Query 014536
Match_columns 423
No_of_seqs 19 out of 21
Neff 1.8
Searched_HMMs 46136
Date Fri Mar 29 06:06:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014536.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014536hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG3937 Uncharacterized conser 94.3 0.25 5.4E-06 43.1 7.9 76 231-315 19-108 (108)
2 PF02060 ISK_Channel: Slow vol 84.0 1.4 3.1E-05 39.6 4.0 35 2-39 39-73 (129)
3 TIGR01837 PHA_granule_1 poly(h 75.0 45 0.00097 28.5 10.0 83 231-318 17-117 (118)
4 cd07596 BAR_SNX The Bin/Amphip 72.2 47 0.001 28.2 9.5 66 259-324 95-172 (218)
5 TIGR01834 PHA_synth_III_E poly 69.3 10 0.00022 38.1 5.6 54 259-319 258-311 (320)
6 PF09712 PHA_synth_III_E: Poly 69.2 9.2 0.0002 37.1 5.2 53 259-318 241-293 (293)
7 PF04799 Fzo_mitofusin: fzo-li 66.3 11 0.00024 35.1 4.9 78 227-332 65-148 (171)
8 PF14362 DUF4407: Domain of un 62.4 1.4E+02 0.003 28.1 11.4 90 230-319 106-204 (301)
9 COG5521 Predicted integral mem 59.8 9.5 0.00021 37.9 3.4 40 6-45 175-218 (275)
10 PF04380 BMFP: Membrane fusoge 59.3 45 0.00098 26.8 6.6 62 255-318 7-78 (79)
11 PRK13182 racA polar chromosome 59.3 39 0.00085 30.9 7.0 77 244-331 47-126 (175)
12 PF02403 Seryl_tRNA_N: Seryl-t 55.3 1.1E+02 0.0024 24.7 9.3 82 237-319 6-89 (108)
13 PRK11832 putative DNA-binding 54.4 15 0.00032 34.8 3.6 42 295-336 135-176 (207)
14 PF04977 DivIC: Septum formati 54.3 44 0.00095 24.9 5.5 42 296-337 16-57 (80)
15 PF06367 Drf_FH3: Diaphanous F 52.9 71 0.0015 27.8 7.3 82 259-347 44-148 (197)
16 PF15079 DUF4546: Domain of un 48.5 70 0.0015 30.8 7.0 65 260-332 50-114 (205)
17 PRK10755 sensor protein BasS/P 48.2 70 0.0015 29.2 6.8 40 7-46 59-98 (356)
18 PF10777 YlaC: Inner membrane 46.2 13 0.00028 34.5 1.8 33 370-402 13-52 (155)
19 TIGR02736 cbb3_Q_epsi cytochro 45.8 31 0.00067 27.6 3.6 32 15-46 3-39 (56)
20 PF09032 Siah-Interact_N: Siah 44.7 53 0.0012 27.2 5.0 39 280-318 8-47 (79)
21 TIGR02894 DNA_bind_RsfA transc 43.2 1.7E+02 0.0036 27.5 8.4 70 251-343 77-148 (161)
22 PF05816 TelA: Toxic anion res 43.1 1.8E+02 0.004 28.3 9.2 118 227-348 17-144 (333)
23 PF10211 Ax_dynein_light: Axon 42.6 2.7E+02 0.0059 25.5 10.0 76 238-320 64-143 (189)
24 PF13933 HRXXH: Putative pepti 41.8 24 0.00053 34.6 3.0 28 222-249 42-70 (245)
25 PF10168 Nup88: Nuclear pore c 41.1 1.2E+02 0.0025 33.3 8.2 75 267-341 557-639 (717)
26 PF14992 TMCO5: TMCO5 family 40.3 54 0.0012 32.7 5.2 51 298-348 124-178 (280)
27 PF05115 PetL: Cytochrome B6-F 39.7 52 0.0011 23.6 3.6 26 10-35 1-29 (31)
28 TIGR02444 conserved hypothetic 39.6 1.5E+02 0.0033 25.7 7.2 66 249-317 43-108 (116)
29 PF00615 RGS: Regulator of G p 39.3 1.6E+02 0.0035 21.9 7.4 76 231-339 43-118 (118)
30 PF12729 4HB_MCP_1: Four helix 39.1 62 0.0013 25.5 4.4 26 13-38 9-34 (181)
31 CHL00106 petL cytochrome b6/f 38.7 47 0.001 23.9 3.3 26 10-35 1-29 (31)
32 PF06103 DUF948: Bacterial pro 38.3 84 0.0018 24.8 5.1 25 10-34 4-28 (90)
33 TIGR02209 ftsL_broad cell divi 38.2 55 0.0012 25.1 3.9 36 299-334 40-75 (85)
34 smart00271 DnaJ DnaJ molecular 37.8 1.1E+02 0.0024 21.5 5.1 44 232-275 12-57 (60)
35 TIGR02229 caa3_sub_IV caa(3)-t 37.8 43 0.00093 28.3 3.5 24 5-28 64-87 (92)
36 PRK11637 AmiB activator; Provi 37.7 4.2E+02 0.0092 26.3 11.8 71 256-326 172-248 (428)
37 PF09006 Surfac_D-trimer: Lung 37.5 54 0.0012 25.4 3.7 25 300-324 2-26 (46)
38 PF06266 HrpF: HrpF protein; 37.3 2.1E+02 0.0045 24.0 7.3 62 229-292 2-71 (74)
39 PF02899 Phage_int_SAM_1: Phag 37.3 1E+02 0.0022 22.5 5.1 38 251-292 41-78 (84)
40 cd06257 DnaJ DnaJ domain or J- 36.0 1.1E+02 0.0024 21.0 4.9 25 231-255 10-34 (55)
41 PRK09835 sensor kinase CusS; P 35.9 1E+02 0.0023 28.9 6.1 36 12-47 188-223 (482)
42 PF05119 Terminase_4: Phage te 35.5 25 0.00055 27.4 1.8 62 281-342 6-69 (100)
43 PHA02562 46 endonuclease subun 35.2 3.9E+02 0.0084 26.7 10.2 40 298-338 380-419 (562)
44 TIGR01870 cas_TM1810_Csm2 CRIS 35.1 2.6E+02 0.0056 23.1 7.8 67 254-320 1-74 (97)
45 PRK11637 AmiB activator; Provi 34.9 2.6E+02 0.0056 27.8 8.9 88 226-318 37-124 (428)
46 TIGR02680 conserved hypothetic 33.9 5.1E+02 0.011 30.3 12.1 46 298-343 291-336 (1353)
47 PF05565 Sipho_Gp157: Siphovir 32.7 2.3E+02 0.0051 25.1 7.5 77 237-317 5-81 (162)
48 PRK11281 hypothetical protein; 32.4 1.3E+02 0.0027 34.9 7.1 139 240-420 383-524 (1113)
49 PF05667 DUF812: Protein of un 31.2 5.9E+02 0.013 27.7 11.3 98 236-333 422-531 (594)
50 PF06305 DUF1049: Protein of u 30.7 1.7E+02 0.0037 21.6 5.4 14 6-19 18-31 (68)
51 PF05597 Phasin: Poly(hydroxya 30.6 3.9E+02 0.0085 23.8 9.2 55 264-318 72-130 (132)
52 PF10046 BLOC1_2: Biogenesis o 29.8 3.2E+02 0.0069 22.5 8.7 66 239-323 20-85 (99)
53 PF04977 DivIC: Septum formati 29.5 1.2E+02 0.0025 22.6 4.4 37 297-333 31-68 (80)
54 cd03572 ENTH_epsin_related ENT 29.5 1.3E+02 0.0029 26.3 5.3 56 241-303 21-77 (122)
55 PF08671 SinI: Anti-repressor 29.3 53 0.0012 23.1 2.3 24 242-265 5-28 (30)
56 PF15086 UPF0542: Uncharacteri 28.9 1.3E+02 0.0027 25.4 4.8 28 14-41 25-52 (74)
57 PF00558 Vpu: Vpu protein; In 28.2 69 0.0015 26.9 3.2 32 17-48 16-47 (81)
58 KOG1962 B-cell receptor-associ 28.1 1.5E+02 0.0033 28.6 5.9 32 297-331 179-210 (216)
59 PRK09039 hypothetical protein; 28.0 1.1E+02 0.0025 30.2 5.2 22 11-32 26-47 (343)
60 PF12606 RELT: Tumour necrosis 27.7 75 0.0016 24.6 3.1 22 11-32 4-25 (50)
61 PF09094 DUF1925: Domain of un 27.2 45 0.00099 28.0 2.0 41 335-385 16-56 (80)
62 PF09079 Cdc6_C: CDC6, C termi 26.9 1.1E+02 0.0024 23.6 4.0 35 233-267 16-50 (85)
63 PF04899 MbeD_MobD: MbeD/MobD 26.6 2.4E+02 0.0053 22.9 5.9 38 280-317 26-69 (70)
64 PF13706 PepSY_TM_3: PepSY-ass 26.3 90 0.002 21.9 3.1 27 9-35 10-36 (37)
65 PRK04778 septation ring format 26.3 1.2E+02 0.0026 31.6 5.2 32 17-48 11-42 (569)
66 COG3352 FlaC Putative archaeal 25.7 2.4E+02 0.0052 26.5 6.5 68 256-323 74-141 (157)
67 PTZ00420 coronin; Provisional 25.7 36 0.00078 36.1 1.4 19 65-83 533-551 (568)
68 PF11932 DUF3450: Protein of u 25.5 5.5E+02 0.012 23.8 9.3 76 237-316 53-133 (251)
69 PF05399 EVI2A: Ectropic viral 25.4 1E+02 0.0022 30.3 4.2 26 6-31 129-156 (227)
70 PF09278 MerR-DNA-bind: MerR, 25.3 2.7E+02 0.0058 20.2 5.7 20 244-263 5-24 (65)
71 KOG4687 Uncharacterized coiled 25.1 2.6E+02 0.0055 29.0 7.1 115 257-375 170-293 (389)
72 PF07200 Mod_r: Modifier of ru 25.1 1.2E+02 0.0026 25.7 4.2 15 365-379 122-136 (150)
73 PRK06718 precorrin-2 dehydroge 24.9 4.2E+02 0.0092 24.0 7.9 51 230-293 132-182 (202)
74 KOG1666 V-SNARE [Intracellular 24.5 1.2E+02 0.0027 29.6 4.6 63 236-298 135-197 (220)
75 PF05103 DivIVA: DivIVA protei 24.2 1.1E+02 0.0025 24.8 3.8 51 252-331 16-66 (131)
76 PF04683 Proteasom_Rpn13: Prot 24.0 32 0.00068 28.1 0.5 16 160-175 54-69 (85)
77 PF07028 DUF1319: Protein of u 24.0 2.5E+02 0.0054 25.5 6.1 44 272-320 40-83 (126)
78 cd01324 cbb3_Oxidase_CcoQ Cyto 23.9 1.6E+02 0.0034 22.1 4.1 32 1-32 1-32 (48)
79 PF13010 pRN1_helical: Primase 23.7 34 0.00073 31.3 0.7 19 94-112 97-119 (135)
80 cd07599 BAR_Rvs167p The Bin/Am 23.4 5.5E+02 0.012 23.1 10.0 19 313-331 155-173 (216)
81 PF12999 PRKCSH-like: Glucosid 23.3 1.3E+02 0.0029 28.1 4.4 47 270-317 127-173 (176)
82 PRK04778 septation ring format 23.1 2.8E+02 0.006 29.0 7.1 16 24-39 21-36 (569)
83 PF13801 Metal_resist: Heavy-m 23.1 3.4E+02 0.0074 20.6 8.6 68 251-318 39-108 (125)
84 TIGR02135 phoU_full phosphate 22.9 4.2E+02 0.0091 22.2 7.0 56 262-321 3-58 (212)
85 PF00226 DnaJ: DnaJ domain; I 22.8 2.5E+02 0.0055 20.1 5.0 45 231-275 10-56 (64)
86 cd08915 V_Alix_like Protein-in 22.7 6E+02 0.013 24.4 8.8 69 256-324 192-277 (342)
87 PHA03030 hypothetical protein; 22.5 65 0.0014 28.9 2.2 20 8-27 4-23 (122)
88 PF12273 RCR: Chitin synthesis 22.5 82 0.0018 26.6 2.7 10 27-36 16-25 (130)
89 cd04785 HTH_CadR-PbrR-like Hel 22.0 2.9E+02 0.0063 23.2 5.8 22 245-266 49-70 (126)
90 cd09238 V_Alix_like_1 Protein- 21.9 4.3E+02 0.0093 25.9 7.8 58 263-322 204-272 (339)
91 PF08514 STAG: STAG domain ; 21.8 5.1E+02 0.011 22.1 8.8 33 221-254 2-37 (118)
92 PRK13922 rod shape-determining 21.7 1.4E+02 0.0031 27.7 4.3 38 299-336 78-115 (276)
93 PRK09039 hypothetical protein; 21.3 4.7E+02 0.01 26.0 8.0 54 266-320 107-160 (343)
94 PF04277 OAD_gamma: Oxaloaceta 21.0 1.9E+02 0.0041 22.2 4.2 14 13-26 13-26 (79)
95 TIGR03017 EpsF chain length de 20.5 8E+02 0.017 23.9 11.3 45 297-341 318-363 (444)
96 PF10018 Med4: Vitamin-D-recep 20.4 6.4E+02 0.014 22.8 9.2 68 298-376 23-90 (188)
97 TIGR01386 cztS_silS_copS heavy 20.2 2.9E+02 0.0063 25.5 5.9 29 19-47 174-202 (457)
98 PRK09966 putative inner membra 20.1 3E+02 0.0066 25.9 6.1 28 319-346 285-312 (407)
No 1
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=94.26 E-value=0.25 Score=43.13 Aligned_cols=76 Identities=33% Similarity=0.526 Sum_probs=58.3
Q ss_pred chhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHH----HHHHHhhhhhhhhhHHHHHHHHhhcCC----------c
Q 014536 231 GSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQ----AREELEDKSETIKRKFSIQKALLSKAD----------R 296 (423)
Q Consensus 231 ~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVd----ARnEL~~KSE~iqRkftI~KALLskAd----------R 296 (423)
...+--+.++.-|+||+ -..+|..|-.+|..-|+. ++.++-.| ++|++.+ ||++.. +
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 45677888999999986 578999999999887774 55566555 8999877 455433 6
Q ss_pred chHHHHHHHHHHHHHHHHh
Q 014536 297 SSIDRLRQQIYNLEKQQRR 315 (423)
Q Consensus 297 SS~DRL~qQIykLE~EqkR 315 (423)
+.+|+|.+||.+||.+++|
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=83.98 E-value=1.4 Score=39.56 Aligned_cols=35 Identities=40% Similarity=0.810 Sum_probs=25.5
Q ss_pred CcchhHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 014536 2 DENNLMLFMLLVISFFFLTIFFTVTLFLTYKKIKRLQE 39 (423)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 (423)
|.+|-.+++|+|++|| -||++.++|.|-+-||+..
T Consensus 39 ~~~~~~lYIL~vmgfF---gff~~gImlsyvRSKK~E~ 73 (129)
T PF02060_consen 39 DDDNEYLYILVVMGFF---GFFTVGIMLSYVRSKKREH 73 (129)
T ss_dssp T-SSTT-HHHHHHHHH---HHHHHHHHHHHHHHHHH--
T ss_pred CCCceeehHHHHHHHH---HHHHHHHHHHHHHHhhhcc
Confidence 3456678888888887 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=74.98 E-value=45 Score=28.50 Aligned_cols=83 Identities=24% Similarity=0.313 Sum_probs=58.7
Q ss_pred chhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHH-HHHHhhhhhh---------------hhhHHHHHHHH--hh
Q 014536 231 GSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQA-REELEDKSET---------------IKRKFSIQKAL--LS 292 (423)
Q Consensus 231 ~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVdA-RnEL~~KSE~---------------iqRkftI~KAL--Ls 292 (423)
.+.+|-++.+.+|+||+- ..++-.+-..|++-+++. +.++.++.+- +.++ |.++| |.
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 356799999999999974 567888999999888753 3344333322 2222 33333 22
Q ss_pred cCCcchHHHHHHHHHHHHHHHHhhhh
Q 014536 293 KADRSSIDRLRQQIYNLEKQQRRLEE 318 (423)
Q Consensus 293 kAdRSS~DRL~qQIykLE~EqkRLek 318 (423)
-+.|.-++.|...|+.||.+..+|+.
T Consensus 92 ~~tk~ev~~L~~RI~~Le~~l~~l~~ 117 (118)
T TIGR01837 92 IPSREEIEALSAKIEQLAVQVEELRR 117 (118)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 36689999999999999999998864
No 4
>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=72.22 E-value=47 Score=28.19 Aligned_cols=66 Identities=14% Similarity=0.228 Sum_probs=40.5
Q ss_pred HHHHHHhHHHHHH------HHhhhhhhhhhHHHHHHHHhhcC------CcchHHHHHHHHHHHHHHHHhhhhhHHHHH
Q 014536 259 VGEFTKCLAQARE------ELEDKSETIKRKFSIQKALLSKA------DRSSIDRLRQQIYNLEKQQRRLEEDVYVYN 324 (423)
Q Consensus 259 V~eF~NcLVdARn------EL~~KSE~iqRkftI~KALLskA------dRSS~DRL~qQIykLE~EqkRLekDa~VYN 324 (423)
++++...+.-+|+ .++...+.++....=+++=+.+. ++..+++|.++|..+|.+.+.+++|....+
T Consensus 95 L~~y~~~~~s~k~~l~~R~~~~~~~~~~~~~l~~k~~~~~kl~~~~~~~~~ki~~l~~~i~~~e~~~~~~~~~~~~i~ 172 (218)
T cd07596 95 LKEYLRYCQAVKETLDDRADALLTLQSLKKDLASKKAQLEKLKAAPGIKPAKVEELEEELEEAESALEEARKRYEEIS 172 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555554444444 44444444444443333333332 457899999999999999999998765543
No 5
>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=69.29 E-value=10 Score=38.12 Aligned_cols=54 Identities=24% Similarity=0.417 Sum_probs=44.9
Q ss_pred HHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhh
Q 014536 259 VGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEED 319 (423)
Q Consensus 259 V~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLekD 319 (423)
.++|+|.+.+.|.++++-.|.+=+. |-=+.||-+|-+++-|+.||.++++|++-
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 4788999999998888877765443 33467999999999999999999999986
No 6
>PF09712 PHA_synth_III_E: Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)
Probab=69.22 E-value=9.2 Score=37.07 Aligned_cols=53 Identities=25% Similarity=0.434 Sum_probs=42.6
Q ss_pred HHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhh
Q 014536 259 VGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEE 318 (423)
Q Consensus 259 V~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLek 318 (423)
.++|+|.+.+.|.+.++=.|.+=+. |-=+-|+-+|-|+.+||.|+.|+++|++
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 4778888888888888766665443 3336799999999999999999999975
No 7
>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=66.32 E-value=11 Score=35.06 Aligned_cols=78 Identities=28% Similarity=0.414 Sum_probs=28.6
Q ss_pred ccccchhHHHHHHHHHHHHHhhhccCcchHHHHHHHH--HhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHH
Q 014536 227 LTSMGSATQRKIKELYHQLVQSCESNELTLAQVGEFT--KCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQ 304 (423)
Q Consensus 227 fTSs~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~--NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~q 304 (423)
++=..+|=-|..|+||-+-+. ++| .-+.+|+ ||=-.+..|| -+-|+|||+
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 2233332 3433333333 247889998
Q ss_pred HHHH----HHHHHHhhhhhHHHHHHHHHHhcc
Q 014536 305 QIYN----LEKQQRRLEEDVYVYNWLQDQLRL 332 (423)
Q Consensus 305 QIyk----LE~EqkRLekDa~VYN~LQqQLKl 332 (423)
||+. ||.|.++|++.....+.+|..+|.
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 8874 777888899999888888877653
No 8
>PF14362 DUF4407: Domain of unknown function (DUF4407)
Probab=62.42 E-value=1.4e+02 Score=28.10 Aligned_cols=90 Identities=12% Similarity=0.171 Sum_probs=67.2
Q ss_pred cchhHHHHHHHHHHHHHhhhccCcch--HHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcC---C----cchHH
Q 014536 230 MGSATQRKIKELYHQLVQSCESNELT--LAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKA---D----RSSID 300 (423)
Q Consensus 230 s~sAtQRRIkeqYDELvran~aK~LT--LaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskA---d----RSS~D 300 (423)
....+.++|.+.|.+......++... -++..+...-+-..++++.++...+.+.-.+...=..-. . -+.+.
T Consensus 106 F~~eI~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~E~~g~~~tg~~G~Gp~~~ 185 (301)
T PF14362_consen 106 FEKEIDQKLDEIRQEKQDAIQAQVQASFDAQIARLDAEIAALQAEIDQLEKEIDRAQQEAQCEIFGTGGTGVPGKGPRYK 185 (301)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCcHHH
Confidence 36788999999999888887776655 566777777777777777777777777777666555442 1 27788
Q ss_pred HHHHHHHHHHHHHHhhhhh
Q 014536 301 RLRQQIYNLEKQQRRLEED 319 (423)
Q Consensus 301 RL~qQIykLE~EqkRLekD 319 (423)
...+++...+.+...+...
T Consensus 186 ~~~~~~~~~~~~l~~l~~~ 204 (301)
T PF14362_consen 186 EKRAQLDAAQAELDTLQAQ 204 (301)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 8888888888888777776
No 9
>COG5521 Predicted integral membrane protein [Function unknown]
Probab=59.83 E-value=9.5 Score=37.92 Aligned_cols=40 Identities=33% Similarity=0.467 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHH----HhHHHHHHHHHHhhhhh
Q 014536 6 LMLFMLLVISFFFLTIFFTVTLF----LTYKKIKRLQELENYAN 45 (423)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~ 45 (423)
.|+||+|++|+.++..+|.|.++ |+.-|+.||-.+-++..
T Consensus 175 i~lflvl~~s~i~~l~tfivagg~sffL~iTKrSrlfsiasFkE 218 (275)
T COG5521 175 IMLFLVLVVSMIQLLLTFIVAGGASFFLWITKRSRLFSIASFKE 218 (275)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhheeeeehhhhhhhHHhHHH
Confidence 57889999999998888888665 88889999887766643
No 10
>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=59.35 E-value=45 Score=26.79 Aligned_cols=62 Identities=24% Similarity=0.271 Sum_probs=33.4
Q ss_pred hHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCC---cchHH-------HHHHHHHHHHHHHHhhhh
Q 014536 255 TLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKAD---RSSID-------RLRQQIYNLEKQQRRLEE 318 (423)
Q Consensus 255 TLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAd---RSS~D-------RL~qQIykLE~EqkRLek 318 (423)
.+.++...++.++.+=+.+.+-.+..=| .+....|++-| |--|| |+++.|..||.+...||+
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 4556666666666533332222221111 23344445543 66666 677888888888777764
No 11
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=59.27 E-value=39 Score=30.94 Aligned_cols=77 Identities=14% Similarity=0.225 Sum_probs=52.5
Q ss_pred HHHhhhccCcchHHHHHHHH--HhHHHHHHHHhhhhh-hhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhH
Q 014536 244 QLVQSCESNELTLAQVGEFT--KCLAQAREELEDKSE-TIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDV 320 (423)
Q Consensus 244 ELvran~aK~LTLaQV~eF~--NcLVdARnEL~~KSE-~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLekDa 320 (423)
+.+++-..-+.+++++.+|. .. .. ..|-.+++ ++..+ .+||.. -.++|.++|..||...+.+-.|+
T Consensus 47 ~~I~~l~~~Gm~i~~i~~~~~~~l-~~--~~l~~~G~~t~~~R----~~lLe~----~~~~l~~ri~eLe~~l~~kad~v 115 (175)
T PRK13182 47 EYVKSQIEEGQNMQDTQKPSSNDV-EE--TQVNTIVQNISSVD----FEQLEA----QLNTITRRLDELERQLQQKADDV 115 (175)
T ss_pred HHHHHHHHcCCCHHHHHHHhhhhh-hH--HHHHHcCCccHHHH----HHHHHH----HHHHHHHHHHHHHHHHHHHHhhh
Confidence 56788889999999998844 32 00 12223333 22222 233322 45678899999999999999999
Q ss_pred HHHHHHHHHhc
Q 014536 321 YVYNWLQDQLR 331 (423)
Q Consensus 321 ~VYN~LQqQLK 331 (423)
+-|.-||.+=-
T Consensus 116 vsYqll~hr~e 126 (175)
T PRK13182 116 VSYQLLQHRRE 126 (175)
T ss_pred hhHHHHHhHHH
Confidence 99999998743
No 12
>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=55.28 E-value=1.1e+02 Score=24.65 Aligned_cols=82 Identities=20% Similarity=0.277 Sum_probs=47.3
Q ss_pred HHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCc--chHHHHHHHHHHHHHHHH
Q 014536 237 KIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADR--SSIDRLRQQIYNLEKQQR 314 (423)
Q Consensus 237 RIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdR--SS~DRL~qQIykLE~Eqk 314 (423)
.|.+-.|...+....+.-....|.++. -|-+.|.+|+++.+.++..-.....-+.+.-+ ...+-|..++..|-.+.+
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 455555555555555544555555554 36788889999999998776544444444333 245555555555544444
Q ss_pred hhhhh
Q 014536 315 RLEED 319 (423)
Q Consensus 315 RLekD 319 (423)
.|++.
T Consensus 85 ~le~~ 89 (108)
T PF02403_consen 85 ELEEQ 89 (108)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 44443
No 13
>PRK11832 putative DNA-binding transcriptional regulator; Provisional
Probab=54.35 E-value=15 Score=34.78 Aligned_cols=42 Identities=17% Similarity=0.376 Sum_probs=39.2
Q ss_pred CcchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHH
Q 014536 295 DRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPAC 336 (423)
Q Consensus 295 dRSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAY 336 (423)
.++||+=+|.++..|-.+-+...++..|||++|++-.||-++
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=54.25 E-value=44 Score=24.87 Aligned_cols=42 Identities=21% Similarity=0.211 Sum_probs=29.3
Q ss_pred cchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHHH
Q 014536 296 RSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPACK 337 (423)
Q Consensus 296 RSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAYK 337 (423)
.+.+-++.+||..|+.+.+.|++...-...--++|+-||.|-
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
>PF06367 Drf_FH3: Diaphanous FH3 Domain; InterPro: IPR010472 Formin homology (FH) proteins play a crucial role in the reorganisation of the actin cytoskeleton, which mediates various functions of the cell cortex including motility, adhesion, and cytokinesis []. Formins are multidomain proteins that interact with diverse signalling molecules and cytoskeletal proteins, although some formins have been assigned functions within the nucleus. Formins are characterised by the presence of three FH domains (FH1, FH2 and FH3), although members of the formin family do not necessarily contain all three domains []. The proline-rich FH1 domain mediates interactions with a variety of proteins, including the actin-binding protein profilin, SH3 (Src homology 3) domain proteins, and WW domain proteins. The FH2 domain (IPR003104 from INTERPRO) is required to inhibit actin polymerisation. The FH3 domain is less well conserved and is required for directing formins to the correct intracellular location, such the mitotic spindle [], or the projection tip during conjugation []. In addition, some formins can contain a GTPase-binding domain (GBD) (IPR010473 from INTERPRO) required for binding to Rho small GTPases, and a C-terminal conserved Dia-autoregulatory domain (DAD). This entry represents the FH3 domain.; GO: 0003779 actin binding, 0016043 cellular component organization; PDB: 3OBV_A 2BNX_A 3EG5_D 2BAP_B 3O4X_B 1Z2C_B 2F31_A.
Probab=52.90 E-value=71 Score=27.76 Aligned_cols=82 Identities=15% Similarity=0.214 Sum_probs=51.9
Q ss_pred HHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhc--------CCcchHHHHHHHHHHHHHHHH---------------h
Q 014536 259 VGEFTKCLAQAREELEDKSETIKRKFSIQKALLSK--------ADRSSIDRLRQQIYNLEKQQR---------------R 315 (423)
Q Consensus 259 V~eF~NcLVdARnEL~~KSE~iqRkftI~KALLsk--------AdRSS~DRL~qQIykLE~Eqk---------------R 315 (423)
+-.|+|+||..- +.++-+..|+..|..- -.....+.|..||...|.+.. .
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 456788887543 4455555555544332 123467788888888776553 3
Q ss_pred hhhhHHHHHHHHHHhccCHHHHHHHHhhhhhh
Q 014536 316 LEEDVYVYNWLQDQLRLSPACKKMFEVCADME 347 (423)
Q Consensus 316 LekDa~VYN~LQqQLKlSpAYKkMlE~ga~~E 347 (423)
+..-..+|..|.++++-++++.-++-+=+..=
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 16
>PF15079 DUF4546: Domain of unknown function (DUF4546)
Probab=48.55 E-value=70 Score=30.79 Aligned_cols=65 Identities=28% Similarity=0.388 Sum_probs=53.4
Q ss_pred HHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhcc
Q 014536 260 GEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRL 332 (423)
Q Consensus 260 ~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKl 332 (423)
.+.-|-|-++|.||.+|-|.|+.--.|- - --||.|++=|.-..+-|+...|-.+|.=++|..-|+
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 279999999999988899999989999889876554
No 17
>PRK10755 sensor protein BasS/PmrB; Provisional
Probab=48.16 E-value=70 Score=29.19 Aligned_cols=40 Identities=18% Similarity=0.188 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhhh
Q 014536 7 MLFMLLVISFFFLTIFFTVTLFLTYKKIKRLQELENYANV 46 (423)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 (423)
+.+.+++++++++.+++.+.+++..+-++.+..|....+-
T Consensus 59 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pl~~l~~~~~~ 98 (356)
T PRK10755 59 AVASLLVPSLVMVSLTLLICFQAVRWITRPLAELQKELEA 98 (356)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHh
Confidence 3444555555556666666666666667778777765543
No 18
>PF10777 YlaC: Inner membrane protein YlaC; InterPro: IPR019713 The extracytoplasmic function (ECF) sigma factors are small regulatory proteins that are quite divergent in sequence relative to most other sigma factors. YlaC, regulated by YlaA, is important in oxidative stress resistance. It contributes to hydrogen peroxide resistance in Bacillus subtilis [].
Probab=46.17 E-value=13 Score=34.51 Aligned_cols=33 Identities=30% Similarity=0.506 Sum_probs=28.2
Q ss_pred HHHHhhhccc-------ccccccccchhhhHHHHHhhhhc
Q 014536 370 EELLAQEKKD-------SFWFVVPLKCLASYIFFFPLLIK 402 (423)
Q Consensus 370 EELLAQEKkD-------sFWqr~~~~~~~~~~~~~~~~~~ 402 (423)
+.+-.+||+| +|-++||--|++-|+.++|+++-
T Consensus 13 d~iN~~E~RDnkprFs~~Fi~~HP~L~~~M~~~y~~~~~l 52 (155)
T PF10777_consen 13 DRINREEKRDNKPRFSSSFIRNHPYLCLAMYAAYLAVAAL 52 (155)
T ss_pred HHHHHHhccCCCccccHHHHHhCcHHHHHHHHHHHHHHHH
Confidence 5667889998 68999999999999999988763
No 19
>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=45.75 E-value=31 Score=27.60 Aligned_cols=32 Identities=28% Similarity=0.686 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHH----hHHHHHH-HHHHhhhhhh
Q 014536 15 SFFFLTIFFTVTLFL----TYKKIKR-LQELENYANV 46 (423)
Q Consensus 15 ~~~~~~~~~~~~~~~----~~~~~~~-~~~~~~~~~~ 46 (423)
.+||+|||++|.|.- .|++-|. -..-|.|+|.
T Consensus 3 ~yf~~ti~lvv~LYgY~yhLYrsek~G~rdYEKY~~L 39 (56)
T TIGR02736 3 AYFAFTLLLVIFLYAYIYHLYRSQKKGERDYEKYANL 39 (56)
T ss_pred chHHHHHHHHHHHHHHHHHhhhhhcccccCHHHHhhh
Confidence 578888888887654 3333332 2567888885
No 20
>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=44.73 E-value=53 Score=27.21 Aligned_cols=39 Identities=28% Similarity=0.481 Sum_probs=30.7
Q ss_pred hhhHHHHHHHHhhcCCcchHHH-HHHHHHHHHHHHHhhhh
Q 014536 280 IKRKFSIQKALLSKADRSSIDR-LRQQIYNLEKQQRRLEE 318 (423)
Q Consensus 280 iqRkftI~KALLskAdRSS~DR-L~qQIykLE~EqkRLek 318 (423)
++-=.-=.++||.+|-|.++.. |-.+|.+||.|.+.+++
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 3333444678999999988874 56899999999999876
No 21
>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=43.18 E-value=1.7e+02 Score=27.47 Aligned_cols=70 Identities=19% Similarity=0.316 Sum_probs=39.7
Q ss_pred cCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCC--cchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHH
Q 014536 251 SNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKAD--RSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQD 328 (423)
Q Consensus 251 aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAd--RSS~DRL~qQIykLE~EqkRLekDa~VYN~LQq 328 (423)
...|||.+|-.|+-.|-+. +... +.+-.... +.-...|.+++..||.|...|+++-.+|.
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 01100000 12334677777788888777777765553
Q ss_pred HhccCHHHHHHHHhh
Q 014536 329 QLRLSPACKKMFEVC 343 (423)
Q Consensus 329 QLKlSpAYKkMlE~g 343 (423)
.-|+.|+.|=
T Consensus 139 -----eDY~~L~~Im 148 (161)
T TIGR02894 139 -----EDYQTLIDIM 148 (161)
T ss_pred -----HHHHHHHHHH
Confidence 2467666653
No 22
>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=43.07 E-value=1.8e+02 Score=28.34 Aligned_cols=118 Identities=22% Similarity=0.263 Sum_probs=77.3
Q ss_pred ccccchhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCC------cchHH
Q 014536 227 LTSMGSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKAD------RSSID 300 (423)
Q Consensus 227 fTSs~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAd------RSS~D 300 (423)
+.+.|...|++|-+.=|.+..-.+.+ +..+|++=++-|+..=+++--..-.-..+-.+..-|+.++. -+.|+
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 66677776666665554443222101111233333555332 26777
Q ss_pred HHHHHHHH----HHHHHHhhhhhHHHHHHHHHHhccCHHHHHHHHhhhhhhc
Q 014536 301 RLRQQIYN----LEKQQRRLEEDVYVYNWLQDQLRLSPACKKMFEVCADMEL 348 (423)
Q Consensus 301 RL~qQIyk----LE~EqkRLekDa~VYN~LQqQLKlSpAYKkMlE~ga~~El 348 (423)
.+.+||++ |+..+..|.+|...+..+.+.+.. .|+.+-+|-+..++
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 77788765 677788999999999999887763 56666666655554
No 23
>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=42.62 E-value=2.7e+02 Score=25.51 Aligned_cols=76 Identities=25% Similarity=0.427 Sum_probs=55.6
Q ss_pred HHHHHHHHHhh----hccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHH
Q 014536 238 IKELYHQLVQS----CESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQ 313 (423)
Q Consensus 238 IkeqYDELvra----n~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~Eq 313 (423)
-.+.+|||+|= +..+++=|..|++...-+++|=..|.+ |.. .|.++|+|-.... -+++..+|..|+.+.
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 346667777777777
Q ss_pred HhhhhhH
Q 014536 314 RRLEEDV 320 (423)
Q Consensus 314 kRLekDa 320 (423)
+.|++=.
T Consensus 137 ~~L~~~~ 143 (189)
T PF10211_consen 137 EELEKQV 143 (189)
T ss_pred HHHHHHH
Confidence 7776533
No 24
>PF13933 HRXXH: Putative peptidase family
Probab=41.84 E-value=24 Score=34.59 Aligned_cols=28 Identities=25% Similarity=0.316 Sum_probs=23.1
Q ss_pred CCCCcccccchhHHHH-HHHHHHHHHhhh
Q 014536 222 GCLCPLTSMGSATQRK-IKELYHQLVQSC 249 (423)
Q Consensus 222 ~c~yPfTSs~sAtQRR-IkeqYDELvran 249 (423)
++.||+.++|.+|||+ |.+.+||.++..
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 25
>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=41.10 E-value=1.2e+02 Score=33.35 Aligned_cols=75 Identities=27% Similarity=0.341 Sum_probs=46.7
Q ss_pred HHHHHHHhhhhhhhhhHHHHHHHHhhcC--C----cchHHHHHHHHHHHHHHHHhhhhhHH-HHHHHHHHhc-cCHHHHH
Q 014536 267 AQAREELEDKSETIKRKFSIQKALLSKA--D----RSSIDRLRQQIYNLEKQQRRLEEDVY-VYNWLQDQLR-LSPACKK 338 (423)
Q Consensus 267 VdARnEL~~KSE~iqRkftI~KALLskA--d----RSS~DRL~qQIykLE~EqkRLekDa~-VYN~LQqQLK-lSpAYKk 338 (423)
.-||.|++++...+++...-.-.=|... . +.+=++|.+.+..++..|+.|.+=+. |.+.++.++. +|.|=+.
T Consensus 557 ~~ar~ei~~rv~~Lk~~~e~Ql~~L~~l~e~~~~l~~~ae~LaeR~e~a~d~Qe~L~~R~~~vl~~l~~~~P~LS~AEr~ 636 (717)
T PF10168_consen 557 DLAREEIQRRVKLLKQQKEQQLKELQELQEERKSLRESAEKLAERYEEAKDKQEKLMKRVDRVLQLLNSQLPVLSEAERE 636 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHH
Confidence 3455555555555544443222222221 1 34446888888888888888888666 7788888877 7887777
Q ss_pred HHH
Q 014536 339 MFE 341 (423)
Q Consensus 339 MlE 341 (423)
|.+
T Consensus 637 ~~~ 639 (717)
T PF10168_consen 637 FKK 639 (717)
T ss_pred HHH
Confidence 743
No 26
>PF14992 TMCO5: TMCO5 family
Probab=40.29 E-value=54 Score=32.71 Aligned_cols=51 Identities=24% Similarity=0.228 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHH---HHHHhhhhhHHHH-HHHHHHhccCHHHHHHHHhhhhhhc
Q 014536 298 SIDRLRQQIYNLE---KQQRRLEEDVYVY-NWLQDQLRLSPACKKMFEVCADMEL 348 (423)
Q Consensus 298 S~DRL~qQIykLE---~EqkRLekDa~VY-N~LQqQLKlSpAYKkMlE~ga~~El 348 (423)
|+-++-.||.|+| .+-..|.+|+.-| ..||+-|+-=.-+|-|+-+....++
T Consensus 124 ~~~~qE~ei~kve~d~~~v~~l~eDq~~~i~klkE~L~rmE~ekE~~lLe~el~k 178 (280)
T PF14992_consen 124 SCASQEKEIAKVEDDYQQVHQLCEDQANEIKKLKEKLRRMEEEKEMLLLEKELSK 178 (280)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5556667777775 3344556776544 3566655443447777766655553
No 27
>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=39.67 E-value=52 Score=23.60 Aligned_cols=26 Identities=50% Similarity=0.874 Sum_probs=16.1
Q ss_pred HHHHHHHH-HHH--HHHHHHHHHhHHHHH
Q 014536 10 MLLVISFF-FLT--IFFTVTLFLTYKKIK 35 (423)
Q Consensus 10 ~~~~~~~~-~~~--~~~~~~~~~~~~~~~ 35 (423)
|+.+||+| ||. ..+|..+|+..+|||
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 28
>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=39.61 E-value=1.5e+02 Score=25.66 Aligned_cols=66 Identities=17% Similarity=0.240 Sum_probs=48.9
Q ss_pred hccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhh
Q 014536 249 CESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLE 317 (423)
Q Consensus 249 n~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLe 317 (423)
.+...++..+......+...-|++..+-.-.+||.. |+-....+=.....+|++|-.+|.+-+|..
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 457788988999988888888888887777776654 233333332456689999999999988864
No 29
>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=39.30 E-value=1.6e+02 Score=21.94 Aligned_cols=76 Identities=21% Similarity=0.429 Sum_probs=47.1
Q ss_pred chhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHH
Q 014536 231 GSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLE 310 (423)
Q Consensus 231 ~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE 310 (423)
.....+.+.+.|+.-+..+....+.+.+ .+|.++.+..+.. ...++.|+.+.++|+.
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 4455566777777777665555555443 3444444443333 5678999999998876
Q ss_pred HHHHhhhhhHHHHHHHHHHhccCHHHHHH
Q 014536 311 KQQRRLEEDVYVYNWLQDQLRLSPACKKM 339 (423)
Q Consensus 311 ~EqkRLekDa~VYN~LQqQLKlSpAYKkM 339 (423)
.|++|.+ .+...|+-|+.|
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 456678888876
No 30
>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=39.13 E-value=62 Score=25.45 Aligned_cols=26 Identities=4% Similarity=0.310 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHH
Q 014536 13 VISFFFLTIFFTVTLFLTYKKIKRLQ 38 (423)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 38 (423)
.++|+++.+++.++.++.+..+..+.
T Consensus 9 ~~~f~~~~~l~~~~~~~~~~~l~~~~ 34 (181)
T PF12729_consen 9 ILGFGLIILLLLIVGIVGLYSLSQIN 34 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444445555555555554443
No 31
>CHL00106 petL cytochrome b6/f complex subunit VI
Probab=38.70 E-value=47 Score=23.85 Aligned_cols=26 Identities=35% Similarity=0.548 Sum_probs=16.5
Q ss_pred HHHHHHHHH---HHHHHHHHHHHhHHHHH
Q 014536 10 MLLVISFFF---LTIFFTVTLFLTYKKIK 35 (423)
Q Consensus 10 ~~~~~~~~~---~~~~~~~~~~~~~~~~~ 35 (423)
|+.+||+|- ....+|..+|+..+|||
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 32
>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=38.27 E-value=84 Score=24.76 Aligned_cols=25 Identities=28% Similarity=0.406 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHH
Q 014536 10 MLLVISFFFLTIFFTVTLFLTYKKI 34 (423)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~ 34 (423)
+++.|+|.+|.||...+|.=.-+.+
T Consensus 4 lI~Aiaf~vLvi~l~~~l~~l~~~l 28 (90)
T PF06103_consen 4 LIAAIAFAVLVIFLIKVLKKLKKTL 28 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4667888888888766655443333
No 33
>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=38.18 E-value=55 Score=25.13 Aligned_cols=36 Identities=19% Similarity=0.280 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCH
Q 014536 299 IDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSP 334 (423)
Q Consensus 299 ~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSp 334 (423)
.+.+.++...|..|..+|..+..|...-.++|+|++
T Consensus 40 ~~~l~~en~~L~~ei~~l~~~~rIe~~Ar~~lgM~~ 75 (85)
T TIGR02209 40 IDKLQKEWRDLQLEVAELSRHERIEKIAKKQLGMKL 75 (85)
T ss_pred HHHHHHHHHHHHHHHHHHcCHHHHHHHHHHhcCCCC
Confidence 444555555666666666666666666666666654
No 34
>smart00271 DnaJ DnaJ molecular chaperone homology domain.
Probab=37.83 E-value=1.1e+02 Score=21.51 Aligned_cols=44 Identities=25% Similarity=0.280 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHHHHHhhhccCcch--HHHHHHHHHhHHHHHHHHhh
Q 014536 232 SATQRKIKELYHQLVQSCESNELT--LAQVGEFTKCLAQAREELED 275 (423)
Q Consensus 232 sAtQRRIkeqYDELvran~aK~LT--LaQV~eF~NcLVdARnEL~~ 275 (423)
+++...|+++|..|++...--... -....+....|.+|-+.|..
T Consensus 12 ~~~~~~ik~ay~~l~~~~HPD~~~~~~~~~~~~~~~l~~Ay~~L~~ 57 (60)
T smart00271 12 DASLDEIKKAYRKLALKYHPDKNPGDKEEAEEKFKEINEAYEVLSD 57 (60)
T ss_pred CCCHHHHHHHHHHHHHHHCcCCCCCchHHHHHHHHHHHHHHHHHcC
Confidence 478899999999999988765555 34444555566666665543
No 35
>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=37.80 E-value=43 Score=28.30 Aligned_cols=24 Identities=25% Similarity=0.406 Sum_probs=18.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHH
Q 014536 5 NLMLFMLLVISFFFLTIFFTVTLF 28 (423)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~ 28 (423)
+-+.-.++..+|+|+.|+|+.|++
T Consensus 64 ~~l~r~~~~~~~~~l~i~~~~t~~ 87 (92)
T TIGR02229 64 HALLRLASAVAFAILAILFVITHG 87 (92)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHH
Confidence 334455677899999999999886
No 36
>PRK11637 AmiB activator; Provisional
Probab=37.71 E-value=4.2e+02 Score=26.35 Aligned_cols=71 Identities=20% Similarity=0.190 Sum_probs=30.3
Q ss_pred HHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcC------CcchHHHHHHHHHHHHHHHHhhhhhHHHHHHH
Q 014536 256 LAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKA------DRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWL 326 (423)
Q Consensus 256 LaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskA------dRSS~DRL~qQIykLE~EqkRLekDa~VYN~L 326 (423)
+.++..=.+-|.+.+.+|..+-..++....-.++-...- .+.-.++|..++...+.+.+.|+++..-...+
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 11234455555555555555555554444333
No 37
>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=37.49 E-value=54 Score=25.37 Aligned_cols=25 Identities=36% Similarity=0.514 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHhhhhhHHHHH
Q 014536 300 DRLRQQIYNLEKQQRRLEEDVYVYN 324 (423)
Q Consensus 300 DRL~qQIykLE~EqkRLekDa~VYN 324 (423)
.=|+|||..||.+.++|..+...|-
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 38
>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=37.33 E-value=2.1e+02 Score=23.98 Aligned_cols=62 Identities=18% Similarity=0.240 Sum_probs=43.8
Q ss_pred ccchhHHHHHH-------HHHHHHH-hhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhh
Q 014536 229 SMGSATQRKIK-------ELYHQLV-QSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLS 292 (423)
Q Consensus 229 Ss~sAtQRRIk-------eqYDELv-ran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLs 292 (423)
++..++|||.- ..+|+.+ .+.++ -|+.+.+.|-.---++-+.=---.+.++=+|.++||.+-
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 899999999776666555555556678889999998763
No 39
>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=37.32 E-value=1e+02 Score=22.49 Aligned_cols=38 Identities=26% Similarity=0.389 Sum_probs=26.7
Q ss_pred cCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhh
Q 014536 251 SNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLS 292 (423)
Q Consensus 251 aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLs 292 (423)
-..+|..+|..|+..|...+ -+..++.+.++..++++.
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 46788899999999987765 567778888888777653
No 40
>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=35.96 E-value=1.1e+02 Score=21.01 Aligned_cols=25 Identities=20% Similarity=0.345 Sum_probs=20.2
Q ss_pred chhHHHHHHHHHHHHHhhhccCcch
Q 014536 231 GSATQRKIKELYHQLVQSCESNELT 255 (423)
Q Consensus 231 ~sAtQRRIkeqYDELvran~aK~LT 255 (423)
.+++...|+.+|..|++...-.+..
T Consensus 10 ~~~~~~~ik~~y~~l~~~~HPD~~~ 34 (55)
T cd06257 10 PDASDEEIKKAYRKLALKYHPDKNP 34 (55)
T ss_pred CCCCHHHHHHHHHHHHHHHCcCCCC
Confidence 4567899999999999988765554
No 41
>PRK09835 sensor kinase CusS; Provisional
Probab=35.89 E-value=1e+02 Score=28.88 Aligned_cols=36 Identities=6% Similarity=0.108 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHhhhhhhh
Q 014536 12 LVISFFFLTIFFTVTLFLTYKKIKRLQELENYANVL 47 (423)
Q Consensus 12 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (423)
+++.++++.+++.+.+|+.+...+.|+.|.+.++-+
T Consensus 188 ~~~~~~~~~~~~~~~~~~~~~~~~pl~~l~~~~~~i 223 (482)
T PRK09835 188 IMTASVISLLIVFIVLLAVHKGHAPIRSVSRQIQNI 223 (482)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444445555666677778888888776644
No 42
>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=35.54 E-value=25 Score=27.38 Aligned_cols=62 Identities=19% Similarity=0.258 Sum_probs=43.7
Q ss_pred hhHHHHHHHH--hhcCCcchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHHHHHHHh
Q 014536 281 KRKFSIQKAL--LSKADRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPACKKMFEV 342 (423)
Q Consensus 281 qRkftI~KAL--LskAdRSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAYKkMlE~ 342 (423)
+|-....+.+ |...|++.++|+|.-+.....-++.|+++-.++..-.-..+.+|++..+..+
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 3444454554 8888999999999888888888888888777654434466777777655443
No 43
>PHA02562 46 endonuclease subunit; Provisional
Probab=35.24 E-value=3.9e+02 Score=26.69 Aligned_cols=40 Identities=18% Similarity=0.312 Sum_probs=31.5
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHHHH
Q 014536 298 SIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPACKK 338 (423)
Q Consensus 298 S~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAYKk 338 (423)
.+++|.+++..+..+...++++...+..+++.|+- +.|+.
T Consensus 380 ~l~~l~~~l~~~~~~~~~~~ke~~~~~~i~~~~~~-~g~~~ 419 (562)
T PHA02562 380 ELAKLQDELDKIVKTKSELVKEKYHRGIVTDLLKD-SGIKA 419 (562)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-hhHHH
Confidence 35577788888888888899998888888888775 55655
No 44
>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=35.07 E-value=2.6e+02 Score=23.07 Aligned_cols=67 Identities=22% Similarity=0.349 Sum_probs=50.5
Q ss_pred chHHHHHHHHHhHHHHHHHHh---hhhhhhhhHHHHHHHHhhcC-Ccc---hHHHHHHHHHHHHHHHHhhhhhH
Q 014536 254 LTLAQVGEFTKCLAQAREELE---DKSETIKRKFSIQKALLSKA-DRS---SIDRLRQQIYNLEKQQRRLEEDV 320 (423)
Q Consensus 254 LTLaQV~eF~NcLVdARnEL~---~KSE~iqRkftI~KALLskA-dRS---S~DRL~qQIykLE~EqkRLekDa 320 (423)
||..|++.|.+-+...++++. ...+.++..+...|+-|-=+ .|- .++.+.+-+..+-...+..+.|.
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 67777777776666666665443
No 45
>PRK11637 AmiB activator; Provisional
Probab=34.91 E-value=2.6e+02 Score=27.81 Aligned_cols=88 Identities=20% Similarity=0.277 Sum_probs=42.1
Q ss_pred cccccchhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHH
Q 014536 226 PLTSMGSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQ 305 (423)
Q Consensus 226 PfTSs~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQ 305 (423)
|++...+.+|.++++.=.++-..... +.++..-.+-+...-+.|..+.+.+++++.-...-|.... ...+.+.++
T Consensus 37 ~~~~~~~~~~~~l~~l~~qi~~~~~~----i~~~~~~~~~~~~~l~~l~~qi~~~~~~i~~~~~~i~~~~-~ei~~l~~e 111 (428)
T PRK11637 37 AFSAHASDNRDQLKSIQQDIAAKEKS----VRQQQQQRASLLAQLKKQEEAISQASRKLRETQNTLNQLN-KQIDELNAS 111 (428)
T ss_pred hhcccchhhHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHH
Confidence 55555567777777776666544432 3333333333444444455555555555544444333221 133444444
Q ss_pred HHHHHHHHHhhhh
Q 014536 306 IYNLEKQQRRLEE 318 (423)
Q Consensus 306 IykLE~EqkRLek 318 (423)
|..++.+.+.+++
T Consensus 112 I~~~q~~l~~~~~ 124 (428)
T PRK11637 112 IAKLEQQQAAQER 124 (428)
T ss_pred HHHHHHHHHHHHH
Confidence 4444444444333
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=33.85 E-value=5.1e+02 Score=30.29 Aligned_cols=46 Identities=20% Similarity=0.238 Sum_probs=30.8
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHHHHHHHhh
Q 014536 298 SIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPACKKMFEVC 343 (423)
Q Consensus 298 S~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAYKkMlE~g 343 (423)
..++.++.+.+++.+.+.|++.......=-++|+-||+|+.--|+.
T Consensus 291 ~~~~~~~~~~~~~~~~~~le~~~~~l~~~~~~l~~~~a~~~~~eL~ 336 (1353)
T TIGR02680 291 ELETAREEERELDARTEALEREADALRTRLEALQGSPAYQDAEELE 336 (1353)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHH
Confidence 4445555555666656666555555555667899999998777776
No 47
>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=32.73 E-value=2.3e+02 Score=25.14 Aligned_cols=77 Identities=22% Similarity=0.388 Sum_probs=50.7
Q ss_pred HHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhh
Q 014536 237 KIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRL 316 (423)
Q Consensus 237 RIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRL 316 (423)
.|++.|.+|....+...++-. .+...|=.-..++..|.+++-.-+.-..|... +-..-..||..-....|...++|
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 578899999988776665443 35566666688899999998776655554433 33445556666666666666655
Q ss_pred h
Q 014536 317 E 317 (423)
Q Consensus 317 e 317 (423)
+
T Consensus 81 k 81 (162)
T PF05565_consen 81 K 81 (162)
T ss_pred H
Confidence 5
No 48
>PRK11281 hypothetical protein; Provisional
Probab=32.41 E-value=1.3e+02 Score=34.87 Aligned_cols=139 Identities=19% Similarity=0.258 Sum_probs=0.0
Q ss_pred HHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhh
Q 014536 240 ELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEED 319 (423)
Q Consensus 240 eqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLekD 319 (423)
+.|.+-........+|-++...+.. |++.|.+|+..-.. ++|..-.+.-+|+.-|+.|..=
T Consensus 383 ~~y~~~l~~~~~~~~~~~~~~~l~~-ll~~r~~LL~~l~~------------------~~~~~l~~~~~l~~~q~Ql~~~ 443 (1113)
T PRK11281 383 DAYIDKLEAGHKSEVTDEVRDALLQ-LLDERRELLDQLNK------------------QLNNQLNLAINLQLNQQQLLSV 443 (1113)
T ss_pred hhHHHHHHhcccCCCCHHHHHHHHH-HHHHHHHHHHHHHH------------------HHHHHHHHHHHHHHHHHHHHHH
Q ss_pred HHHHH-HHHHHhccCHHHHHHHHhhhhhhccccCCCCCCCCcccccccC--CHHHHHhhhcccccccccccchhhhHHHH
Q 014536 320 VYVYN-WLQDQLRLSPACKKMFEVCADMELKTKSSKPLENTETDEFADI--SFEELLAQEKKDSFWFVVPLKCLASYIFF 396 (423)
Q Consensus 320 a~VYN-~LQqQLKlSpAYKkMlE~ga~~Elk~~~~~~le~~~a~E~adi--SFEELLAQEKkDsFWqr~~~~~~~~~~~~ 396 (423)
+.-|. .|+||+ +=-.+..|+. .+-+.++ +....++......=|......-...+.+|
T Consensus 444 ~~~l~~~L~~~l-----------------fWv~s~~pid---~~w~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 (1113)
T PRK11281 444 SDSLQSTLTQQI-----------------FWVNSNKPMD---LDWLKAFPQALKDQFKSLKITVSFSNLWDGLFIALLLF 503 (1113)
T ss_pred HHHHHHHHHHhh-----------------hccCCCCCcC---HHHHHHHHHHHHHHHhhhhhhhhHHHHHHhhHhHHHHH
Q ss_pred Hhhhhcccceeeeeeecccccccc
Q 014536 397 FPLLIKLPCFCIFLYRQKNWKSRM 420 (423)
Q Consensus 397 ~~~~~~~~~~~~~~~~~~~~~~~~ 420 (423)
+|+++ |+.+.+++.+.++.++
T Consensus 504 ~~lll---~~~~~~~~r~~~~~~l 524 (1113)
T PRK11281 504 LPLLL---IAGLIRWRKKWIKARL 524 (1113)
T ss_pred HHHHH---HHHHHHHHHHHHHHHH
No 49
>PF05667 DUF812: Protein of unknown function (DUF812); InterPro: IPR008530 This family consists of several eukaryotic proteins of unknown function.
Probab=31.24 E-value=5.9e+02 Score=27.67 Aligned_cols=98 Identities=19% Similarity=0.269 Sum_probs=54.8
Q ss_pred HHHHHHHHHHHhhhccCcchH----HHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHH-HHHH---HHH
Q 014536 236 RKIKELYHQLVQSCESNELTL----AQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSID-RLRQ---QIY 307 (423)
Q Consensus 236 RRIkeqYDELvran~aK~LTL----aQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~D-RL~q---QIy 307 (423)
..+.+-|+.|-.....+.... .+|.++-...=+.-.|++.|.+.++.--+.-+.|=....||+|= ||.+ .|.
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 33333333333344444444444444444444444456798886 7774 555
Q ss_pred HHHHHHHhhhhhHHHH----HHHHHHhccC
Q 014536 308 NLEKQQRRLEEDVYVY----NWLQDQLRLS 333 (423)
Q Consensus 308 kLE~EqkRLekDa~VY----N~LQqQLKlS 333 (423)
|=..|..+.-.|+--+ |.|+.+|.-+
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 5566666666677654 5666666544
No 50
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=30.74 E-value=1.7e+02 Score=21.60 Aligned_cols=14 Identities=36% Similarity=0.560 Sum_probs=6.9
Q ss_pred hHHHHHHHHHHHHH
Q 014536 6 LMLFMLLVISFFFL 19 (423)
Q Consensus 6 ~~~~~~~~~~~~~~ 19 (423)
+-+.++++++|++-
T Consensus 18 ~pl~l~il~~f~~G 31 (68)
T PF06305_consen 18 LPLGLLILIAFLLG 31 (68)
T ss_pred chHHHHHHHHHHHH
Confidence 34455555555443
No 51
>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=30.59 E-value=3.9e+02 Score=23.79 Aligned_cols=55 Identities=20% Similarity=0.362 Sum_probs=39.3
Q ss_pred HhHHHHHHHHhhhhhhhhhHH--HHHHHHh--hcCCcchHHHHHHHHHHHHHHHHhhhh
Q 014536 264 KCLAQAREELEDKSETIKRKF--SIQKALL--SKADRSSIDRLRQQIYNLEKQQRRLEE 318 (423)
Q Consensus 264 NcLVdARnEL~~KSE~iqRkf--tI~KALL--skAdRSS~DRL~qQIykLE~EqkRLek 318 (423)
+..=++++...+.-+.+...| +|.+||= --+.|.-+|=|...|+.|+.+..+|..
T Consensus 72 ~~~~~~~~~~~~~~dklE~~fd~rV~~aL~rLgvPs~~dv~~L~~rId~L~~~v~~l~~ 130 (132)
T PF05597_consen 72 SRVDDVKERATGQWDKLEQAFDERVARALNRLGVPSRKDVEALSARIDQLTAQVERLAN 130 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344466777777777777766 5667663 235578888899999999988888753
No 52
>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=29.84 E-value=3.2e+02 Score=22.55 Aligned_cols=66 Identities=27% Similarity=0.372 Sum_probs=45.4
Q ss_pred HHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhh
Q 014536 239 KELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEE 318 (423)
Q Consensus 239 keqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLek 318 (423)
..-|+=|-+.|.+-..-...+.+.++-|-..-+.|.+|.+. ++...+||+.+|.+...|+.
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 35677777888877777777777777777777777777664 44555666666666666666
Q ss_pred hHHHH
Q 014536 319 DVYVY 323 (423)
Q Consensus 319 Da~VY 323 (423)
=|+.-
T Consensus 81 ~v~~L 85 (99)
T PF10046_consen 81 TVYEL 85 (99)
T ss_pred HHHHH
Confidence 55543
No 53
>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=29.54 E-value=1.2e+02 Score=22.59 Aligned_cols=37 Identities=19% Similarity=0.395 Sum_probs=28.5
Q ss_pred chHHHHHHHHHHHHHHHHhh-hhhHHHHHHHHHHhccC
Q 014536 297 SSIDRLRQQIYNLEKQQRRL-EEDVYVYNWLQDQLRLS 333 (423)
Q Consensus 297 SS~DRL~qQIykLE~EqkRL-ekDa~VYN~LQqQLKlS 333 (423)
+-.+.+.+++.+|+.+.++| .-+..|-..-.++|+++
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 35667888888888888888 66677777777788775
No 54
>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=29.52 E-value=1.3e+02 Score=26.33 Aligned_cols=56 Identities=20% Similarity=0.253 Sum_probs=40.6
Q ss_pred HHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhh-hhHHHHHHHHhhcCCcchHHHHH
Q 014536 241 LYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETI-KRKFSIQKALLSKADRSSIDRLR 303 (423)
Q Consensus 241 qYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~i-qRkftI~KALLskAdRSS~DRL~ 303 (423)
.|.|+++...+..-+..+|.+|+. .+|.+|+-.| ....+|.|.|+.+. .+.|.|-.
T Consensus 21 ~~~Eia~~t~~s~~~~~ei~d~L~------kRL~~~~~hVK~K~Lrilk~l~~~G-~~~f~~~~ 77 (122)
T cd03572 21 LYEEIAKLTRKSVGSCQELLEYLL------KRLKRSSPHVKLKVLKIIKHLCEKG-NSDFKREL 77 (122)
T ss_pred HHHHHHHHHHcCHHHHHHHHHHHH------HHhcCCCCcchHHHHHHHHHHHhhC-CHHHHHHH
Confidence 688999888885555555555543 5789999888 55678888888776 47777654
No 55
>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=29.32 E-value=53 Score=23.08 Aligned_cols=24 Identities=17% Similarity=0.439 Sum_probs=18.7
Q ss_pred HHHHHhhhccCcchHHHHHHHHHh
Q 014536 242 YHQLVQSCESNELTLAQVGEFTKC 265 (423)
Q Consensus 242 YDELvran~aK~LTLaQV~eF~Nc 265 (423)
+-+|++-+..-++|..||++|+..
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 56
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=28.89 E-value=1.3e+02 Score=25.38 Aligned_cols=28 Identities=25% Similarity=0.456 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHh
Q 014536 14 ISFFFLTIFFTVTLFLTYKKIKRLQELE 41 (423)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (423)
-.+..||-||.++.||.||-.|.++.=|
T Consensus 25 ~vll~LtPlfiisa~lSwkLaK~ie~~e 52 (74)
T PF15086_consen 25 TVLLILTPLFIISAVLSWKLAKAIEKEE 52 (74)
T ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence 3445688899999999999888776443
No 57
>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=28.16 E-value=69 Score=26.95 Aligned_cols=32 Identities=19% Similarity=0.544 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHhhhhhhhc
Q 014536 17 FFLTIFFTVTLFLTYKKIKRLQELENYANVLK 48 (423)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 48 (423)
++++|..-...|..|+|+||-+++.....-+.
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 33455555567899999999888877766554
No 58
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=28.06 E-value=1.5e+02 Score=28.62 Aligned_cols=32 Identities=34% Similarity=0.551 Sum_probs=26.8
Q ss_pred chHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhc
Q 014536 297 SSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLR 331 (423)
Q Consensus 297 SS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLK 331 (423)
...+=|..|...+-.|+.||.|| |+.||+|+.
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 45677888999999999999988 789999875
No 59
>PRK09039 hypothetical protein; Validated
Probab=28.00 E-value=1.1e+02 Score=30.19 Aligned_cols=22 Identities=36% Similarity=0.794 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhHH
Q 014536 11 LLVISFFFLTIFFTVTLFLTYK 32 (423)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~ 32 (423)
||.+.+|.||||..+-.||...
T Consensus 26 ll~~~~f~l~~f~~~q~fLs~~ 47 (343)
T PRK09039 26 LLLVIMFLLTVFVVAQFFLSRE 47 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4444567899999999998764
No 60
>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=27.72 E-value=75 Score=24.58 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhHH
Q 014536 11 LLVISFFFLTIFFTVTLFLTYK 32 (423)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~ 32 (423)
+++|++||+++...+.+.-+-|
T Consensus 4 ~~iV~i~iv~~lLg~~I~~~~K 25 (50)
T PF12606_consen 4 FLIVSIFIVMGLLGLSICTTLK 25 (50)
T ss_pred hHHHHHHHHHHHHHHHHHHHhh
Confidence 4667777777776666554444
No 61
>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=27.23 E-value=45 Score=27.98 Aligned_cols=41 Identities=22% Similarity=0.414 Sum_probs=25.4
Q ss_pred HHHHHHHhhhhhhccccCCCCCCCCcccccccCCHHHHHhhhccccccccc
Q 014536 335 ACKKMFEVCADMELKTKSSKPLENTETDEFADISFEELLAQEKKDSFWFVV 385 (423)
Q Consensus 335 AYKkMlE~ga~~Elk~~~~~~le~~~a~E~adiSFEELLAQEKkDsFWqr~ 385 (423)
.||+|+.++.-.. .+ ++ ....+-..++|+.-.=-|+||+-.
T Consensus 16 mhkRMl~vs~~~~-------~~--~~-~~~~~~a~~~L~~aQcNd~yWHG~ 56 (80)
T PF09094_consen 16 MHKRMLYVSSKVR-------QL--PD-KKRKEEAREELYRAQCNDAYWHGL 56 (80)
T ss_dssp HHHHHHHHHHHHT-------T----------HHHHHHHHHTTBGGGG--SS
T ss_pred HHHHHHHHHHHHH-------Hh--hh-hhhhHHHHHHHHHhccCcchhccc
Confidence 5899999996655 11 11 223334689999999999999853
No 62
>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=26.88 E-value=1.1e+02 Score=23.59 Aligned_cols=35 Identities=20% Similarity=0.381 Sum_probs=26.2
Q ss_pred hHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHH
Q 014536 233 ATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLA 267 (423)
Q Consensus 233 AtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLV 267 (423)
++=++|-++|.+++.......+|-.+|.++++-|-
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 34478999999999999999999999999888764
No 63
>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=26.60 E-value=2.4e+02 Score=22.89 Aligned_cols=38 Identities=18% Similarity=0.363 Sum_probs=22.4
Q ss_pred hhhHHHHHHHHhhcCC------cchHHHHHHHHHHHHHHHHhhh
Q 014536 280 IKRKFSIQKALLSKAD------RSSIDRLRQQIYNLEKQQRRLE 317 (423)
Q Consensus 280 iqRkftI~KALLskAd------RSS~DRL~qQIykLE~EqkRLe 317 (423)
.+.+|.=...|+..+. +..++.|.+||..|..+-+||.
T Consensus 26 Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql~rLs 69 (70)
T PF04899_consen 26 WQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLSEQLERLS 69 (70)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3444444445554432 4567777777777777776664
No 64
>PF13706 PepSY_TM_3: PepSY-associated TM helix
Probab=26.27 E-value=90 Score=21.93 Aligned_cols=27 Identities=19% Similarity=0.501 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHH
Q 014536 9 FMLLVISFFFLTIFFTVTLFLTYKKIK 35 (423)
Q Consensus 9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 35 (423)
.+-++++.+++.+++|-++..-...|.
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 65
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=26.26 E-value=1.2e+02 Score=31.62 Aligned_cols=32 Identities=28% Similarity=0.447 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHhhhhhhhc
Q 014536 17 FFLTIFFTVTLFLTYKKIKRLQELENYANVLK 48 (423)
Q Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 48 (423)
..+.|++++.+|+.-+..+++.+||+.-+-|.
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 66
>COG3352 FlaC Putative archaeal flagellar protein C [Cell motility and secretion]
Probab=25.72 E-value=2.4e+02 Score=26.54 Aligned_cols=68 Identities=18% Similarity=0.221 Sum_probs=50.2
Q ss_pred HHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhHHHH
Q 014536 256 LAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDVYVY 323 (423)
Q Consensus 256 LaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLekDa~VY 323 (423)
++...+=++-|=..=..|---.|++-|.|-+-++.+.+--|+-.|-|.+||.+|+...+-..+|+..+
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 33333334443333334445577788889999999988888889999999999999999999998653
No 67
>PTZ00420 coronin; Provisional
Probab=25.67 E-value=36 Score=36.07 Aligned_cols=19 Identities=53% Similarity=0.707 Sum_probs=15.4
Q ss_pred CCCCCCCCCCCcccccccc
Q 014536 65 NNDNNNNNNNDNTLHQNQN 83 (423)
Q Consensus 65 ~~~~~~~~~~~~~~~~~~~ 83 (423)
|.|.|||+|++|||....|
T Consensus 533 ~~~~~~~~~~~~~~~~~~~ 551 (568)
T PTZ00420 533 NDDDNNNLNRGNTLRSEGN 551 (568)
T ss_pred cCcccccccCCcceecccc
Confidence 5677889999999987665
No 68
>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=25.53 E-value=5.5e+02 Score=23.83 Aligned_cols=76 Identities=28% Similarity=0.278 Sum_probs=41.7
Q ss_pred HHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHH-----HHHH
Q 014536 237 KIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIY-----NLEK 311 (423)
Q Consensus 237 RIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIy-----kLE~ 311 (423)
.+.+.|+.|-+-.+.-..-..+..+-+..+-....+|.++.+.+...-.=...++. ..+|+|.+.|. ..++
T Consensus 53 ~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~~~~~~~~~l~p~m~----~m~~~L~~~v~~d~Pf~~~e 128 (251)
T PF11932_consen 53 ELLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIEQIEETRQELVPLME----QMIDELEQFVELDLPFLLEE 128 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHhcCCCCChHH
Confidence 34455555555555555556666666666666667777666666554433333332 24555555554 4444
Q ss_pred HHHhh
Q 014536 312 QQRRL 316 (423)
Q Consensus 312 EqkRL 316 (423)
.++||
T Consensus 129 R~~Rl 133 (251)
T PF11932_consen 129 RQERL 133 (251)
T ss_pred HHHHH
Confidence 44444
No 69
>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=25.37 E-value=1e+02 Score=30.28 Aligned_cols=26 Identities=38% Similarity=0.704 Sum_probs=17.2
Q ss_pred hHHHHHHHHHHHHH--HHHHHHHHHHhH
Q 014536 6 LMLFMLLVISFFFL--TIFFTVTLFLTY 31 (423)
Q Consensus 6 ~~~~~~~~~~~~~~--~~~~~~~~~~~~ 31 (423)
.||..|++|...|| ||.|..|..|.-
T Consensus 129 amLIClIIIAVLfLICT~LfLSTVVLAN 156 (227)
T PF05399_consen 129 AMLICLIIIAVLFLICTLLFLSTVVLAN 156 (227)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67777777765554 677777766643
No 70
>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=25.31 E-value=2.7e+02 Score=20.20 Aligned_cols=20 Identities=15% Similarity=0.335 Sum_probs=15.1
Q ss_pred HHHhhhccCcchHHHHHHHH
Q 014536 244 QLVQSCESNELTLAQVGEFT 263 (423)
Q Consensus 244 ELvran~aK~LTLaQV~eF~ 263 (423)
+++++.++=++||+++.+|.
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 35677788899999999999
No 71
>KOG4687 consensus Uncharacterized coiled-coil protein [Function unknown]
Probab=25.10 E-value=2.6e+02 Score=29.04 Aligned_cols=115 Identities=22% Similarity=0.202 Sum_probs=80.7
Q ss_pred HHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhh---cC--CcchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhc
Q 014536 257 AQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLS---KA--DRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLR 331 (423)
Q Consensus 257 aQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLs---kA--dRSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLK 331 (423)
+|...=+...||-+.||.-.-+..+|+---..-=|+ ++ +|+. -++|+.|=.|-+=|..-+.+-..=-+-.|
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 455555667777777777766666665332222121 22 2332 36788888888888877777776667777
Q ss_pred cCHH-HHHHHHhhhhhhccccCCCCCCCCcccccccCCH---HHHHhh
Q 014536 332 LSPA-CKKMFEVCADMELKTKSSKPLENTETDEFADISF---EELLAQ 375 (423)
Q Consensus 332 lSpA-YKkMlE~ga~~Elk~~~~~~le~~~a~E~adiSF---EELLAQ 375 (423)
+|-+ ||.|.+--..--|+.+.....++-+..+++=|+- .|+||.
T Consensus 246 ~siaKYKqM~dAknvqtmrkkgi~a~~G~dknedaiin~kQikeiLaS 293 (389)
T KOG4687|consen 246 MSIAKYKQMADAKNVQTMRKKGIKAGEGDDKNEDAIINMKQIKEILAS 293 (389)
T ss_pred HHHHHHHHHHHHHhHHHHHhcCCccCCCCCCcchheecHHHHHHHHHc
Confidence 7754 9999999888888899999999888888888885 466665
No 72
>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=25.09 E-value=1.2e+02 Score=25.69 Aligned_cols=15 Identities=27% Similarity=0.501 Sum_probs=11.8
Q ss_pred ccCCHHHHHhhhccc
Q 014536 365 ADISFEELLAQEKKD 379 (423)
Q Consensus 365 adiSFEELLAQEKkD 379 (423)
.+|++++.+.++++-
T Consensus 122 g~~d~~~Fl~~f~~~ 136 (150)
T PF07200_consen 122 GEIDVDDFLKQFKEK 136 (150)
T ss_dssp SHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHH
Confidence 368889999988765
No 73
>PRK06718 precorrin-2 dehydrogenase; Reviewed
Probab=24.91 E-value=4.2e+02 Score=24.01 Aligned_cols=51 Identities=14% Similarity=0.315 Sum_probs=37.7
Q ss_pred cchhHHHHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhc
Q 014536 230 MGSATQRKIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSK 293 (423)
Q Consensus 230 s~sAtQRRIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLsk 293 (423)
+++.+.++|.+.|. ...++|+..|-..|..+.++..+...+-.+-+.+++.
T Consensus 132 la~~lr~~ie~~~~-------------~~~~~~~~~~~~~R~~~k~~~~~~~~R~~~~~~~~~~ 182 (202)
T PRK06718 132 LAKKIRDELEALYD-------------ESYESYIDFLYECRQKIKELQIEKREKQILLQEVLSS 182 (202)
T ss_pred HHHHHHHHHHHHcc-------------hhHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhhh
Confidence 45666666666554 3456788889999999999888777777777777754
No 74
>KOG1666 consensus V-SNARE [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.53 E-value=1.2e+02 Score=29.59 Aligned_cols=63 Identities=14% Similarity=0.205 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHhhhccCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcch
Q 014536 236 RKIKELYHQLVQSCESNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSS 298 (423)
Q Consensus 236 RRIkeqYDELvran~aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS 298 (423)
+||++.|+-.+---+-..==|.+.+.=-+.|-.||..|.+-++++-|+-+|.+.|.-.+-+..
T Consensus 135 ~rl~ds~Ria~ETEqIG~~IL~dL~~QRe~L~rar~rL~~td~~lgkS~kiL~tM~RR~~~nk 197 (220)
T KOG1666|consen 135 DRLKDSQRIALETEQIGSEILEDLHGQREQLERARERLRETDANLGKSRKILTTMTRRLIRNK 197 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchhhhhHHHHHHHHHHHHHHHHH
Confidence 578888887665444333345566666788999999999999999999999999986554433
No 75
>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=24.22 E-value=1.1e+02 Score=24.79 Aligned_cols=51 Identities=18% Similarity=0.263 Sum_probs=27.1
Q ss_pred CcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhc
Q 014536 252 NELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLR 331 (423)
Q Consensus 252 K~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLK 331 (423)
++.+-.||.+|+.-|.+.= ++|..++..|..+...|.....-|......|+
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 4667789999988887644 44446666666666666666666654444443
No 76
>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=24.01 E-value=32 Score=28.10 Aligned_cols=16 Identities=44% Similarity=0.702 Sum_probs=11.2
Q ss_pred Cccccccccccceehh
Q 014536 160 RQETVDGCATGRVLVV 175 (423)
Q Consensus 160 ~~~~~~~~~~~~~~~~ 175 (423)
.-..|+.|.||||.|.
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 3457899999999876
No 77
>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=23.98 E-value=2.5e+02 Score=25.49 Aligned_cols=44 Identities=25% Similarity=0.352 Sum_probs=33.7
Q ss_pred HHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhH
Q 014536 272 ELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDV 320 (423)
Q Consensus 272 EL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLekDa 320 (423)
.+....+.|+.-+.|.++ -||..+.|.+.+..|+.|..+|++|.
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 48889999999999999999998875
No 78
>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=23.92 E-value=1.6e+02 Score=22.15 Aligned_cols=32 Identities=16% Similarity=0.339 Sum_probs=17.3
Q ss_pred CCcchhHHHHHHHHHHHHHHHHHHHHHHHhHH
Q 014536 1 MDENNLMLFMLLVISFFFLTIFFTVTLFLTYK 32 (423)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 (423)
||.++.+--..-+.+++++.++|...++..|.
T Consensus 1 Md~~~~lr~~a~~~~l~~~~~~Figiv~wa~~ 32 (48)
T cd01324 1 MDIGETLRGLADSWGLLYLALFFLGVVVWAFR 32 (48)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 66664333334445555555666666666664
No 79
>PF13010 pRN1_helical: Primase helical domain; PDB: 1RO0_A 1RNI_A 1RO2_A 3M1M_A.
Probab=23.69 E-value=34 Score=31.27 Aligned_cols=19 Identities=42% Similarity=0.962 Sum_probs=13.2
Q ss_pred hhhhhccCCCC----hhhhhhcc
Q 014536 94 TLLLEILPSKS----AKWDRLLS 112 (423)
Q Consensus 94 sll~eilps~s----~kw~~l~~ 112 (423)
..|..+||+|| |||+..|.
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 89998763
No 80
>cd07599 BAR_Rvs167p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 167 and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 167 (Rvs167p) and Schizosaccharomyces pombe Hob1 (homolog of Bin1). S. cerevisiae Rvs167p plays a role in regulation of the actin cytoskeleton, endocytosis, and sporulation. It forms a heterodimer with another BAR domain protein Rvs161p. Rvs161p and Rvs167p share common functions but are not interchangeable. Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. Rvs167p also interacts with the GTPase activating protein (GAP) Gyp5p, which is involved in ER to Golgi vesicle trafficking. BAR domains fo
Probab=23.44 E-value=5.5e+02 Score=23.13 Aligned_cols=19 Identities=37% Similarity=0.550 Sum_probs=14.2
Q ss_pred HHhhhhhHHHHHHHHHHhc
Q 014536 313 QRRLEEDVYVYNWLQDQLR 331 (423)
Q Consensus 313 qkRLekDa~VYN~LQqQLK 331 (423)
++.|++=..+|+.|-.+|+
T Consensus 155 e~~l~~a~~~y~~lN~~Lk 173 (216)
T cd07599 155 ERKLEEAKEEYEALNELLK 173 (216)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5566666678888888886
No 81
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=23.25 E-value=1.3e+02 Score=28.13 Aligned_cols=47 Identities=30% Similarity=0.511 Sum_probs=27.5
Q ss_pred HHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhh
Q 014536 270 REELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLE 317 (423)
Q Consensus 270 RnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLe 317 (423)
|.++.++.+.++.-+.++..|+..+.+ -.+.+..++.+|+.|.+..+
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 24566667777777666544
No 82
>PRK04778 septation ring formation regulator EzrA; Provisional
Probab=23.14 E-value=2.8e+02 Score=28.99 Aligned_cols=16 Identities=31% Similarity=0.443 Sum_probs=10.6
Q ss_pred HHHHHHhHHHHHHHHH
Q 014536 24 TVTLFLTYKKIKRLQE 39 (423)
Q Consensus 24 ~~~~~~~~~~~~~~~~ 39 (423)
.+.=--.|+.|.+|.+
T Consensus 21 ~~~rr~~~~~i~~Le~ 36 (569)
T PRK04778 21 LILRKRNYKRIDELEE 36 (569)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3344677888887754
No 83
>PF13801 Metal_resist: Heavy-metal resistance; PDB: 3EPV_C 2Y3D_A 2Y3H_D 2Y3G_B 2Y3B_A 2Y39_A 3LAY_H.
Probab=23.08 E-value=3.4e+02 Score=20.57 Aligned_cols=68 Identities=19% Similarity=0.256 Sum_probs=42.1
Q ss_pred cCcchHHHHHHHHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhc--CCcchHHHHHHHHHHHHHHHHhhhh
Q 014536 251 SNELTLAQVGEFTKCLAQAREELEDKSETIKRKFSIQKALLSK--ADRSSIDRLRQQIYNLEKQQRRLEE 318 (423)
Q Consensus 251 aK~LTLaQV~eF~NcLVdARnEL~~KSE~iqRkftI~KALLsk--AdRSS~DRL~qQIykLE~EqkRLek 318 (423)
.-.||=.|-.++-.-+-+.+.+...--..++....=..++|.. .|+.-++.+.++|..++.+.....-
T Consensus 39 ~l~Lt~eQ~~~l~~~~~~~~~~~~~~r~~~~~~r~~l~~ll~~~~~D~~~i~a~~~~~~~~~~~l~~~~~ 108 (125)
T PF13801_consen 39 MLNLTPEQQAKLRALMDEFRQEMRALRQELRAARQELRALLAAPPPDEAAIEALLEEIREAQAELRQERL 108 (125)
T ss_dssp HS-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556666666666666666655555555555555555666665 4577888888888888776655443
No 84
>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=22.90 E-value=4.2e+02 Score=22.22 Aligned_cols=56 Identities=21% Similarity=0.299 Sum_probs=42.0
Q ss_pred HHHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhHH
Q 014536 262 FTKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDVY 321 (423)
Q Consensus 262 F~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLekDa~ 321 (423)
|..-|..+|.++..=++.+..-+.-....+.+.+ ..+.++|.+.|.+-.+|...+.
T Consensus 3 ~~~~l~~~~~el~~m~~~~~~ml~~~~~~~~~~d----~~~~~~i~~~e~~id~l~~~i~ 58 (212)
T TIGR02135 3 FDEELKELREELLEMGGLVEEQLEDAVRALTEKD----RELARKVIEDDDQINALEVKIE 58 (212)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC----HHHHHHHHHChHHHHHHHHHHH
Confidence 5566888999999888888888888877777655 2456677777777777776654
No 85
>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=22.81 E-value=2.5e+02 Score=20.12 Aligned_cols=45 Identities=24% Similarity=0.286 Sum_probs=30.4
Q ss_pred chhHHHHHHHHHHHHHhhhccCcchH--HHHHHHHHhHHHHHHHHhh
Q 014536 231 GSATQRKIKELYHQLVQSCESNELTL--AQVGEFTKCLAQAREELED 275 (423)
Q Consensus 231 ~sAtQRRIkeqYDELvran~aK~LTL--aQV~eF~NcLVdARnEL~~ 275 (423)
..|.+-.|+++|.+|++...--++.- +...+....|..|.+-|..
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 3344555555555555543
No 86
>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=22.71 E-value=6e+02 Score=24.45 Aligned_cols=69 Identities=17% Similarity=0.224 Sum_probs=46.5
Q ss_pred HHHHHHHHH---hHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcc---h-----------HHHHHHHHHHHHHHHHhhhh
Q 014536 256 LAQVGEFTK---CLAQAREELEDKSETIKRKFSIQKALLSKADRS---S-----------IDRLRQQIYNLEKQQRRLEE 318 (423)
Q Consensus 256 LaQV~eF~N---cLVdARnEL~~KSE~iqRkftI~KALLskAdRS---S-----------~DRL~qQIykLE~EqkRLek 318 (423)
+..+..+.+ -|...|..+.+.-...-+...|+..||.+..+. . ||-+..+|...-..|+.|-+
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 334444543 447778888888888888889999998887543 2 55555666666677777776
Q ss_pred hHHHHH
Q 014536 319 DVYVYN 324 (423)
Q Consensus 319 Da~VYN 324 (423)
+....|
T Consensus 272 ~i~~~~ 277 (342)
T cd08915 272 EIDAAN 277 (342)
T ss_pred HHHHHH
Confidence 665444
No 87
>PHA03030 hypothetical protein; Provisional
Probab=22.54 E-value=65 Score=28.94 Aligned_cols=20 Identities=40% Similarity=0.999 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 014536 8 LFMLLVISFFFLTIFFTVTL 27 (423)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~ 27 (423)
.|.++.+.|.|+.|||-++.
T Consensus 4 i~~ili~lfifl~iffYI~~ 23 (122)
T PHA03030 4 IFLILIFLFIFLFIFFYIRI 23 (122)
T ss_pred ehHHHHHHHHHHHHHHHhee
Confidence 35666677777777776543
No 88
>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=22.53 E-value=82 Score=26.64 Aligned_cols=10 Identities=50% Similarity=0.766 Sum_probs=4.4
Q ss_pred HHHhHHHHHH
Q 014536 27 LFLTYKKIKR 36 (423)
Q Consensus 27 ~~~~~~~~~~ 36 (423)
+|+++..-+|
T Consensus 16 ~~~~~~~~rR 25 (130)
T PF12273_consen 16 LFLFYCHNRR 25 (130)
T ss_pred HHHHHHHHHH
Confidence 3444544443
No 89
>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=21.99 E-value=2.9e+02 Score=23.19 Aligned_cols=22 Identities=5% Similarity=0.184 Sum_probs=17.1
Q ss_pred HHhhhccCcchHHHHHHHHHhH
Q 014536 245 LVQSCESNELTLAQVGEFTKCL 266 (423)
Q Consensus 245 Lvran~aK~LTLaQV~eF~NcL 266 (423)
++++-..-+++|+++.+|+...
T Consensus 49 ~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04785 49 FIRRARDLGFSLEEIRALLALS 70 (126)
T ss_pred HHHHHHHCCCCHHHHHHHHhhh
Confidence 4566677889999999988753
No 90
>cd09238 V_Alix_like_1 Protein-interacting V-domain of an uncharacterized family of the V_Alix_like superfamily. This domain family is comprised of uncharacterized plant proteins. It belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), (His-Domain) type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. 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. Alix, HD-PTP, Bro1, a
Probab=21.92 E-value=4.3e+02 Score=25.92 Aligned_cols=58 Identities=21% Similarity=0.251 Sum_probs=36.6
Q ss_pred HHhHHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHH-----------HHHHHHHHHHHhhhhhHHH
Q 014536 263 TKCLAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLR-----------QQIYNLEKQQRRLEEDVYV 322 (423)
Q Consensus 263 ~NcLVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~-----------qQIykLE~EqkRLekDa~V 322 (423)
++-|...|..+.+.-....+...|+..|+.... ++++|+ .+|...-..|+.|-++...
T Consensus 204 l~~lk~eR~~l~~~Lk~~~~~DDI~~~ll~~~~--~~e~lF~~eL~kf~~~~~~v~~~~~~Q~~ll~~i~~ 272 (339)
T cd09238 204 LEALGNERAGIEDMMKALKRNDNILAKVMATTG--SYDALFKEELKKYDSVREAVSKNISSQDDLLSRLRA 272 (339)
T ss_pred HHHHHHHHHHHHHHHHHHhhcCCcHHHHHHhhh--hhHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence 345666777777777777888889988987653 255544 4444444555555555544
No 91
>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=21.80 E-value=5.1e+02 Score=22.13 Aligned_cols=33 Identities=27% Similarity=0.506 Sum_probs=27.3
Q ss_pred CCCCCcccccc---hhHHHHHHHHHHHHHhhhccCcc
Q 014536 221 LGCLCPLTSMG---SATQRKIKELYHQLVQSCESNEL 254 (423)
Q Consensus 221 ~~c~yPfTSs~---sAtQRRIkeqYDELvran~aK~L 254 (423)
...-|||.+.+ ...+..+.+-.+.||..+. ..+
T Consensus 2 ~~~~YPli~k~~~~k~Fr~~~~~F~~~lv~~~~-~~~ 37 (118)
T PF08514_consen 2 DSSDYPLISKGKKFKKFRKNFCEFFDQLVEQCH-SSI 37 (118)
T ss_pred CcccCCCcCCCcccHHHHHHHHHHHHHHHHHhc-ccc
Confidence 34579999997 7788999999999999888 554
No 92
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=21.73 E-value=1.4e+02 Score=27.68 Aligned_cols=38 Identities=21% Similarity=0.295 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHH
Q 014536 299 IDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPAC 336 (423)
Q Consensus 299 ~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAY 336 (423)
-++|.+|+..|+.+..++++-..-...|++.|.+.+.+
T Consensus 78 n~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL~~~~~~ 115 (276)
T PRK13922 78 NEELKKELLELESRLQELEQLEAENARLRELLNLKESL 115 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccC
Confidence 34555555555555555554444555556665555443
No 93
>PRK09039 hypothetical protein; Validated
Probab=21.26 E-value=4.7e+02 Score=25.98 Aligned_cols=54 Identities=24% Similarity=0.346 Sum_probs=35.5
Q ss_pred HHHHHHHHhhhhhhhhhHHHHHHHHhhcCCcchHHHHHHHHHHHHHHHHhhhhhH
Q 014536 266 LAQAREELEDKSETIKRKFSIQKALLSKADRSSIDRLRQQIYNLEKQQRRLEEDV 320 (423)
Q Consensus 266 LVdARnEL~~KSE~iqRkftI~KALLskAdRSS~DRL~qQIykLE~EqkRLekDa 320 (423)
+.++..+++.+...+++...=.|+..+. .++-+.||.+||..|+.+..+|+...
T Consensus 107 ~~~~~~~~~~~~~~l~~~L~~~k~~~se-~~~~V~~L~~qI~aLr~Qla~le~~L 160 (343)
T PRK09039 107 LAGAGAAAEGRAGELAQELDSEKQVSAR-ALAQVELLNQQIAALRRQLAALEAAL 160 (343)
T ss_pred hhhhcchHHHHHHHHHHHHHHHHHHHHH-hhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344556666666677777666665543 35577888888888887777766543
No 94
>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=21.01 E-value=1.9e+02 Score=22.20 Aligned_cols=14 Identities=29% Similarity=0.465 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHHHH
Q 014536 13 VISFFFLTIFFTVT 26 (423)
Q Consensus 13 ~~~~~~~~~~~~~~ 26 (423)
.|.|+||.+.+.+.
T Consensus 13 ~iVF~~L~lL~~~i 26 (79)
T PF04277_consen 13 GIVFLVLILLILVI 26 (79)
T ss_pred HHHHHHHHHHHHHH
Confidence 34444444444333
No 95
>TIGR03017 EpsF chain length determinant protein EpsF. Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=20.50 E-value=8e+02 Score=23.92 Aligned_cols=45 Identities=16% Similarity=0.139 Sum_probs=27.2
Q ss_pred chHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCH-HHHHHHH
Q 014536 297 SSIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSP-ACKKMFE 341 (423)
Q Consensus 297 SS~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSp-AYKkMlE 341 (423)
.....|..++..++.+...+.....-|..|+.++...- -|..+++
T Consensus 318 ~~~~~l~~~l~~~~~~~~~l~~~~~~~~~L~r~~~~~~~~y~~ll~ 363 (444)
T TIGR03017 318 QREAELREALENQKAKVLELNRQRDEMSVLQRDVENAQRAYDAAMQ 363 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666666666666666666667777777766543 3444444
No 96
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=20.45 E-value=6.4e+02 Score=22.75 Aligned_cols=68 Identities=19% Similarity=0.276 Sum_probs=37.2
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCHHHHHHHHhhhhhhccccCCCCCCCCcccccccCCHHHHHhhh
Q 014536 298 SIDRLRQQIYNLEKQQRRLEEDVYVYNWLQDQLRLSPACKKMFEVCADMELKTKSSKPLENTETDEFADISFEELLAQE 376 (423)
Q Consensus 298 S~DRL~qQIykLE~EqkRLekDa~VYN~LQqQLKlSpAYKkMlE~ga~~Elk~~~~~~le~~~a~E~adiSFEELLAQE 376 (423)
.++.++.+|..|+.|.+.|.+.+ ..++. +|+.|.+.+.-+-.... ..+......+-..++|+|||.=-
T Consensus 23 ~hq~~~~~I~~L~~e~~~ld~~i---~~~~~--~L~~~~~~L~~~~~~~~------~~~~~~~~~~~~~v~~~eLL~YA 90 (188)
T PF10018_consen 23 EHQENQARIQQLRAEIEELDEQI---RDILK--QLKEARKELRTLPDQAD------EKLKSIPKAEKRPVDYEELLSYA 90 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH---HHHHH--HHHHHHHHHHHHHHHhh------hccccccccccCCCCHHHHHHHH
Confidence 46677777777777777776532 22222 34455554443331111 11122333557789999999633
No 97
>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=20.22 E-value=2.9e+02 Score=25.51 Aligned_cols=29 Identities=14% Similarity=0.187 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHhhhhhhh
Q 014536 19 LTIFFTVTLFLTYKKIKRLQELENYANVL 47 (423)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 47 (423)
+.+++.+.+|+...-++.|..+...++-+
T Consensus 174 ~~~~~~~~~~~~r~i~~pl~~l~~~~~~i 202 (457)
T TIGR01386 174 VLLTALLGWWITRLGLEPLRRLSAVAARI 202 (457)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHh
Confidence 33444455566666667777777766655
No 98
>PRK09966 putative inner membrane diguanylate cyclase; Provisional
Probab=20.10 E-value=3e+02 Score=25.89 Aligned_cols=28 Identities=11% Similarity=0.283 Sum_probs=17.5
Q ss_pred hHHHHHHHHHHhccCHHHHHHHHhhhhh
Q 014536 319 DVYVYNWLQDQLRLSPACKKMFEVCADM 346 (423)
Q Consensus 319 Da~VYN~LQqQLKlSpAYKkMlE~ga~~ 346 (423)
|.+=|..+.+.++-.-.=..+.+++...
T Consensus 285 ~id~f~~in~~~G~~~gd~~l~~~a~~L 312 (407)
T PRK09966 285 DGDNFKYINDTWGHATGDRVLIEIAKRL 312 (407)
T ss_pred ECccchHHHhhhchHHHHHHHHHHHHHH
Confidence 4455667777777666656666666544
Done!