHH
Q psy18081 15 PPLYVMTTVTPEKADGLKALQEAIDTIKAK 44 (82)
Q Consensus 15 pPlYvltt~tlDK~~Gi~~L~~Aie~I~~~ 44 (82)
.+.+++..-...+.+|++.+-+|++.+.+.
T Consensus 178 ~~~~i~~~g~~~~~k~~~~l~~~~~~l~~~ 207 (355)
T cd03799 178 EPLRILSVGRLVEKKGLDYLLEALALLKDR 207 (355)
T ss_pred CCeEEEEEeeeccccCHHHHHHHHHHHhhc
Confidence 455677777788899999999999887654
No 23
>cd07029 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to ass
Probab=41.37 E-value=35 Score=21.88 Aligned_cols=31 Identities=6% Similarity=0.215 Sum_probs=24.6
Q ss_pred EEEEeeeCCHHHHHHHHHHHHHHHHHHHhhc
Q psy18081 18 YVMTTVTPEKADGLKALQEAIDTIKAKIEQL 48 (82)
Q Consensus 18 Yvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~ 48 (82)
-.++.+|.+...-+++|++|++.|.+.....
T Consensus 51 ~~lriqT~~~~~p~~al~~a~~~l~~~~~~~ 81 (85)
T cd07029 51 INLRIQTKGGEPAVDVLKKGLEDLEQICDHI 81 (85)
T ss_pred cEEEEEeCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 4566777777888999999999998877654
No 24
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=41.06 E-value=22 Score=23.72 Aligned_cols=37 Identities=38% Similarity=0.624 Sum_probs=29.4
Q ss_pred CCcceEEEEecCCeEEEEeeeCCHHHHHHHHHHHHHHHHH
Q psy18081 4 EKMPIKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKA 43 (82)
Q Consensus 4 e~~~IkIkLIApPlYvltt~tlDK~~Gi~~L~~Aie~I~~ 43 (82)
+.-||-+=|.|==+|++. .||+.|.+.++++++.|+.
T Consensus 40 ~~epIaFGLkal~l~vvv---~D~Eg~td~~ee~l~~veg 76 (88)
T COG2092 40 EEEPIAFGLKALKLYVVV---EDKEGGTDALEEALEEVEG 76 (88)
T ss_pred eeEeeeeeeeeEEEEEEE---cccccCcHHHHHHHhhccC
Confidence 445777777776677666 8999999999999998764
No 25
>PRK11190 Fe/S biogenesis protein NfuA; Provisional
Probab=39.82 E-value=25 Score=25.76 Aligned_cols=28 Identities=11% Similarity=0.236 Sum_probs=24.7
Q ss_pred HHHHHHHHHHH-HHHHHHhhcCCeEEEEe
Q psy18081 29 DGLKALQEAID-TIKAKIEQLGGVFQVQM 56 (82)
Q Consensus 29 ~Gi~~L~~Aie-~I~~~I~~~gG~~~Vk~ 56 (82)
+=++.++++|+ .||-.+.++||.+.+..
T Consensus 106 ~~~~~i~~~l~~~irP~l~~dGGdielv~ 134 (192)
T PRK11190 106 PLMERVEYVLQSQINPQLAGHGGRVSLME 134 (192)
T ss_pred HHHHHHHHHHHhccChhHHhcCCcEEEEE
Confidence 45888999997 99999999999998875
No 26
>KOG1588|consensus
Probab=38.90 E-value=65 Score=25.21 Aligned_cols=32 Identities=25% Similarity=0.358 Sum_probs=28.3
Q ss_pred cCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHH
Q psy18081 14 APPLYVMTTVTPEKADGLKALQEAIDTIKAKI 45 (82)
Q Consensus 14 ApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I 45 (82)
.-||-|+..+-.+.+..-.+|..|++.|++-.
T Consensus 158 ~epLHVlIe~~~p~~ea~~rl~~AleeI~klL 189 (259)
T KOG1588|consen 158 NEPLHVLIETEAPPAEAYARLAYALEEIKKLL 189 (259)
T ss_pred CCCcEEEEEEeCCHHHHHHHHHHHHHHHHHhc
Confidence 45888999999999999999999999998754
No 27
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=38.87 E-value=51 Score=21.35 Aligned_cols=20 Identities=20% Similarity=0.202 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHhhcCCeE
Q psy18081 33 ALQEAIDTIKAKIEQLGGVF 52 (82)
Q Consensus 33 ~L~~Aie~I~~~I~~~gG~~ 52 (82)
-+++.++.+++.|++.||+.
T Consensus 22 ~~~~~~~~~~~~i~~~gg~i 41 (97)
T CHL00123 22 ELLKWIENYKKLLRKRGAKN 41 (97)
T ss_pred HHHHHHHHHHHHHHHCCCEE
Confidence 46778899999999999986
No 28
>PF12224 Amidoligase_2: Putative amidoligase enzyme; InterPro: IPR022025 This family of proteins are likely to act as amidoligase enzymes [] Protein in this family are found in conserved gene neighbourhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes) [].
Probab=38.01 E-value=54 Score=23.43 Aligned_cols=46 Identities=15% Similarity=0.322 Sum_probs=31.5
Q ss_pred eEEEEecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHH---HhhcCCeEEEEeceeEe
Q psy18081 8 IKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAK---IEQLGGVFQVQMAVSIL 61 (82)
Q Consensus 8 IkIkLIApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~---I~~~gG~~~Vk~~PkvV 61 (82)
+-+.||+||++.-. + ++.|++.++++++. +....-.|.|-..|...
T Consensus 76 ~~~ElvSP~l~~~~------~--~~~i~~~~~~lr~~~~~~~~~scg~HVHv~~~~~ 124 (252)
T PF12224_consen 76 VPVELVSPPLPYDE------E--LEEIDKVLEALRRNGAIGTNDSCGFHVHVGPEPP 124 (252)
T ss_pred eeEEEECCCcCchh------h--HHHHHHHHHHHHHcCCccccCCeeEEEEECCCCC
Confidence 67899999998633 1 77777777777773 33455667777666543
No 29
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=37.60 E-value=75 Score=18.77 Aligned_cols=29 Identities=28% Similarity=0.312 Sum_probs=22.6
Q ss_pred eEEEEeeeCCHHHHHHHHHHHHHHHHHHH
Q psy18081 17 LYVMTTVTPEKADGLKALQEAIDTIKAKI 45 (82)
Q Consensus 17 lYvltt~tlDK~~Gi~~L~~Aie~I~~~I 45 (82)
.|+++..|..--.-.++|.+|++.+++..
T Consensus 37 ~~~~~IeT~g~~~p~~~l~~A~~~l~~~~ 65 (66)
T PF01193_consen 37 KFVFRIETDGSLTPKEALLKAIKILKEKL 65 (66)
T ss_dssp EEEEEEEEBSSS-HHHHHHHHHHHHHHHH
T ss_pred EEEEEEEECCCCCHHHHHHHHHHHHHHhc
Confidence 46777777777788999999999998764
No 30
>PF00534 Glycos_transf_1: Glycosyl transferases group 1; InterPro: IPR001296 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. Proteins containign this domain transfer UDP, ADP, GDP or CMP linked sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. The bacterial enzymes are involved in various biosynthetic processes that include exopolysaccharide biosynthesis, lipopolysaccharide core biosynthesis and the biosynthesis of the slime polysaccaride colanic acid. Mutations in this domain of the human N-acetylglucosaminyl-phosphatidylinositol biosynthetic protein are the cause of paroxysmal nocturnal hemoglobinuria (PNH), an acquired hemolytic blood disorder characterised by venous thrombosis, erythrocyte hemolysis, infections and defective hematopoiesis.; GO: 0009058 biosynthetic process; PDB: 2L7C_A 2IV3_B 2IUY_B 2XA9_A 2XA1_B 2X6R_A 2XMP_B 2XA2_B 2X6Q_A 3QHP_B ....
Probab=37.04 E-value=1.1e+02 Score=19.58 Aligned_cols=30 Identities=20% Similarity=0.263 Sum_probs=26.5
Q ss_pred CCeEEEEeeeCCHHHHHHHHHHHHHHHHHH
Q psy18081 15 PPLYVMTTVTPEKADGLKALQEAIDTIKAK 44 (82)
Q Consensus 15 pPlYvltt~tlDK~~Gi~~L~~Aie~I~~~ 44 (82)
.+.+++....+++.+|+..|=+|+..+.+.
T Consensus 14 ~~~~il~~g~~~~~K~~~~li~a~~~l~~~ 43 (172)
T PF00534_consen 14 KKKIILFIGRLDPEKGIDLLIEAFKKLKEK 43 (172)
T ss_dssp TSEEEEEESESSGGGTHHHHHHHHHHHHHH
T ss_pred CCeEEEEEecCccccCHHHHHHHHHHHHhh
Confidence 467888899999999999999999988776
No 31
>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=35.40 E-value=40 Score=25.46 Aligned_cols=50 Identities=16% Similarity=0.310 Sum_probs=31.3
Q ss_pred eEEEEecCCeEEEEeeeCCHHHHHHHHHH----HHHHHHHHHhhcCCeEEEEece
Q psy18081 8 IKINLIAPPLYVMTTVTPEKADGLKALQE----AIDTIKAKIEQLGGVFQVQMAV 58 (82)
Q Consensus 8 IkIkLIApPlYvltt~tlDK~~Gi~~L~~----Aie~I~~~I~~~gG~~~Vk~~P 58 (82)
+.|+|...=-+ +..+=.|-=.|+..-+. -+.-|++.++..||+|.|...|
T Consensus 300 v~V~l~~~~~~-l~l~V~DnG~Gf~~~~~~~~~GL~~mreRv~~lgG~l~i~S~~ 353 (365)
T COG4585 300 VRVTLERTDDE-LRLEVIDNGVGFDPDKEGGGFGLLGMRERVEALGGTLTIDSAP 353 (365)
T ss_pred EEEEEEEcCCE-EEEEEEECCcCCCccccCCCcchhhHHHHHHHcCCEEEEEecC
Confidence 44444444443 22222233345544443 5778999999999999999988
No 32
>TIGR00166 S6 ribosomal protein S6. MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6.
Probab=35.18 E-value=60 Score=20.45 Aligned_cols=20 Identities=20% Similarity=0.222 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHhhcCCeEE
Q psy18081 34 LQEAIDTIKAKIEQLGGVFQ 53 (82)
Q Consensus 34 L~~Aie~I~~~I~~~gG~~~ 53 (82)
+++.++.+.+.|++.||...
T Consensus 17 ~~~~~~~~~~~i~~~gg~i~ 36 (93)
T TIGR00166 17 VKGQIERYKKVITLNGAEIV 36 (93)
T ss_pred HHHHHHHHHHHHHhCCCEEE
Confidence 67889999999999999864
No 33
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=34.78 E-value=72 Score=24.34 Aligned_cols=42 Identities=19% Similarity=0.248 Sum_probs=30.1
Q ss_pred EEEeeeCCHHHHHHHHHHHHHHHHH--HHhhcCCeEEEEeceeEe
Q psy18081 19 VMTTVTPEKADGLKALQEAIDTIKA--KIEQLGGVFQVQMAVSIL 61 (82)
Q Consensus 19 vltt~tlDK~~Gi~~L~~Aie~I~~--~I~~~gG~~~Vk~~PkvV 61 (82)
.+..+|.+ -.||+.+++|+.+..+ +.+...=++++..+|+=+
T Consensus 179 ~ie~~~~~-~dGi~~Ik~aL~~~~~~~~~~~~~v~i~~ig~P~Y~ 222 (262)
T PRK03987 179 YVDLTSPE-PDGVEIIKKALKAAEKANKYEDVEVEIYYVGAPRYR 222 (262)
T ss_pred EEEEEeCC-CChHHHHHHHHHHHHhhcCCCCCcEEEEEECCCeEE
Confidence 34556766 6799999999999887 333344467788899743
No 34
>PF12691 Minor_capsid_3: Minor capsid protein from bacteriophage; InterPro: IPR024411 This entry represents a minor capsid protein from bacteriophages.
Probab=34.75 E-value=1.3e+02 Score=20.74 Aligned_cols=47 Identities=11% Similarity=0.135 Sum_probs=35.8
Q ss_pred eEEEEeeeCCHHHHHHHHHHHHHHHHH----HHhhcCCeEEEE-----eceeEeec
Q psy18081 17 LYVMTTVTPEKADGLKALQEAIDTIKA----KIEQLGGVFQVQ-----MAVSILLM 63 (82)
Q Consensus 17 lYvltt~tlDK~~Gi~~L~~Aie~I~~----~I~~~gG~~~Vk-----~~PkvVse 63 (82)
.|.+...|.|..++...|.+.-..+.+ .+.+..|+|... ..|..++.
T Consensus 58 ~feI~~K~~d~~~a~~tl~~Is~~Ld~~~~~~L~S~dgSy~f~~lev~~~P~~~~~ 113 (135)
T PF12691_consen 58 PFEIAIKSKDQQKANNTLWEISDYLDNLNDRDLPSQDGSYEFESLEVYSQPFINGK 113 (135)
T ss_pred eEEEEEecCcHhHHHHHHHHHHHHHHHhhhcCcCcCCCcEEEEEeEeecCCccccc
Confidence 588999999999999888766555544 688899998753 56766555
No 35
>cd07302 CHD cyclase homology domain. Catalytic domains of the mononucleotidyl cyclases (MNC's), also called cyclase homology domains (CHDs), are part of the class III nucleotidyl cyclases. This class includes eukaryotic and prokaryotic adenylate cyclases (AC's) and guanylate cyclases (GC's). They seem to share a common catalytic mechanism in their requirement for two magnesium ions to bind the polyphosphate moiety of the nucleotide.
Probab=33.99 E-value=84 Score=19.99 Aligned_cols=31 Identities=19% Similarity=0.254 Sum_probs=27.1
Q ss_pred eCCHHHHHHHHHHHHHHHHHHHhhcCCeEEE
Q psy18081 24 TPEKADGLKALQEAIDTIKAKIEQLGGVFQV 54 (82)
Q Consensus 24 tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~V 54 (82)
.++.++.+..|+...+.+.+.+.++||...-
T Consensus 18 ~~~~~~~~~~l~~~~~~~~~~~~~~~g~~~~ 48 (177)
T cd07302 18 RLGPEELVELLNEYFSAFDEIIERHGGTVDK 48 (177)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHcCCEEEE
Confidence 3478999999999999999999999998753
No 36
>PF05773 RWD: RWD domain; InterPro: IPR006575 The RWD eukaryotic domain is found in RING finger (IPR001841 from INTERPRO) and WD repeat (IPR001680 from INTERPRO) containing proteins and DEXDc-like helicase (IPR001410 from INTERPRO) subfamily related to the ubiquitin-conjugating enzymes domain (IPR000608 from INTERPRO). ; GO: 0005515 protein binding; PDB: 2EBM_A 2EBK_A 2DAX_A 2DAW_A 2DAY_A 2DMF_A 1UKX_A 2YZ0_A.
Probab=33.49 E-value=1.1e+02 Score=18.57 Aligned_cols=31 Identities=13% Similarity=0.412 Sum_probs=20.2
Q ss_pred cCCeEEEEeeeCCHHHHHHHHHHHHHHHHHH
Q psy18081 14 APPLYVMTTVTPEKADGLKALQEAIDTIKAK 44 (82)
Q Consensus 14 ApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~ 44 (82)
+||.+.+++.....+.-...|.+.+..+-+.
T Consensus 64 ~~P~i~l~~~~~~~~~~~~~l~~~l~~~~~~ 94 (113)
T PF05773_consen 64 SPPKISLESPKNSRNEQIEKLNKELEQIAEE 94 (113)
T ss_dssp S--EEEEEEESSSHCHHHHHHHHHHHHHHHH
T ss_pred cCCEEEEEcCCCCCHHHHHHHHHHHHHHHHH
Confidence 6889999998888866666666665554433
No 37
>cd03798 GT1_wlbH_like This family is most closely related to the GT1 family of glycosyltransferases. wlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core (band B), generates band A LPS.
Probab=33.22 E-value=1.5e+02 Score=20.15 Aligned_cols=30 Identities=17% Similarity=0.140 Sum_probs=24.7
Q ss_pred CCeEEEEeeeCCHHHHHHHHHHHHHHHHHH
Q psy18081 15 PPLYVMTTVTPEKADGLKALQEAIDTIKAK 44 (82)
Q Consensus 15 pPlYvltt~tlDK~~Gi~~L~~Aie~I~~~ 44 (82)
.+.+++..-..+..+|++.+=+|++.+.+.
T Consensus 201 ~~~~i~~~g~~~~~k~~~~li~~~~~~~~~ 230 (377)
T cd03798 201 DKKVILFVGRLVPRKGIDYLIEALARLLKK 230 (377)
T ss_pred CceEEEEeccCccccCHHHHHHHHHHHHhc
Confidence 567788888888899999999988887754
No 38
>PF10719 ComFB: Late competence development protein ComFB; InterPro: IPR019657 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. The development of genetic competence in Bacillus subtilis is a highly regulated adaptive response to stationary-phase stress. For competence to develop, the transcriptional regulator, ComK, must be activated. ComK is required for the expression of genes encoding proteins that function in DNA uptake. In log-phase cultures, ComK is inactive in a complex with MecA and ClpC. The comS gene is induced in response to high culture cell density and nutritional stress and its product functions to release active ComK from the complex. ComK then stimulates the transcription initiation of its own gene as well as that of the late competence operons []. The comF locus has three open reading frames and is driven by a single sigma A-like promoter in front of comFORF1. It is dependent on early regulatory competence genes and is only expressed in competence medium. ComFORF1 is similar to an extensive family of ATP-dependent RNA/DNA helicases with closer similarity to the DEAD protein subfamily and to the PriA protein in Escherichia coli. ComFORF1 late gene product plays an essential role during the binding and uptake events involved in B. subtilis transformation []. ComFB is the second protein encoded within the late competence locus ComF []. The function of ComFB within late competence development is not known.
Probab=32.04 E-value=79 Score=19.65 Aligned_cols=10 Identities=50% Similarity=0.982 Sum_probs=7.8
Q ss_pred CCeEEEEeee
Q psy18081 15 PPLYVMTTVT 24 (82)
Q Consensus 15 pPlYvltt~t 24 (82)
||+|+.+..-
T Consensus 42 PPrYv~~~~~ 51 (85)
T PF10719_consen 42 PPRYVVSEVG 51 (85)
T ss_pred CCeEEEecCc
Confidence 8999988543
No 39
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=31.26 E-value=83 Score=24.68 Aligned_cols=40 Identities=23% Similarity=0.381 Sum_probs=30.6
Q ss_pred CeEEEEeeeCC----------HHHHHHHHHHHHHHHHHHHhhcCCeEEEE
Q psy18081 16 PLYVMTTVTPE----------KADGLKALQEAIDTIKAKIEQLGGVFQVQ 55 (82)
Q Consensus 16 PlYvltt~tlD----------K~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk 55 (82)
|+|++...-.. -..-..-|-++++.+++..++.|+.|.|.
T Consensus 31 ~vfi~dp~~~~~~~~~~~~~~~~~r~~Fl~esL~~L~~~L~~~g~~L~v~ 80 (429)
T TIGR02765 31 PLYCFDPRQFKLTHFFGFPKTGPARGKFLLESLKDLRTSLRKLGSDLLVR 80 (429)
T ss_pred EEEEECchHhccccccccCCCCHHHHHHHHHHHHHHHHHHHHcCCCeEEE
Confidence 67777653333 23356778999999999999999999886
No 40
>PF00828 Ribosomal_L18e: Ribosomal protein L18e/L15; InterPro: IPR021131 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 entry represents both L15 and L18e ribosomal proteins, which share a common structure consisting mainly of parallel beta sheets (beta-alpha-beta units) with a core of three turns of irregular (beta-beta-alpha)n superhelix [, ].; PDB: 3O58_Y 1S1I_V 3O5H_Y 3IZS_O 3IZR_R 2OTL_L 1M1K_M 3G6E_L 1VQ9_L 1YIT_L ....
Probab=30.91 E-value=45 Score=22.19 Aligned_cols=14 Identities=43% Similarity=0.518 Sum_probs=10.9
Q ss_pred HHHHHhhcCCeEEE
Q psy18081 41 IKAKIEQLGGVFQV 54 (82)
Q Consensus 41 I~~~I~~~gG~~~V 54 (82)
-++.||+.||++.+
T Consensus 115 A~ekIe~aGG~v~~ 128 (129)
T PF00828_consen 115 AKEKIEAAGGEVVT 128 (129)
T ss_dssp HHHHHHHTSEEEEE
T ss_pred HHHHHHHcCCEEEe
Confidence 46678899999864
No 41
>PRK06419 rpl15p 50S ribosomal protein L15P; Reviewed
Probab=30.84 E-value=56 Score=22.97 Aligned_cols=18 Identities=28% Similarity=0.357 Sum_probs=13.0
Q ss_pred HHHHHHHhhcCCeEEEEe
Q psy18081 39 DTIKAKIEQLGGVFQVQM 56 (82)
Q Consensus 39 e~I~~~I~~~gG~~~Vk~ 56 (82)
+.-++.||+.||++.+..
T Consensus 129 ~~A~ekIe~aGG~v~l~~ 146 (148)
T PRK06419 129 EKAIEKIEAAGGEVVLSE 146 (148)
T ss_pred HHHHHHHHHcCCEEEEee
Confidence 345667888899997753
No 42
>COG3469 Chitinase [Carbohydrate transport and metabolism]
Probab=30.83 E-value=57 Score=26.32 Aligned_cols=27 Identities=22% Similarity=0.385 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHhhcCCeEEEEecee
Q psy18081 33 ALQEAIDTIKAKIEQLGGVFQVQMAVS 59 (82)
Q Consensus 33 ~L~~Aie~I~~~I~~~gG~~~Vk~~Pk 59 (82)
++-.|++++++.=++.|+.|-|.|||.
T Consensus 155 v~p~alk~vk~hyk~~Gk~f~itMAPE 181 (332)
T COG3469 155 VIPAALKAVKDHYKNQGKNFFITMAPE 181 (332)
T ss_pred ehHHHHHHHHHHHHhcCCceEEEecCC
Confidence 456688888988899999999999995
No 43
>COG0694 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]
Probab=30.66 E-value=37 Score=22.54 Aligned_cols=27 Identities=22% Similarity=0.374 Sum_probs=22.5
Q ss_pred HHHHHHHHHH-HHHHHHhhcCCeEEEEe
Q psy18081 30 GLKALQEAID-TIKAKIEQLGGVFQVQM 56 (82)
Q Consensus 30 Gi~~L~~Aie-~I~~~I~~~gG~~~Vk~ 56 (82)
=++.++++++ .|+-.+..+||.+.+..
T Consensus 10 ~~e~v~~~l~~~irP~l~~dGGdve~~~ 37 (93)
T COG0694 10 LLERVEEVLDEKIRPQLAMDGGDVELVG 37 (93)
T ss_pred HHHHHHHHHHhccCcceeccCCeEEEEE
Confidence 3677888888 88899999999998763
No 44
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=30.11 E-value=1.4e+02 Score=18.76 Aligned_cols=31 Identities=19% Similarity=0.359 Sum_probs=25.2
Q ss_pred eEEEEeeeCCHHHHHHHHHHHHHHHHHHHhh
Q psy18081 17 LYVMTTVTPEKADGLKALQEAIDTIKAKIEQ 47 (82)
Q Consensus 17 lYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~ 47 (82)
.|.++..|..--.-.++|.+|++.+++....
T Consensus 55 ~~~~~VeT~Gs~~P~~al~~Ai~~L~~~~~~ 85 (86)
T cd00460 55 KFILRIETVGSIPPEEALRRAVEILRKKLEH 85 (86)
T ss_pred eEEEEEEECCCCCHHHHHHHHHHHHHHHHhh
Confidence 5788888887677889999999999887653
No 45
>cd00756 MoaE MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits.
Probab=29.73 E-value=1.3e+02 Score=20.38 Aligned_cols=33 Identities=15% Similarity=0.342 Sum_probs=28.5
Q ss_pred ecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHH
Q psy18081 13 IAPPLYVMTTVTPEKADGLKALQEAIDTIKAKI 45 (82)
Q Consensus 13 IApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I 45 (82)
+.-+...+...+.-+.++++.++.+|+.|+...
T Consensus 77 vGe~~v~i~v~a~hR~~af~A~~~~id~lK~~~ 109 (124)
T cd00756 77 PGEAIVLVAVSSPHRKEAFEACEFLIDRLKHRA 109 (124)
T ss_pred CCCEEEEEEEecCCHHHHHHHHHHHHHHHHhhC
Confidence 456777888999999999999999999998764
No 46
>KOG4513|consensus
Probab=29.50 E-value=1e+02 Score=26.24 Aligned_cols=48 Identities=35% Similarity=0.422 Sum_probs=35.5
Q ss_pred ceEEEEecCCeEEEEeeeCCH-HHHHHHHHHHHHHHHHHHhhcCCeEEEE
Q psy18081 7 PIKINLIAPPLYVMTTVTPEK-ADGLKALQEAIDTIKAKIEQLGGVFQVQ 55 (82)
Q Consensus 7 ~IkIkLIApPlYvltt~tlDK-~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk 55 (82)
.|.+| +|||-.|--|--.+- ....+.-..||..|-+.|++.||.+.|.
T Consensus 407 ~v~vN-lappDMVGHTG~~EAtv~AcEatD~aig~Iy~A~~~~~y~lvvT 455 (531)
T KOG4513|consen 407 QVRVN-LAPPDMVGHTGDIEATVVACEATDEAIGKIYDAIEQVGYILVVT 455 (531)
T ss_pred eEEEc-CCCccccCcccchhhhhhHHHHHHHHHHHHHHHHHhcCcEEEEE
Confidence 46677 688877765543332 2456777789999999999999999875
No 47
>PF00586 AIRS: AIR synthase related protein, N-terminal domain; InterPro: IPR000728 This family includes Hydrogen expression/formation protein, HypE, which may be involved in the maturation of NifE hydrogenase; AIR synthase and FGAM synthase, which are involved in de novo purine biosynthesis; and selenide, water dikinase, an enzyme which synthesizes selenophosphate from selenide and ATP.; GO: 0003824 catalytic activity; PDB: 3VIU_A 2Z1T_A 2Z1U_A 3C9U_B 3C9S_A 3C9R_A 1VQV_A 3C9T_B 3M84_A 3QTY_A ....
Probab=29.49 E-value=83 Score=19.36 Aligned_cols=38 Identities=16% Similarity=0.313 Sum_probs=29.0
Q ss_pred CCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeE
Q psy18081 15 PPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVF 52 (82)
Q Consensus 15 pPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~ 52 (82)
-|+|.+..-.+.+..=.+.+++.++-|.+.-++.|-.+
T Consensus 54 ~P~~~~~~l~~~~~~~~~~l~~~~~Gi~~~~~~~g~~i 91 (96)
T PF00586_consen 54 KPLAILDSLGLPNPESPEELKEIVKGIAEACREFGIPI 91 (96)
T ss_dssp EEEEEEEEEEESTTSBHHHHHHHHHHHHHHHHHHT-EE
T ss_pred eeeEEEEEEEcCCCCCHHHHHHHHHHHHHHHHHhCCcE
Confidence 48888888887776566679999999999888877543
No 48
>PF03197 FRD2: Bacteriophage FRD2 protein; InterPro: IPR004885 This is group of bacteriophage proteins has no known function.
Probab=29.30 E-value=44 Score=22.91 Aligned_cols=17 Identities=35% Similarity=0.425 Sum_probs=13.5
Q ss_pred HHHHhhcCCeEEEEece
Q psy18081 42 KAKIEQLGGVFQVQMAV 58 (82)
Q Consensus 42 ~~~I~~~gG~~~Vk~~P 58 (82)
-+.|+++||.|+|+.--
T Consensus 3 Vklie~~G~~F~V~dm~ 19 (102)
T PF03197_consen 3 VKLIEENGGWFEVKDMS 19 (102)
T ss_pred hHHHHHcCCcEEEeeeE
Confidence 45689999999998543
No 49
>cd03817 GT1_UGDG_like This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1,2-diacylglycerol forming 3-D-glucosyl-1,2-diacylglycerol.
Probab=28.59 E-value=2e+02 Score=19.80 Aligned_cols=30 Identities=10% Similarity=0.050 Sum_probs=23.9
Q ss_pred CCeEEEEeeeCCHHHHHHHHHHHHHHHHHH
Q psy18081 15 PPLYVMTTVTPEKADGLKALQEAIDTIKAK 44 (82)
Q Consensus 15 pPlYvltt~tlDK~~Gi~~L~~Aie~I~~~ 44 (82)
.+..++..-..++.+|++.+-+|+..+++.
T Consensus 201 ~~~~i~~~G~~~~~k~~~~l~~~~~~~~~~ 230 (374)
T cd03817 201 DEPVLLYVGRLAKEKNIDFLIRAFARLLKE 230 (374)
T ss_pred CCeEEEEEeeeecccCHHHHHHHHHHHHHh
Confidence 456677777788889999999999887764
No 50
>COG4443 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.57 E-value=33 Score=22.18 Aligned_cols=32 Identities=22% Similarity=0.537 Sum_probs=25.9
Q ss_pred cCCeEEEEeeeCCHHH---HHHHHHHHHHHHHHHH
Q psy18081 14 APPLYVMTTVTPEKAD---GLKALQEAIDTIKAKI 45 (82)
Q Consensus 14 ApPlYvltt~tlDK~~---Gi~~L~~Aie~I~~~I 45 (82)
+||.|-|++=+.|+.+ ||-+-++-+.++++..
T Consensus 35 ~~~KyDiR~Wspdh~KMGKGiTLt~eE~~~l~d~l 69 (72)
T COG4443 35 RPPKYDIRAWSPDHSKMGKGITLTNEEFKALKDLL 69 (72)
T ss_pred CCCcCcccccCcchhhhcCceeecHHHHHHHHHHH
Confidence 7999999999999974 7877777777776654
No 51
>COG0525 ValS Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=27.56 E-value=22 Score=32.03 Aligned_cols=56 Identities=13% Similarity=0.184 Sum_probs=43.4
Q ss_pred cCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEE----EEeceeEeeccccchh
Q psy18081 14 APPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQ----VQMAVSILLMSMIQNS 69 (82)
Q Consensus 14 ApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~----Vk~~PkvVse~d~~~l 69 (82)
..+.|.-..-..|+..-++.|++.+++++.++++..+.+. +..||..|-++|..-|
T Consensus 799 ~~~~~~~l~~~id~~~e~~rl~k~~~k~~~e~~~~~~kl~ne~f~~kAp~~vv~~e~~~~ 858 (877)
T COG0525 799 GAELFLPLAGLIDLAAELARLEKELEKLEKEIDRIEKKLSNEGFVAKAPEEVVEKEKEKL 858 (877)
T ss_pred cceEEEeccchhhHHHHHhhHHHHHHHHHHHHHHHHHhhcchhhhhcCCHHHHHHHHHHH
Confidence 4677777888899999999999999999999986554444 6667777766665444
No 52
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 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 [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=27.38 E-value=97 Score=19.17 Aligned_cols=21 Identities=33% Similarity=0.618 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHhhcCCeEE
Q psy18081 33 ALQEAIDTIKAKIEQLGGVFQ 53 (82)
Q Consensus 33 ~L~~Aie~I~~~I~~~gG~~~ 53 (82)
-+++.++.+.+.|++.||...
T Consensus 17 ~~~~~~~~~~~~i~~~gg~v~ 37 (92)
T PF01250_consen 17 EIKKLIERVKKIIEKNGGVVR 37 (92)
T ss_dssp HHHHHHHHHHHHHHHTTEEEE
T ss_pred HHHHHHHHHHHHHHHCCCEEE
Confidence 466788889999999999874
No 53
>cd07027 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/
Probab=27.29 E-value=1.1e+02 Score=19.38 Aligned_cols=29 Identities=17% Similarity=0.195 Sum_probs=21.9
Q ss_pred EEEeeeCCHHHHHHHHHHHHHHHHHHHhh
Q psy18081 19 VMTTVTPEKADGLKALQEAIDTIKAKIEQ 47 (82)
Q Consensus 19 vltt~tlDK~~Gi~~L~~Aie~I~~~I~~ 47 (82)
.++.+|...-.-.++|++|++.+.+..+.
T Consensus 52 ~lrI~T~~~~~P~~al~~a~~~l~~~~~~ 80 (83)
T cd07027 52 QIRIQTKSGIKPKDALKRAVNKLSKLYEH 80 (83)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence 45555555567889999999999887765
No 54
>TIGR01046 S10_Arc_S20_Euk ribosomal protein S10(archaeal)/S20(eukaryotic). its equivalents in eukaryotes.
Probab=26.93 E-value=1.9e+02 Score=19.08 Aligned_cols=29 Identities=17% Similarity=0.253 Sum_probs=22.4
Q ss_pred EEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeE
Q psy18081 20 MTTVTPEKADGLKALQEAIDTIKAKIEQLGGVF 52 (82)
Q Consensus 20 ltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~ 52 (82)
|+.++.|. ..|+++++.|.+..++.|..+
T Consensus 5 I~L~S~d~----~~Ld~~~~~I~~~ak~~g~~~ 33 (99)
T TIGR01046 5 IKLTSTNV----RSLEKVCAQIKRIAEKTGVRM 33 (99)
T ss_pred EEEEECCH----HHHHHHHHHHHHHHHHcCCEE
Confidence 45556665 689999999999999877643
No 55
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=26.79 E-value=66 Score=17.00 Aligned_cols=21 Identities=33% Similarity=0.520 Sum_probs=15.8
Q ss_pred HHHHHHHHHhhcCCeEEEEec
Q psy18081 37 AIDTIKAKIEQLGGVFQVQMA 57 (82)
Q Consensus 37 Aie~I~~~I~~~gG~~~Vk~~ 57 (82)
.-+.+++.|++.||.+.-...
T Consensus 14 ~~~~l~~~i~~~Gg~v~~~~~ 34 (72)
T cd00027 14 ERDELKELIEKLGGKVTSSVS 34 (72)
T ss_pred CHHHHHHHHHHcCCEEecccc
Confidence 346788999999998866544
No 56
>PF03147 FDX-ACB: Ferredoxin-fold anticodon binding domain; InterPro: IPR005121 Aminoacyl-tRNA synthetases (aaRSs) play a crucial role in the translation of the genetic code by means of covalent attachment of amino acids to their cognate tRNAs. Phenylalanine-tRNA synthetase (PheRS) is known to be among the most complex enzymes of the aaRS family. Bacterial and mitochondrial PheRSs share a ferredoxin-fold anticodon binding (FDX-ACB) domain, which represents a canonical double split alpha+beta motif having no insertions. The FDX-ACB domain displays a typical RNA recognition fold (RRM) (see PDOC00030 from PROSITEDOC) formed by the four-stranded antiparallel beta sheet, with two helices packed against it [, , , , ].; GO: 0000049 tRNA binding, 0000287 magnesium ion binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation, 0008033 tRNA processing; PDB: 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 3PCO_D 2RHS_D 2RHQ_B 2AKW_B 1B70_B ....
Probab=26.67 E-value=1.7e+02 Score=18.29 Aligned_cols=36 Identities=25% Similarity=0.387 Sum_probs=25.3
Q ss_pred eEEEEeeeCCHHHHHHHHHHHHHHHHHHHhh-cCCeE
Q psy18081 17 LYVMTTVTPEKADGLKALQEAIDTIKAKIEQ-LGGVF 52 (82)
Q Consensus 17 lYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~-~gG~~ 52 (82)
.|.++-+..||.-.=+-+++..+.|.+.+++ .|.++
T Consensus 57 ~~rl~~~~~~~TLt~~ev~~~~~~i~~~l~~~~~~~l 93 (94)
T PF03147_consen 57 TYRLTYQSPDRTLTDEEVNEIHDKIIKALEKKLGAEL 93 (94)
T ss_dssp EEEEEE--SSS---HHHHHHHHHHHHHHHHHTCT-BE
T ss_pred EEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHhCcEe
Confidence 4788889999999999999999999999965 56654
No 57
>cd03794 GT1_wbuB_like This family is most closely related to the GT1 family of glycosyltransferases. wbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase.
Probab=26.48 E-value=1.8e+02 Score=20.05 Aligned_cols=31 Identities=26% Similarity=0.325 Sum_probs=25.6
Q ss_pred cCCeEEEEeeeCCHHHHHHHHHHHHHHHHHH
Q psy18081 14 APPLYVMTTVTPEKADGLKALQEAIDTIKAK 44 (82)
Q Consensus 14 ApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~ 44 (82)
..+..++..-..++.+|++.+-+|+..+.+.
T Consensus 218 ~~~~~i~~~G~~~~~k~~~~l~~~~~~l~~~ 248 (394)
T cd03794 218 DDKFVVLYAGNIGRAQGLDTLLEAAALLKDR 248 (394)
T ss_pred CCcEEEEEecCcccccCHHHHHHHHHHHhhc
Confidence 4566777888889999999999999988764
No 58
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=26.32 E-value=1.5e+02 Score=17.62 Aligned_cols=46 Identities=13% Similarity=0.203 Sum_probs=30.6
Q ss_pred eEEEEecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEE
Q psy18081 8 IKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQ 53 (82)
Q Consensus 8 IkIkLIApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~ 53 (82)
|.|++---.--+-..-..+..+-.+.|++.+..+++...+.|-...
T Consensus 27 v~v~l~~~~~~l~v~~~~~~~~~~~~L~~~~~~L~~~L~~~G~~~~ 72 (85)
T PF02120_consen 27 VEVKLRLQGGNLSVQFTAENPETKELLRQNLPELKERLQAQGLEVV 72 (85)
T ss_dssp EEEEEEEETTEEEEEEE--SSHHHHHHHHTHHHHHHHHHTTT-EEE
T ss_pred EEEEEEEeCCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCeE
Confidence 3333333333444445567788999999999999999999986554
No 59
>cd01514 Elongation_Factor_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p. This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain. EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the
Probab=26.24 E-value=1.5e+02 Score=17.55 Aligned_cols=29 Identities=14% Similarity=0.352 Sum_probs=22.3
Q ss_pred CeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEE
Q psy18081 16 PLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQ 53 (82)
Q Consensus 16 PlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~ 53 (82)
|.|-++.++.+. ++-.+-+.+.+++|.+.
T Consensus 2 Pi~~~~I~~p~~---------~~g~v~~~l~~rrg~v~ 30 (79)
T cd01514 2 PIMKVEITVPEE---------YLGAVIGDLSKRRGEIL 30 (79)
T ss_pred CEEEEEEEcCHH---------HHHHHHHHHHhcCCeeE
Confidence 888888888887 55556777778888875
No 60
>PF04455 Saccharop_dh_N: LOR/SDH bifunctional enzyme conserved region ; InterPro: IPR007545 Lysine-oxoglutarate reductase/Saccharopine dehydrogenase (LOR/SDH) is a bifunctional enzyme. This conserved region is commonly found immediately N-terminal to saccharopine dehydrogenase conserved region (IPR005097 from INTERPRO) in eukaryotes [, ].; PDB: 3C2Q_B 3MGJ_A.
Probab=26.06 E-value=89 Score=21.03 Aligned_cols=19 Identities=32% Similarity=0.632 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHhhcCCeEEEE
Q psy18081 33 ALQEAIDTIKAKIEQLGGVFQVQ 55 (82)
Q Consensus 33 ~L~~Aie~I~~~I~~~gG~~~Vk 55 (82)
+|++|+. .|...||+|.|.
T Consensus 17 il~~vLD----~I~d~GG~F~i~ 35 (103)
T PF04455_consen 17 ILNRVLD----IIMDMGGDFEIL 35 (103)
T ss_dssp HHHHHHH----HHHHTT-EEEEE
T ss_pred hHHHHHH----HHHhcCCCEEEE
Confidence 3555555 566899999986
No 61
>PF04155 Ground-like: Ground-like domain; InterPro: IPR007284 This group of proteins contain one or more copies of the ground-like domain, which are specific to Caenorhabditis elegans and Caenorhabditis briggsae. It has been proposed that the ground-like domain containing proteins may bind and modulate the activity of Patched-like membrane molecules, reminiscent of the modulating activities of neuropeptides [].
Probab=25.90 E-value=1.2e+02 Score=18.48 Aligned_cols=19 Identities=32% Similarity=0.564 Sum_probs=12.0
Q ss_pred HHHHHhh-cCCeEEEEecee
Q psy18081 41 IKAKIEQ-LGGVFQVQMAVS 59 (82)
Q Consensus 41 I~~~I~~-~gG~~~Vk~~Pk 59 (82)
|....++ .||.|.|..++.
T Consensus 31 Iq~~~e~~f~~~f~vIcs~~ 50 (76)
T PF04155_consen 31 IQKAAEKRFGGSFEVICSEG 50 (76)
T ss_pred HHHHHHHHhCCCEEEEEeCC
Confidence 3344433 889999986553
No 62
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=25.87 E-value=1.6e+02 Score=18.27 Aligned_cols=24 Identities=25% Similarity=0.534 Sum_probs=18.3
Q ss_pred Ce--EEEEeeeCCHHHHHHHHHHHHHHHHHHH
Q psy18081 16 PL--YVMTTVTPEKADGLKALQEAIDTIKAKI 45 (82)
Q Consensus 16 Pl--Yvltt~tlDK~~Gi~~L~~Aie~I~~~I 45 (82)
|. |.+| ++|.+.+++-++.+++-|
T Consensus 55 p~t~~~lT------~~Gr~~~~~~~~~L~~~i 80 (80)
T PF13601_consen 55 PRTWYSLT------DKGREAFERYVAALREII 80 (80)
T ss_dssp -EEEEEE-------HHHHHHHHHHHHHHHHHH
T ss_pred CeEEEEEC------HHHHHHHHHHHHHHHHhC
Confidence 66 6666 889999999999888754
No 63
>COG1303 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.76 E-value=83 Score=23.51 Aligned_cols=21 Identities=24% Similarity=0.646 Sum_probs=18.2
Q ss_pred HHHHHHHHHHhhcCCeEEEEe
Q psy18081 36 EAIDTIKAKIEQLGGVFQVQM 56 (82)
Q Consensus 36 ~Aie~I~~~I~~~gG~~~Vk~ 56 (82)
...+.+++.++..||.|.|+.
T Consensus 44 ~v~esv~dVv~rwGG~F~v~~ 64 (179)
T COG1303 44 KVVESVEDVVERWGGPFFVKF 64 (179)
T ss_pred HHHHHHHHHHHhcCCCEEEEE
Confidence 467889999999999998874
No 64
>KOG0005|consensus
Probab=25.69 E-value=1.7e+02 Score=18.72 Aligned_cols=34 Identities=21% Similarity=0.417 Sum_probs=20.3
Q ss_pred eEEEEecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCe
Q psy18081 8 IKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGV 51 (82)
Q Consensus 8 IkIkLIApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~ 51 (82)
||++-..--.--+...-.|| ++.|++.||+.-|-
T Consensus 3 iKvktLt~KeIeidIep~Dk----------verIKErvEEkeGI 36 (70)
T KOG0005|consen 3 IKVKTLTGKEIEIDIEPTDK----------VERIKERVEEKEGI 36 (70)
T ss_pred eeEeeeccceEEEeeCcchH----------HHHHHHHhhhhcCC
Confidence 44444444444444444444 78899999887774
No 65
>PRK12271 rps10p 30S ribosomal protein S10P; Reviewed
Probab=25.53 E-value=2e+02 Score=19.11 Aligned_cols=29 Identities=24% Similarity=0.290 Sum_probs=22.5
Q ss_pred EEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeE
Q psy18081 20 MTTVTPEKADGLKALQEAIDTIKAKIEQLGGVF 52 (82)
Q Consensus 20 ltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~ 52 (82)
|+.++.|. ..|+++++.|.+..++.|-.+
T Consensus 6 I~L~S~d~----~~Ld~~~~~I~~~~k~~g~~~ 34 (102)
T PRK12271 6 IRLSSTNP----EDLDEVCDQIKEIAEKTGVDM 34 (102)
T ss_pred EEEEeCCH----HHHHHHHHHHHHHHHHcCCeE
Confidence 44556665 689999999999999877644
No 66
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=25.40 E-value=57 Score=18.42 Aligned_cols=14 Identities=21% Similarity=0.534 Sum_probs=12.0
Q ss_pred HHHHHHHhhcCCeE
Q psy18081 39 DTIKAKIEQLGGVF 52 (82)
Q Consensus 39 e~I~~~I~~~gG~~ 52 (82)
+.++..|+++||.+
T Consensus 22 ~~l~~~i~~~GG~v 35 (78)
T PF00533_consen 22 EELEQLIKKHGGTV 35 (78)
T ss_dssp HHHHHHHHHTTEEE
T ss_pred HHHHHHHHHcCCEE
Confidence 45688999999999
No 67
>cd03805 GT1_ALG2_like This family is most closely related to the GT1 family of glycosyltransferases. ALG2, a 1,3-mannosyltransferase, in yeast catalyzes the mannosylation of Man(2)GlcNAc(2)-dolichol diphosphate and Man(1)GlcNAc(2)-dolichol diphosphate to form Man(3)GlcNAc(2)-dolichol diphosphate. A deficiency of this enzyme causes an abnormal accumulation of Man1GlcNAc2-PP-dolichol and Man2GlcNAc2-PP-dolichol, which is associated with a type of congenital disorders of glycosylation (CDG), designated CDG-Ii, in humans.
Probab=25.09 E-value=78 Score=23.14 Aligned_cols=32 Identities=16% Similarity=0.160 Sum_probs=25.6
Q ss_pred cCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHH
Q psy18081 14 APPLYVMTTVTPEKADGLKALQEAIDTIKAKI 45 (82)
Q Consensus 14 ApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I 45 (82)
..+.+++..-.+++.+|++.|=+|++.+.+..
T Consensus 209 ~~~~~i~~~grl~~~Kg~~~ll~a~~~l~~~~ 240 (392)
T cd03805 209 SGKKTFLSINRFERKKNIALAIEAFAILKDKL 240 (392)
T ss_pred CCceEEEEEeeecccCChHHHHHHHHHHHhhc
Confidence 34467778888999999999999998886643
No 68
>smart00044 CYCc Adenylyl- / guanylyl cyclase, catalytic domain. Present in two copies in mammalian adenylyl cyclases. Eubacterial homologues are known. Two residues (Asn, Arg) are thought to be involved in catalysis. These cyclases have important roles in a diverse range of cellular processes.
Probab=24.78 E-value=1.7e+02 Score=19.76 Aligned_cols=30 Identities=13% Similarity=0.180 Sum_probs=26.3
Q ss_pred eCCHHHHHHHHHHHHHHHHHHHhhcCCeEE
Q psy18081 24 TPEKADGLKALQEAIDTIKAKIEQLGGVFQ 53 (82)
Q Consensus 24 tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~ 53 (82)
..+.++-...|+.-...+.+.|+++||...
T Consensus 53 ~~~~~~~~~~l~~~~~~~~~~i~~~gg~v~ 82 (194)
T smart00044 53 EATPEQVVTLLNDLYSRFDRIIDRHGGYKV 82 (194)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHhcCeEEE
Confidence 467888999999999999999999998754
No 69
>PRK01146 DNA-directed RNA polymerase subunit L; Provisional
Probab=24.47 E-value=1.3e+02 Score=19.15 Aligned_cols=29 Identities=31% Similarity=0.319 Sum_probs=21.0
Q ss_pred EEEeeeCCHHHHHHHHHHHHHHHHHHHhh
Q psy18081 19 VMTTVTPEKADGLKALQEAIDTIKAKIEQ 47 (82)
Q Consensus 19 vltt~tlDK~~Gi~~L~~Aie~I~~~I~~ 47 (82)
.++.+|.+...-.++|.+|++.+.+....
T Consensus 54 ~lrIqt~~~~~p~~al~~a~~~L~~~~~~ 82 (85)
T PRK01146 54 VLKIKTDGGIDPLEALKEAAKRIIDLCDE 82 (85)
T ss_pred EEEEEECCCCCHHHHHHHHHHHHHHHHHH
Confidence 34455555566889999999999887654
No 70
>smart00864 Tubulin Tubulin/FtsZ family, GTPase domain. This domain is found in all tubulin chains, as well as the bacterial FtsZ family of proteins. These proteins are involved in polymer formation. Tubulin is the major component of microtubules, while FtsZ is the polymer-forming protein of bacterial cell division, it is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases, this entry is the GTPase domain. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in bacteria and archaea.
Probab=23.48 E-value=1.6e+02 Score=20.68 Aligned_cols=27 Identities=33% Similarity=0.605 Sum_probs=21.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHhhcCCeE
Q psy18081 26 EKADGLKALQEAIDTIKAKIEQLGGVF 52 (82)
Q Consensus 26 DK~~Gi~~L~~Aie~I~~~I~~~gG~~ 52 (82)
|.+.|=++.++..+.|+..+++..|-+
T Consensus 61 ~~~~g~~~~~~~~~~ir~~le~~d~~~ 87 (192)
T smart00864 61 DPEVGREAAEESLDEIREELEGADGVF 87 (192)
T ss_pred ChHHHHHHHHHHHHHHHHHhcCCCEEE
Confidence 455788999999999999998864433
No 71
>cd03820 GT1_amsD_like This family is most closely related to the GT1 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be responsible for the formation of galactose alpha-1,6 linkages in amylovoran.
Probab=23.17 E-value=2.5e+02 Score=18.98 Aligned_cols=29 Identities=17% Similarity=0.135 Sum_probs=23.7
Q ss_pred CCeEEEEeeeCCHHHHHHHHHHHHHHHHH
Q psy18081 15 PPLYVMTTVTPEKADGLKALQEAIDTIKA 43 (82)
Q Consensus 15 pPlYvltt~tlDK~~Gi~~L~~Aie~I~~ 43 (82)
.+.+++..-...+.+|++.+-+|++.+++
T Consensus 177 ~~~~i~~~g~~~~~K~~~~l~~~~~~l~~ 205 (348)
T cd03820 177 KSKRILAVGRLVPQKGFDLLIEAWAKIAK 205 (348)
T ss_pred CCcEEEEEEeeccccCHHHHHHHHHHHHh
Confidence 34567777788889999999999988865
No 72
>PRK02255 putrescine carbamoyltransferase; Provisional
Probab=23.08 E-value=80 Score=24.89 Aligned_cols=39 Identities=21% Similarity=0.285 Sum_probs=23.8
Q ss_pred cceEEEEecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEEec
Q psy18081 6 MPIKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMA 57 (82)
Q Consensus 6 ~~IkIkLIApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~ 57 (82)
+.++|.+++||-|-+. .+-++.+++..++.||.+.+...
T Consensus 177 ~g~~v~~~~P~~~~~~-------------~~~~~~~~~~~~~~g~~~~~~~d 215 (338)
T PRK02255 177 MGMDFVHFGPKGYQLP-------------EEHLAIAEENCEVSGGSVLVTDD 215 (338)
T ss_pred CCCEEEEECCCccccC-------------HHHHHHHHHHHHhcCCeEEEEcC
Confidence 4578999999998542 11233444555567777765433
No 73
>PF05949 DUF881: Bacterial protein of unknown function (DUF881); InterPro: IPR010273 This family consists of a series of hypothetical bacterial proteins. One of the family members Q45543 from SWISSPROT from Bacillus subtilis is thought to be involved in cell division and sporulation [].; PDB: 3GMG_B.
Probab=22.87 E-value=2.7e+02 Score=19.28 Aligned_cols=45 Identities=22% Similarity=0.388 Sum_probs=30.5
Q ss_pred EEecCCeEEEEeeeCCHHHHHHHHHHHHH---HHHHHHhhcCCeEEEEeceeEe
Q psy18081 11 NLIAPPLYVMTTVTPEKADGLKALQEAID---TIKAKIEQLGGVFQVQMAVSIL 61 (82)
Q Consensus 11 kLIApPlYvltt~tlDK~~Gi~~L~~Aie---~I~~~I~~~gG~~~Vk~~PkvV 61 (82)
+-++|| |++..-.. =+.|..|+. -+.+..+..|-.+.+.....+.
T Consensus 86 ~~i~~P-y~I~AIGd-----p~~L~~al~~~~~~~~~~~~~gi~v~i~~~~~i~ 133 (149)
T PF05949_consen 86 RPISPP-YVIKAIGD-----PETLYSALNIPGGVVDSLRQRGIRVTIEKSDDIT 133 (149)
T ss_dssp EEE-SS-EEEEEES------HHHHHHHHTSTTSCHHHHHCTT-EEEEEEEEEEE
T ss_pred EEccCC-EEEEEEeC-----HHHHHHHHccccHHHHHHHHcCCEEEEEecCeEE
Confidence 567888 99887654 456777877 4566777788888888776554
No 74
>PRK04005 50S ribosomal protein L18e; Provisional
Probab=22.27 E-value=88 Score=21.31 Aligned_cols=16 Identities=44% Similarity=0.553 Sum_probs=12.6
Q ss_pred HHHHHHHhhcCCeEEE
Q psy18081 39 DTIKAKIEQLGGVFQV 54 (82)
Q Consensus 39 e~I~~~I~~~gG~~~V 54 (82)
+.-++.|++.||.+.+
T Consensus 78 k~A~ekIe~aGG~v~~ 93 (111)
T PRK04005 78 ETAKEKIEEAGGKALT 93 (111)
T ss_pred HHHHHHHHHcCCEEEE
Confidence 3467889999999865
No 75
>cd01479 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24
Probab=22.26 E-value=2.3e+02 Score=20.79 Aligned_cols=34 Identities=21% Similarity=0.401 Sum_probs=24.0
Q ss_pred cCCeEEEEeeeCCHHHHHH--HHHHHHHHHHHHHhhcC
Q psy18081 14 APPLYVMTTVTPEKADGLK--ALQEAIDTIKAKIEQLG 49 (82)
Q Consensus 14 ApPlYvltt~tlDK~~Gi~--~L~~Aie~I~~~I~~~g 49 (82)
.||.|+.-.-+.-- .++ .++.+++.|++.|+...
T Consensus 2 ~pp~~~FvIDvs~~--a~~~g~~~~~~~si~~~L~~lp 37 (244)
T cd01479 2 QPAVYVFLIDVSYN--AIKSGLLATACEALLSNLDNLP 37 (244)
T ss_pred CCCEEEEEEEccHH--HHhhChHHHHHHHHHHHHHhcC
Confidence 48888877655432 233 68888999999998744
No 76
>PF05166 YcgL: YcgL domain; InterPro: IPR007840 This family of proteins formerly called DUF709 includes the Escherichia coli gene ycgL. Homologues of YcgL are found in gammaproteobacteria. The structure of this protein shows a novel alpha/beta/alpha sandwich structure []. The proteins in this entry are functionally uncharacterised.; PDB: 2H7A_A.
Probab=22.08 E-value=46 Score=21.35 Aligned_cols=41 Identities=24% Similarity=0.407 Sum_probs=21.2
Q ss_pred ecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEEece
Q psy18081 13 IAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAV 58 (82)
Q Consensus 13 IApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~P 58 (82)
.+.|.+||.. .++++.-+. +.-++.+.+.|++.| |-++|+|
T Consensus 33 fG~p~~vm~l-~L~~~r~La--~~d~~~V~~~l~~~G--fyLQ~PP 73 (74)
T PF05166_consen 33 FGKPQFVMEL-NLTPERKLA--RADAEKVLAALEEQG--FYLQMPP 73 (74)
T ss_dssp H-SEEEEEEE--SSS----S--SS-HHHHHHHHHHTS--EEEE---
T ss_pred cCCCeEEEEe-cCCCCceec--cCCHHHHHHHHHhCC--EEEecCC
Confidence 3578899885 555544333 334566777777776 6678777
No 77
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=21.98 E-value=1.3e+02 Score=18.66 Aligned_cols=19 Identities=32% Similarity=0.461 Sum_probs=14.3
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q psy18081 26 EKADGLKALQEAIDTIKAK 44 (82)
Q Consensus 26 DK~~Gi~~L~~Aie~I~~~ 44 (82)
+.+++++.+++||...++.
T Consensus 56 ~~~~A~~~l~eAi~~Are~ 74 (94)
T PF12862_consen 56 HYEEALQALEEAIRLAREN 74 (94)
T ss_pred CHHHHHHHHHHHHHHHHHH
Confidence 5677888888888876653
No 78
>PLN02390 molybdopterin synthase catalytic subunit
Probab=21.52 E-value=2.2e+02 Score=19.19 Aligned_cols=33 Identities=24% Similarity=0.342 Sum_probs=28.3
Q ss_pred ecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHH
Q psy18081 13 IAPPLYVMTTVTPEKADGLKALQEAIDTIKAKI 45 (82)
Q Consensus 13 IApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I 45 (82)
+.-+..++...+.-+.++++..+.+|+.++...
T Consensus 66 vge~~v~v~v~s~HR~~Af~A~~~~id~lK~~v 98 (111)
T PLN02390 66 VGETSVFVAVSSVHRADALDACKFLIDELKASV 98 (111)
T ss_pred CCCEEEEEEEECCCHHHHHHHHHHHHHHHhhcC
Confidence 456778889999999999999999999998753
No 79
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.51 E-value=1.4e+02 Score=18.71 Aligned_cols=40 Identities=13% Similarity=0.089 Sum_probs=25.8
Q ss_pred HHHHHHHHhhcCCeEEEEeceeEeecccc-chhhhccccCcce
Q psy18081 38 IDTIKAKIEQLGGVFQVQMAVSILLMSMI-QNSQTDLFNSDVI 79 (82)
Q Consensus 38 ie~I~~~I~~~gG~~~Vk~~PkvVse~d~-~~l~~~~~~~~~~ 79 (82)
...+++.++++||++..- .++ -+.+.. ..+...+-..|++
T Consensus 12 ~~~~~~~~~~~G~~~~~h-g~~-~~~~~~~~~l~~~i~~aD~V 52 (97)
T PF10087_consen 12 ERRYKRILEKYGGKLIHH-GRD-GGDEKKASRLPSKIKKADLV 52 (97)
T ss_pred HHHHHHHHHHcCCEEEEE-ecC-CCCccchhHHHHhcCCCCEE
Confidence 456788899999999887 222 222222 2477777676754
No 80
>PF08651 DASH_Duo1: DASH complex subunit Duo1; InterPro: IPR013960 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 [, ].
Probab=21.28 E-value=55 Score=20.85 Aligned_cols=24 Identities=8% Similarity=0.257 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCeE
Q psy18081 29 DGLKALQEAIDTIKAKIEQLGGVF 52 (82)
Q Consensus 29 ~Gi~~L~~Aie~I~~~I~~~gG~~ 52 (82)
+++.-++.+|+.+.+++++.+|.+
T Consensus 8 ~~Lr~IN~~ie~~~~~L~~a~~~~ 31 (78)
T PF08651_consen 8 EQLRKINPVIEGLIETLRSAKSNM 31 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578889999999999998877654
No 81
>TIGR00658 orni_carb_tr ornithine carbamoyltransferase. Most OTCases are homotrimers, but the homotrimers are organized into dodecamers built from four trimers in at least two species; the catabolic OTCase of Pseudomonas aeruginosa is allosterically regulated, while OTCase of the extreme thermophile Pyrococcus furiosus shows both allostery and thermophily.
Probab=21.27 E-value=1.5e+02 Score=22.89 Aligned_cols=36 Identities=11% Similarity=0.296 Sum_probs=22.7
Q ss_pred cceEEEEecCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEE
Q psy18081 6 MPIKINLIAPPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQV 54 (82)
Q Consensus 6 ~~IkIkLIApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~V 54 (82)
..+.+.+++||.|.+. .+-++.+++.+.+.||++.+
T Consensus 171 ~g~~v~~~~P~~~~~~-------------~~~~~~~~~~~~~~g~~~~~ 206 (304)
T TIGR00658 171 LGMDVVVATPEGYEPD-------------ADIVKKAQEIAKENGGSVEL 206 (304)
T ss_pred cCCEEEEECCchhcCC-------------HHHHHHHHHHHHHcCCeEEE
Confidence 4678999999988543 11234455555666776643
No 82
>PF08416 PTB: Phosphotyrosine-binding domain; InterPro: IPR013625 The phosphotyrosine-binding domain (PTB, also phosphotyrosine-interaction or PI domain) of tensin tends to be found at the C terminus of a protein. Tensin is a multi-domain protein that binds to actin filaments and functions as a focal-adhesion molecule (focal adhesions are regions of plasma membrane through which cells attach to the extracellular matrix). Human tensin has actin-binding sites, an SH2 (IPR000980 from INTERPRO) domain and a region similar to the tumour suppressor PTEN []. The PTB domain interacts with the cytoplasmic tails of beta integrin by binding to an NPXY motif []. ; GO: 0005515 protein binding; PDB: 3HQC_A 2DKQ_A 2LOZ_A 2CY5_A 2CY4_A 2GJY_A 1WVH_A.
Probab=21.22 E-value=98 Score=21.06 Aligned_cols=47 Identities=23% Similarity=0.282 Sum_probs=29.7
Q ss_pred EEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCe------EEEEeceeEeeccccc
Q psy18081 20 MTTVTPEKADGLKALQEAIDTIKAKIEQLGGV------FQVQMAVSILLMSMIQ 67 (82)
Q Consensus 20 ltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~------~~Vk~~PkvVse~d~~ 67 (82)
+.|-.+|+..|+..+++|++.+. ..++.|+- |+|...=-.++|.+.+
T Consensus 7 L~T~~~e~~~g~~~v~d~i~~l~-~l~~~~~~w~q~~~lkV~~~~v~L~D~~~k 59 (131)
T PF08416_consen 7 LATFDVESLTGPQAVEDAIRRLK-LLEAKGRIWPQEMHLKVSDQGVTLTDIETK 59 (131)
T ss_dssp EEEEEECTTSCCCHHHHHHHHHH-HHHCSS-SS-EEEEEEEETTEEEEEESSTS
T ss_pred EEEEEcCCCcchhhHHHHHHHHH-hhccCCCcccEEEEEEEeCCeEEEEECccc
Confidence 45667788889999999999873 44555554 5555444444454443
No 83
>PF09702 Cas_Csa5: CRISPR-associated protein (Cas_Csa5); InterPro: IPR010157 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a minor family of Cas protein found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus.
Probab=21.21 E-value=1.5e+02 Score=20.44 Aligned_cols=40 Identities=10% Similarity=-0.095 Sum_probs=29.1
Q ss_pred eeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEEeceeEee
Q psy18081 23 VTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQMAVSILL 62 (82)
Q Consensus 23 ~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~PkvVs 62 (82)
+.+.++.-..+|.+|+..++..+++..=+-.+.+.++-+.
T Consensus 16 NALs~E~v~~aL~dAlR~~~s~~~s~ei~~~~~~~~~~y~ 55 (105)
T PF09702_consen 16 NALSPEAVEVALYDALRIFRSIIDSAEIDKSQVEEGRRYI 55 (105)
T ss_pred hhcCHHHHHHHHHHHHHHHHHHhccccccccccccCcccc
Confidence 5678999999999999999988876533332333666555
No 84
>cd02749 Macro Macro domain, a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes.
Probab=21.12 E-value=1.5e+02 Score=19.10 Aligned_cols=41 Identities=17% Similarity=0.350 Sum_probs=28.0
Q ss_pred CeEEEEeeeCCH-----HHHHHHHHHHHHHHHHHHhhcCCeEEEEec
Q psy18081 16 PLYVMTTVTPEK-----ADGLKALQEAIDTIKAKIEQLGGVFQVQMA 57 (82)
Q Consensus 16 PlYvltt~tlDK-----~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~ 57 (82)
+.|++-+-+... ....+.|++|++.+-+.+... |--.|.++
T Consensus 73 ~~~vih~~~p~~~~~~~~~~~~~l~~a~~~~L~~~~~~-~~~sIa~P 118 (147)
T cd02749 73 AKYLIHIVGPKYNQGNNKAAFELLKNAYENCLKEAEEK-GIKSIAFP 118 (147)
T ss_pred CCEEEEeCCCCCCCCCCchHHHHHHHHHHHHHHHHHHc-CCCEEEEC
Confidence 677777666543 346889999999998888765 33345544
No 85
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=20.99 E-value=88 Score=21.11 Aligned_cols=16 Identities=56% Similarity=0.927 Sum_probs=12.2
Q ss_pred HHHHHHHHhhcCCeEE
Q psy18081 38 IDTIKAKIEQLGGVFQ 53 (82)
Q Consensus 38 ie~I~~~I~~~gG~~~ 53 (82)
.+.|++.|++.||...
T Consensus 60 ~d~i~~~Ie~~Gg~IH 75 (95)
T PF02680_consen 60 FDEIKEAIEELGGVIH 75 (95)
T ss_dssp HHHHHHHHHHTT-EEE
T ss_pred HHHHHHHHHHcCCeEE
Confidence 3678899999999875
No 86
>PF04811 Sec23_trunk: Sec23/Sec24 trunk domain; InterPro: IPR006896 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 (IPR006895 from INTERPRO), an alpha/beta trunk domain, an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes the Sec23/24 alpha/beta trunk domain, which is formed from a single, approximately 250-residue segment plugged into the beta-barrel between strands beta-1 and beta-19. The trunk has an alpha/beta fold with a vWA topology, and it forms the dimer interface, primarily involving strand beta-14 on Sec23 and Sec24; in addition, the trunk domain of Sec23 contacts Sar1.; GO: 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EGD_A 2NUP_A 3EG9_A 3EFO_A 3EGX_A 2NUT_A 1PD0_A 1PD1_A 1M2V_B 1PCX_A ....
Probab=20.98 E-value=2.1e+02 Score=20.57 Aligned_cols=36 Identities=28% Similarity=0.444 Sum_probs=24.4
Q ss_pred cCCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcC
Q psy18081 14 APPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLG 49 (82)
Q Consensus 14 ApPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~g 49 (82)
.||.|+.-.-+.=-.-.-..++.+++.|++.|+...
T Consensus 2 ~pp~y~FvID~s~~av~~g~~~~~~~sl~~~l~~l~ 37 (243)
T PF04811_consen 2 QPPVYVFVIDVSYEAVQSGLLQSLIESLKSALDSLP 37 (243)
T ss_dssp S--EEEEEEE-SHHHHHHTHHHHHHHHHHHHGCTSS
T ss_pred CCCEEEEEEECchhhhhccHHHHHHHHHHHHHHhcc
Confidence 488998877766443344578889999999998866
No 87
>KOG0177|consensus
Probab=20.82 E-value=1.7e+02 Score=22.28 Aligned_cols=32 Identities=13% Similarity=0.126 Sum_probs=23.2
Q ss_pred eCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEE
Q psy18081 24 TPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ 55 (82)
Q Consensus 24 tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk 55 (82)
...-++|+++|++|+..+++..--.=-.|.|+
T Consensus 150 dmt~eea~~lmkKCv~El~kRlvin~~~f~v~ 181 (200)
T KOG0177|consen 150 DMTIEEALDLMKKCVLELKKRLVINLPGFIVK 181 (200)
T ss_pred CCCHHHHHHHHHHHHHHHHHhcccCCCCcEEE
Confidence 34568999999999999998765433334443
No 88
>PF02112 PDEase_II: cAMP phosphodiesterases class-II; InterPro: IPR000396 Cyclic-AMP phosphodiesterase (3.1.4.17 from EC) (PDE) catalyses the hydrolysis of cAMP to the corresponding nucleoside 5' monophosphate. On the basis of sequence similarity, most PDEs can be grouped together [], but some enzymes lie apart from the main family and represent a second distinct class [] that includes PDEs from Dictyostelium and yeast. This entry contains class-II cyclic-AMP phosphodiesterases.; GO: 0004115 3',5'-cyclic-AMP phosphodiesterase activity, 0006198 cAMP catabolic process
Probab=20.57 E-value=41 Score=26.75 Aligned_cols=15 Identities=40% Similarity=0.992 Sum_probs=11.8
Q ss_pred ccchhhhccccCccee
Q psy18081 65 MIQNSQTDLFNSDVIW 80 (82)
Q Consensus 65 d~~~l~~~~~~~~~~~ 80 (82)
=-+-|++|+|| |+||
T Consensus 119 ti~alk~hiFN-~~iW 133 (335)
T PF02112_consen 119 TIEALKNHIFN-DIIW 133 (335)
T ss_pred HHHHHHHcccC-CccC
Confidence 34678999998 6788
No 89
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=20.53 E-value=1.6e+02 Score=17.59 Aligned_cols=29 Identities=17% Similarity=0.297 Sum_probs=19.0
Q ss_pred eEEEEeeeCCHHHHHHHHHHHHHHHHHHH
Q psy18081 17 LYVMTTVTPEKADGLKALQEAIDTIKAKI 45 (82)
Q Consensus 17 lYvltt~tlDK~~Gi~~L~~Aie~I~~~I 45 (82)
.|++|..|.|+..=++.+-+.+..-.-.|
T Consensus 1 ~~iltv~g~Dr~GiVa~vs~~la~~g~nI 29 (77)
T cd04893 1 HLVISALGTDRPGILNELTRAVSESGCNI 29 (77)
T ss_pred CEEEEEEeCCCChHHHHHHHHHHHcCCCE
Confidence 37899999999765555555554433333
No 90
>PF13250 DUF4041: Domain of unknown function (DUF4041)
Probab=20.53 E-value=1.9e+02 Score=17.26 Aligned_cols=29 Identities=14% Similarity=0.375 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHhhcCCeEEEEece
Q psy18081 30 GLKALQEAIDTIKAKIEQLGGVFQVQMAV 58 (82)
Q Consensus 30 Gi~~L~~Aie~I~~~I~~~gG~~~Vk~~P 58 (82)
-+..+++.|+..-+.|.+.|..+.+...|
T Consensus 22 Ni~~~~~rI~ksf~~iNkl~~~~~i~I~~ 50 (56)
T PF13250_consen 22 NIDTMEKRIEKSFEQINKLGKTNNIRISP 50 (56)
T ss_pred hHHHHHHHHHHHHHHHHHcCccceeeECH
Confidence 46788899999999999999988887654
No 91
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=20.37 E-value=1.1e+02 Score=16.47 Aligned_cols=22 Identities=32% Similarity=0.474 Sum_probs=18.0
Q ss_pred HHHHHHHHHhhcCCeEEEEece
Q psy18081 37 AIDTIKAKIEQLGGVFQVQMAV 58 (82)
Q Consensus 37 Aie~I~~~I~~~gG~~~Vk~~P 58 (82)
..+.+++.|.+.||.+.....+
T Consensus 18 ~~~~l~~~i~~~Gg~~~~~~~~ 39 (80)
T smart00292 18 ERDELKELIEALGGKVTSSLSS 39 (80)
T ss_pred cHHHHHHHHHHcCCEEecccCc
Confidence 4567889999999999877665
No 92
>COG4274 Uncharacterized conserved protein [Function unknown]
Probab=20.32 E-value=1.4e+02 Score=20.61 Aligned_cols=37 Identities=30% Similarity=0.513 Sum_probs=25.4
Q ss_pred EEEEeeeCCHHHHHHHHHHH---HHHHHHHHhhcCCeEEEEe
Q psy18081 18 YVMTTVTPEKADGLKALQEA---IDTIKAKIEQLGGVFQVQM 56 (82)
Q Consensus 18 Yvltt~tlDK~~Gi~~L~~A---ie~I~~~I~~~gG~~~Vk~ 56 (82)
|++-.+-. ++|++-|++- .++.+...++.||+++=.+
T Consensus 11 yvvL~n~T--d~Gaktlke~p~R~~av~~~les~G~k~~~~y 50 (104)
T COG4274 11 YVVLSNFT--DQGAKTLKETPKRAAAVRALLESMGGKVKEQY 50 (104)
T ss_pred hhhhhhcc--HhHHHHHhhCHHHHHHHHHHHHHcCcEEEEEE
Confidence 44433333 4588888764 5677888999999987654
No 93
>COG0643 CheA Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]
Probab=20.08 E-value=1.1e+02 Score=26.87 Aligned_cols=21 Identities=43% Similarity=0.683 Sum_probs=17.0
Q ss_pred HHHHHHHHhhcCCeEEEEece
Q psy18081 38 IDTIKAKIEQLGGVFQVQMAV 58 (82)
Q Consensus 38 ie~I~~~I~~~gG~~~Vk~~P 58 (82)
++++|..|++.||...|...|
T Consensus 541 MDVVk~~I~~LgG~I~V~S~~ 561 (716)
T COG0643 541 MDVVKTNIEQLGGSISVSSEP 561 (716)
T ss_pred HHHHHHHHHHcCCEEEEEecC
Confidence 566788888889999988776
No 94
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=20.06 E-value=2e+02 Score=18.19 Aligned_cols=25 Identities=24% Similarity=0.310 Sum_probs=19.8
Q ss_pred eEEEEeeeCCHHHHHHHHHHHHHHHHHHHhh
Q psy18081 17 LYVMTTVTPEKADGLKALQEAIDTIKAKIEQ 47 (82)
Q Consensus 17 lYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~ 47 (82)
.|.|| ++|-+.|+++.+..++.++.
T Consensus 70 ~y~iT------~~Gr~~l~~~~~~~~~~~~~ 94 (100)
T TIGR03433 70 FYRLT------AAGRKQLAAETESWARLSAA 94 (100)
T ss_pred EEEEC------HHHHHHHHHHHHHHHHHHHH
Confidence 47777 88999999998888776654
No 95
>cd01569 PBEF_like pre-B-cell colony-enhancing factor (PBEF)-like. The mammalian members of this group of nicotinate phosphoribosyltransferases (NAPRTases) were originally identified as genes whose expression is upregulated upon activation in lymphoid cells. In general, nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis.
Probab=20.05 E-value=2.8e+02 Score=22.91 Aligned_cols=38 Identities=16% Similarity=0.177 Sum_probs=29.3
Q ss_pred CCeEEEEeeeCCHHHHHHHHHHHHHHHHHHHhhcCCeEEEE
Q psy18081 15 PPLYVMTTVTPEKADGLKALQEAIDTIKAKIEQLGGVFQVQ 55 (82)
Q Consensus 15 pPlYvltt~tlDK~~Gi~~L~~Aie~I~~~I~~~gG~~~Vk 55 (82)
++.+.+-.-|.|=-.+ ++.+++..++.|.+.||.+.|+
T Consensus 253 ~~~~~lv~DTYD~~~~---~~~~~~~lk~~i~~~g~~lviR 290 (407)
T cd01569 253 PGIVSVVSDSYDFWNA---LTLWGPRLKDEILARGGTLVIR 290 (407)
T ss_pred CCcEEEEecCccHHHH---HHHHHHHHHHHHHhcCCcEEEE
Confidence 4467777888885444 7789999999999999998554
Done!