Query 016200
Match_columns 393
No_of_seqs 19 out of 21
Neff 1.9
Searched_HMMs 46136
Date Fri Mar 29 04:42:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016200.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016200hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3937 Uncharacterized conser 93.9 0.33 7.3E-06 42.1 7.9 76 231-315 19-108 (108)
2 PF02060 ISK_Channel: Slow vol 86.3 0.97 2.1E-05 40.3 4.0 34 3-39 40-73 (129)
3 TIGR01837 PHA_granule_1 poly(h 74.1 51 0.0011 28.0 10.1 83 231-318 17-117 (118)
4 PF04799 Fzo_mitofusin: fzo-li 70.8 8 0.00017 35.7 4.9 78 227-332 65-148 (171)
5 cd07596 BAR_SNX The Bin/Amphip 70.6 56 0.0012 27.6 9.6 65 259-323 95-171 (218)
6 TIGR01834 PHA_synth_III_E poly 69.0 10 0.00022 37.9 5.5 54 259-319 258-311 (320)
7 COG5521 Predicted integral mem 66.1 6.3 0.00014 38.9 3.4 40 6-45 175-218 (275)
8 PRK13182 racA polar chromosome 60.8 37 0.00079 30.9 7.1 79 243-332 46-127 (175)
9 PF04380 BMFP: Membrane fusoge 57.1 55 0.0012 26.1 6.7 62 255-318 7-78 (79)
10 PRK10755 sensor protein BasS/P 53.9 39 0.00085 30.6 6.1 39 7-45 59-97 (356)
11 PF06367 Drf_FH3: Diaphanous F 53.8 68 0.0015 27.7 7.3 82 259-347 44-148 (197)
12 TIGR02736 cbb3_Q_epsi cytochro 53.6 20 0.00044 28.4 3.6 32 15-46 3-39 (56)
13 PRK11832 putative DNA-binding 53.5 16 0.00035 34.3 3.6 42 295-336 135-176 (207)
14 PF04977 DivIC: Septum formati 50.7 55 0.0012 24.2 5.5 42 296-337 16-57 (80)
15 PF10211 Ax_dynein_light: Axon 50.5 1.9E+02 0.0042 26.3 9.9 76 238-320 64-143 (189)
16 PF02403 Seryl_tRNA_N: Seryl-t 48.2 1.4E+02 0.0031 23.9 9.4 83 237-320 6-90 (108)
17 PF12273 RCR: Chitin synthesis 48.1 17 0.00037 30.5 2.7 10 27-36 16-25 (130)
18 PF09032 Siah-Interact_N: Siah 47.4 46 0.00099 27.4 4.9 39 280-318 8-47 (79)
19 PF15079 DUF4546: Domain of un 47.3 77 0.0017 30.3 7.0 65 260-332 50-114 (205)
20 PF12729 4HB_MCP_1: Four helix 47.1 40 0.00087 26.4 4.5 26 13-38 9-34 (181)
21 PF09712 PHA_synth_III_E: Poly 46.7 75 0.0016 30.8 7.1 53 259-318 241-293 (293)
22 PF06103 DUF948: Bacterial pro 46.6 53 0.0012 25.7 5.1 26 10-35 4-29 (90)
23 PF05115 PetL: Cytochrome B6-F 45.8 36 0.00078 24.2 3.6 26 10-35 1-29 (31)
24 CHL00106 petL cytochrome b6/f 45.5 32 0.0007 24.5 3.3 26 10-35 1-29 (31)
25 PF13933 HRXXH: Putative pepti 44.5 21 0.00046 34.8 3.0 28 222-249 42-70 (245)
26 TIGR02229 caa3_sub_IV caa(3)-t 44.4 30 0.00064 29.0 3.5 23 6-28 65-87 (92)
27 PRK09835 sensor kinase CusS; P 43.5 69 0.0015 29.9 6.1 36 12-47 188-223 (482)
28 PF05119 Terminase_4: Phage te 41.9 19 0.0004 28.0 1.9 62 281-342 6-69 (100)
29 TIGR02894 DNA_bind_RsfA transc 41.5 1.9E+02 0.0041 26.9 8.4 70 251-343 77-148 (161)
30 PF05816 TelA: Toxic anion res 40.6 3.5E+02 0.0076 26.3 10.6 118 227-348 17-144 (333)
31 PF02899 Phage_int_SAM_1: Phag 40.1 89 0.0019 22.7 5.1 38 251-292 41-78 (84)
32 smart00271 DnaJ DnaJ molecular 39.8 99 0.0021 21.6 5.2 44 232-275 12-57 (60)
33 TIGR02444 conserved hypothetic 38.6 1.7E+02 0.0036 25.2 7.3 66 249-317 43-108 (116)
34 PF10168 Nup88: Nuclear pore c 38.5 1.4E+02 0.003 32.6 8.2 76 266-341 556-639 (717)
35 PF06305 DUF1049: Protein of u 37.8 1.1E+02 0.0025 22.4 5.4 14 6-19 18-31 (68)
36 PF06266 HrpF: HrpF protein; 37.6 2.1E+02 0.0046 23.8 7.3 62 229-292 2-71 (74)
37 cd06257 DnaJ DnaJ domain or J- 37.4 1E+02 0.0022 21.0 4.9 25 231-255 10-34 (55)
38 PF00615 RGS: Regulator of G p 36.9 1.7E+02 0.0038 21.6 7.2 76 231-339 43-118 (118)
39 TIGR01870 cas_TM1810_Csm2 CRIS 35.9 2.4E+02 0.0053 23.0 7.8 67 254-320 1-74 (97)
40 PF15086 UPF0542: Uncharacteri 35.8 85 0.0018 26.2 4.8 28 14-41 25-52 (74)
41 TIGR02209 ftsL_broad cell divi 35.2 67 0.0014 24.5 3.9 36 299-334 40-75 (85)
42 PRK11637 AmiB activator; Provi 34.9 2.7E+02 0.0059 27.5 9.0 60 226-289 37-96 (428)
43 PF12606 RELT: Tumour necrosis 34.6 49 0.0011 25.3 3.1 22 11-32 4-25 (50)
44 PF00558 Vpu: Vpu protein; In 34.6 47 0.001 27.7 3.2 32 17-48 16-47 (81)
45 PRK09039 hypothetical protein; 34.3 78 0.0017 31.1 5.2 22 11-32 26-47 (343)
46 TIGR02680 conserved hypothetic 33.5 5.4E+02 0.012 29.9 12.1 46 298-343 291-336 (1353)
47 cd03572 ENTH_epsin_related ENT 33.5 1.1E+02 0.0023 26.7 5.4 57 241-304 21-78 (122)
48 PRK11637 AmiB activator; Provi 33.5 4.9E+02 0.011 25.8 11.8 71 256-326 172-248 (428)
49 PF09006 Surfac_D-trimer: Lung 33.5 69 0.0015 24.6 3.7 25 300-324 2-26 (46)
50 PF05399 EVI2A: Ectropic viral 33.4 62 0.0013 31.5 4.3 26 6-31 129-156 (227)
51 PRK04778 septation ring format 32.7 81 0.0018 32.6 5.2 32 17-48 11-42 (569)
52 PHA02562 46 endonuclease subun 32.7 4.7E+02 0.01 26.0 10.2 40 298-338 380-419 (562)
53 PF08671 SinI: Anti-repressor 31.0 49 0.0011 23.1 2.3 24 242-265 5-28 (30)
54 PF05565 Sipho_Gp157: Siphovir 30.4 2.6E+02 0.0057 24.6 7.3 77 237-317 5-81 (162)
55 PHA03030 hypothetical protein; 30.4 38 0.00083 30.1 2.2 20 8-27 4-23 (122)
56 PF13706 PepSY_TM_3: PepSY-ass 30.3 89 0.0019 21.8 3.6 27 9-35 10-36 (37)
57 PF10046 BLOC1_2: Biogenesis o 30.2 3.1E+02 0.0067 22.5 8.7 67 239-324 20-86 (99)
58 PF09079 Cdc6_C: CDC6, C termi 29.7 95 0.0021 23.8 4.0 35 233-267 16-50 (85)
59 cd01324 cbb3_Oxidase_CcoQ Cyto 29.4 1.1E+02 0.0024 22.8 4.2 32 1-32 1-32 (48)
60 PF04899 MbeD_MobD: MbeD/MobD 28.8 2.2E+02 0.0047 23.0 6.0 39 279-317 25-69 (70)
61 PF04277 OAD_gamma: Oxaloaceta 27.9 1.2E+02 0.0026 23.2 4.2 14 13-26 13-26 (79)
62 PF09278 MerR-DNA-bind: MerR, 27.0 2.4E+02 0.0053 20.3 5.7 20 244-263 5-24 (65)
63 PF13010 pRN1_helical: Primase 26.8 28 0.00061 31.6 0.7 19 94-112 97-119 (135)
64 PF04977 DivIC: Septum formati 26.4 1.4E+02 0.0031 21.9 4.4 37 297-333 31-68 (80)
65 PF05597 Phasin: Poly(hydroxya 26.3 4.6E+02 0.0099 23.2 9.3 54 264-317 72-129 (132)
66 TIGR01386 cztS_silS_copS heavy 26.2 1.9E+02 0.0042 26.5 6.0 30 18-47 173-202 (457)
67 PF03908 Sec20: Sec20; InterP 25.9 67 0.0014 25.6 2.7 17 17-33 75-91 (92)
68 PF05667 DUF812: Protein of un 25.8 8.7E+02 0.019 26.3 11.4 98 236-333 422-531 (594)
69 KOG1666 V-SNARE [Intracellular 25.5 1.2E+02 0.0026 29.5 4.6 64 236-299 135-198 (220)
70 PF07200 Mod_r: Modifier of ru 25.4 1.8E+02 0.0039 24.5 5.2 21 365-385 122-144 (150)
71 COG3352 FlaC Putative archaeal 25.2 2.6E+02 0.0055 26.2 6.5 68 256-323 74-141 (157)
72 PRK09966 putative inner membra 25.1 2.2E+02 0.0047 26.7 6.2 15 38-52 50-64 (407)
73 PF09094 DUF1925: Domain of un 25.0 59 0.0013 27.1 2.2 39 335-383 16-54 (80)
74 KOG4687 Uncharacterized coiled 24.6 2.8E+02 0.0061 28.6 7.2 115 257-375 170-293 (389)
75 PF04683 Proteasom_Rpn13: Prot 24.0 26 0.00056 28.4 0.0 16 160-175 54-69 (85)
76 KOG1962 B-cell receptor-associ 23.9 2.1E+02 0.0045 27.6 5.9 32 297-331 179-210 (216)
77 TIGR02135 phoU_full phosphate 23.9 4E+02 0.0087 22.2 7.0 57 262-322 3-59 (212)
78 TIGR01558 sm_term_P27 phage te 23.7 44 0.00096 27.5 1.3 35 290-324 26-60 (116)
79 PF00226 DnaJ: DnaJ domain; I 23.5 2.8E+02 0.0061 19.8 5.3 45 231-275 10-56 (64)
80 PF00672 HAMP: HAMP domain; I 23.3 71 0.0015 22.6 2.2 24 22-45 12-35 (70)
81 PLN02302 ent-kaurenoic acid ox 23.3 1.5E+02 0.0033 28.3 4.9 29 5-33 4-32 (490)
82 PF05103 DivIVA: DivIVA protei 23.2 1.2E+02 0.0027 24.4 3.8 51 252-331 16-66 (131)
83 PRK11677 hypothetical protein; 23.1 1E+02 0.0023 27.3 3.5 42 7-48 1-53 (134)
84 cd04785 HTH_CadR-PbrR-like Hel 22.9 2.7E+02 0.006 23.2 5.8 23 244-266 48-70 (126)
85 PTZ00420 coronin; Provisional 22.8 44 0.00095 35.2 1.4 19 65-83 533-551 (568)
86 COG4864 Uncharacterized protei 22.8 83 0.0018 31.5 3.1 22 5-26 3-24 (328)
87 PF09451 ATG27: Autophagy-rela 22.8 61 0.0013 30.5 2.2 23 11-33 206-228 (268)
88 PF07028 DUF1319: Protein of u 22.5 2.8E+02 0.0062 24.9 6.1 44 272-320 40-83 (126)
89 PF06305 DUF1049: Protein of u 22.5 2.2E+02 0.0047 20.9 4.6 33 6-38 22-54 (68)
90 PF08514 STAG: STAG domain ; 22.2 4.9E+02 0.011 22.1 8.8 32 222-254 3-37 (118)
91 smart00721 BAR BAR domain. 22.1 4E+02 0.0086 23.1 6.9 57 280-342 6-66 (239)
92 PRK06718 precorrin-2 dehydroge 22.0 5.1E+02 0.011 23.3 7.8 51 230-293 132-182 (202)
93 PHA02849 putative transmembran 21.6 2.3E+02 0.005 24.1 5.0 22 10-31 16-37 (82)
94 PRK04778 septation ring format 21.3 3.2E+02 0.007 28.4 7.1 16 24-39 21-36 (569)
95 PF12999 PRKCSH-like: Glucosid 21.3 1.6E+02 0.0034 27.5 4.5 47 270-317 127-173 (176)
96 PF13801 Metal_resist: Heavy-m 21.3 3.7E+02 0.0079 20.3 8.6 69 251-319 39-109 (125)
97 cd08915 V_Alix_like Protein-in 21.2 6.8E+02 0.015 24.0 8.8 69 256-324 192-277 (342)
98 PF14584 DUF4446: Protein of u 20.9 2.2E+02 0.0048 25.5 5.2 26 24-51 15-40 (151)
99 PF11932 DUF3450: Protein of u 20.9 6.7E+02 0.014 23.1 9.4 67 237-307 53-119 (251)
100 PF07172 GRP: Glycine rich pro 20.8 89 0.0019 26.1 2.5 15 16-30 6-20 (95)
101 PRK09470 cpxA two-component se 20.8 3.2E+02 0.0069 25.3 6.3 26 22-47 179-204 (461)
102 PF06692 MNSV_P7B: Melon necro 20.7 99 0.0021 25.0 2.6 17 6-22 14-30 (61)
103 PF00674 DUP: DUP family; Int 20.7 1.3E+02 0.0029 24.6 3.5 27 4-30 6-32 (108)
104 PF01445 SH: Viral small hydro 20.5 2.8E+02 0.006 22.3 5.0 31 8-38 11-41 (57)
105 PF10066 DUF2304: Uncharacteri 20.1 2.8E+02 0.006 23.1 5.3 17 22-38 76-92 (115)
106 COG4537 ComGC Competence prote 20.1 81 0.0018 27.8 2.2 15 7-21 19-33 (107)
107 PF09125 COX2-transmemb: Cytoc 20.0 1.5E+02 0.0032 22.2 3.2 22 5-26 15-36 (38)
108 PF11337 DUF3139: Protein of u 20.0 2.6E+02 0.0057 22.1 4.9 38 6-43 8-49 (85)
109 PRK05886 yajC preprotein trans 20.0 2.1E+02 0.0045 24.8 4.6 16 95-110 63-78 (109)
No 1
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=93.93 E-value=0.33 Score=42.08 Aligned_cols=76 Identities=33% Similarity=0.526 Sum_probs=58.3
Q ss_pred chhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHH----HHHHHhhhhhhhhhHHHHHHHHhhcCC----------c
Q 016200 231 GSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQ----AREELEDKSETIKRKFSIQKALLSKAD----------R 296 (393)
Q Consensus 231 ~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVd----ARnEL~~KSE~iqRkftI~KALLskad----------R 296 (393)
...+--+.+..-|+||+ -..+|..|-.+|..-|+. ++.++-.| ++|++.+ ||++.. +
T Consensus 19 ~a~~~ek~~klvDelVk---kGeln~eEak~~vddl~~q~k~~~~e~e~K---~~r~i~~---ml~~~~~~r~~~~~~l~ 89 (108)
T COG3937 19 AAETAEKVQKLVDELVK---KGELNAEEAKRFVDDLLRQAKEAQGELEEK---IPRKIEE---MLSDLEVARQSEMDELT 89 (108)
T ss_pred HHHHHHHHHHHHHHHHH---cCCCCHHHHHHHHHHHHHHHHHHhhhHHHh---hhHHHHH---HHhhccccccchHHHHH
Confidence 45677888899999986 568999999999888774 55566655 8999877 455433 6
Q ss_pred chHHHHHHHHHHHHHHHHh
Q 016200 297 SSIDRLRQQIYNLEKQQRR 315 (393)
Q Consensus 297 SS~DRL~qQIykLE~EqkR 315 (393)
+.+|+|.+||.+||.+++|
T Consensus 90 ~rvd~Lerqv~~Lenk~kr 108 (108)
T COG3937 90 ERVDALERQVADLENKLKR 108 (108)
T ss_pred HHHHHHHHHHHHHHHHhcC
Confidence 7788888888888888765
No 2
>PF02060 ISK_Channel: Slow voltage-gated potassium channel; InterPro: IPR000369 Potassium channels are the most diverse group of the ion channel family [, ]. They are important in shaping the action potential, and in neuronal excitability and plasticity []. The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups []: the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers []. In eukaryotic cells, K+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes []. In prokaryotic cells, they play a role in the maintenance of ionic homeostasis []. All K+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K+ channels; and three types of calcium (Ca)-activated K+ channels (BK, IK and SK) []. The 2TM domain family comprises inward-rectifying K+ channels. In addition, there are K+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K+ selective leak channels. Two types of beta subunit (KCNE and KCNAB) are presently known to associate with voltage-gated alpha subunits (Kv, KCNQ and eag-like). However, not all combinations of alpha and beta subunits are possible. The KCNE family of K+ channel subunits are membrane glycoproteins that possess a single transmembrane (TM) domain. They share no structural relationship with the alpha subunit proteins, which possess pore forming domains. The subunits appear to have a regulatory function, modulating the kinetics and voltage dependence of the alpha subunits of voltage-dependent K+ channels. KCNE subunits are formed from short polypeptides of ~130 amino acids, and are divided into five subfamilies: KCNE1 (MinK/IsK), KCNE2 (MiRP1), KCNE3 (MiRP2), KCNE4 (MiRP3) and KCNE1L (AMMECR2). ; GO: 0005249 voltage-gated potassium channel activity, 0006811 ion transport, 0016020 membrane; PDB: 2K21_A.
Probab=86.33 E-value=0.97 Score=40.33 Aligned_cols=34 Identities=38% Similarity=0.788 Sum_probs=25.1
Q ss_pred cchhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 016200 3 ENNLMLFMLLVISFFFLTIFFTVTLFLTYKKIKRLQE 39 (393)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 (393)
.+|-.+++|+|++|| -||++.++|.|-+-||+..
T Consensus 40 ~~~~~lYIL~vmgfF---gff~~gImlsyvRSKK~E~ 73 (129)
T PF02060_consen 40 DDNEYLYILVVMGFF---GFFTVGIMLSYVRSKKREH 73 (129)
T ss_dssp -SSTT-HHHHHHHHH---HHHHHHHHHHHHHHHHH--
T ss_pred CCceeehHHHHHHHH---HHHHHHHHHHHHHHhhhcc
Confidence 456678888888887 4788999999999988764
No 3
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=74.10 E-value=51 Score=27.98 Aligned_cols=83 Identities=24% Similarity=0.313 Sum_probs=58.6
Q ss_pred chhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHH-HHHHhhhhhh---------------hhhHHHHHHHH--hh
Q 016200 231 GSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQA-REELEDKSET---------------IKRKFSIQKAL--LS 292 (393)
Q Consensus 231 ~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVdA-RnEL~~KSE~---------------iqRkftI~KAL--Ls 292 (393)
.+.+|-++.+.+|+||+- ..++-.+-..|++-+++. +.++.++.+- +.++ |.++| |.
T Consensus 17 ~a~~~ek~~k~~~~LVkk---Ge~~~ee~k~~~~e~~~~~~e~~~~~~~~~~~~~~~~~~~le~~~~~~--v~~~L~~lg 91 (118)
T TIGR01837 17 LARVQEEGSKFFNRLVKE---GELAEKRGQKRFDESVDAAREEVKTALEQTRDQVQRNWDKLEKAFDER--VEQALNRLN 91 (118)
T ss_pred HHHHHHHHHHHHHHHHHh---ccccHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhhHHHHHHHHHHH--HHHHHHHcC
Confidence 356789999999999974 567888999999888753 3334333322 2222 33333 22
Q ss_pred cCCcchHHHHHHHHHHHHHHHHhhhh
Q 016200 293 KADRSSIDRLRQQIYNLEKQQRRLEE 318 (393)
Q Consensus 293 kadRSS~DRL~qQIykLE~EqkRLek 318 (393)
-+.|.-++.|...|+.||.+..+|+.
T Consensus 92 ~~tk~ev~~L~~RI~~Le~~l~~l~~ 117 (118)
T TIGR01837 92 IPSREEIEALSAKIEQLAVQVEELRR 117 (118)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 36689999999999999999988864
No 4
>PF04799 Fzo_mitofusin: fzo-like conserved region; InterPro: IPR006884 This entry represents the heptad repeat domain which is conserved at the C terminus of Fzo/mitofusion family of GTPases. Fzo is a mediator of mitochondrial fusion during spermatogenesis []. This conserved region is also found in the human mitofusin protein []. This domain forms a dimeric antiparallel coiled coil structure, which has been proposed to act as a mitochodrial tether before vesicle fusion [].; GO: 0003924 GTPase activity, 0006184 GTP catabolic process, 0008053 mitochondrial fusion, 0005741 mitochondrial outer membrane, 0016021 integral to membrane; PDB: 1T3J_A.
Probab=70.85 E-value=8 Score=35.74 Aligned_cols=78 Identities=27% Similarity=0.406 Sum_probs=29.1
Q ss_pred ccccchhHHHHHHHHHHHHHhhhccCcchHHHHHHH--HHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHH
Q 016200 227 LTSMGSATQRKIKELYHQLVQSCESNELTLAQVGEF--TKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQ 304 (393)
Q Consensus 227 fTS~~sAtQRRIkeqYDELvran~aK~LTLaQV~eF--~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~q 304 (393)
++=..+|=-|..|+||-+-+. ++| .-+.+| +||=-.+..|| -+-|+|||+
T Consensus 65 LtWT~~AKER~fK~Qfv~hAt----~KL--r~iv~~tsancs~QVqqeL----------------------~~tf~rL~~ 116 (171)
T PF04799_consen 65 LTWTNKAKERAFKRQFVDHAT----EKL--RLIVSFTSANCSHQVQQEL----------------------SSTFARLCQ 116 (171)
T ss_dssp -------------------------------------------------------------------------HHHHHHH
T ss_pred HhcCchHHHHHHHHHHHHHHH----HHH--HHHHHHHhcchHHHHHHHH----------------------HHHHHHHHH
Confidence 444578888999999976542 222 223333 24433333333 247889999
Q ss_pred HHHH----HHHHHHhhhhhHHHHHHHHHHhcc
Q 016200 305 QIYN----LEKQQRRLEEDVYVYNWLQDQLRL 332 (393)
Q Consensus 305 QIyk----LE~EqkRLekDa~VYN~LQqQLKl 332 (393)
||+. ||.|.++|++.....+.+|..+|.
T Consensus 117 ~Vd~~~~eL~~eI~~L~~~i~~le~~~~~~k~ 148 (171)
T PF04799_consen 117 QVDQTKNELEDEIKQLEKEIQRLEEIQSKSKT 148 (171)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9874 778888999999999888887663
No 5
>cd07596 BAR_SNX The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=70.58 E-value=56 Score=27.57 Aligned_cols=65 Identities=14% Similarity=0.227 Sum_probs=40.0
Q ss_pred HHHHHHhHHHHHH------HHhhhhhhhhhHHHHHHHHhhcC------CcchHHHHHHHHHHHHHHHHhhhhhHHHH
Q 016200 259 VGEFTKCLAQARE------ELEDKSETIKRKFSIQKALLSKA------DRSSIDRLRQQIYNLEKQQRRLEEDVYVY 323 (393)
Q Consensus 259 V~eF~NcLVdARn------EL~~KSE~iqRkftI~KALLska------dRSS~DRL~qQIykLE~EqkRLekDa~VY 323 (393)
+.++..++.-+|+ .++...+.++....=+++=+.+. ++..+++|-++|..+|.+.+.+++|....
T Consensus 95 L~~y~~~~~s~k~~l~~R~~~~~~~~~~~~~l~~k~~~~~kl~~~~~~~~~ki~~l~~~i~~~e~~~~~~~~~~~~i 171 (218)
T cd07596 95 LKEYLRYCQAVKETLDDRADALLTLQSLKKDLASKKAQLEKLKAAPGIKPAKVEELEEELEEAESALEEARKRYEEI 171 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555554444444 44444444444443333333322 45789999999999999999999876554
No 6
>TIGR01834 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit. This model represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. This model must be designated subfamily to indicate the heterogeneity of PHAs.
Probab=68.99 E-value=10 Score=37.91 Aligned_cols=54 Identities=24% Similarity=0.417 Sum_probs=44.7
Q ss_pred HHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhh
Q 016200 259 VGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEED 319 (393)
Q Consensus 259 V~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLekD 319 (393)
.++|+|.+.+.|.++++-.|.+=+. |-=+.|+-+|-++.-|+.||.++++|++-
T Consensus 258 ~G~lvna~m~lr~~~qe~~e~~L~~-------LnlPTRsElDe~~krL~ELrR~vr~L~k~ 311 (320)
T TIGR01834 258 HGKFINALMRLRIQQQEIVEALLKM-------LNLPTRSELDEAHQRIQQLRREVKSLKKR 311 (320)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh-------CCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788899999998888777665443 34467999999999999999999999985
No 7
>COG5521 Predicted integral membrane protein [Function unknown]
Probab=66.10 E-value=6.3 Score=38.87 Aligned_cols=40 Identities=33% Similarity=0.467 Sum_probs=32.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH----HhHHHHHHHHHHhhHhh
Q 016200 6 LMLFMLLVISFFFLTIFFTVTLF----LTYKKIKRLQELENYAN 45 (393)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~ 45 (393)
.|+||+|++|+.++..+|.|.++ |+.-|+.||-.+-++..
T Consensus 175 i~lflvl~~s~i~~l~tfivagg~sffL~iTKrSrlfsiasFkE 218 (275)
T COG5521 175 IMLFLVLVVSMIQLLLTFIVAGGASFFLWITKRSRLFSIASFKE 218 (275)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhheeeeehhhhhhhHHhHHH
Confidence 57889999999999888888665 88889999887766643
No 8
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=60.78 E-value=37 Score=30.94 Aligned_cols=79 Identities=14% Similarity=0.223 Sum_probs=53.0
Q ss_pred HHHHhhhccCcchHHHHHHHH--HhHHHHHHHHhhhhh-hhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhh
Q 016200 243 HQLVQSCESNELTLAQVGEFT--KCLAQAREELEDKSE-TIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEED 319 (393)
Q Consensus 243 DELvran~aK~LTLaQV~eF~--NcLVdARnEL~~KSE-~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLekD 319 (393)
=+.++|-..-+++++++.+|. .+ .. ..|-.+++ ++..+ .+||.. -.++|-++|..||.....+-.|
T Consensus 46 L~~I~~l~~~Gm~i~~i~~~~~~~l-~~--~~l~~~G~~t~~~R----~~lLe~----~~~~l~~ri~eLe~~l~~kad~ 114 (175)
T PRK13182 46 LEYVKSQIEEGQNMQDTQKPSSNDV-EE--TQVNTIVQNISSVD----FEQLEA----QLNTITRRLDELERQLQQKADD 114 (175)
T ss_pred HHHHHHHHHcCCCHHHHHHHhhhhh-hH--HHHHHcCCccHHHH----HHHHHH----HHHHHHHHHHHHHHHHHHHHhh
Confidence 356788889999999998844 32 00 12222333 22222 233322 4567888999999999999999
Q ss_pred HHHHHHHHHHhcc
Q 016200 320 VYVYNWLQDQLRL 332 (393)
Q Consensus 320 a~VYN~LQqQLKl 332 (393)
++-|.-||.+=-+
T Consensus 115 vvsYqll~hr~e~ 127 (175)
T PRK13182 115 VVSYQLLQHRREM 127 (175)
T ss_pred hhhHHHHHhHHHH
Confidence 9999999987433
No 9
>PF04380 BMFP: Membrane fusogenic activity; InterPro: IPR007475 BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro.
Probab=57.09 E-value=55 Score=26.15 Aligned_cols=62 Identities=24% Similarity=0.271 Sum_probs=33.4
Q ss_pred hHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCC---cchHH-------HHHHHHHHHHHHHHhhhh
Q 016200 255 TLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKAD---RSSID-------RLRQQIYNLEKQQRRLEE 318 (393)
Q Consensus 255 TLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskad---RSS~D-------RL~qQIykLE~EqkRLek 318 (393)
.+.++...++.++.+=..+.+-.+..=| .+....|++-| |--|| |+++.|..||.+...||+
T Consensus 7 ~~d~~~~~~~~~~~~~~~~~~e~e~~~r--~~l~~~l~kldlVtREEFd~q~~~L~~~r~kl~~LEarl~~LE~ 78 (79)
T PF04380_consen 7 IFDDLAKQISEALPAAQGPREEIEKNIR--ARLQSALSKLDLVTREEFDAQKAVLARTREKLEALEARLAALEA 78 (79)
T ss_pred HHHHHHHHHHHHHHhhhhhHHHHHHHHH--HHHHHHHHHCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4556666666666633333222221111 23344445543 66666 667888888887777763
No 10
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=53.87 E-value=39 Score=30.62 Aligned_cols=39 Identities=18% Similarity=0.192 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhHhh
Q 016200 7 MLFMLLVISFFFLTIFFTVTLFLTYKKIKRLQELENYAN 45 (393)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 45 (393)
+++.+++++++++.+++.+.+++..+-++.+..|....+
T Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pl~~l~~~~~ 97 (356)
T PRK10755 59 AVASLLVPSLVMVSLTLLICFQAVRWITRPLAELQKELE 97 (356)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 344455555555666666666666666777777766544
No 11
>PF06367 Drf_FH3: Diaphanous FH3 Domain; InterPro: IPR010472 Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of the cell cortex including motility, adhesion, and cytokinesis []. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain (IPR003104 from INTERPRO) is required to inhibit actin polymerisation. The FH3 domain is less well conserved and is required for directing formins to the correct intracellular location, such the mitotic spindle [], or the projection tip during conjugation []. In addition, some formins can contain a GTPase-binding domain (GBD) (IPR010473 from INTERPRO) required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD). This entry represents the FH3 domain.; GO: 0003779 actin binding, 0016043 cellular component organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=53.80 E-value=68 Score=27.72 Aligned_cols=82 Identities=15% Similarity=0.214 Sum_probs=51.9
Q ss_pred HHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhc--------CCcchHHHHHHHHHHHHHHHH---------------h
Q 016200 259 VGEFTKCLAQAREELEDKSETIKRKFSIQKALLSK--------ADRSSIDRLRQQIYNLEKQQR---------------R 315 (393)
Q Consensus 259 V~eF~NcLVdARnEL~~KSE~iqRkftI~KALLsk--------adRSS~DRL~qQIykLE~Eqk---------------R 315 (393)
+-.|+|+||..- +.++-+..|+..|..- -.....+.|..||...|.+.. .
T Consensus 44 ~l~~IN~li~~~-------~d~~~R~~lr~e~~~~GL~~il~~l~~~~~~~L~~Qi~~f~~~~~~D~~el~~~~~~~~~~ 116 (197)
T PF06367_consen 44 CLQFINSLINSP-------EDLNFRVHLRNEFERLGLLDILEKLRNLEDDDLQEQIDIFEENEEEDEEELLERFDSKTVD 116 (197)
T ss_dssp HHHHHHHHHTT--------SSHHHHHHHHHHHHHTTHHHHHHHHTTS--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCC-------CCHHHHHHHHHHHHHCCcHHHHHHHHhcchHHHHHHHHHHHHHHHhhHHHHHHhhcccccc
Confidence 456888887653 4455555555544332 123467788888887776543 2
Q ss_pred hhhhHHHHHHHHHHhccCHHHHHHHHhhhhhh
Q 016200 316 LEEDVYVYNWLQDQLRLSPACKKMFEVCADME 347 (393)
Q Consensus 316 LekDa~VYN~LQqQLKlSpAYKkMlE~ga~~E 347 (393)
+..-..+|..|..+++-++++.-++-+=+..=
T Consensus 117 ~~~~~~l~~~l~~~~~~~~~~~~~~siLq~ll 148 (197)
T PF06367_consen 117 LSDPQELFEALLEKLKDTEAEDYFLSILQHLL 148 (197)
T ss_dssp SSSHHHHHHHHHHHHTTSTTHHHHHHHHHHHT
T ss_pred cccHHHHHHHHHHHHhCcccHHHHHHHHHHHH
Confidence 44456789999999999999988765544443
No 12
>TIGR02736 cbb3_Q_epsi cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial. Members of this protein family are restricted to the epsilon branch of the Proteobacteria. All members are found in operons containing the other three structural subunits of the cbb3 type of cytochrome c oxidase. These small proteins show remote sequence similarity to the CcoQ subunit in other cytochrome c oxidase systems, so this family is assumed to represent the epsilonproteobacterial variant of CcoQ.
Probab=53.58 E-value=20 Score=28.40 Aligned_cols=32 Identities=28% Similarity=0.680 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHh----HHHHHH-HHHHhhHhhh
Q 016200 15 SFFFLTIFFTVTLFLT----YKKIKR-LQELENYANV 46 (393)
Q Consensus 15 ~~~~~~~~~~~~~~~~----~~~~~~-~~~~~~~~~~ 46 (393)
.+||+|||++|.|.-- |++-|. -..-|.|+|.
T Consensus 3 ~yf~~ti~lvv~LYgY~yhLYrsek~G~rdYEKY~~L 39 (56)
T TIGR02736 3 AYFAFTLLLVIFLYAYIYHLYRSQKKGERDYEKYANL 39 (56)
T ss_pred chHHHHHHHHHHHHHHHHHhhhhhcccccCHHHHhhh
Confidence 5788888888776543 333332 2567888885
No 13
>PRK11832 putative DNA-binding transcriptional regulator; Provisional
Probab=53.45 E-value=16 Score=34.35 Aligned_cols=42 Identities=17% Similarity=0.376 Sum_probs=39.2
Q ss_pred CcchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHH
Q 016200 295 DRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPAC 336 (393)
Q Consensus 295 dRSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAY 336 (393)
.++||+=+|.++..|-.+=....++..|||+||++-.||-++
T Consensus 135 g~~sY~~IR~~L~eL~~~~e~~R~~I~v~~YIq~RT~LSRS~ 176 (207)
T PRK11832 135 GHNSYEQIRATLLSMIDWNEELRSRIGVMNYIHQRTRISRSV 176 (207)
T ss_pred cCcHHHHHHHHHHHHHhCCHHHHhhccHHHHHHHhccccHHH
Confidence 378999999999999999999999999999999999999876
No 14
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=50.67 E-value=55 Score=24.15 Aligned_cols=42 Identities=21% Similarity=0.211 Sum_probs=29.1
Q ss_pred cchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHHH
Q 016200 296 RSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPACK 337 (393)
Q Consensus 296 RSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAYK 337 (393)
.+.+-++.+||..|+.+.+.|++...-...--++|+-||.|-
T Consensus 16 ~~~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~i 57 (80)
T PF04977_consen 16 YSRYYQLNQEIAELQKEIEELKKENEELKEEIERLKNDPDYI 57 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHH
Confidence 345556777777777777777777766666667776678774
No 15
>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].
Probab=50.48 E-value=1.9e+02 Score=26.26 Aligned_cols=76 Identities=25% Similarity=0.427 Sum_probs=55.7
Q ss_pred HHHHHHHHHhh----hccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHH
Q 016200 238 IKELYHQLVQS----CESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQ 313 (393)
Q Consensus 238 IkeqYDELvra----n~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~Eq 313 (393)
-.+.+|||+|= |..+++=|..|+....-+++|=..|.+ |.. .|.++|+|-.... -+++..+|..|+.+.
T Consensus 64 y~~~F~ELIRQVTi~C~ERGlLL~rvrde~~~~l~~y~~l~~-s~~---~f~~rk~l~~e~~---~~~l~~~i~~L~~e~ 136 (189)
T PF10211_consen 64 YSQCFDELIRQVTIDCPERGLLLLRVRDEYRMTLDAYQTLYE-SSI---AFGMRKALQAEQG---KQELEEEIEELEEEK 136 (189)
T ss_pred HHHHHHHHHHHHHhCcHHHhHHHHHHHHHHHHHHHHHHHHHH-HHH---HHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Confidence 35589999984 457889999999999999998766644 332 4788888877543 346677777777777
Q ss_pred HhhhhhH
Q 016200 314 RRLEEDV 320 (393)
Q Consensus 314 kRLekDa 320 (393)
+.|++=.
T Consensus 137 ~~L~~~~ 143 (189)
T PF10211_consen 137 EELEKQV 143 (189)
T ss_pred HHHHHHH
Confidence 7776533
No 16
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=48.19 E-value=1.4e+02 Score=23.86 Aligned_cols=83 Identities=19% Similarity=0.281 Sum_probs=48.2
Q ss_pred HHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCc--chHHHHHHHHHHHHHHHH
Q 016200 237 KIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADR--SSIDRLRQQIYNLEKQQR 314 (393)
Q Consensus 237 RIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadR--SS~DRL~qQIykLE~Eqk 314 (393)
.|.+-.|........+.-....|.+++ -|-+.|.+|+++.+.++..-.....-+...-+ ...+-|..++..|-.+.+
T Consensus 6 ~ir~n~e~v~~~l~~R~~~~~~vd~i~-~ld~~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~ 84 (108)
T PF02403_consen 6 LIRENPEEVRENLKKRGGDEEDVDEII-ELDQERRELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIK 84 (108)
T ss_dssp HHHHHHHHHHHHHHHTTCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHH
T ss_pred HHHhCHHHHHHHHHHcCCCHhhHHHHH-HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHH
Confidence 455556655555555544555555554 36788889999999998776544444444333 245555555555555555
Q ss_pred hhhhhH
Q 016200 315 RLEEDV 320 (393)
Q Consensus 315 RLekDa 320 (393)
.|++..
T Consensus 85 ~le~~~ 90 (108)
T PF02403_consen 85 ELEEQL 90 (108)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 544443
No 17
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=48.10 E-value=17 Score=30.48 Aligned_cols=10 Identities=50% Similarity=0.766 Sum_probs=4.5
Q ss_pred HHHhHHHHHH
Q 016200 27 LFLTYKKIKR 36 (393)
Q Consensus 27 ~~~~~~~~~~ 36 (393)
+|+++..-+|
T Consensus 16 ~~~~~~~~rR 25 (130)
T PF12273_consen 16 LFLFYCHNRR 25 (130)
T ss_pred HHHHHHHHHH
Confidence 3444544443
No 18
>PF09032 Siah-Interact_N: Siah interacting protein, N terminal ; InterPro: IPR015120 The N-terminal domain of Siah interacting protein (SIP) adopts a helical hairpin structure with a hydrophobic core stabilised by a classic knobs-and-holes arrangement of side chains contributed by the two amphipathic helices. Little is known about this domain's function, except that it is crucial for interactions with Siah. It has also been hypothesised that SIP can dimerise through this N-terminal domain []. ; PDB: 1YSM_A 2A26_C 2A25_B 1X5M_A.
Probab=47.36 E-value=46 Score=27.41 Aligned_cols=39 Identities=28% Similarity=0.481 Sum_probs=31.0
Q ss_pred hhhHHHHHHHHhhcCCcchHHH-HHHHHHHHHHHHHhhhh
Q 016200 280 IKRKFSIQKALLSKADRSSIDR-LRQQIYNLEKQQRRLEE 318 (393)
Q Consensus 280 iqRkftI~KALLskadRSS~DR-L~qQIykLE~EqkRLek 318 (393)
++-=+-=.++||.+|-|.++.. |-.+|.+||.|.+.+++
T Consensus 8 L~~Dl~El~~Ll~~a~R~rVk~~L~~ei~klE~eI~~~~~ 47 (79)
T PF09032_consen 8 LQLDLEELKSLLEQAKRKRVKDLLTNEIRKLETEIKKLKE 47 (79)
T ss_dssp HHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHCHH
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444678999999988875 58899999999999876
No 19
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=47.34 E-value=77 Score=30.32 Aligned_cols=65 Identities=28% Similarity=0.388 Sum_probs=53.2
Q ss_pred HHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhcc
Q 016200 260 GEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRL 332 (393)
Q Consensus 260 ~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKl 332 (393)
.+.-|-|-++|.||.+|-|.|+.--.|- - --||.|++=|.-..+-|+...|-.+|.=++|..-|+
T Consensus 50 ~eLkNeLREVREELkEKmeEIKQIKdiM----D----KDFDKL~EFVEIMKeMQkDMDEKMDvLiNiQKnnKl 114 (205)
T PF15079_consen 50 QELKNELREVREELKEKMEEIKQIKDIM----D----KDFDKLHEFVEIMKEMQKDMDEKMDVLINIQKNNKL 114 (205)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH----h----hhHHHHHHHHHHHHHHHHhHHHhhhHHhhccccccC
Confidence 5677899999999999999998643332 2 279999999999988899999988998888866554
No 20
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=47.08 E-value=40 Score=26.36 Aligned_cols=26 Identities=4% Similarity=0.310 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHH
Q 016200 13 VISFFFLTIFFTVTLFLTYKKIKRLQ 38 (393)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 38 (393)
.++|+++.+++.++.++.+..+..+.
T Consensus 9 ~~~f~~~~~l~~~~~~~~~~~l~~~~ 34 (181)
T PF12729_consen 9 ILGFGLIILLLLIVGIVGLYSLSQIN 34 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444555555555555554443
No 21
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=46.67 E-value=75 Score=30.78 Aligned_cols=53 Identities=25% Similarity=0.434 Sum_probs=42.5
Q ss_pred HHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhh
Q 016200 259 VGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEE 318 (393)
Q Consensus 259 V~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLek 318 (393)
.+.|+|.+.+.|.+.++=.|.+=+. |-=+-|+-+|-|+..||.|+.|+++|++
T Consensus 241 ~g~~~~a~m~~r~~~~~~~e~~L~~-------l~lPTr~evd~l~k~l~eLrre~r~Lkr 293 (293)
T PF09712_consen 241 YGQLVNALMDLRKQQQEVVEEYLRS-------LNLPTRSEVDELYKRLHELRREVRALKR 293 (293)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-------CCCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4778888888888887766655443 3336799999999999999999999975
No 22
>PF06103 DUF948: Bacterial protein of unknown function (DUF948); InterPro: IPR009293 This family consists of bacterial sequences several of which are thought to be general stress proteins.
Probab=46.64 E-value=53 Score=25.70 Aligned_cols=26 Identities=27% Similarity=0.397 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHH
Q 016200 10 MLLVISFFFLTIFFTVTLFLTYKKIK 35 (393)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 35 (393)
+++.|+|.+|.||...+|.=.-+.++
T Consensus 4 lI~Aiaf~vLvi~l~~~l~~l~~~l~ 29 (90)
T PF06103_consen 4 LIAAIAFAVLVIFLIKVLKKLKKTLD 29 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46678888888887666554433333
No 23
>PF05115 PetL: Cytochrome B6-F complex subunit VI (PetL); InterPro: IPR007802 This family consists of several Cytochrome B6-F complex subunit VI (PetL) proteins found in a number of plant species. PetL is one of the small subunits which make up the cytochrome b(6)f complex. PetL is not absolutely required for either the accumulation or for the function of cytochrome b6f; in its absence, however, the complex becomes unstable in vivo in aging cells and labile in vitro. It has been suggested that the N terminus of the protein is likely to lie in the thylakoid lumen [].; GO: 0009055 electron carrier activity, 0009512 cytochrome b6f complex; PDB: 2ZT9_E 1Q90_L.
Probab=45.80 E-value=36 Score=24.20 Aligned_cols=26 Identities=50% Similarity=0.874 Sum_probs=16.1
Q ss_pred HHHHHHHH-HHH--HHHHHHHHHhHHHHH
Q 016200 10 MLLVISFF-FLT--IFFTVTLFLTYKKIK 35 (393)
Q Consensus 10 ~~~~~~~~-~~~--~~~~~~~~~~~~~~~ 35 (393)
|+.+||+| ||. ..+|..+|+..+|||
T Consensus 1 M~tiisYf~fL~~al~~t~~lfiGL~kIk 29 (31)
T PF05115_consen 1 MLTIISYFGFLLAALTLTLVLFIGLSKIK 29 (31)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHCTT
T ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 55666655 333 345666788888886
No 24
>CHL00106 petL cytochrome b6/f complex subunit VI
Probab=45.51 E-value=32 Score=24.46 Aligned_cols=26 Identities=35% Similarity=0.548 Sum_probs=16.5
Q ss_pred HHHHHHHHH---HHHHHHHHHHHhHHHHH
Q 016200 10 MLLVISFFF---LTIFFTVTLFLTYKKIK 35 (393)
Q Consensus 10 ~~~~~~~~~---~~~~~~~~~~~~~~~~~ 35 (393)
|+.+||+|- ....+|..+|+..+|||
T Consensus 1 M~tiisYf~~L~~a~~~t~~lfigL~kIk 29 (31)
T CHL00106 1 MLTITSYFGFLLAALTITSGLFIGLSKIR 29 (31)
T ss_pred ChhHHHHHHHHHHHHHHHHHHHHHHHhhe
Confidence 445555542 33446677899999985
No 25
>PF13933 HRXXH: Putative peptidase family
Probab=44.46 E-value=21 Score=34.78 Aligned_cols=28 Identities=25% Similarity=0.316 Sum_probs=23.1
Q ss_pred CCCCcccccchhHHHH-HHHHHHHHHhhh
Q 016200 222 GCLCPLTSMGSATQRK-IKELYHQLVQSC 249 (393)
Q Consensus 222 ~c~yPfTS~~sAtQRR-IkeqYDELvran 249 (393)
++.||+.++|.+|||+ |.+.+||.++..
T Consensus 42 ~~~fpih~SCN~T~r~qL~~al~ea~~lA 70 (245)
T PF13933_consen 42 VPVFPIHSSCNATQRRQLNSALDEAVELA 70 (245)
T ss_pred ccCCccccchhHHHHHHHHHHHHHHHHHH
Confidence 6789999999999987 567788877543
No 26
>TIGR02229 caa3_sub_IV caa(3)-type oxidase, subunit IV. This model represents a small set of proteins with weak similarity to the sequences in Pfam family pfam03626, which describes the cytochrome C oxidase subunit IV.
Probab=44.36 E-value=30 Score=29.03 Aligned_cols=23 Identities=26% Similarity=0.407 Sum_probs=18.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Q 016200 6 LMLFMLLVISFFFLTIFFTVTLF 28 (393)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~ 28 (393)
-+.-.++.++|+|+.|||..|++
T Consensus 65 ~l~r~~~~~~~~~l~i~~~~t~~ 87 (92)
T TIGR02229 65 ALLRLASAVAFAILAILFVITHG 87 (92)
T ss_pred chHHHHHHHHHHHHHHHHHHHHH
Confidence 34455677899999999999886
No 27
>PRK09835 sensor kinase CusS; Provisional
Probab=43.45 E-value=69 Score=29.87 Aligned_cols=36 Identities=6% Similarity=0.108 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhHhhhh
Q 016200 12 LVISFFFLTIFFTVTLFLTYKKIKRLQELENYANVL 47 (393)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (393)
+++.++++.+++.+.+|+.+...+.|+.|.+.++-+
T Consensus 188 ~~~~~~~~~~~~~~~~~~~~~~~~pl~~l~~~~~~i 223 (482)
T PRK09835 188 IMTASVISLLIVFIVLLAVHKGHAPIRSVSRQIQNI 223 (482)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444445555666677778888888877644
No 28
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=41.92 E-value=19 Score=27.97 Aligned_cols=62 Identities=19% Similarity=0.258 Sum_probs=45.0
Q ss_pred hhHHHHHHHH--hhcCCcchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHHHHHHHh
Q 016200 281 KRKFSIQKAL--LSKADRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPACKKMFEV 342 (393)
Q Consensus 281 qRkftI~KAL--LskadRSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAYKkMlE~ 342 (393)
+|-....+.+ |...|+.-++|+|.-+.....-++.|+++=.++..-.-..+.+|++..+..+
T Consensus 6 ~~i~~~L~~~~~l~~~D~~~l~~yc~~~~~~~~~~~~l~~~G~~~~~~~G~~~~nP~~~~~~~~ 69 (100)
T PF05119_consen 6 KRIVPELKELGILSNLDVPLLERYCEAYSRYREAEKELKKEGFVVETKNGNPKKNPAVSILNKA 69 (100)
T ss_pred HHHHHHHHHcCCCcHhHHHHHHHHHHHHHHHHHHHHHHHHcCceeeCCCCCcccCHHHHHHHHH
Confidence 4444555554 8888999999999999988888888888777754444467778877655443
No 29
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=41.48 E-value=1.9e+02 Score=26.91 Aligned_cols=70 Identities=19% Similarity=0.316 Sum_probs=39.9
Q ss_pred cCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCC--cchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Q 016200 251 SNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKAD--RSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQD 328 (393)
Q Consensus 251 aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskad--RSS~DRL~qQIykLE~EqkRLekDa~VYN~LQq 328 (393)
...|||.+|-.|+-.|-+. +... +.+-.-.. +.-...|.+++..||.|...|+++..+|.
T Consensus 77 ~~~ltl~~vI~fLq~l~~~-------~~~~-------~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~---- 138 (161)
T TIGR02894 77 AGSLTLQDVISFLQNLKTT-------NPSD-------QALQKENERLKNQNESLQKRNEELEKELEKLRQRLSTIE---- 138 (161)
T ss_pred cccCCHHHHHHHHHHHHhc-------chhH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----
Confidence 3679999999998655321 1101 11100000 12334677777888888777777766553
Q ss_pred HhccCHHHHHHHHhh
Q 016200 329 QLRLSPACKKMFEVC 343 (393)
Q Consensus 329 QLKlSpAYKkMlE~g 343 (393)
.-|+.|+.|=
T Consensus 139 -----eDY~~L~~Im 148 (161)
T TIGR02894 139 -----EDYQTLIDIM 148 (161)
T ss_pred -----HHHHHHHHHH
Confidence 2467766653
No 30
>PF05816 TelA: Toxic anion resistance protein (TelA); InterPro: IPR008863 This family consists of several prokaryotic TelA like proteins. TelA and KlA are associated with tellurite resistance [] and plasmid fertility inhibition [].
Probab=40.57 E-value=3.5e+02 Score=26.29 Aligned_cols=118 Identities=22% Similarity=0.263 Sum_probs=76.9
Q ss_pred ccccchhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCC------cchHH
Q 016200 227 LTSMGSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKAD------RSSID 300 (393)
Q Consensus 227 fTS~~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskad------RSS~D 300 (393)
+.+.|...|++|-..=|.+..-.+.+ +..+|++=++-|+..=+++--..-.-..+-.+..-|+.++. -+.|+
T Consensus 17 i~~~G~~~~~~~a~~s~~iL~~v~~~--d~~~vg~~L~~L~~~~~~~dp~~~~~~~~~~~l~klf~k~~~~~~~~~~ky~ 94 (333)
T PF05816_consen 17 ILSFGAEAQEKIAQFSDRILDRVRNK--DSGEVGELLNELRKEMDELDPSELKDEKKKGFLGKLFGKAKNSLERYFAKYQ 94 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh--ccchHhHHHHHHHHHHHhCChhhhhhhhhhhHHHHhhhhhhhHHHHHHHHHH
Confidence 45678899999999888987775555 66667766666665544443222101111233333555332 26677
Q ss_pred HHHHHHHH----HHHHHHhhhhhHHHHHHHHHHhccCHHHHHHHHhhhhhhh
Q 016200 301 RLRQQIYN----LEKQQRRLEEDVYVYNWLQDQLRLSPACKKMFEVCADMEL 348 (393)
Q Consensus 301 RL~qQIyk----LE~EqkRLekDa~VYN~LQqQLKlSpAYKkMlE~ga~~El 348 (393)
.+-+||++ |+..+..|.+|...+..+.+.+.. .|+.+-.|-+..++
T Consensus 95 sv~~qId~I~~~L~~~~~~L~~d~~~L~~l~~~n~~--~~~~L~~~I~ag~~ 144 (333)
T PF05816_consen 95 SVQSQIDKIIAELESGQDELLRDNAMLDQLYEKNWE--YYQELEKYIAAGEL 144 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHH
Confidence 77778765 677788999999999999887763 56666666655554
No 31
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=40.10 E-value=89 Score=22.65 Aligned_cols=38 Identities=26% Similarity=0.389 Sum_probs=26.9
Q ss_pred cCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhh
Q 016200 251 SNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLS 292 (393)
Q Consensus 251 aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLs 292 (393)
-..+|..+|..|+..|...+ -+..++.+.++..++++.
T Consensus 41 ~~~i~~~~v~~f~~~~~~~~----~s~~T~~~~~~alr~f~~ 78 (84)
T PF02899_consen 41 WEDITEEDVRDFLEYLAKEG----LSPSTINRRLSALRAFFR 78 (84)
T ss_dssp GGG--HHHHHHHHHHHHCTT------HHHHHHHHHHHHHHHH
T ss_pred hhhhhhHHHHHHHHHHHccC----CCHHHHHHHHHHHHHHHH
Confidence 46788999999999997765 567788888888777653
No 32
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=39.82 E-value=99 Score=21.58 Aligned_cols=44 Identities=25% Similarity=0.280 Sum_probs=31.2
Q ss_pred hhHHHHHHHHHHHHHhhhccCcch--HHHHHHHHHhHHHHHHHHhh
Q 016200 232 SATQRKIKELYHQLVQSCESNELT--LAQVGEFTKCLAQAREELED 275 (393)
Q Consensus 232 sAtQRRIkeqYDELvran~aK~LT--LaQV~eF~NcLVdARnEL~~ 275 (393)
+++...|+.+|..|++...--... -....+....|.+|-+.|..
T Consensus 12 ~~~~~~ik~ay~~l~~~~HPD~~~~~~~~~~~~~~~l~~Ay~~L~~ 57 (60)
T smart00271 12 DASLDEIKKAYRKLALKYHPDKNPGDKEEAEEKFKEINEAYEVLSD 57 (60)
T ss_pred CCCHHHHHHHHHHHHHHHCcCCCCCchHHHHHHHHHHHHHHHHHcC
Confidence 478899999999999988765555 34455555666666666543
No 33
>TIGR02444 conserved hypothetical protein TIGR02444. Members of this family are bacterial hypothetical proteins, about 160 amino acids in length, found in various Proteobacteria, including members of the genera Pseudomonas and Vibrio. The C-terminal region is poorly conserved and is not included in the model.
Probab=38.62 E-value=1.7e+02 Score=25.25 Aligned_cols=66 Identities=17% Similarity=0.240 Sum_probs=49.0
Q ss_pred hccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhh
Q 016200 249 CESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLE 317 (393)
Q Consensus 249 n~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLe 317 (393)
.+...++..+......+...-|++..+-.-.+||.. |+-....+=.....+|++|-.+|.+-+|+.
T Consensus 43 ~~g~~l~~~~~~~l~~~~~~w~~~vv~PlR~lRr~~---K~~~~~~~~~~~~~lr~~lk~~EL~aEr~~ 108 (116)
T TIGR02444 43 ERGLAFDEQEIAQVQACAGTWSEDVVRPLRAVRRQL---KQHLPDTPEEINAALRAAVKALELQGEKLL 108 (116)
T ss_pred HcCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hccCCCCcchhHHHHHHHHHHHHHHHHHHH
Confidence 457788989999998888888888887777776654 233333332456679999999999988864
No 34
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=38.54 E-value=1.4e+02 Score=32.59 Aligned_cols=76 Identities=26% Similarity=0.330 Sum_probs=47.6
Q ss_pred HHHHHHHHhhhhhhhhhHHHHHHHHhhcC--C----cchHHHHHHHHHHHHHHHHhhhhhHH-HHHHHHHHhc-cCHHHH
Q 016200 266 LAQAREELEDKSETIKRKFSIQKALLSKA--D----RSSIDRLRQQIYNLEKQQRRLEEDVY-VYNWLQDQLR-LSPACK 337 (393)
Q Consensus 266 LVdARnEL~~KSE~iqRkftI~KALLska--d----RSS~DRL~qQIykLE~EqkRLekDa~-VYN~LQqQLK-lSpAYK 337 (393)
+.-||.+++++...+++...-.-.-|... . +.+=++|.+.+..++..|+.|.+=+. |.+.++.++. +|.|=+
T Consensus 556 ~~~ar~ei~~rv~~Lk~~~e~Ql~~L~~l~e~~~~l~~~ae~LaeR~e~a~d~Qe~L~~R~~~vl~~l~~~~P~LS~AEr 635 (717)
T PF10168_consen 556 QDLAREEIQRRVKLLKQQKEQQLKELQELQEERKSLRESAEKLAERYEEAKDKQEKLMKRVDRVLQLLNSQLPVLSEAER 635 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHH
Confidence 33455555555555544443222222221 1 34446888888888888888888666 7788888887 888877
Q ss_pred HHHH
Q 016200 338 KMFE 341 (393)
Q Consensus 338 kMlE 341 (393)
.|.+
T Consensus 636 ~~~~ 639 (717)
T PF10168_consen 636 EFKK 639 (717)
T ss_pred HHHH
Confidence 7753
No 35
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=37.84 E-value=1.1e+02 Score=22.37 Aligned_cols=14 Identities=36% Similarity=0.560 Sum_probs=6.9
Q ss_pred hHHHHHHHHHHHHH
Q 016200 6 LMLFMLLVISFFFL 19 (393)
Q Consensus 6 ~~~~~~~~~~~~~~ 19 (393)
+-+.++++++|++-
T Consensus 18 ~pl~l~il~~f~~G 31 (68)
T PF06305_consen 18 LPLGLLILIAFLLG 31 (68)
T ss_pred chHHHHHHHHHHHH
Confidence 34455555555443
No 36
>PF06266 HrpF: HrpF protein; InterPro: IPR009371 The species Pseudomonas syringae encompasses plant pathogens with differing host specificities and corresponding pathovar designations. P. syringae requires the Hrp (type III protein secretion) system, encoded by a 25-kb cluster of hrp and hrc genes, in order to elicit the hypersensitive response (HR) in nonhosts or to be pathogenic in hosts. The exact function of HrpF is unknown but the protein is needed for pathogenicity [].
Probab=37.61 E-value=2.1e+02 Score=23.77 Aligned_cols=62 Identities=18% Similarity=0.240 Sum_probs=43.8
Q ss_pred ccchhHHHHHH-------HHHHHHH-hhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhh
Q 016200 229 SMGSATQRKIK-------ELYHQLV-QSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLS 292 (393)
Q Consensus 229 S~~sAtQRRIk-------eqYDELv-ran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLs 292 (393)
++..++|||.- ..+|+.+ .+.+. -|+.+.+.|-..--++-+.=---.+.++=+|.++||.+-
T Consensus 2 ~s~~~LqrrLD~~~~rA~~~~d~aal~a~e~--~s~~D~~AF~ea~~q~s~As~A~~Q~l~vkH~L~KaiId 71 (74)
T PF06266_consen 2 SSFNALQRRLDSQFERAQTNLDDAALNASEG--FSPEDIQAFNEASMQASVASWAANQELRVKHGLAKAIID 71 (74)
T ss_pred cchHHHHHHHHHHHHHHHhhHHHHHHhhhcC--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHH
Confidence 56788999664 4566644 33443 899999999776666655555556678888999998763
No 37
>cd06257 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification.
Probab=37.43 E-value=1e+02 Score=21.02 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=20.1
Q ss_pred chhHHHHHHHHHHHHHhhhccCcch
Q 016200 231 GSATQRKIKELYHQLVQSCESNELT 255 (393)
Q Consensus 231 ~sAtQRRIkeqYDELvran~aK~LT 255 (393)
.+++...|+.+|..|++...--+..
T Consensus 10 ~~~~~~~ik~~y~~l~~~~HPD~~~ 34 (55)
T cd06257 10 PDASDEEIKKAYRKLALKYHPDKNP 34 (55)
T ss_pred CCCCHHHHHHHHHHHHHHHCcCCCC
Confidence 3567899999999999988765554
No 38
>PF00615 RGS: Regulator of G protein signaling domain; InterPro: IPR000342 RGS (Regulator of G Protein Signalling) proteins are multi-functional, GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways []. Upon activation by GPCRs, heterotrimeric G proteins exchange GDP for GTP, are released from the receptor, and dissociate into free, active GTP-bound alpha subunit and beta-gamma dimer, both of which activate downstream effectors. The response is terminated upon GTP hydrolysis by the alpha subunit (IPR001019 from INTERPRO), which can then bind the beta-gamma dimer (IPR001632 from INTERPRO, IPR001770 from INTERPRO) and the receptor. RGS proteins markedly reduce the lifespan of GTP-bound alpha subunits by stabilising the G protein transition state. All RGS proteins contain an 'RGS-box' (or RGS domain), which is required for activity. Some small RGS proteins such as RGS1 and RGS4 are comprised of little more than an RGS domain, while others also contain additional domains that confer further functionality []. RGS domains can be found in conjunction with a variety of domains, including: DEP for membrane targeting (IPR000591 from INTERPRO), PDZ for binding to GPCRs (IPR001478 from INTERPRO), PTB for phosphotyrosine-binding (IPR006020 from INTERPRO), RBD for Ras-binding (IPR003116 from INTERPRO), GoLoco for guanine nucleotide inhibitor activity (IPR003109 from INTERPRO), PX for phosphatidylinositol-binding (IPR001683 from INTERPRO), PXA that is associated with PX (IPR003114 from INTERPRO), PH for stimulating guanine nucleotide exchange (IPR001849 from INTERPRO), and GGL (G protein gamma subunit-like) for binding G protein beta subunits (IPR001770 from INTERPRO) []. Those RGS proteins that contain GGL domains can interact with G protein beta subunits to form novel dimers that prevent G protein gamma subunit binding and G protein alpha subunit association, thereby preventing heterotrimer formation.; GO: 0004871 signal transducer activity; PDB: 2BCJ_A 3PSC_A 3PVU_A 1YM7_B 3PVW_A 1OMW_A 2EBZ_A 2BV1_B 2GTP_D 1CMZ_A ....
Probab=36.93 E-value=1.7e+02 Score=21.63 Aligned_cols=76 Identities=21% Similarity=0.429 Sum_probs=45.9
Q ss_pred chhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHH
Q 016200 231 GSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLE 310 (393)
Q Consensus 231 ~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE 310 (393)
.....+.+.+.|+.-+..+....+.|.+ .+|.++.+..+.. ...+..|+.+..+|+.
T Consensus 43 ~~~~~~~a~~I~~~fi~~~s~~~l~i~~---------~~~~~~~~~~~~~------------~~~~~~f~~a~~~v~~-- 99 (118)
T PF00615_consen 43 EEQRKKLAQQIYNKFISPGSPNELNIPS---------KIRKEVQDALENA------------PPSPDLFDEAQEEVYE-- 99 (118)
T ss_dssp HHHHHHHHHHHHHHHTSTTSTTCCSSTH---------HHHHHHHHHHTST------------STTTTTTHHHHHHHHH--
T ss_pred hhhHHHHHHHHHHHHhcccccccccccH---------HHHHHHHHHHHHh------------cccHHHHHHHHHHHHH--
Confidence 3445556666777666555555554433 3344444333332 5678999999998876
Q ss_pred HHHHhhhhhHHHHHHHHHHhccCHHHHHH
Q 016200 311 KQQRRLEEDVYVYNWLQDQLRLSPACKKM 339 (393)
Q Consensus 311 ~EqkRLekDa~VYN~LQqQLKlSpAYKkM 339 (393)
.|++|.+ .+...|+.|+.|
T Consensus 100 ----~L~~~~~------~~F~~S~~y~~~ 118 (118)
T PF00615_consen 100 ----MLEEDWF------PKFLKSEEYKQF 118 (118)
T ss_dssp ----HHHHTHH------HHHHTSHHHHHH
T ss_pred ----HHhhchH------HhHccCHhhhcC
Confidence 3554442 456778888876
No 39
>TIGR01870 cas_TM1810_Csm2 CRISPR-associated protein, Csm2 family. These proteins are found adjacent to a characteristic short, palidromic repeat cluster termed CRISPR, a probable mobile DNA element. This model represents the C-terminal domain of a minor family of CRISPR-associated protein from the Mtube subtype of CRISPR/Cas locus. The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2.
Probab=35.91 E-value=2.4e+02 Score=23.05 Aligned_cols=67 Identities=22% Similarity=0.349 Sum_probs=50.6
Q ss_pred chHHHHHHHHHhHHHHHHHHh---hhhhhhhhHHHHHHHHhhcC-Ccc---hHHHHHHHHHHHHHHHHhhhhhH
Q 016200 254 LTLAQVGEFTKCLAQAREELE---DKSETIKRKFSIQKALLSKA-DRS---SIDRLRQQIYNLEKQQRRLEEDV 320 (393)
Q Consensus 254 LTLaQV~eF~NcLVdARnEL~---~KSE~iqRkftI~KALLska-dRS---S~DRL~qQIykLE~EqkRLekDa 320 (393)
||..|++.|.+-+...++++. ...+.++..+...|+-|-=+ .|- .++.+++-+..+-...+..+.|.
T Consensus 1 lttsQlRk~~~~v~~i~~~~~~~~~~~~~~~~~l~~Lk~klaY~~GR~~~~~~~~~~~~~~~~~~~i~~~~~~~ 74 (97)
T TIGR01870 1 LTTTQLRRFYDELRRIEEKIRRSEQKNEDITAELHMLKPKLAYAVGREGIREFEGFVELLEDLLDKIDKIDNDD 74 (97)
T ss_pred CcHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHcCccccchhHHHHHHHHHHHHHhcccchH
Confidence 688999999999999999885 56777888888888877553 453 67788877777766666665443
No 40
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=35.76 E-value=85 Score=26.17 Aligned_cols=28 Identities=25% Similarity=0.456 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHh
Q 016200 14 ISFFFLTIFFTVTLFLTYKKIKRLQELE 41 (393)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (393)
-.+..||-||.++.||.||-.|.|+.=|
T Consensus 25 ~vll~LtPlfiisa~lSwkLaK~ie~~e 52 (74)
T PF15086_consen 25 TVLLILTPLFIISAVLSWKLAKAIEKEE 52 (74)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence 3445688899999999999888776443
No 41
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=35.16 E-value=67 Score=24.51 Aligned_cols=36 Identities=19% Similarity=0.280 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCH
Q 016200 299 IDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSP 334 (393)
Q Consensus 299 ~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSp 334 (393)
.+.+.++...|..|..+|..+..|...-.++|+|++
T Consensus 40 ~~~l~~en~~L~~ei~~l~~~~rIe~~Ar~~lgM~~ 75 (85)
T TIGR02209 40 IDKLQKEWRDLQLEVAELSRHERIEKIAKKQLGMKL 75 (85)
T ss_pred HHHHHHHHHHHHHHHHHHcCHHHHHHHHHHhcCCCC
Confidence 344455555555666666666666666666666654
No 42
>PRK11637 AmiB activator; Provisional
Probab=34.92 E-value=2.7e+02 Score=27.53 Aligned_cols=60 Identities=13% Similarity=0.194 Sum_probs=30.2
Q ss_pred cccccchhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHH
Q 016200 226 PLTSMGSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKA 289 (393)
Q Consensus 226 PfTS~~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KA 289 (393)
|++.....+|.++++.=.++-..... +.++..-.+-+...-+.|..+.+.+++.+.-...
T Consensus 37 ~~~~~~~~~~~~l~~l~~qi~~~~~~----i~~~~~~~~~~~~~l~~l~~qi~~~~~~i~~~~~ 96 (428)
T PRK11637 37 AFSAHASDNRDQLKSIQQDIAAKEKS----VRQQQQQRASLLAQLKKQEEAISQASRKLRETQN 96 (428)
T ss_pred hhcccchhhHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55555567777777776666544332 3333333333444444444555555554444433
No 43
>PF12606 RELT: Tumour necrosis factor receptor superfamily member 19; InterPro: IPR022248 The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the "guardians of the immune system" due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). RELT (receptor expressed in lymphoid tissues) is a member of the TNFR superfamily. The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1 []. RELT like proteins 1 and 2 (RELL1 and RELL2) are two RELT homologues that bind to RELT. The expression of RELL1 at the mRNA level is ubiquitous, whereas expression of RELL2 mRNA is more restricted to particular tissues [].
Probab=34.61 E-value=49 Score=25.34 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhHH
Q 016200 11 LLVISFFFLTIFFTVTLFLTYK 32 (393)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~ 32 (393)
+++|++||+++...+.+.-+-|
T Consensus 4 ~~iV~i~iv~~lLg~~I~~~~K 25 (50)
T PF12606_consen 4 FLIVSIFIVMGLLGLSICTTLK 25 (50)
T ss_pred hHHHHHHHHHHHHHHHHHHHhh
Confidence 4667777777776666654444
No 44
>PF00558 Vpu: Vpu protein; InterPro: IPR008187 The Human immunodeficiency virus 1 (HIV-1) Vpu protein acts in the degradation of CD4 in the endoplasmic reticulum and in the enhancement of virion release from the plasma membrane of infected cells [].; GO: 0019076 release of virus from host; PDB: 2JPX_A 1PI8_A 2GOH_A 2GOF_A 1PI7_A 1PJE_A 1VPU_A 2K7Y_A.
Probab=34.55 E-value=47 Score=27.71 Aligned_cols=32 Identities=19% Similarity=0.544 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHhhHhhhhc
Q 016200 17 FFLTIFFTVTLFLTYKKIKRLQELENYANVLK 48 (393)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 48 (393)
++++|..-...|..|+|+||-.++.....-+.
T Consensus 16 ~iiaIvvW~iv~ieYrk~~rqrkId~li~RIr 47 (81)
T PF00558_consen 16 LIIAIVVWTIVYIEYRKIKRQRKIDRLIERIR 47 (81)
T ss_dssp HHHHHHHHHHH------------CHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 34455555567899999999888877766554
No 45
>PRK09039 hypothetical protein; Validated
Probab=34.27 E-value=78 Score=31.10 Aligned_cols=22 Identities=36% Similarity=0.794 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhHH
Q 016200 11 LLVISFFFLTIFFTVTLFLTYK 32 (393)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~ 32 (393)
||.+.+|.||||..+-+||...
T Consensus 26 ll~~~~f~l~~f~~~q~fLs~~ 47 (343)
T PRK09039 26 LLLVIMFLLTVFVVAQFFLSRE 47 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4444567889999999998754
No 46
>TIGR02680 conserved hypothetical protein TIGR02680. Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length.
Probab=33.54 E-value=5.4e+02 Score=29.94 Aligned_cols=46 Identities=20% Similarity=0.238 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHHHHHHHhh
Q 016200 298 SIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPACKKMFEVC 343 (393)
Q Consensus 298 S~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAYKkMlE~g 343 (393)
.+++.++.+.+++.+...|++.......=-++|+-||+|+.--|+.
T Consensus 291 ~~~~~~~~~~~~~~~~~~le~~~~~l~~~~~~l~~~~a~~~~~eL~ 336 (1353)
T TIGR02680 291 ELETAREEERELDARTEALEREADALRTRLEALQGSPAYQDAEELE 336 (1353)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 4455566666666666666666655666667899999998877776
No 47
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=33.50 E-value=1.1e+02 Score=26.72 Aligned_cols=57 Identities=21% Similarity=0.264 Sum_probs=40.8
Q ss_pred HHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhh-hhHHHHHHHHhhcCCcchHHHHHH
Q 016200 241 LYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETI-KRKFSIQKALLSKADRSSIDRLRQ 304 (393)
Q Consensus 241 qYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~i-qRkftI~KALLskadRSS~DRL~q 304 (393)
.|.|+++...+..-+..+|.+|+- .+|.+|+-.| ....+|.|.|+.+. .+.|.|-++
T Consensus 21 ~~~Eia~~t~~s~~~~~ei~d~L~------kRL~~~~~hVK~K~Lrilk~l~~~G-~~~f~~~~~ 78 (122)
T cd03572 21 LYEEIAKLTRKSVGSCQELLEYLL------KRLKRSSPHVKLKVLKIIKHLCEKG-NSDFKRELQ 78 (122)
T ss_pred HHHHHHHHHHcCHHHHHHHHHHHH------HHhcCCCCcchHHHHHHHHHHHhhC-CHHHHHHHH
Confidence 688999888875555555555543 5789999888 55678888887776 477876543
No 48
>PRK11637 AmiB activator; Provisional
Probab=33.50 E-value=4.9e+02 Score=25.79 Aligned_cols=71 Identities=20% Similarity=0.190 Sum_probs=30.0
Q ss_pred HHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcC------CcchHHHHHHHHHHHHHHHHhhhhhHHHHHHH
Q 016200 256 LAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKA------DRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWL 326 (393)
Q Consensus 256 LaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLska------dRSS~DRL~qQIykLE~EqkRLekDa~VYN~L 326 (393)
+.++..-..-|.+.+.+|..+-..++....-.++-...- .+.-.++|..++...+.+...|+.+..-...+
T Consensus 172 l~~l~~~~~~L~~~k~~le~~~~~l~~~~~e~~~~k~~L~~~k~e~~~~l~~L~~~~~~~~~~l~~l~~~~~~L~~~ 248 (428)
T PRK11637 172 IAELKQTREELAAQKAELEEKQSQQKTLLYEQQAQQQKLEQARNERKKTLTGLESSLQKDQQQLSELRANESRLRDS 248 (428)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444555555555444443333222222211110 11234455555555555555555554443333
No 49
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=33.46 E-value=69 Score=24.58 Aligned_cols=25 Identities=36% Similarity=0.514 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHhhhhhHHHHH
Q 016200 300 DRLRQQIYNLEKQQRRLEEDVYVYN 324 (393)
Q Consensus 300 DRL~qQIykLE~EqkRLekDa~VYN 324 (393)
.=|++||..||.+.++|..+...|-
T Consensus 2 ~aLrqQv~aL~~qv~~Lq~~fs~yK 26 (46)
T PF09006_consen 2 NALRQQVEALQGQVQRLQAAFSQYK 26 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3589999999999999988776654
No 50
>PF05399 EVI2A: Ectropic viral integration site 2A protein (EVI2A); InterPro: IPR008608 This family contains several mammalian ectropic viral integration site 2A (EVI2A) proteins. The function of this protein is unknown although it is thought to be a membrane protein and may function as an oncogene in retrovirus induced myeloid tumours [, ].; GO: 0016021 integral to membrane
Probab=33.45 E-value=62 Score=31.52 Aligned_cols=26 Identities=38% Similarity=0.704 Sum_probs=17.1
Q ss_pred hHHHHHHHHHHHHH--HHHHHHHHHHhH
Q 016200 6 LMLFMLLVISFFFL--TIFFTVTLFLTY 31 (393)
Q Consensus 6 ~~~~~~~~~~~~~~--~~~~~~~~~~~~ 31 (393)
+||..|++|...|| ||.|..|..|.-
T Consensus 129 amLIClIIIAVLfLICT~LfLSTVVLAN 156 (227)
T PF05399_consen 129 AMLICLIIIAVLFLICTLLFLSTVVLAN 156 (227)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67777777765544 677777766653
No 51
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=32.68 E-value=81 Score=32.61 Aligned_cols=32 Identities=28% Similarity=0.447 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHhhHhhhhc
Q 016200 17 FFLTIFFTVTLFLTYKKIKRLQELENYANVLK 48 (393)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 48 (393)
..+.|++++.+|+.-+..+++.+||+.-+-|.
T Consensus 11 ii~i~~~~~~~~~rr~~~~~i~~Le~~k~~l~ 42 (569)
T PRK04778 11 VIIIIAYLAGLILRKRNYKRIDELEERKQELE 42 (569)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34445555557777777788888888766554
No 52
>PHA02562 46 endonuclease subunit; Provisional
Probab=32.66 E-value=4.7e+02 Score=25.98 Aligned_cols=40 Identities=18% Similarity=0.312 Sum_probs=31.4
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHHHH
Q 016200 298 SIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPACKK 338 (393)
Q Consensus 298 S~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAYKk 338 (393)
.+.+|.+++..+..+...++++...+..+++.|+- +.|+.
T Consensus 380 ~l~~l~~~l~~~~~~~~~~~ke~~~~~~i~~~~~~-~g~~~ 419 (562)
T PHA02562 380 ELAKLQDELDKIVKTKSELVKEKYHRGIVTDLLKD-SGIKA 419 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hhHHH
Confidence 35577888888888888899998888888888775 55654
No 53
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=31.01 E-value=49 Score=23.09 Aligned_cols=24 Identities=17% Similarity=0.439 Sum_probs=18.7
Q ss_pred HHHHHhhhccCcchHHHHHHHHHh
Q 016200 242 YHQLVQSCESNELTLAQVGEFTKC 265 (393)
Q Consensus 242 YDELvran~aK~LTLaQV~eF~Nc 265 (393)
+-+|++-+..-++|..||++|+..
T Consensus 5 W~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 5 WVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHh
Confidence 457888888999999999999864
No 54
>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].
Probab=30.38 E-value=2.6e+02 Score=24.65 Aligned_cols=77 Identities=22% Similarity=0.388 Sum_probs=51.1
Q ss_pred HHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhh
Q 016200 237 KIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRL 316 (393)
Q Consensus 237 RIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRL 316 (393)
.|++.|.+|....+...++-. .+..+|=.-..++..|.+++-.-+.-..|... +-..-..||..-....|...++|
T Consensus 5 el~~~~~~l~~~~e~~~~d~e---~~~dtLe~i~~~~~~K~~~~~~~Ik~~ea~~e-~~k~E~krL~~rkk~~e~~~~~L 80 (162)
T PF05565_consen 5 ELTDEYLELLELLEEGDLDEE---AIADTLESIEDEIEEKADNIAKVIKNLEADIE-AIKAEIKRLQERKKSIENRIDRL 80 (162)
T ss_pred HHHHHHHHHHHHHhcCCCCHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 578899999987776665543 35566666688899999998776665555433 33445556666666666666665
Q ss_pred h
Q 016200 317 E 317 (393)
Q Consensus 317 e 317 (393)
+
T Consensus 81 k 81 (162)
T PF05565_consen 81 K 81 (162)
T ss_pred H
Confidence 5
No 55
>PHA03030 hypothetical protein; Provisional
Probab=30.37 E-value=38 Score=30.12 Aligned_cols=20 Identities=40% Similarity=0.999 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 016200 8 LFMLLVISFFFLTIFFTVTL 27 (393)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~ 27 (393)
.|.+|.+.|.|+.|||-++.
T Consensus 4 i~~ili~lfifl~iffYI~~ 23 (122)
T PHA03030 4 IFLILIFLFIFLFIFFYIRI 23 (122)
T ss_pred ehHHHHHHHHHHHHHHHhee
Confidence 46667777777777776543
No 56
>PF13706 PepSY_TM_3: PepSY-associated TM helix
Probab=30.27 E-value=89 Score=21.78 Aligned_cols=27 Identities=19% Similarity=0.501 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 016200 9 FMLLVISFFFLTIFFTVTLFLTYKKIK 35 (393)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 35 (393)
.+-++++.+++.+|+|-++..-...|.
T Consensus 10 W~Gl~~g~~l~~~~~tG~~~~f~~ei~ 36 (37)
T PF13706_consen 10 WLGLILGLLLFVIFLTGAVMVFRDEID 36 (37)
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHhhc
Confidence 455778888888888887776655554
No 57
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=30.20 E-value=3.1e+02 Score=22.48 Aligned_cols=67 Identities=27% Similarity=0.377 Sum_probs=46.3
Q ss_pred HHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhh
Q 016200 239 KELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEE 318 (393)
Q Consensus 239 keqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLek 318 (393)
..-|+=|-+.|.+-..-...+.+.++-|-..-+.|.+|.+. ++...+||+.+|.+...|+.
T Consensus 20 ~~d~~LLe~mN~~~~~kY~~~~~~~~~l~~~~~~l~~k~~~-------------------l~~~l~~Id~Ie~~V~~LE~ 80 (99)
T PF10046_consen 20 NEDYNLLENMNKATSLKYKKMKDIAAGLEKNLEDLNQKYEE-------------------LQPYLQQIDQIEEQVTELEQ 80 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------------------HHHHHHHHHHHHHHHHHHHH
Confidence 35677777888877777777777777777777777776654 44556677777777777766
Q ss_pred hHHHHH
Q 016200 319 DVYVYN 324 (393)
Q Consensus 319 Da~VYN 324 (393)
=|+.-+
T Consensus 81 ~v~~LD 86 (99)
T PF10046_consen 81 TVYELD 86 (99)
T ss_pred HHHHHH
Confidence 665433
No 58
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=29.66 E-value=95 Score=23.83 Aligned_cols=35 Identities=20% Similarity=0.381 Sum_probs=26.2
Q ss_pred hHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHH
Q 016200 233 ATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLA 267 (393)
Q Consensus 233 AtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLV 267 (393)
++=+.|-++|.++|.......++-.+|.++++-|-
T Consensus 16 ~~~~~vy~~Y~~lc~~~~~~pls~~r~~~~l~eL~ 50 (85)
T PF09079_consen 16 VTTGEVYEVYEELCESLGVDPLSYRRFSDYLSELE 50 (85)
T ss_dssp EEHHHHHHHHHHHHHHTTS----HHHHHHHHHHHH
T ss_pred eeHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 34468999999999999999999999999988764
No 59
>cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322
Probab=29.38 E-value=1.1e+02 Score=22.76 Aligned_cols=32 Identities=16% Similarity=0.339 Sum_probs=17.3
Q ss_pred CCcchhHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 016200 1 MDENNLMLFMLLVISFFFLTIFFTVTLFLTYK 32 (393)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 (393)
||.++.+--..-+..++++.++|...++..|.
T Consensus 1 Md~~~~lr~~a~~~~l~~~~~~Figiv~wa~~ 32 (48)
T cd01324 1 MDIGETLRGLADSWGLLYLALFFLGVVVWAFR 32 (48)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 66664333334445555555666666666664
No 60
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=28.83 E-value=2.2e+02 Score=22.99 Aligned_cols=39 Identities=18% Similarity=0.353 Sum_probs=22.6
Q ss_pred hhhhHHHHHHHHhhcCC------cchHHHHHHHHHHHHHHHHhhh
Q 016200 279 TIKRKFSIQKALLSKAD------RSSIDRLRQQIYNLEKQQRRLE 317 (393)
Q Consensus 279 ~iqRkftI~KALLskad------RSS~DRL~qQIykLE~EqkRLe 317 (393)
..+.+|.=...|+..+. +..++.|.+||..|..+-+||.
T Consensus 25 ~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql~rLs 69 (70)
T PF04899_consen 25 EWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLSEQLERLS 69 (70)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34444554555555432 4566777777777777666664
No 61
>PF04277 OAD_gamma: Oxaloacetate decarboxylase, gamma chain ; InterPro: IPR005899 This family comprises distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases. These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit [].; GO: 0008948 oxaloacetate decarboxylase activity, 0015081 sodium ion transmembrane transporter activity, 0071436 sodium ion export, 0016020 membrane
Probab=27.94 E-value=1.2e+02 Score=23.15 Aligned_cols=14 Identities=29% Similarity=0.465 Sum_probs=6.1
Q ss_pred HHHHHHHHHHHHHH
Q 016200 13 VISFFFLTIFFTVT 26 (393)
Q Consensus 13 ~~~~~~~~~~~~~~ 26 (393)
.|.|+||.+.+.+.
T Consensus 13 ~iVF~~L~lL~~~i 26 (79)
T PF04277_consen 13 GIVFLVLILLILVI 26 (79)
T ss_pred HHHHHHHHHHHHHH
Confidence 34444444444333
No 62
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=27.03 E-value=2.4e+02 Score=20.28 Aligned_cols=20 Identities=15% Similarity=0.335 Sum_probs=15.3
Q ss_pred HHHhhhccCcchHHHHHHHH
Q 016200 244 QLVQSCESNELTLAQVGEFT 263 (393)
Q Consensus 244 ELvran~aK~LTLaQV~eF~ 263 (393)
+++++.++=++||+++.+|.
T Consensus 5 ~~I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 5 QFIRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 35777888899999999999
No 63
>PF13010 pRN1_helical: Primase helical domain; PDB: 1RO0_A 1RNI_A 1RO2_A 3M1M_A.
Probab=26.85 E-value=28 Score=31.55 Aligned_cols=19 Identities=42% Similarity=0.962 Sum_probs=13.2
Q ss_pred hhhhhccCCCC----hhhhhhcc
Q 016200 94 TLLLEILPSKS----AKWDRLLS 112 (393)
Q Consensus 94 sll~eilps~s----~kw~~l~~ 112 (393)
..|..+||+|| |||+..|.
T Consensus 97 d~l~qlLP~DSKvf~pKWdkYf~ 119 (135)
T PF13010_consen 97 DVLLQLLPEDSKVFAPKWDKYFV 119 (135)
T ss_dssp HHHHHHS-TT-TTTS-HHHHHHH
T ss_pred HHHHHHCcccccccccchhHHHH
Confidence 46889999997 89998773
No 64
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=26.40 E-value=1.4e+02 Score=21.94 Aligned_cols=37 Identities=19% Similarity=0.395 Sum_probs=28.3
Q ss_pred chHHHHHHHHHHHHHHHHhh-hhhHHHHHHHHHHhccC
Q 016200 297 SSIDRLRQQIYNLEKQQRRL-EEDVYVYNWLQDQLRLS 333 (393)
Q Consensus 297 SS~DRL~qQIykLE~EqkRL-ekDa~VYN~LQqQLKlS 333 (393)
.-.+.+.+++..|+.+.++| .-+.+|-..-.++|+++
T Consensus 31 ~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~AR~~lgm~ 68 (80)
T PF04977_consen 31 KEIEELKKENEELKEEIERLKNDPDYIEKVAREKLGMV 68 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcCCc
Confidence 35567788888888888888 66677777777788775
No 65
>PF05597 Phasin: Poly(hydroxyalcanoate) granule associated protein (phasin); InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=26.26 E-value=4.6e+02 Score=23.19 Aligned_cols=54 Identities=20% Similarity=0.363 Sum_probs=38.4
Q ss_pred HhHHHHHHHHhhhhhhhhhHH--HHHHHHh--hcCCcchHHHHHHHHHHHHHHHHhhh
Q 016200 264 KCLAQAREELEDKSETIKRKF--SIQKALL--SKADRSSIDRLRQQIYNLEKQQRRLE 317 (393)
Q Consensus 264 NcLVdARnEL~~KSE~iqRkf--tI~KALL--skadRSS~DRL~qQIykLE~EqkRLe 317 (393)
...=++++...+.-+.+...| +|.+||= --+.|.-+|=|...|+.|+.+..+|.
T Consensus 72 ~~~~~~~~~~~~~~dklE~~fd~rV~~aL~rLgvPs~~dv~~L~~rId~L~~~v~~l~ 129 (132)
T PF05597_consen 72 SRVDDVKERATGQWDKLEQAFDERVARALNRLGVPSRKDVEALSARIDQLTAQVERLA 129 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 344466777777777777766 5666662 23557788888888888888888775
No 66
>TIGR01386 cztS_silS_copS heavy metal sensor kinase. Members of this family contain a sensor histidine kinase domain (Pfam:PF00512) and a domain found in bacterial signal proteins (Pfam:PF00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc.
Probab=26.19 E-value=1.9e+02 Score=26.50 Aligned_cols=30 Identities=13% Similarity=0.203 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHhhHhhhh
Q 016200 18 FLTIFFTVTLFLTYKKIKRLQELENYANVL 47 (393)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (393)
++.+++.+.+|+...-++.|..|...++-+
T Consensus 173 ~~~~~~~~~~~~~r~i~~pl~~l~~~~~~i 202 (457)
T TIGR01386 173 LVLLTALLGWWITRLGLEPLRRLSAVAARI 202 (457)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHh
Confidence 333444455566666667777777776655
No 67
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway.
Probab=25.90 E-value=67 Score=25.64 Aligned_cols=17 Identities=24% Similarity=0.737 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHhHHH
Q 016200 17 FFLTIFFTVTLFLTYKK 33 (393)
Q Consensus 17 ~~~~~~~~~~~~~~~~~ 33 (393)
|.+.+|+.|.+|+.+|.
T Consensus 75 ~~~~~f~~~v~yI~~rR 91 (92)
T PF03908_consen 75 FAFLFFLLVVLYILWRR 91 (92)
T ss_pred HHHHHHHHHHHHHhhhc
Confidence 33444555666665553
No 68
>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function.
Probab=25.78 E-value=8.7e+02 Score=26.26 Aligned_cols=98 Identities=19% Similarity=0.269 Sum_probs=54.7
Q ss_pred HHHHHHHHHHHhhhccCcchH----HHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHH-HHHH---HHH
Q 016200 236 RKIKELYHQLVQSCESNELTL----AQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSID-RLRQ---QIY 307 (393)
Q Consensus 236 RRIkeqYDELvran~aK~LTL----aQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~D-RL~q---QIy 307 (393)
..+.+-|+.|-.....+.... .+|.++-...=+.-.|++.|.+.++.--+.-+.|=....|++|= ||.+ .|.
T Consensus 422 ~pL~~e~r~lk~~~~~~~~e~~~~~~~ik~~r~~~k~~~~e~~~Kee~~~qL~~e~e~~~k~~~Rs~Yt~RIlEIv~NI~ 501 (594)
T PF05667_consen 422 APLIEEYRRLKEKASNRESESKQKLQEIKELREEIKEIEEEIRQKEELYKQLVKELEKLPKDVNRSAYTRRILEIVKNIR 501 (594)
T ss_pred hHHHHHHHHHHHHHhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHHHhHH
Confidence 345566777776666555444 33334333333444444444444444444444444556799886 7754 455
Q ss_pred HHHHHHHhhhhhHHHH----HHHHHHhccC
Q 016200 308 NLEKQQRRLEEDVYVY----NWLQDQLRLS 333 (393)
Q Consensus 308 kLE~EqkRLekDa~VY----N~LQqQLKlS 333 (393)
|=..+..+.-.|+--+ |+|+.+|.-+
T Consensus 502 KQk~eI~KIl~DTr~lQkeiN~l~gkL~Rt 531 (594)
T PF05667_consen 502 KQKEEIEKILSDTRELQKEINSLTGKLDRT 531 (594)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 5555566666676554 6677776654
No 69
>KOG1666 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.54 E-value=1.2e+02 Score=29.52 Aligned_cols=64 Identities=14% Similarity=0.207 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchH
Q 016200 236 RKIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSI 299 (393)
Q Consensus 236 RRIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~ 299 (393)
+||++.|+-.+---+-..==|.+.+.=-+.|-.||..|.+-++++-|+-+|.+.|.-.+-+..|
T Consensus 135 ~rl~ds~Ria~ETEqIG~~IL~dL~~QRe~L~rar~rL~~td~~lgkS~kiL~tM~RR~~~nk~ 198 (220)
T KOG1666|consen 135 DRLKDSQRIALETEQIGSEILEDLHGQREQLERARERLRETDANLGKSRKILTTMTRRLIRNKF 198 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhhHHHHHHHHHHHHHHHHHH
Confidence 5788888876654443333455666667889999999999999999999999999865554433
No 70
>PF07200 Mod_r: Modifier of rudimentary (Mod(r)) protein; InterPro: IPR009851 This entry represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic [], and both of these regions are represented in this family.; PDB: 2CAZ_F 2P22_C 2F66_F.
Probab=25.39 E-value=1.8e+02 Score=24.54 Aligned_cols=21 Identities=19% Similarity=0.415 Sum_probs=15.6
Q ss_pred ccccHHHHHhhhhhh--hhhhhc
Q 016200 365 ADISFEELLAQEKKD--SFWQKN 385 (393)
Q Consensus 365 adiSFEELLAqEKkD--sFWqrn 385 (393)
.+|++++.+.+++.- -|+-|.
T Consensus 122 g~~d~~~Fl~~f~~~R~~yH~R~ 144 (150)
T PF07200_consen 122 GEIDVDDFLKQFKEKRKLYHLRR 144 (150)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Confidence 378899999998876 555543
No 71
>COG3352 FlaC Putative archaeal flagellar protein C [Cell motility and secretion]
Probab=25.22 E-value=2.6e+02 Score=26.17 Aligned_cols=68 Identities=18% Similarity=0.221 Sum_probs=50.5
Q ss_pred HHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhHHHH
Q 016200 256 LAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDVYVY 323 (393)
Q Consensus 256 LaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLekDa~VY 323 (393)
++...+=++-|=.-=..|---.|++-|.|-+-++.+.+--|+-.|-|.+||.+|+...+-..+|+..+
T Consensus 74 ~~~~~eelerLe~~iKdl~~lye~Vs~d~Npf~s~~~qes~~~veel~eqV~el~~i~emv~~d~~~l 141 (157)
T COG3352 74 LQDIKEELERLEENIKDLVSLYELVSRDFNPFMSKTPQESRGIVEELEEQVNELKMIVEMVIKDLREL 141 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHhccchhh
Confidence 33444444444333334445577888889999999998888889999999999999999999998653
No 72
>PRK09966 putative inner membrane diguanylate cyclase; Provisional
Probab=25.10 E-value=2.2e+02 Score=26.69 Aligned_cols=15 Identities=27% Similarity=0.200 Sum_probs=10.8
Q ss_pred HHHhhHhhhhccccc
Q 016200 38 QELENYANVLKGSLS 52 (393)
Q Consensus 38 ~~~~~~~~~~~~~~~ 52 (393)
++|+..++++.-++.
T Consensus 50 ~~l~~~a~~~a~~l~ 64 (407)
T PRK09966 50 KNLALTAATMTYSLE 64 (407)
T ss_pred hhHHHHHHHHhcccc
Confidence 567788888776664
No 73
>PF09094 DUF1925: Domain of unknown function (DUF1925); InterPro: IPR015178 Alpha-amylase is classified as family 13 of the glycosyl hydrolases and is present in archaea, bacteria, plants and animals. Alpha-amylase is an essential enzyme in alpha-glucan metabolism, acting to catalyse the hydrolysis of alpha-1,4-glucosidic bonds of glycogen, starch and related polysaccharides. Although all alpha-amylases possess the same catalytic function, they can vary with respect to sequence. In general, they are composed of three domains: a TIM barrel containing the active site residues and chloride ion-binding site (domain A), a long loop region inserted between the third beta strand and the alpha-helix of domain A that contains calcium-binding site(s) (domain B), and a C-terminal beta-sheet domain that appears to show some variability in sequence and length between amylases (domain C) []. Amylases have at least one conserved calcium-binding site, as calcium is essential for the stability of the enzyme. The chloride-binding functions to activate the enzyme, which acts by a two-step mechanism involving a catalytic nucleophile base (usually an Asp) and a catalytic proton donor (usually a Glu) that are responsible for the formation of the beta-linked glycosyl-enzyme intermediate. This entry represents a domain found in prokaryotic alpha-amylase (3.2.1.1 from EC) and 4-alpha-glucanotransferase (2.4.1.25 from EC). It is adjacent to the C-terminal domain (see IPR015179 from INTERPRO). The exact function of this domain is, as yet, unknown. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; PDB: 1K1X_B 1K1W_A 1K1Y_A.
Probab=25.03 E-value=59 Score=27.12 Aligned_cols=39 Identities=23% Similarity=0.459 Sum_probs=24.5
Q ss_pred HHHHHHHhhhhhhhcccCCCCCCCCcccccccccHHHHHhhhhhhhhhh
Q 016200 335 ACKKMFEVCADMELKTKSSKPLENTETDEFADISFEELLAQEKKDSFWQ 383 (393)
Q Consensus 335 AYKkMlE~ga~~Elk~~~~~~le~~~a~e~adiSFEELLAqEKkDsFWq 383 (393)
.||+|+.++.-.. .+ ++ ....+-..++|+.-.=-|+||.
T Consensus 16 mhkRMl~vs~~~~-------~~--~~-~~~~~~a~~~L~~aQcNd~yWH 54 (80)
T PF09094_consen 16 MHKRMLYVSSKVR-------QL--PD-KKRKEEAREELYRAQCNDAYWH 54 (80)
T ss_dssp HHHHHHHHHHHHT-------T----------HHHHHHHHHTTBGGGG--
T ss_pred HHHHHHHHHHHHH-------Hh--hh-hhhhHHHHHHHHHhccCcchhc
Confidence 5899999996655 11 11 1233346899999999999996
No 74
>KOG4687 consensus Uncharacterized coiled-coil protein [Function unknown]
Probab=24.57 E-value=2.8e+02 Score=28.59 Aligned_cols=115 Identities=22% Similarity=0.213 Sum_probs=80.1
Q ss_pred HHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHH-----HHhhcCCcchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhc
Q 016200 257 AQVGEFTKCLAQAREELEDKSETIKRKFSIQK-----ALLSKADRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLR 331 (393)
Q Consensus 257 aQV~eF~NcLVdARnEL~~KSE~iqRkftI~K-----ALLskadRSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLK 331 (393)
+|...=+...||-+.||.-.-+..+|+---.. +|=-+.+|+. -++|+.|=.|-+=|..-+.+-..=-+-.|
T Consensus 170 a~LafDLkamideKEELimERDa~kcKa~RLnhELfvaLnadkrhpr----~~DiDgll~ENkfLhaklkiadeElEliK 245 (389)
T KOG4687|consen 170 AGLAFDLKAMIDEKEELIMERDAMKCKAARLNHELFVALNADKRHPR----AEDIDGLLAENKFLHAKLKIADEELELIK 245 (389)
T ss_pred hhhhhHHHHHhchHHHHHHHHHHHHHHHHHhhhHHHHHHcCCCCCch----hhhhHHHHHhhHHHHHHhcccHHHHHHHH
Confidence 45555566777777777776666666533222 2211222332 36788888888888877777776666777
Q ss_pred cCHH-HHHHHHhhhhhhhcccCCCCCCCCcccccccccH---HHHHhh
Q 016200 332 LSPA-CKKMFEVCADMELKTKSSKPLENTETDEFADISF---EELLAQ 375 (393)
Q Consensus 332 lSpA-YKkMlE~ga~~Elk~~~~~~le~~~a~e~adiSF---EELLAq 375 (393)
+|-+ ||.|.+--..--|+.+.....++-+..+++=|+- .|+||-
T Consensus 246 ~siaKYKqM~dAknvqtmrkkgi~a~~G~dknedaiin~kQikeiLaS 293 (389)
T KOG4687|consen 246 MSIAKYKQMADAKNVQTMRKKGIKAGEGDDKNEDAIINMKQIKEILAS 293 (389)
T ss_pred HHHHHHHHHHHHHhHHHHHhcCCccCCCCCCcchheecHHHHHHHHHc
Confidence 7754 9999999888888889999998888888888875 466664
No 75
>PF04683 Proteasom_Rpn13: Proteasome complex subunit Rpn13 ubiquitin receptor; InterPro: IPR006773 This family was thought originally to be involved in cell-adhesion [, ], but the members are now known to be proteasome subunit Rpn13, a novel ubiquitin receptor. The 26S proteasome is a huge macromolecular protein-degradation machine consisting of a proteolytically active 20S core, in the form of four disc-like proteins, and one or two 19S regulatory particles. The regulatory particle(s) sit on the top and or bottom of the core, de-ubiquitinate the substrate peptides, unfold them and guide them into the narrow channel through the centre of the core. Rpn13 and its homologues dock onto the regulatory particle through the N-terminal region which binds Rpn2. The C-terminal part of the domain binds de-ubiquitinating enzyme Uch37/UCHL5 and enhances its isopeptidase activity. Rpn13 binds ubiquitin via a conserved amino-terminal region called the pleckstrin-like receptor for ubiquitin, termed Pru, domain []. The domain forms two contiguous anti-parallel beta-sheets with a configuration similar to the pleckstrin-homology domain (PHD) fold []. Rpn13's ability to bind ubiquitin and the proteasome subunit Rpn2/S1 simultaneously supports evidence of its role as a ubiquitin receptor. Finally, when complexed to di-ubiquitin, via the Pru, and Uch37 via the C-terminal part, it frees up the distal ubiquitin for de-ubiquitination by the Uch37 []. ; GO: 0005634 nucleus, 0005737 cytoplasm; PDB: 2Z4D_A 2KR0_A 2Z59_A 2R2Y_A.
Probab=23.99 E-value=26 Score=28.38 Aligned_cols=16 Identities=44% Similarity=0.702 Sum_probs=11.1
Q ss_pred Cccccccccccchhhh
Q 016200 160 RQETVDGCATGRVLVV 175 (393)
Q Consensus 160 ~~~~~~~~~~~~~~~~ 175 (393)
.-..|+.|.||||.|.
T Consensus 54 ~f~~V~~c~tGRVy~L 69 (85)
T PF04683_consen 54 TFKKVPQCKTGRVYVL 69 (85)
T ss_dssp EEEE-TTSSTS-EEEE
T ss_pred EEEECCcCCCCeEEEE
Confidence 3457899999999875
No 76
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=23.92 E-value=2.1e+02 Score=27.57 Aligned_cols=32 Identities=34% Similarity=0.551 Sum_probs=26.4
Q ss_pred chHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhc
Q 016200 297 SSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLR 331 (393)
Q Consensus 297 SS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLK 331 (393)
...+=|..|...+-.|+.||.+| |+.||+|+.
T Consensus 179 ~~~~al~Kq~e~~~~EydrLlee---~~~Lq~~i~ 210 (216)
T KOG1962|consen 179 KKVDALKKQSEGLQDEYDRLLEE---YSKLQEQIE 210 (216)
T ss_pred HHHHHHHHHHHHcccHHHHHHHH---HHHHHHHHh
Confidence 35667788889999999999888 789999875
No 77
>TIGR02135 phoU_full phosphate transport system regulatory protein PhoU. This model describes PhoU, a regulatory protein of unknown mechanism for high-affinity phosphate ABC transporter systems. The protein consists of two copies of the domain described by Pfam model pfam01895. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect and so likely has some second function.
Probab=23.92 E-value=4e+02 Score=22.20 Aligned_cols=57 Identities=21% Similarity=0.283 Sum_probs=43.0
Q ss_pred HHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhHHH
Q 016200 262 FTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDVYV 322 (393)
Q Consensus 262 F~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLekDa~V 322 (393)
|..-|..+|.++..=++.+..-+.-....+.+.+ ..+.++|.+.|.+-.+|...+.-
T Consensus 3 ~~~~l~~~~~el~~m~~~~~~ml~~~~~~~~~~d----~~~~~~i~~~e~~id~l~~~i~~ 59 (212)
T TIGR02135 3 FDEELKELREELLEMGGLVEEQLEDAVRALTEKD----RELARKVIEDDDQINALEVKIEE 59 (212)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC----HHHHHHHHHChHHHHHHHHHHHH
Confidence 5566888999999888888888888777777655 24567777777777777776643
No 78
>TIGR01558 sm_term_P27 phage terminase, small subunit, putative, P27 family. Members tend to be adjacent to the phage terminase large subunit gene.
Probab=23.68 E-value=44 Score=27.45 Aligned_cols=35 Identities=17% Similarity=0.204 Sum_probs=27.0
Q ss_pred HhhcCCcchHHHHHHHHHHHHHHHHhhhhhHHHHH
Q 016200 290 LLSKADRSSIDRLRQQIYNLEKQQRRLEEDVYVYN 324 (393)
Q Consensus 290 LLskadRSS~DRL~qQIykLE~EqkRLekDa~VYN 324 (393)
+|+.+|...+.++|.-+.....-.+.++++-.+|.
T Consensus 26 ~l~~~D~~~l~~yc~a~~~~~~a~~~i~~~G~~~~ 60 (116)
T TIGR01558 26 ILTNLDRDALLRYCEAYDRYREATDDLEATGITAT 60 (116)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHcCeeEE
Confidence 67888888999998888888777777776665553
No 79
>PF00226 DnaJ: DnaJ domain; InterPro: IPR001623 The prokaryotic heat shock protein DnaJ interacts with the chaperone hsp70-like DnaK protein []. Structurally, the DnaJ protein consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acids, a glycine-rich region ('G' domain') of about 30 residues, a central domain containing four repeats of a CXXCXGXG motif ('CRR' domain) and a C-terminal region of 120 to 170 residues. Such a structure is shown in the following schematic representation: +------------+-+-------+-----+-----------+--------------------------------+ | N-terminal | | Gly-R | | CXXCXGXG | C-terminal | +------------+-+-------+-----+-----------+--------------------------------+ It is thought that the 'J' domain of DnaJ mediates the interaction with the dnaK protein and consists of four helices, the second of which has a charged surface that includes at least one pair of basic residues that are essential for interaction with the ATPase domain of Hsp70. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins [], either together or separately. In yeast, J-domains have been classified into 3 groups; the class III proteins are functionally distinct and do not appear to act as molecular chaperones []. ; GO: 0031072 heat shock protein binding; PDB: 2GUZ_C 2L6L_A 1HDJ_A 2EJ7_A 1FPO_C 2CUG_A 2QSA_A 2OCH_A 3BVO_B 3APQ_A ....
Probab=23.47 E-value=2.8e+02 Score=19.75 Aligned_cols=45 Identities=24% Similarity=0.286 Sum_probs=30.7
Q ss_pred chhHHHHHHHHHHHHHhhhccCcchH--HHHHHHHHhHHHHHHHHhh
Q 016200 231 GSATQRKIKELYHQLVQSCESNELTL--AQVGEFTKCLAQAREELED 275 (393)
Q Consensus 231 ~sAtQRRIkeqYDELvran~aK~LTL--aQV~eF~NcLVdARnEL~~ 275 (393)
..|.+-.|+++|..|++...--++.- +...+....|..|..-|..
T Consensus 10 ~~~~~~eik~~y~~l~~~~HPD~~~~~~~~~~~~~~~i~~Ay~~L~~ 56 (64)
T PF00226_consen 10 PDASDEEIKKAYRRLSKQYHPDKNSGDEAEAEEKFARINEAYEILSD 56 (64)
T ss_dssp TTSSHHHHHHHHHHHHHHTSTTTGTSTHHHHHHHHHHHHHHHHHHHS
T ss_pred CCCCHHHHHHHHHhhhhccccccchhhhhhhhHHHHHHHHHHHHhCC
Confidence 37789999999999999987655433 3445555555556555543
No 80
>PF00672 HAMP: HAMP domain; InterPro: IPR003660 The HAMP linker domain (present in Histidine kinases, Adenyl cyclases, Methyl-accepting proteins and Phosphatases) is an approximately 50-amino acid alpha-helical region. It is found in bacterial sensor and chemotaxis proteins and in eukaryotic histidine kinases. The bacterial proteins are usually integral membrane proteins and part of a two-component signal transduction pathway. One or several copies of the HAMP domain can be found in association with other domains, such as the histidine kinase domain, the bacterial chemotaxis sensory transducer domain, the PAS repeat, the EAL domain, the GGDEF domain, the protein phosphatase 2C-like domain, the guanylate cyclase domain, or the response regulatory domain. It has been suggested that the HAMP domain possesses a role of regulating the phosphorylation or methylation of homodimeric receptors by transmitting the conformational changes in periplasmic ligand-binding domains to cytoplasmic signalling kinase and methyl-acceptor domains.; GO: 0004871 signal transducer activity, 0007165 signal transduction, 0016021 integral to membrane; PDB: 3PJX_A 3PJW_A 3ZX6_B 2Y20_B 2Y0Q_D 2Y21_H 3ZRW_C 2L7H_B 2LFS_B 2L7I_B ....
Probab=23.34 E-value=71 Score=22.64 Aligned_cols=24 Identities=13% Similarity=0.228 Sum_probs=13.3
Q ss_pred HHHHHHHHhHHHHHHHHHHhhHhh
Q 016200 22 FFTVTLFLTYKKIKRLQELENYAN 45 (393)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~ 45 (393)
.+.+.+++...-.+.+++|...+.
T Consensus 12 ~~~~~~~~~~~i~~pl~~l~~~~~ 35 (70)
T PF00672_consen 12 SLLLAWLLARRITRPLRRLSDAMQ 35 (70)
T ss_dssp HHHHHHH--HTTCCCHHHHHHHCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333445556666677777776654
No 81
>PLN02302 ent-kaurenoic acid oxidase
Probab=23.30 E-value=1.5e+02 Score=28.29 Aligned_cols=29 Identities=7% Similarity=0.010 Sum_probs=15.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHhHHH
Q 016200 5 NLMLFMLLVISFFFLTIFFTVTLFLTYKK 33 (393)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (393)
|.|.++|+++.+.|+++++.+--++.|+.
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 (490)
T PLN02302 4 GSIWVWLAAIVAGVFVLKWVLRRVNSWLY 32 (490)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45556666666566665555433334433
No 82
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=23.20 E-value=1.2e+02 Score=24.43 Aligned_cols=51 Identities=18% Similarity=0.263 Sum_probs=27.2
Q ss_pred CcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhc
Q 016200 252 NELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLR 331 (393)
Q Consensus 252 K~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLK 331 (393)
++.+..||.+|+.-|.+.= ++|..++..|..+...|.....-|......|+
T Consensus 16 rGYd~~eVD~fl~~l~~~~-----------------------------~~l~~e~~~L~~~~~~l~~~l~~~~~~~~~l~ 66 (131)
T PF05103_consen 16 RGYDPDEVDDFLDELAEEL-----------------------------ERLQRENAELKEEIEELQAQLEELREEEESLQ 66 (131)
T ss_dssp EEEEHHHHHHHHHHHHHHH-----------------------------HHHHHHHHHHHHHHHCCCCT------------
T ss_pred CCcCHHHHHHHHHHHHHHH-----------------------------HHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHH
Confidence 3667789999988887644 44446666666666666666666654444443
No 83
>PRK11677 hypothetical protein; Provisional
Probab=23.05 E-value=1e+02 Score=27.35 Aligned_cols=42 Identities=26% Similarity=0.324 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhH---HHHHHHH--------HHhhHhhhhc
Q 016200 7 MLFMLLVISFFFLTIFFTVTLFLTY---KKIKRLQ--------ELENYANVLK 48 (393)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~--------~~~~~~~~~~ 48 (393)
|.+++.+|+|..-.|+-.+...++. ++.+.|+ |||.|..-+.
T Consensus 1 M~W~~a~i~livG~iiG~~~~R~~~~~~~~q~~le~eLe~~k~ele~YkqeV~ 53 (134)
T PRK11677 1 MTWEYALIGLVVGIIIGAVAMRFGNRKLRQQQALQYELEKNKAELEEYRQELV 53 (134)
T ss_pred CcHHHHHHHHHHHHHHHHHHHhhccchhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345555555444333333333333 3444443 6777765543
No 84
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.90 E-value=2.7e+02 Score=23.17 Aligned_cols=23 Identities=4% Similarity=0.197 Sum_probs=17.6
Q ss_pred HHHhhhccCcchHHHHHHHHHhH
Q 016200 244 QLVQSCESNELTLAQVGEFTKCL 266 (393)
Q Consensus 244 ELvran~aK~LTLaQV~eF~NcL 266 (393)
.++++-..-+++|+++.+|+.+.
T Consensus 48 ~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04785 48 RFIRRARDLGFSLEEIRALLALS 70 (126)
T ss_pred HHHHHHHHCCCCHHHHHHHHhhh
Confidence 35566677889999999998753
No 85
>PTZ00420 coronin; Provisional
Probab=22.83 E-value=44 Score=35.23 Aligned_cols=19 Identities=53% Similarity=0.707 Sum_probs=15.3
Q ss_pred CCCCCCCCCCCcccccccc
Q 016200 65 NNDNNNNNNNDNTLHQNQN 83 (393)
Q Consensus 65 ~~~~~~~~~~~~~~~~~~~ 83 (393)
|.|.|||+|++|||....|
T Consensus 533 ~~~~~~~~~~~~~~~~~~~ 551 (568)
T PTZ00420 533 NDDDNNNLNRGNTLRSEGN 551 (568)
T ss_pred cCcccccccCCcceecccc
Confidence 5677889999999987665
No 86
>COG4864 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.82 E-value=83 Score=31.49 Aligned_cols=22 Identities=27% Similarity=0.452 Sum_probs=17.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHH
Q 016200 5 NLMLFMLLVISFFFLTIFFTVT 26 (393)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~ 26 (393)
.|++..++|+.|.||.+|||+.
T Consensus 3 ~l~~iii~~viii~l~v~ftfv 24 (328)
T COG4864 3 MLGPIIIAVVIIIALAVFFTFV 24 (328)
T ss_pred chHHHHHHHHHHHHHHHHHHHh
Confidence 3677888888999999999853
No 87
>PF09451 ATG27: Autophagy-related protein 27; InterPro: IPR018939 Autophagy is a degradative transport pathway that delivers cytosolic proteins to the lysosome (vacuole) [] and is induced by starvation []. Cytosolic proteins appear inside the vacuole enclosed in autophagic vesicles. Autophagy significantly differs from other transport pathways by using double membrane layered transport intermediates, called autophagosomes [, ]. The breakdown of vesicular transport intermediates is a unique feature of autophagy []. Autophagy can also function in the elimination of invading bacteria and antigens []. There are more than 25 AuTophaGy-related (ATG) genes that are essential for autophagy, although it is still not known how the autophagosome is made. Atg9 is a potential membrane carrier to deliver lipids that are used to form the vesicle. Atg27 is another transmembrane protein, and is a cycling protein []. It acts as an effector of VPS34 phosphatidylinositol 3-phosphate kinase signalling and regulates the cytoplasm to vacuole transport (Cvt) vesicle formation. It is also required for autophagy-dependent cycling of ATG9.
Probab=22.76 E-value=61 Score=30.47 Aligned_cols=23 Identities=26% Similarity=0.719 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHH
Q 016200 11 LLVISFFFLTIFFTVTLFLTYKK 33 (393)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~ 33 (393)
|++|.|+|+.++|.+..++.|.+
T Consensus 206 l~i~~~l~~~~Y~i~g~~~n~~~ 228 (268)
T PF09451_consen 206 LFIILFLFLAAYLIFGSWYNYNR 228 (268)
T ss_pred HHHHHHHHHHHHhhhhhheeecc
Confidence 44556666677777777776654
No 88
>PF07028 DUF1319: Protein of unknown function (DUF1319); InterPro: IPR010746 This entry is represented by Commelina yellow mottle virus, Orf1. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains a number of viral proteins of unknown function approximately 200 residues long. Family members seem to be restricted to badnaviruses.
Probab=22.53 E-value=2.8e+02 Score=24.94 Aligned_cols=44 Identities=25% Similarity=0.352 Sum_probs=33.5
Q ss_pred HHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhH
Q 016200 272 ELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDV 320 (393)
Q Consensus 272 EL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLekDa 320 (393)
.+....+.|+.-+.|.++ -|+..+.|.+.+..|+.|..+|++|.
T Consensus 40 ~~~~~~~~lk~~~ki~~~-----Qr~~l~~l~~~l~~l~~eL~~Lr~~~ 83 (126)
T PF07028_consen 40 SQKKLLEELKNLSKIQES-----QRSELKELKQELDVLSKELQALRKEY 83 (126)
T ss_pred HHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444445677777777654 48888999999999999999998875
No 89
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=22.53 E-value=2.2e+02 Score=20.89 Aligned_cols=33 Identities=12% Similarity=0.313 Sum_probs=20.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 016200 6 LMLFMLLVISFFFLTIFFTVTLFLTYKKIKRLQ 38 (393)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 38 (393)
+.+++.+++.+.+..++.....+-...++++++
T Consensus 22 l~il~~f~~G~llg~l~~~~~~~~~r~~~~~~~ 54 (68)
T PF06305_consen 22 LLILIAFLLGALLGWLLSLPSRLRLRRRIRRLR 54 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666666666666666666666666665
No 90
>PF08514 STAG: STAG domain ; InterPro: IPR013721 STAG domain proteins are subunits of cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes. The STAG domain is present in Schizosaccharomyces pombe (Fission yeast) mitotic cohesin Psc3, and the meiosis specific cohesin Rec11. Many organisms express a meiosis-specific STAG protein, for example, mice and humans have a meiosis specific variant called STAG3, although budding yeast does not have a meiosis specific version [].
Probab=22.20 E-value=4.9e+02 Score=22.08 Aligned_cols=32 Identities=28% Similarity=0.563 Sum_probs=27.0
Q ss_pred CCCCcccccc---hhHHHHHHHHHHHHHhhhccCcc
Q 016200 222 GCLCPLTSMG---SATQRKIKELYHQLVQSCESNEL 254 (393)
Q Consensus 222 ~c~yPfTS~~---sAtQRRIkeqYDELvran~aK~L 254 (393)
..-|||.+.+ ...+..+.+-.+.||..+. ..+
T Consensus 3 ~~~YPli~k~~~~k~Fr~~~~~F~~~lv~~~~-~~~ 37 (118)
T PF08514_consen 3 SSDYPLISKGKKFKKFRKNFCEFFDQLVEQCH-SSI 37 (118)
T ss_pred cccCCCcCCCcccHHHHHHHHHHHHHHHHHhc-ccc
Confidence 4579999997 7788999999999999888 554
No 91
>smart00721 BAR BAR domain.
Probab=22.09 E-value=4e+02 Score=23.07 Aligned_cols=57 Identities=21% Similarity=0.366 Sum_probs=40.8
Q ss_pred hhhHHHHHHHHhhcCCcch----HHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHHHHHHHh
Q 016200 280 IKRKFSIQKALLSKADRSS----IDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPACKKMFEV 342 (393)
Q Consensus 280 iqRkftI~KALLskadRSS----~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAYKkMlE~ 342 (393)
+.|.....+--+-.+.+.. |+.+.+++..+|...++|-+|+..| +| -.|+.+.|...
T Consensus 6 ~~R~~q~~~ek~G~~e~T~~D~~f~~le~~~~~~~~~~~kl~k~~~~y--~q----~~~~~~~~~~~ 66 (239)
T smart00721 6 FNRAKQKVGEKVGKAEKTKLDEDFEELERRFDTTEAEIEKLQKDTKLY--LQ----PNPAVRAKLAS 66 (239)
T ss_pred hHHHHHHHHHHhCCCCcCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHH--cC----CChhhHHHHHH
Confidence 4455555555555666544 7799999999999999999999988 33 26666666543
No 92
>PRK06718 precorrin-2 dehydrogenase; Reviewed
Probab=21.99 E-value=5.1e+02 Score=23.33 Aligned_cols=51 Identities=14% Similarity=0.315 Sum_probs=37.5
Q ss_pred cchhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhc
Q 016200 230 MGSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSK 293 (393)
Q Consensus 230 ~~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLsk 293 (393)
+++.+.++|.+.|. ...++|+..|-..|..+.++..+...+-.+.+.++..
T Consensus 132 la~~lr~~ie~~~~-------------~~~~~~~~~~~~~R~~~k~~~~~~~~R~~~~~~~~~~ 182 (202)
T PRK06718 132 LAKKIRDELEALYD-------------ESYESYIDFLYECRQKIKELQIEKREKQILLQEVLSS 182 (202)
T ss_pred HHHHHHHHHHHHcc-------------hhHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence 45666666666553 3456788889999999999888777777777777754
No 93
>PHA02849 putative transmembrane protein; Provisional
Probab=21.56 E-value=2.3e+02 Score=24.12 Aligned_cols=22 Identities=32% Similarity=0.425 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhH
Q 016200 10 MLLVISFFFLTIFFTVTLFLTY 31 (393)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~ 31 (393)
|.+||+.|.++|.|++.+.+-.
T Consensus 16 ~v~vi~v~v~vI~i~~flLlyL 37 (82)
T PHA02849 16 AVTVILVFVLVISFLAFMLLYL 37 (82)
T ss_pred hHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666666666665554433
No 94
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=21.29 E-value=3.2e+02 Score=28.39 Aligned_cols=16 Identities=31% Similarity=0.443 Sum_probs=10.6
Q ss_pred HHHHHHhHHHHHHHHH
Q 016200 24 TVTLFLTYKKIKRLQE 39 (393)
Q Consensus 24 ~~~~~~~~~~~~~~~~ 39 (393)
.+.=--.|+.|.+|.+
T Consensus 21 ~~~rr~~~~~i~~Le~ 36 (569)
T PRK04778 21 LILRKRNYKRIDELEE 36 (569)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3344677888887754
No 95
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=21.29 E-value=1.6e+02 Score=27.47 Aligned_cols=47 Identities=30% Similarity=0.511 Sum_probs=27.3
Q ss_pred HHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhh
Q 016200 270 REELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLE 317 (393)
Q Consensus 270 RnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIykLE~EqkRLe 317 (393)
|.++.++.+.++.-+.++..|+..+.+ -.+.+..++..|+.|.+..+
T Consensus 127 ~~~~~~~~~~~~~G~~~r~~~i~~a~~-~~~e~~~~l~~l~~ei~~~~ 173 (176)
T PF12999_consen 127 REELEEEEEIYKEGLKIRQELIEEAKK-KREELEKKLEELEKEIQAAK 173 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHh
Confidence 444455555556666666666655532 24566667777776666544
No 96
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=21.27 E-value=3.7e+02 Score=20.27 Aligned_cols=69 Identities=19% Similarity=0.265 Sum_probs=43.2
Q ss_pred cCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhc--CCcchHHHHHHHHHHHHHHHHhhhhh
Q 016200 251 SNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSK--ADRSSIDRLRQQIYNLEKQQRRLEED 319 (393)
Q Consensus 251 aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLsk--adRSS~DRL~qQIykLE~EqkRLekD 319 (393)
.-.||=.|-.++-.-+-+.+.+...--..++....=..++|.. .|+.-++.+.++|..++.+.....-+
T Consensus 39 ~l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~ll~~~~~D~~~i~a~~~~~~~~~~~l~~~~~~ 109 (125)
T PF13801_consen 39 MLNLTPEQQAKLRALMDEFRQEMRALRQELRAARQELRALLAAPPPDEAAIEALLEEIREAQAELRQERLE 109 (125)
T ss_dssp HS-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSS-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566667766666666666665555555555555555666665 46788888888888887776554433
No 97
>cd08915 V_Alix_like Protein-interacting V-domain of mammalian Alix and related domains. This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains
Probab=21.21 E-value=6.8e+02 Score=23.96 Aligned_cols=69 Identities=17% Similarity=0.224 Sum_probs=46.9
Q ss_pred HHHHHHHHH---hHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcc---h-----------HHHHHHHHHHHHHHHHhhhh
Q 016200 256 LAQVGEFTK---CLAQAREELEDKSETIKRKFSIQKALLSKADRS---S-----------IDRLRQQIYNLEKQQRRLEE 318 (393)
Q Consensus 256 LaQV~eF~N---cLVdARnEL~~KSE~iqRkftI~KALLskadRS---S-----------~DRL~qQIykLE~EqkRLek 318 (393)
+..+..+++ -|...|..+.+.-...-+...|+..||.+..+. . ||-+..+|...-..|+.|-+
T Consensus 192 v~~Lr~~l~~l~~lk~eR~~~~~~lk~~~~~ddI~~~ll~~~~~~~~~~~e~lf~~eL~kf~~~~~~i~~~~~~Q~~ll~ 271 (342)
T cd08915 192 VSSLRPLLNEVSELEKERERFISELEIKSRNNDILPKLITEYKKNGTTEFEDLFEEHLKKFDKDLTYVEKTKKKQIELIK 271 (342)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCcHHHHHHhhccccchhHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 334444443 447778888888887888888999998886542 2 55556666666677777777
Q ss_pred hHHHHH
Q 016200 319 DVYVYN 324 (393)
Q Consensus 319 Da~VYN 324 (393)
+....|
T Consensus 272 ~i~~~~ 277 (342)
T cd08915 272 EIDAAN 277 (342)
T ss_pred HHHHHH
Confidence 766444
No 98
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=20.89 E-value=2.2e+02 Score=25.47 Aligned_cols=26 Identities=15% Similarity=0.477 Sum_probs=14.9
Q ss_pred HHHHHHhHHHHHHHHHHhhHhhhhcccc
Q 016200 24 TVTLFLTYKKIKRLQELENYANVLKGSL 51 (393)
Q Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 51 (393)
.+.++..+.|++||+. .|...++|.-
T Consensus 15 li~~~~~~~kl~kl~r--~Y~~lm~g~~ 40 (151)
T PF14584_consen 15 LILIIILNIKLRKLKR--RYDALMRGKD 40 (151)
T ss_pred HHHHHHHHHHHHHHHH--HHHHHhCCCC
Confidence 3334444556666653 6777777753
No 99
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=20.87 E-value=6.7e+02 Score=23.13 Aligned_cols=67 Identities=24% Similarity=0.220 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHH
Q 016200 237 KIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIY 307 (393)
Q Consensus 237 RIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskadRSS~DRL~qQIy 307 (393)
.+.+.|+.|-+-.+.-..-..+....+..+-....+|.++.+.+...-.=...++. ..+|+|.+.|.
T Consensus 53 ~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~~~~~~~~~l~p~m~----~m~~~L~~~v~ 119 (251)
T PF11932_consen 53 ELLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIEQIEETRQELVPLME----QMIDELEQFVE 119 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHh
Confidence 34445555555444444455555566666666666666666555544333333332 24445544444
No 100
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=20.78 E-value=89 Score=26.10 Aligned_cols=15 Identities=20% Similarity=0.676 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHHHh
Q 016200 16 FFFLTIFFTVTLFLT 30 (393)
Q Consensus 16 ~~~~~~~~~~~~~~~ 30 (393)
|+||.+||++.|++.
T Consensus 6 ~llL~l~LA~lLlis 20 (95)
T PF07172_consen 6 FLLLGLLLAALLLIS 20 (95)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344444444444443
No 101
>PRK09470 cpxA two-component sensor protein; Provisional
Probab=20.75 E-value=3.2e+02 Score=25.33 Aligned_cols=26 Identities=23% Similarity=0.312 Sum_probs=15.9
Q ss_pred HHHHHHHHhHHHHHHHHHHhhHhhhh
Q 016200 22 FFTVTLFLTYKKIKRLQELENYANVL 47 (393)
Q Consensus 22 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (393)
++.+.+++.++-++.|..|...++-+
T Consensus 179 ~~~~~~~~~~~i~~pl~~l~~~~~~i 204 (461)
T PRK09470 179 STPLLLWLAWSLAKPARKLKNAADEV 204 (461)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344455555667788877776654
No 102
>PF06692 MNSV_P7B: Melon necrotic spot virus P7B protein; InterPro: IPR009575 This family consists of several Melon necrotic spot virus (MNSV) P7B proteins. The function of this family is unknown.
Probab=20.73 E-value=99 Score=24.98 Aligned_cols=17 Identities=35% Similarity=0.581 Sum_probs=9.5
Q ss_pred hHHHHHHHHHHHHHHHH
Q 016200 6 LMLFMLLVISFFFLTIF 22 (393)
Q Consensus 6 ~~~~~~~~~~~~~~~~~ 22 (393)
+.+|+.|+|+|.|..|.
T Consensus 14 ~~~lLiliis~~f~lI~ 30 (61)
T PF06692_consen 14 SGPLLILIISFVFFLIT 30 (61)
T ss_pred hhHHHHHHHHHHHHHHh
Confidence 44566666666554443
No 103
>PF00674 DUP: DUP family; InterPro: IPR001142 A number of uncharacterised integral membrane proteins from yeast contain an internal duplication due to duplicated genes. Duplicated copies of genes may be classified in two types of cluster organisation. The first type includes genes sharing a significant level of identity in the amino acid sequences of their predicted protein product. They are recovered on two different chromosomes, transcribed in the same orientation and the distance between them is conserved. The second type of cluster is based on one gene unit tandemly repeated. This duplication is itself repeated elsewhere in the genome. The basic gene unit is recovered many times in the genome and is a component of a multigene family of unknown function. These organisations in clusters of genes suggest a 'Lego organisation' of the yeast chromosomes []. The proteins belonging to this family are of unknown function.
Probab=20.65 E-value=1.3e+02 Score=24.64 Aligned_cols=27 Identities=37% Similarity=0.736 Sum_probs=15.8
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHh
Q 016200 4 NNLMLFMLLVISFFFLTIFFTVTLFLT 30 (393)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 30 (393)
||....+++++++++++++|.+.+..-
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 (108)
T PF00674_consen 6 NNVFFSLLIIIVFLFLSIIFLVLIIRF 32 (108)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344555556666677666666555443
No 104
>PF01445 SH: Viral small hydrophobic protein; InterPro: IPR001477 The mumps virus SH protein is a membrane protein and not essential for virus growth []. Its function is unknown.; GO: 0016020 membrane
Probab=20.53 E-value=2.8e+02 Score=22.29 Aligned_cols=31 Identities=29% Similarity=0.635 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 016200 8 LFMLLVISFFFLTIFFTVTLFLTYKKIKRLQ 38 (393)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 38 (393)
.|.+|+.....+|.+.-+++-.|||..-|-.
T Consensus 11 tfLlLill~liiTLyVwi~ltItyKTavrha 41 (57)
T PF01445_consen 11 TFLLLILLYLIITLYVWIILTITYKTAVRHA 41 (57)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 4666666677778888888889999876643
No 105
>PF10066 DUF2304: Uncharacterized conserved protein (DUF2304); InterPro: IPR019277 This entry represents hypothetical archaeal and bacterial proteins that have no known function.
Probab=20.13 E-value=2.8e+02 Score=23.07 Aligned_cols=17 Identities=41% Similarity=0.788 Sum_probs=7.6
Q ss_pred HHHHHHHHhHHHHHHHH
Q 016200 22 FFTVTLFLTYKKIKRLQ 38 (393)
Q Consensus 22 ~~~~~~~~~~~~~~~~~ 38 (393)
++.+..|-.|-++.+++
T Consensus 76 ~ll~~~~~l~~~is~le 92 (115)
T PF10066_consen 76 FLLVIIFSLYVRISRLE 92 (115)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33334444455555443
No 106
>COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion]
Probab=20.10 E-value=81 Score=27.81 Aligned_cols=15 Identities=47% Similarity=0.820 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHH
Q 016200 7 MLFMLLVISFFFLTI 21 (393)
Q Consensus 7 ~~~~~~~~~~~~~~~ 21 (393)
||..|++||..+|.+
T Consensus 19 MLiVLlIISiLlLl~ 33 (107)
T COG4537 19 MLIVLLIISILLLLF 33 (107)
T ss_pred HHHHHHHHHHHHHHH
Confidence 788888888776644
No 107
>PF09125 COX2-transmemb: Cytochrome C oxidase subunit II, transmembrane; InterPro: IPR015209 This N-terminal domain forms the transmembrane region in subunit II of cytochrome c oxidase from Thermus thermophilus. This domain adopts a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold []. ; PDB: 1EHK_B 2QPE_B 3S8F_B 4EV3_B 3BVD_B 3S8G_B 3EH3_B 3S3C_B 3S39_B 3QJQ_B ....
Probab=20.04 E-value=1.5e+02 Score=22.22 Aligned_cols=22 Identities=27% Similarity=0.425 Sum_probs=14.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHH
Q 016200 5 NLMLFMLLVISFFFLTIFFTVT 26 (393)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~ 26 (393)
....|-|..|..|...|-||++
T Consensus 15 ~Wi~F~l~mi~vFi~li~ytl~ 36 (38)
T PF09125_consen 15 GWIAFALAMILVFIALIGYTLA 36 (38)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHh
Confidence 3456666666667667777764
No 108
>PF11337 DUF3139: Protein of unknown function (DUF3139); InterPro: IPR021486 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=20.02 E-value=2.6e+02 Score=22.09 Aligned_cols=38 Identities=24% Similarity=0.397 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHHHHHHH----HHHHHHhHHHHHHHHHHhhH
Q 016200 6 LMLFMLLVISFFFLTIFF----TVTLFLTYKKIKRLQELENY 43 (393)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~ 43 (393)
+.++++++|+.|++..+| .+.-....+.+..--+-+.|
T Consensus 8 ~iii~li~i~li~~~~~~~~~~~~~k~~~~k~i~~yL~e~gy 49 (85)
T PF11337_consen 8 LIIIILIVISLIIGIYYFFNGNPYQKHKAEKAIDWYLQEQGY 49 (85)
T ss_pred HHHHHHHHHHHHHHHHHhhcCchhhHHHHHHHHHHHHHHcCC
No 109
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=20.01 E-value=2.1e+02 Score=24.80 Aligned_cols=16 Identities=38% Similarity=0.669 Sum_probs=7.3
Q ss_pred hhhhccCCCChhhhhh
Q 016200 95 LLLEILPSKSAKWDRL 110 (393)
Q Consensus 95 ll~eilps~s~kw~~l 110 (393)
+.+||-|.---+|.+-
T Consensus 63 v~leia~gv~i~~~r~ 78 (109)
T PRK05886 63 VDLEIAPGVVTTWMKL 78 (109)
T ss_pred EEEEECCCeEEEEEhh
Confidence 4445544444445443
Done!