Query 035942
Match_columns 53
No_of_seqs 103 out of 260
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 07:51:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035942.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035942hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04099 Sybindin: Sybindin-li 99.8 2.6E-21 5.6E-26 119.3 6.9 53 1-53 65-125 (142)
2 KOG3368 Transport protein part 99.8 2.4E-20 5.3E-25 116.1 7.1 49 2-50 60-116 (140)
3 KOG3369 Transport protein part 99.8 1.1E-18 2.3E-23 113.2 7.1 51 2-52 122-179 (199)
4 COG5122 TRS23 Transport protei 99.5 3.2E-13 7E-18 83.2 7.0 51 2-52 58-115 (134)
5 PF04628 Sedlin_N: Sedlin, N-t 98.3 1.8E-06 3.9E-11 52.3 5.7 47 6-53 57-115 (132)
6 KOG3444 Uncharacterized conser 96.3 0.014 3.1E-07 35.9 4.9 47 6-53 63-121 (121)
7 KOG3487 TRAPP 20 K subunit [In 96.1 0.017 3.6E-07 36.3 4.8 39 14-53 79-118 (139)
8 COG5603 TRS20 Subunit of TRAPP 95.2 0.048 1E-06 34.0 4.1 36 17-53 81-117 (136)
9 PF13774 Longin: Regulated-SNA 92.2 1.1 2.4E-05 24.5 5.9 38 4-41 17-62 (83)
10 PF03090 Replicase: Replicase 77.4 7.6 0.00016 24.0 4.5 41 10-50 60-115 (137)
11 PF07599 DUF1563: Protein of u 75.1 4.3 9.2E-05 20.8 2.4 20 29-48 11-30 (43)
12 COG3260 Ni,Fe-hydrogenase III 69.7 6.7 0.00014 25.0 2.9 21 17-37 52-72 (148)
13 COG0817 RuvC Holliday junction 63.8 35 0.00076 22.0 5.4 38 1-38 10-48 (160)
14 PLN00180 NDF6 (NDH-dependent f 60.6 8.6 0.00019 25.1 2.2 25 29-53 94-127 (180)
15 PF09888 DUF2115: Uncharacteri 58.2 16 0.00036 23.1 3.2 20 34-53 104-123 (163)
16 KOG0861 SNARE protein YKT6, sy 56.8 27 0.00059 23.2 4.1 38 2-39 55-101 (198)
17 PF14894 Lsm_C: Lsm C-terminal 56.1 12 0.00026 20.8 2.0 26 20-45 36-61 (64)
18 KOG0862 Synaptobrevin/VAMP-lik 49.3 23 0.00051 23.8 2.9 24 3-26 51-80 (216)
19 COG4066 Uncharacterized protei 45.6 28 0.00062 22.5 2.8 22 32-53 101-122 (165)
20 PRK13886 conjugal transfer pro 44.6 32 0.0007 23.0 3.1 41 10-50 113-157 (241)
21 PRK01022 hypothetical protein; 41.0 45 0.00097 21.3 3.2 22 32-53 104-125 (167)
22 PHA00731 hypothetical protein 39.4 32 0.00069 20.5 2.2 27 17-43 47-73 (96)
23 KOG1299 Vacuolar sorting prote 37.6 35 0.00076 25.8 2.6 24 25-48 112-135 (549)
24 PRK11778 putative inner membra 37.5 14 0.0003 25.9 0.5 43 4-46 211-254 (330)
25 PF00309 Sigma54_AID: Sigma-54 35.6 50 0.0011 16.7 2.3 18 36-53 32-49 (49)
26 PF01343 Peptidase_S49: Peptid 35.4 9.3 0.0002 23.1 -0.6 22 25-46 85-106 (154)
27 PF14837 INTS5_N: Integrator c 34.8 63 0.0014 21.5 3.3 26 23-48 75-100 (213)
28 COG3012 Uncharacterized protei 34.0 54 0.0012 21.0 2.7 27 23-52 25-51 (151)
29 COG2271 UhpC Sugar phosphate p 33.4 20 0.00042 26.5 0.7 13 36-48 241-253 (448)
30 TIGR00706 SppA_dom signal pept 32.7 19 0.00041 22.8 0.5 22 26-47 141-162 (207)
31 PF10407 Cytokin_check_N: Cdc1 32.2 81 0.0018 17.6 3.0 23 17-39 5-30 (73)
32 PF08684 ocr: DNA mimic ocr; 31.1 57 0.0012 19.5 2.3 18 24-41 72-91 (101)
33 PF08610 Pex16: Peroxisomal me 30.7 19 0.00042 24.7 0.3 11 37-47 2-12 (335)
34 PF05952 ComX: Bacillus compet 30.4 23 0.00051 19.1 0.6 8 40-47 6-13 (57)
35 COG2213 MtlA Phosphotransferas 30.1 10 0.00023 28.0 -1.1 21 28-48 249-269 (472)
36 cd07018 S49_SppA_67K_type Sign 30.0 20 0.00043 23.0 0.3 26 21-46 154-179 (222)
37 PF03324 Herpes_HEPA: Herpesvi 29.3 64 0.0014 18.6 2.3 17 26-42 43-60 (93)
38 PF08465 Herpes_TK_C: Thymidin 29.0 45 0.00098 16.2 1.4 11 38-49 13-23 (33)
39 cd07984 LPLAT_LABLAT-like Lyso 28.8 1.3E+02 0.0029 17.8 3.8 37 9-47 144-181 (192)
40 PF10100 DUF2338: Uncharacteri 28.2 55 0.0012 24.1 2.3 23 31-53 305-329 (429)
41 PHA02436 hypothetical protein 28.1 78 0.0017 16.7 2.3 23 17-39 9-32 (52)
42 PF05819 NolX: NolX protein; 27.7 45 0.00097 25.5 1.8 23 23-46 361-383 (624)
43 PF03164 Mon1: Trafficking pro 26.8 2.4E+02 0.0052 20.1 5.9 35 3-37 55-97 (415)
44 KOG4651 Chondroitin 6-sulfotra 26.3 41 0.00088 23.4 1.3 18 27-46 296-313 (324)
45 PF09949 DUF2183: Uncharacteri 26.1 1E+02 0.0022 17.9 2.8 13 17-29 67-79 (100)
46 PF07002 Copine: Copine; Inte 25.9 1.2E+02 0.0025 18.7 3.2 25 13-37 107-132 (146)
47 cd07022 S49_Sppa_36K_type Sign 25.8 27 0.00058 22.2 0.3 23 24-46 151-173 (214)
48 PF11530 Pilin_PilX: Minor typ 25.4 59 0.0013 20.2 1.8 23 27-49 10-32 (127)
49 PHA02097 hypothetical protein 25.4 1.2E+02 0.0027 16.3 2.9 22 4-25 28-51 (59)
50 PRK14818 NADH dehydrogenase su 23.3 1.1E+02 0.0024 19.8 2.9 21 17-37 73-93 (173)
51 PF03607 DCX: Doublecortin; I 23.2 90 0.0019 16.2 2.0 20 18-37 1-20 (60)
52 PF08701 GN3L_Grn1: GNL3L/Grn1 22.6 71 0.0015 18.1 1.6 15 22-36 34-52 (79)
53 COG1658 Small primase-like pro 22.6 43 0.00094 20.6 0.8 32 17-48 58-95 (127)
54 PF08442 ATP-grasp_2: ATP-gras 22.6 70 0.0015 20.7 1.8 17 26-42 174-190 (202)
55 PF01004 Flavi_M: Flavivirus e 22.4 30 0.00064 19.6 0.0 22 25-50 22-43 (75)
56 KOG3120 Predicted haloacid deh 22.2 1.7E+02 0.0037 20.2 3.6 32 17-49 104-137 (256)
57 PF10170 C6_DPF: Cysteine-rich 22.1 36 0.00078 20.2 0.3 9 42-50 32-40 (97)
58 cd07023 S49_Sppa_N_C Signal pe 21.9 39 0.00086 21.2 0.5 22 25-46 145-166 (208)
59 PHA02705 hypothetical protein; 21.3 70 0.0015 17.7 1.4 17 21-37 1-17 (72)
60 PF01325 Fe_dep_repress: Iron 20.5 1E+02 0.0022 16.0 1.9 15 25-39 3-17 (60)
61 COG4939 Major membrane immunog 20.3 89 0.0019 19.8 1.9 16 1-16 19-39 (147)
62 COG2122 Uncharacterized conser 20.1 2.7E+02 0.0058 19.3 4.2 33 17-49 24-58 (256)
No 1
>PF04099 Sybindin: Sybindin-like family ; InterPro: IPR007233 Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. Syndecan-2 induces spine formation by recruiting intracellular vesicles toward postsynaptic sites through the interaction with synbindin []. ; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005801 cis-Golgi network; PDB: 3CUE_C 2J3T_C 2ZMV_B 2JSN_A.
Probab=99.85 E-value=2.6e-21 Score=119.29 Aligned_cols=53 Identities=40% Similarity=0.590 Sum_probs=41.6
Q ss_pred CceeEEEeCCeEEEEE-------EEEeeCCCCccHHHHHHHH-HHHhHhhhhcCCCCCCCC
Q 035942 1 CLFHSSHTHTYKLCFM-------IILVTHARTGGQRESLKCI-YNLYVESIDKNPLYSPGT 53 (53)
Q Consensus 1 ~~f~s~~T~~yklh~~-------Fvl~td~~~~~~~~~L~~i-Y~~YvdyV~KNPfy~~~~ 53 (53)
++|++++|++|||||+ ||++||++++++++.|+++ |++|+|||+|||||++|.
T Consensus 65 ~g~~~~~T~~yklh~~eT~TGlKFvl~td~~~~~~~~~l~~~~~~lY~dyV~KNPfy~~~~ 125 (142)
T PF04099_consen 65 SGFESFETDTYKLHCFETPTGLKFVLITDPNVPSLRDELLRIYYELYVDYVVKNPFYSLEM 125 (142)
T ss_dssp -SEEEEEESS-EEEEEE-TTS-EEEEEE-TTCCHCHHHHHHHHHHHHHHHHHS-TTS-TTS
T ss_pred eeEEEEEeCCEEEEEEEcCcCcEEEEEecCCCccHHHHHHHHHHHHHHHHHhhCCCCCCCC
Confidence 5799999999999999 9999999997665555554 559999999999999874
No 2
>KOG3368 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.83 E-value=2.4e-20 Score=116.07 Aligned_cols=49 Identities=47% Similarity=0.756 Sum_probs=48.2
Q ss_pred ceeEEEeCCeEEEEE-------EEEeeCCCCccHHHHHHHHHH-HhHhhhhcCCCCC
Q 035942 2 LFHSSHTHTYKLCFM-------IILVTHARTGGQRESLKCIYN-LYVESIDKNPLYS 50 (53)
Q Consensus 2 ~f~s~~T~~yklh~~-------Fvl~td~~~~~~~~~L~~iY~-~YvdyV~KNPfy~ 50 (53)
+|++++|++||||++ ||++|||++++++++|++||+ +||+||+|||+++
T Consensus 60 ~f~sy~Ts~YklhfyeTptglk~vl~Tdpk~~~ir~vLq~IYs~lyVE~Vvknpl~~ 116 (140)
T KOG3368|consen 60 GFLSYKTSKYKLHFYETPTGLKFVLNTDPKAGSIRDVLQYIYSHLYVEYVVKNPLYT 116 (140)
T ss_pred CeeEEeeceeEEEEEEcCCCcEEEEecCCCcccHHHHHHHHHHHHHHHHHHcCcccc
Confidence 689999999999999 999999999999999999999 9999999999999
No 3
>KOG3369 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.77 E-value=1.1e-18 Score=113.20 Aligned_cols=51 Identities=29% Similarity=0.498 Sum_probs=49.2
Q ss_pred ceeEEEeCCeEEEEE-------EEEeeCCCCccHHHHHHHHHHHhHhhhhcCCCCCCC
Q 035942 2 LFHSSHTHTYKLCFM-------IILVTHARTGGQRESLKCIYNLYVESIDKNPLYSPG 52 (53)
Q Consensus 2 ~f~s~~T~~yklh~~-------Fvl~td~~~~~~~~~L~~iY~~YvdyV~KNPfy~~~ 52 (53)
|..-++|++|+|||| ||+++|+..+.++.+|++||++|.|||+|||||++|
T Consensus 122 Gie~LetdtF~l~~~QTlTG~KFVvis~~~~~~aD~lLrKiYelYsDyvlKNPfYSlE 179 (199)
T KOG3369|consen 122 GIEVLETDTFTLHIFQTLTGTKFVVIAEPGTQGADSLLRKIYELYSDYVLKNPFYSLE 179 (199)
T ss_pred ceEEEEeccEEEEEEEccCCcEEEEEecCCchhHHHHHHHHHHHHHHHhhcCCccCcc
Confidence 677899999999999 999999999999999999999999999999999986
No 4
>COG5122 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]
Probab=99.46 E-value=3.2e-13 Score=83.20 Aligned_cols=51 Identities=27% Similarity=0.421 Sum_probs=47.6
Q ss_pred ceeEEEeCCeEEEEE-------EEEeeCCCCccHHHHHHHHHHHhHhhhhcCCCCCCC
Q 035942 2 LFHSSHTHTYKLCFM-------IILVTHARTGGQRESLKCIYNLYVESIDKNPLYSPG 52 (53)
Q Consensus 2 ~f~s~~T~~yklh~~-------Fvl~td~~~~~~~~~L~~iY~~YvdyV~KNPfy~~~ 52 (53)
+.+.+.+++|.+|.+ ||.++...+.|+.--|++||++|+|||+|||||++|
T Consensus 58 g~~~l~~~~f~m~I~qT~TG~kFV~~~~k~t~na~~ql~kiY~lYsdYV~knPfys~E 115 (134)
T COG5122 58 GRLVLYFRNFVMTIFQTTTGTKFVFVAEKRTVNALFQLQKIYSLYSDYVTKNPFYSPE 115 (134)
T ss_pred ceEEEEeccEEEEEEEecCCcEEEEEecCCchhHHHHHHHHHHHHHHHhhcCCCCCcc
Confidence 567788999999999 999999999999988999999999999999999986
No 5
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=98.34 E-value=1.8e-06 Score=52.29 Aligned_cols=47 Identities=32% Similarity=0.496 Sum_probs=38.5
Q ss_pred EEeCCeEEEEE-------EEEeeC-----CCCccHHHHHHHHHHHhHhhhhcCCCCCCCC
Q 035942 6 SHTHTYKLCFM-------IILVTH-----ARTGGQRESLKCIYNLYVESIDKNPLYSPGT 53 (53)
Q Consensus 6 ~~T~~yklh~~-------Fvl~td-----~~~~~~~~~L~~iY~~YvdyV~KNPfy~~~~ 53 (53)
+..+.|+++-| ||++.+ .+..+++.++++||++|++ ++-||||++++
T Consensus 57 ~~~~~~~vygyvT~t~~Kfvl~~~~~~~~~~d~~ik~fF~~vh~~Y~~-~~~NPF~~~~~ 115 (132)
T PF04628_consen 57 DPFEDYKVYGYVTNTGIKFVLVHDMSDNSIRDEDIKQFFKEVHELYVK-ALCNPFYQPGT 115 (132)
T ss_dssp EEETTEEEEEEETTT--EEEEEECGGG-S--HHHHHHHHHHHHHHHHH-HHTSTTCGCT-
T ss_pred ehhhhHHHHhhhccCceeEEEEEecccCCcchHHHHHHHHHHHHHHHH-HccCCCCCCCC
Confidence 45688999988 999888 4566899999999999999 67799999874
No 6
>KOG3444 consensus Uncharacterized conserved protein [Function unknown]
Probab=96.29 E-value=0.014 Score=35.86 Aligned_cols=47 Identities=30% Similarity=0.501 Sum_probs=38.0
Q ss_pred EEeCCeEEEEE-------EEEeeCCC-----CccHHHHHHHHHHHhHhhhhcCCCCCCCC
Q 035942 6 SHTHTYKLCFM-------IILVTHAR-----TGGQRESLKCIYNLYVESIDKNPLYSPGT 53 (53)
Q Consensus 6 ~~T~~yklh~~-------Fvl~td~~-----~~~~~~~L~~iY~~YvdyV~KNPfy~~~~ 53 (53)
+.|..||..-| ||+.+|.. ...+|.+.|..+-+|.| ++-||||-+|+
T Consensus 63 y~ted~kvYgfvtNTkVKFIlvvdssd~avreteiRsv~r~~h~l~td-~~~npfy~pg~ 121 (121)
T KOG3444|consen 63 YPTEDYKVYGFVTNTKVKFILVVDSSDYAVRETEIRSVFRILHLLYTD-LSCNPFYLPGL 121 (121)
T ss_pred ccccceeEEEEEeccEEEEEEEEcCCcceehhHHHHHHHHHHHHHHHH-heecceeccCC
Confidence 46888999888 99988664 34667888887779999 89999999874
No 7
>KOG3487 consensus TRAPP 20 K subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=96.12 E-value=0.017 Score=36.33 Aligned_cols=39 Identities=18% Similarity=0.339 Sum_probs=31.6
Q ss_pred EEEEEEeeCCCC-ccHHHHHHHHHHHhHhhhhcCCCCCCCC
Q 035942 14 CFMIILVTHART-GGQRESLKCIYNLYVESIDKNPLYSPGT 53 (53)
Q Consensus 14 h~~Fvl~td~~~-~~~~~~L~~iY~~YvdyV~KNPfy~~~~ 53 (53)
|..|+++-+.++ .++....+.+|++|+.. +.||||++.+
T Consensus 79 ~i~f~mlh~~~~~~~ik~Ffqev~elyik~-lmnpFy~~~d 118 (139)
T KOG3487|consen 79 HIRFIMLHINRADDNIKLFFQEVHELYIKT-LMNPFYEIND 118 (139)
T ss_pred cEEEEEEeeccccccHHHHHHHHHHHHHHH-HhCcccccCC
Confidence 334888877765 48999999999999994 6799999864
No 8
>COG5603 TRS20 Subunit of TRAPP, an ER-Golgi tethering complex [Cell motility and secretion]
Probab=95.15 E-value=0.048 Score=34.04 Aligned_cols=36 Identities=19% Similarity=0.479 Sum_probs=29.8
Q ss_pred EEEeeCCC-CccHHHHHHHHHHHhHhhhhcCCCCCCCC
Q 035942 17 IILVTHAR-TGGQRESLKCIYNLYVESIDKNPLYSPGT 53 (53)
Q Consensus 17 Fvl~td~~-~~~~~~~L~~iY~~YvdyV~KNPfy~~~~ 53 (53)
|+++-..+ ..|++..++.++++|++. +.||||++++
T Consensus 81 f~~iH~n~s~~N~rsF~qevHely~kt-Lmspfy~~~~ 117 (136)
T COG5603 81 FLFIHQNQSRKNARSFLQEVHELYAKT-LMSPFYEPDE 117 (136)
T ss_pred EEEEeccchhhhHHHHHHHHHHHHHHH-hhCcccCCCc
Confidence 77777554 569999999999999995 5699999874
No 9
>PF13774 Longin: Regulated-SNARE-like domain; PDB: 1IOU_A 3BW6_A 1H8M_A 3EGX_C 2NUP_C 3EGD_C 2NUT_C 3KYQ_A 1IFQ_B 2VX8_D ....
Probab=92.24 E-value=1.1 Score=24.49 Aligned_cols=38 Identities=13% Similarity=0.193 Sum_probs=29.2
Q ss_pred eEEEeCCeEEEEE------EEEeeCCCCcc--HHHHHHHHHHHhHh
Q 035942 4 HSSHTHTYKLCFM------IILVTHARTGG--QRESLKCIYNLYVE 41 (53)
Q Consensus 4 ~s~~T~~yklh~~------Fvl~td~~~~~--~~~~L~~iY~~Yvd 41 (53)
.+++.+.|..|++ ++++||.+.+. .=..|++|.+.|..
T Consensus 17 ~s~~~~~~~fh~~~~~~i~~~citd~~~~~r~aF~fL~~i~~~F~~ 62 (83)
T PF13774_consen 17 MSYESGNYVFHYLVEDGIAYLCITDKSYPKRVAFAFLEEIKQEFIQ 62 (83)
T ss_dssp EEEEETTEEEEEEEETTEEEEEEEETTS-HHHHHHHHHHHHHHHHH
T ss_pred EEEEECCEEEEEEEcCCeEEEEEEcCCCCcchHHHHHHHHHHHHHH
Confidence 5788999999999 99999998774 45667777764443
No 10
>PF03090 Replicase: Replicase family; InterPro: IPR004322 This is a family of bacterial plasmid DNA replication initiator proteins. These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or may be mediated by Hsp70 chaperones. A similar RepA family of proteins found mainly in Escherichia coli is involved in plasmid replication (see IPR000525 from INTERPRO).
Probab=77.41 E-value=7.6 Score=23.96 Aligned_cols=41 Identities=20% Similarity=0.168 Sum_probs=29.6
Q ss_pred CeEEEEE-----EEEeeCCCCccHHHHHHHHHH----------HhHhhhhcCCCCC
Q 035942 10 TYKLCFM-----IILVTHARTGGQRESLKCIYN----------LYVESIDKNPLYS 50 (53)
Q Consensus 10 ~yklh~~-----Fvl~td~~~~~~~~~L~~iY~----------~YvdyV~KNPfy~ 50 (53)
+-+-|++ -|..|+.+...-...|+.|.+ .|+--+.||||++
T Consensus 60 nghaHl~y~L~~PV~~t~~ar~kpl~ylaav~~~L~~~L~aD~~ysg~i~KNP~h~ 115 (137)
T PF03090_consen 60 NGHAHLIYALDAPVCTTENARSKPLRYLAAVERALTRKLGADPGYSGLITKNPLHP 115 (137)
T ss_pred CCcEEEEEEECCcEeeCccccchHHHHHHHHHHHHHHHhCCCcccCCcccCCCCCc
Confidence 3455666 666788877777777777776 3677899999986
No 11
>PF07599 DUF1563: Protein of unknown function (DUF1563); InterPro: IPR011457 This is a small family of short hypothetical proteins in Leptospira interrogans.
Probab=75.08 E-value=4.3 Score=20.77 Aligned_cols=20 Identities=35% Similarity=0.521 Sum_probs=16.4
Q ss_pred HHHHHHHHHHhHhhhhcCCC
Q 035942 29 RESLKCIYNLYVESIDKNPL 48 (53)
Q Consensus 29 ~~~L~~iY~~YvdyV~KNPf 48 (53)
-+.|..+|+-||+|-+|--|
T Consensus 11 L~TLeNlYatyve~~lkq~f 30 (43)
T PF07599_consen 11 LETLENLYATYVEYFLKQTF 30 (43)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999988544
No 12
>COG3260 Ni,Fe-hydrogenase III small subunit [Energy production and conversion]
Probab=69.72 E-value=6.7 Score=25.01 Aligned_cols=21 Identities=52% Similarity=0.575 Sum_probs=19.8
Q ss_pred EEEeeCCCCccHHHHHHHHHH
Q 035942 17 IILVTHARTGGQRESLKCIYN 37 (53)
Q Consensus 17 Fvl~td~~~~~~~~~L~~iY~ 37 (53)
..|+|.+-+..+++-|+++|+
T Consensus 52 iLlVTG~vT~~~~e~lkk~Ye 72 (148)
T COG3260 52 ILLVTGAVTRQMREPLKKAYE 72 (148)
T ss_pred EEEEeccccHHHHHHHHHHHH
Confidence 788999999999999999998
No 13
>COG0817 RuvC Holliday junction resolvasome, endonuclease subunit [DNA replication, recombination, and repair]
Probab=63.85 E-value=35 Score=21.95 Aligned_cols=38 Identities=13% Similarity=0.175 Sum_probs=31.2
Q ss_pred CceeEEEeCCeEEEEE-EEEeeCCCCccHHHHHHHHHHH
Q 035942 1 CLFHSSHTHTYKLCFM-IILVTHARTGGQRESLKCIYNL 38 (53)
Q Consensus 1 ~~f~s~~T~~yklh~~-Fvl~td~~~~~~~~~L~~iY~~ 38 (53)
||+--++.+.-++|+. .-++..++...+.+-|++||+-
T Consensus 10 ~G~gvI~~~~~~l~~v~~G~I~t~~~~~l~~RL~~l~~~ 48 (160)
T COG0817 10 TGYGVIEVEGRQLSYLASGVIRTSSDAPLAERLKQLYDG 48 (160)
T ss_pred cceEEEEccCCeEEEEeeeEEecCCCccHHHHHHHHHHH
Confidence 6788888888899999 6667777777888899999873
No 14
>PLN00180 NDF6 (NDH-dependent flow 6); Provisional
Probab=60.56 E-value=8.6 Score=25.08 Aligned_cols=25 Identities=24% Similarity=0.567 Sum_probs=19.0
Q ss_pred HHHHHHHHHHhHhh---------hhcCCCCCCCC
Q 035942 29 RESLKCIYNLYVES---------IDKNPLYSPGT 53 (53)
Q Consensus 29 ~~~L~~iY~~Yvdy---------V~KNPfy~~~~ 53 (53)
...++.+|..|+=+ -||.|||+.++
T Consensus 94 D~aiKnVYtfY~mFT~WG~~fFgSmKDPfYDSe~ 127 (180)
T PLN00180 94 DAAIKNVYTFYIMFTCWGCLFFGSMKDPFYDSEE 127 (180)
T ss_pred HHHHhHHHHHHHHHHHHHHhheeccCCcccchHH
Confidence 46788888877765 37999998763
No 15
>PF09888 DUF2115: Uncharacterized protein conserved in archaea (DUF2115); InterPro: IPR019215 This entry represents various hypothetical archaeal proteins, has no known function.
Probab=58.16 E-value=16 Score=23.08 Aligned_cols=20 Identities=30% Similarity=0.374 Sum_probs=16.6
Q ss_pred HHHHHhHhhhhcCCCCCCCC
Q 035942 34 CIYNLYVESIDKNPLYSPGT 53 (53)
Q Consensus 34 ~iY~~YvdyV~KNPfy~~~~ 53 (53)
.|=++|+=+|++-|++++|+
T Consensus 104 ~lis~Y~~FI~~~PlHPvG~ 123 (163)
T PF09888_consen 104 YLISPYLIFILKEPLHPVGM 123 (163)
T ss_pred HHHHHHHHHHhCCCCCCCCC
Confidence 33348999999999999984
No 16
>KOG0861 consensus SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport]
Probab=56.80 E-value=27 Score=23.18 Aligned_cols=38 Identities=11% Similarity=0.075 Sum_probs=28.2
Q ss_pred ceeEEEeCCeEEEEE-------EEEeeCCCCc--cHHHHHHHHHHHh
Q 035942 2 LFHSSHTHTYKLCFM-------IILVTHARTG--GQRESLKCIYNLY 39 (53)
Q Consensus 2 ~f~s~~T~~yklh~~-------Fvl~td~~~~--~~~~~L~~iY~~Y 39 (53)
.++|++-+.|++|+| -|+++|..-| ..-.+|.+|-.-|
T Consensus 55 ~rqsvk~~~Y~~h~yvrndgL~~V~~~D~eYP~rvA~tLL~kvld~~ 101 (198)
T KOG0861|consen 55 QRQSVKHEEYLVHVYVRNDGLCGVLIADDEYPVRVAFTLLNKVLDEF 101 (198)
T ss_pred cccccccceeEEEEEEecCCeeEEEEecCcCchhHHHHHHHHHHHHH
Confidence 367888999999999 8999999765 3445666665433
No 17
>PF14894 Lsm_C: Lsm C-terminal; PDB: 1M5Q_1.
Probab=56.05 E-value=12 Score=20.81 Aligned_cols=26 Identities=31% Similarity=0.494 Sum_probs=18.6
Q ss_pred eeCCCCccHHHHHHHHHHHhHhhhhc
Q 035942 20 VTHARTGGQRESLKCIYNLYVESIDK 45 (53)
Q Consensus 20 ~td~~~~~~~~~L~~iY~~YvdyV~K 45 (53)
+|..++.+.-.+-++||++|-+|+-+
T Consensus 36 Vse~GVEGsGPlAerv~~ly~eyi~~ 61 (64)
T PF14894_consen 36 VSENGVEGSGPLAERVYDLYNEYIEK 61 (64)
T ss_dssp EETTEEE--SHHHHHHHHHHHHHHH-
T ss_pred EeccccccCChHHHHHHHHHHHHHHh
Confidence 56667778888889999999988743
No 18
>KOG0862 consensus Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.31 E-value=23 Score=23.78 Aligned_cols=24 Identities=13% Similarity=0.199 Sum_probs=21.0
Q ss_pred eeEEEeCCeEEEEE------EEEeeCCCCc
Q 035942 3 FHSSHTHTYKLCFM------IILVTHARTG 26 (53)
Q Consensus 3 f~s~~T~~yklh~~------Fvl~td~~~~ 26 (53)
..|.+|+.|.+|+. +++++|.+-+
T Consensus 51 r~Sietg~f~fHfli~~~Vcylvicd~~yP 80 (216)
T KOG0862|consen 51 RCSIETGPFVFHFLIESGVCYLVICDKSYP 80 (216)
T ss_pred ccccccCCeEEEEEecCCEEEEEEecCCCc
Confidence 46889999999999 8889999866
No 19
>COG4066 Uncharacterized protein conserved in archaea [Function unknown]
Probab=45.56 E-value=28 Score=22.51 Aligned_cols=22 Identities=36% Similarity=0.608 Sum_probs=18.1
Q ss_pred HHHHHHHhHhhhhcCCCCCCCC
Q 035942 32 LKCIYNLYVESIDKNPLYSPGT 53 (53)
Q Consensus 32 L~~iY~~YvdyV~KNPfy~~~~ 53 (53)
+.+|=.+|+-||-|-|++++|+
T Consensus 101 i~~i~~~Y~tfvrkEPlHPpgt 122 (165)
T COG4066 101 ISKILCPYLTFVRKEPLHPPGT 122 (165)
T ss_pred HHHHHHHHHHHHhCCCCCCCCC
Confidence 3455558999999999999985
No 20
>PRK13886 conjugal transfer protein TraL; Provisional
Probab=44.58 E-value=32 Score=23.01 Aligned_cols=41 Identities=7% Similarity=-0.002 Sum_probs=26.5
Q ss_pred CeEEEEEEEEeeCCCCccHHHHHHHHHHH---hHhhhh-cCCCCC
Q 035942 10 TYKLCFMIILVTHARTGGQRESLKCIYNL---YVESID-KNPLYS 50 (53)
Q Consensus 10 ~yklh~~Fvl~td~~~~~~~~~L~~iY~~---YvdyV~-KNPfy~ 50 (53)
..++..++|+.-..+..+.-.-|.++.+- -+++|+ +||++-
T Consensus 113 g~~lvvh~vi~gg~~~~dtl~~~~~l~~~~~~~~~~Vvw~N~~~G 157 (241)
T PRK13886 113 GHELVVHTVVTGGQALLDTVSGFAQLASQFPAECLFVVWLNPYWG 157 (241)
T ss_pred CceEEEEEEECCCcccHHHHHHHHHHHHHcCCCceEEEEecCccC
Confidence 44555556665554445555666666774 489999 999764
No 21
>PRK01022 hypothetical protein; Provisional
Probab=41.00 E-value=45 Score=21.27 Aligned_cols=22 Identities=36% Similarity=0.375 Sum_probs=17.3
Q ss_pred HHHHHHHhHhhhhcCCCCCCCC
Q 035942 32 LKCIYNLYVESIDKNPLYSPGT 53 (53)
Q Consensus 32 L~~iY~~YvdyV~KNPfy~~~~ 53 (53)
|..|=++|+=||+|=|++++|+
T Consensus 104 ~~~lv~~Y~~FI~~~PlHPvG~ 125 (167)
T PRK01022 104 LYKLVSPYLIFILKEPLHPVGT 125 (167)
T ss_pred HHHHHHHHHHHHhCCCCCCCCC
Confidence 3333348999999999999985
No 22
>PHA00731 hypothetical protein
Probab=39.43 E-value=32 Score=20.46 Aligned_cols=27 Identities=19% Similarity=0.251 Sum_probs=20.1
Q ss_pred EEEeeCCCCccHHHHHHHHHHHhHhhh
Q 035942 17 IILVTHARTGGQRESLKCIYNLYVESI 43 (53)
Q Consensus 17 Fvl~td~~~~~~~~~L~~iY~~YvdyV 43 (53)
|+..-|.+-.+.-.-|+++|++|.|-.
T Consensus 47 ~~~~e~i~~e~vl~klkrLYevy~d~~ 73 (96)
T PHA00731 47 FFFTEKIALEEVLLKLKRLYEVYEDSE 73 (96)
T ss_pred eeecccccHHHHHHHHHHHHHHHHHHH
Confidence 666666666677777888999998854
No 23
>KOG1299 consensus Vacuolar sorting protein VPS45/Stt10 (Sec1 family) [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.57 E-value=35 Score=25.82 Aligned_cols=24 Identities=17% Similarity=0.411 Sum_probs=21.1
Q ss_pred CccHHHHHHHHHHHhHhhhhcCCC
Q 035942 25 TGGQRESLKCIYNLYVESIDKNPL 48 (53)
Q Consensus 25 ~~~~~~~L~~iY~~YvdyV~KNPf 48 (53)
..+-+++-++|-|+|.||+.-||.
T Consensus 112 esD~~E~V~eVqE~y~Df~~~n~~ 135 (549)
T KOG1299|consen 112 ESDEQEVVREVQEIYLDFFKVNPD 135 (549)
T ss_pred hcchHHHHHHHHHHHHhhhccCCc
Confidence 456688999999999999999996
No 24
>PRK11778 putative inner membrane peptidase; Provisional
Probab=37.46 E-value=14 Score=25.94 Aligned_cols=43 Identities=16% Similarity=0.130 Sum_probs=29.0
Q ss_pred eEEEeCCeEEEEE-EEEeeCCCCccHHHHHHHHHHHhHhhhhcC
Q 035942 4 HSSHTHTYKLCFM-IILVTHARTGGQRESLKCIYNLYVESIDKN 46 (53)
Q Consensus 4 ~s~~T~~yklh~~-Fvl~td~~~~~~~~~L~~iY~~YvdyV~KN 46 (53)
+.++++.||=-.- |--.|+.+...+++.|..+|+.|++.|.+|
T Consensus 211 evi~aG~yK~a~~pf~~~see~Re~~q~~Ld~~y~~F~~~Va~~ 254 (330)
T PRK11778 211 ELHTAGEYKRTLTLFGENTEEGREKFREELEETHQLFKDFVQRY 254 (330)
T ss_pred EEEEecCccCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4455555553211 333455555678999999999999999876
No 25
>PF00309 Sigma54_AID: Sigma-54 factor, Activator interacting domain (AID) ; InterPro: IPR000394 Sigma factors [] are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes: the sigma-54 and sigma-70 families. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor [, ] required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognised by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions: A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent
Probab=35.62 E-value=50 Score=16.73 Aligned_cols=18 Identities=17% Similarity=0.266 Sum_probs=12.7
Q ss_pred HHHhHhhhhcCCCCCCCC
Q 035942 36 YNLYVESIDKNPLYSPGT 53 (53)
Q Consensus 36 Y~~YvdyV~KNPfy~~~~ 53 (53)
.+.--+.+..|||-++++
T Consensus 32 ~~~i~~~~~eNP~Le~~e 49 (49)
T PF00309_consen 32 EEYIEEEAEENPFLEVDE 49 (49)
T ss_pred HHHHHHHHHhCcCcccCC
Confidence 333446788999988764
No 26
>PF01343 Peptidase_S49: Peptidase family S49 peptidase classification.; InterPro: IPR002142 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. The domain defines sequences in viruses, archaea, bacteria and plants. These sequences are variously annotated in the different taxonomic groups, examples are: Viruses: capsid protein Archaea: proteinase IV homolog Bacteria: proteinase IV, sohB, SppA, pfaP, putative protease Plants: SppA, protease IV This group also contains proteins classified as non-peptidase homologues that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. Related proteins, non-peptidase homologs and unclassified S49 members are also to be found in IPR002810 from INTERPRO.; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3RST_B 3BEZ_D 3BF0_A.
Probab=35.41 E-value=9.3 Score=23.14 Aligned_cols=22 Identities=18% Similarity=0.422 Sum_probs=17.5
Q ss_pred CccHHHHHHHHHHHhHhhhhcC
Q 035942 25 TGGQRESLKCIYNLYVESIDKN 46 (53)
Q Consensus 25 ~~~~~~~L~~iY~~YvdyV~KN 46 (53)
.+.+++.|..+|+.|++-|.+|
T Consensus 85 r~~~~~~l~~~~~~f~~~Va~~ 106 (154)
T PF01343_consen 85 RENLQELLDELYDQFVNDVAEG 106 (154)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHc
Confidence 3467888999999999888765
No 27
>PF14837 INTS5_N: Integrator complex subunit 5 N-terminus
Probab=34.85 E-value=63 Score=21.52 Aligned_cols=26 Identities=15% Similarity=0.273 Sum_probs=22.5
Q ss_pred CCCccHHHHHHHHHHHhHhhhhcCCC
Q 035942 23 ARTGGQRESLKCIYNLYVESIDKNPL 48 (53)
Q Consensus 23 ~~~~~~~~~L~~iY~~YvdyV~KNPf 48 (53)
.+.+++++.+++|.+.+.++|-+||=
T Consensus 75 ~~~~~~~~ai~ei~~~L~~fv~~npk 100 (213)
T PF14837_consen 75 QDEADLDEAIQEIHDVLSRFVEANPK 100 (213)
T ss_pred CCCccHHHHHHHHHHHHHHHHhcCCc
Confidence 34668899999999999999999983
No 28
>COG3012 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.04 E-value=54 Score=21.00 Aligned_cols=27 Identities=15% Similarity=0.092 Sum_probs=19.1
Q ss_pred CCCccHHHHHHHHHHHhHhhhhcCCCCCCC
Q 035942 23 ARTGGQRESLKCIYNLYVESIDKNPLYSPG 52 (53)
Q Consensus 23 ~~~~~~~~~L~~iY~~YvdyV~KNPfy~~~ 52 (53)
..++..+.+||.=| +-||+||+-|-+.
T Consensus 25 ~~a~t~e~LMRSRy---~Ayvlkn~dYli~ 51 (151)
T COG3012 25 QVAPTPEALMRSRY---CAYVLKNADYLIK 51 (151)
T ss_pred cCCCCHHHHHHHHH---HHHHhcCchheee
Confidence 34567788888765 4568999888654
No 29
>COG2271 UhpC Sugar phosphate permease [Carbohydrate transport and metabolism]
Probab=33.43 E-value=20 Score=26.48 Aligned_cols=13 Identities=31% Similarity=0.639 Sum_probs=10.9
Q ss_pred HHHhHhhhhcCCC
Q 035942 36 YNLYVESIDKNPL 48 (53)
Q Consensus 36 Y~~YvdyV~KNPf 48 (53)
.++..+||+|||.
T Consensus 241 ~~i~~~YVL~Nk~ 253 (448)
T COG2271 241 WQIFVKYVLKNKL 253 (448)
T ss_pred HHHHHHHHHcChH
Confidence 4479999999995
No 30
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively.
Probab=32.68 E-value=19 Score=22.82 Aligned_cols=22 Identities=14% Similarity=0.212 Sum_probs=18.6
Q ss_pred ccHHHHHHHHHHHhHhhhhcCC
Q 035942 26 GGQRESLKCIYNLYVESIDKNP 47 (53)
Q Consensus 26 ~~~~~~L~~iY~~YvdyV~KNP 47 (53)
+.++..|..+|+.|++.|.+|-
T Consensus 141 e~~~~~l~~~~~~f~~~va~~R 162 (207)
T TIGR00706 141 DILQNLVNESYEQFVQVVAKGR 162 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHhcC
Confidence 4678899999999999998774
No 31
>PF10407 Cytokin_check_N: Cdc14 phosphatase binding protein N-terminus ; InterPro: IPR018844 Cytokinesis in yeasts involves a family of proteins whose essential function is to bind Cdc14-family phosphatase and prevent this from being sequestered and inhibited in the nucleolus. This is the highly conserved N terminus of a family of proteins which act as cytokinesis checkpoint controls by allowing cells to cope with cytokinesis defects. These proteins are required for rDNA silencing and mini-chromosome maintenance [].
Probab=32.18 E-value=81 Score=17.60 Aligned_cols=23 Identities=17% Similarity=0.390 Sum_probs=14.2
Q ss_pred EEEeeCCCCc--cHHHHHHHHHH-Hh
Q 035942 17 IILVTHARTG--GQRESLKCIYN-LY 39 (53)
Q Consensus 17 Fvl~td~~~~--~~~~~L~~iY~-~Y 39 (53)
|+.+|+|+.. .+.+.+.+-|+ +|
T Consensus 5 FLhlt~~~~tl~~L~~eI~~~f~kLY 30 (73)
T PF10407_consen 5 FLHLTDPNNTLSQLKEEIEERFKKLY 30 (73)
T ss_pred EEEEeCCCCcHHHHHHHHHHHHHHHC
Confidence 7888999643 44444555555 55
No 32
>PF08684 ocr: DNA mimic ocr; InterPro: IPR014798 The structure of an Ocr protein from bacteriophage T7 has shown that this protein mimics the size and shape of a bent DNA molecule []. Ocr has also been shown to be an inhibitor of the complex type I DNA restriction enzymes []. ; PDB: 1S7Z_A 2Y7C_E.
Probab=31.11 E-value=57 Score=19.51 Aligned_cols=18 Identities=33% Similarity=0.490 Sum_probs=10.8
Q ss_pred CCccHHHHHH-HHHH-HhHh
Q 035942 24 RTGGQRESLK-CIYN-LYVE 41 (53)
Q Consensus 24 ~~~~~~~~L~-~iY~-~Yvd 41 (53)
++.++..+|+ +||+ +|.|
T Consensus 72 dtkDV~~IlqaRIyE~L~nd 91 (101)
T PF08684_consen 72 DTKDVTRILQARIYEQLYND 91 (101)
T ss_dssp --S-HHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHHH
Confidence 4556666665 7999 8766
No 33
>PF08610 Pex16: Peroxisomal membrane protein (Pex16); InterPro: IPR013919 Pex16 is a peripheral protein located at the matrix face of the peroxisomal membrane [].
Probab=30.70 E-value=19 Score=24.73 Aligned_cols=11 Identities=27% Similarity=0.664 Sum_probs=9.9
Q ss_pred HHhHhhhhcCC
Q 035942 37 NLYVESIDKNP 47 (53)
Q Consensus 37 ~~YvdyV~KNP 47 (53)
+.|.|+|.+||
T Consensus 2 ~~Y~~~V~~N~ 12 (335)
T PF08610_consen 2 EAYEDWVRRNP 12 (335)
T ss_pred hHHHHHHHHCH
Confidence 57999999998
No 34
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=30.37 E-value=23 Score=19.10 Aligned_cols=8 Identities=38% Similarity=0.634 Sum_probs=6.8
Q ss_pred HhhhhcCC
Q 035942 40 VESIDKNP 47 (53)
Q Consensus 40 vdyV~KNP 47 (53)
+.|.++||
T Consensus 6 V~YLv~nP 13 (57)
T PF05952_consen 6 VNYLVQNP 13 (57)
T ss_pred HHHHHHCh
Confidence 67899998
No 35
>COG2213 MtlA Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]
Probab=30.14 E-value=10 Score=27.97 Aligned_cols=21 Identities=14% Similarity=0.115 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHhHhhhhcCCC
Q 035942 28 QRESLKCIYNLYVESIDKNPL 48 (53)
Q Consensus 28 ~~~~L~~iY~~YvdyV~KNPf 48 (53)
.-..+--|+|+|-.||+.||.
T Consensus 249 iIHffGGIHEIYFPyVLMkP~ 269 (472)
T COG2213 249 IIHFFGGIHEIYFPYVLMKPR 269 (472)
T ss_pred eeeeccccceEeehhhhcchH
Confidence 345667789999999999995
No 36
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=30.00 E-value=20 Score=22.98 Aligned_cols=26 Identities=8% Similarity=0.293 Sum_probs=20.4
Q ss_pred eCCCCccHHHHHHHHHHHhHhhhhcC
Q 035942 21 THARTGGQRESLKCIYNLYVESIDKN 46 (53)
Q Consensus 21 td~~~~~~~~~L~~iY~~YvdyV~KN 46 (53)
|+.....++..|..+|+.|++-|.+|
T Consensus 154 s~~~r~~~~~~l~~~~~~f~~~Va~~ 179 (222)
T cd07018 154 SPEAREQTQALLDSLWDQYLADVAAS 179 (222)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44445677899999999999988875
No 37
>PF03324 Herpes_HEPA: Herpesvirus DNA helicase/primase complex associated protein; InterPro: IPR004996 This is a family of proteins expressed by members of the Herpesviridae.; GO: 0019079 viral genome replication
Probab=29.32 E-value=64 Score=18.60 Aligned_cols=17 Identities=18% Similarity=0.286 Sum_probs=14.4
Q ss_pred ccHHHHHHHHHH-HhHhh
Q 035942 26 GGQRESLKCIYN-LYVES 42 (53)
Q Consensus 26 ~~~~~~L~~iY~-~Yvdy 42 (53)
..+...++++|+ +|.+.
T Consensus 43 ~~L~~~~r~l~~~ly~~~ 60 (93)
T PF03324_consen 43 LALMAFFRQLYEKLYSDF 60 (93)
T ss_pred HHHHHHHHHHHHHHhcCC
Confidence 578999999999 99754
No 38
>PF08465 Herpes_TK_C: Thymidine kinase from Herpesvirus C-terminal; InterPro: IPR013672 This domain is found towards the C terminus in Herpesvirus Thymidine kinases. ; GO: 0004797 thymidine kinase activity, 0005524 ATP binding
Probab=28.95 E-value=45 Score=16.23 Aligned_cols=11 Identities=45% Similarity=0.757 Sum_probs=7.1
Q ss_pred HhHhhhhcCCCC
Q 035942 38 LYVESIDKNPLY 49 (53)
Q Consensus 38 ~YvdyV~KNPfy 49 (53)
+|.. |+|||-.
T Consensus 13 IY~q-i~kn~aI 23 (33)
T PF08465_consen 13 IYTQ-ILKNPAI 23 (33)
T ss_pred HHHH-HHhCccc
Confidence 4444 8888854
No 39
>cd07984 LPLAT_LABLAT-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are such LPLATs as lipid A biosynthesis lauroyl/myristoyl (LABLAT, HtrB) acyltransferases and similar proteins.
Probab=28.83 E-value=1.3e+02 Score=17.85 Aligned_cols=37 Identities=14% Similarity=0.253 Sum_probs=27.2
Q ss_pred CCeEEEEE-EEEeeCCCCccHHHHHHHHHHHhHhhhhcCC
Q 035942 9 HTYKLCFM-IILVTHARTGGQRESLKCIYNLYVESIDKNP 47 (53)
Q Consensus 9 ~~yklh~~-Fvl~td~~~~~~~~~L~~iY~~YvdyV~KNP 47 (53)
+.|++|+. .+- .+...+.++..+++.+.+-+.+-++|
T Consensus 144 ~~~~i~~~~~i~--~~~~~~~~~~~~~~~~~lE~~i~~~P 181 (192)
T cd07984 144 GGYRIEFEPPLE--NPPSEDVEEDTQRLNDALEAAIREHP 181 (192)
T ss_pred CCEEEEEeCCCC--CCCCCCHHHHHHHHHHHHHHHHHhCc
Confidence 46888877 321 12256889999999998888888888
No 40
>PF10100 DUF2338: Uncharacterized protein conserved in bacteria (DUF2338); InterPro: IPR016935 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.17 E-value=55 Score=24.15 Aligned_cols=23 Identities=30% Similarity=0.486 Sum_probs=18.6
Q ss_pred HHHHHHHHhHhh--hhcCCCCCCCC
Q 035942 31 SLKCIYNLYVES--IDKNPLYSPGT 53 (53)
Q Consensus 31 ~L~~iY~~Yvdy--V~KNPfy~~~~ 53 (53)
-.++-|-+||.| ++=.||++||+
T Consensus 305 ~i~QEYLLYVRYtsiLIDPFS~PD~ 329 (429)
T PF10100_consen 305 AIHQEYLLYVRYTSILIDPFSEPDE 329 (429)
T ss_pred hHHhhHHHHHHhhhheeCCCCCCCC
Confidence 356778899998 57899999985
No 41
>PHA02436 hypothetical protein
Probab=28.09 E-value=78 Score=16.70 Aligned_cols=23 Identities=22% Similarity=0.332 Sum_probs=17.2
Q ss_pred EEEeeCCCCccHHHHHHHHHH-Hh
Q 035942 17 IILVTHARTGGQRESLKCIYN-LY 39 (53)
Q Consensus 17 Fvl~td~~~~~~~~~L~~iY~-~Y 39 (53)
|++----+..+++++.+++|+ +|
T Consensus 9 fiiKE~yGeRkIEEVFeE~YE~~Y 32 (52)
T PHA02436 9 FIIKETYGERNIEEVFKEAYESFY 32 (52)
T ss_pred EEeehhhchhhHHHHHHHHHHHhc
Confidence 444444466789999999999 77
No 42
>PF05819 NolX: NolX protein; InterPro: IPR008718 This family consists of Rhizobium NolX and Xanthomonas HrpF proteins. The interaction between the plant pathogen Xanthomonas campestris pv. vesicatoria (strain 85-10) and its host plants is controlled by hrp genes (hypersensitive reaction and pathogenicity), which encode a type III protein secretion system. Among type III-secreted proteins are avirulence proteins, effectors involved in the induction of plant defence reactions. HrpF is dispensable for protein secretion but required for AvrBs3 recognition in planta, is thought to function as a translocator of effector proteins into the host cell []. NolX, a Glycine max (Soybean) cultivar specificity protein, is secreted by a type III secretion system (TTSS) and shows homology to HrpF. It is not known whether NolX functions at the bacterium-plant interface or acts inside the host cell. NolX is expressed in planta only during the early stages of nodule development [].; GO: 0009877 nodulation
Probab=27.72 E-value=45 Score=25.53 Aligned_cols=23 Identities=17% Similarity=0.420 Sum_probs=18.7
Q ss_pred CCCccHHHHHHHHHHHhHhhhhcC
Q 035942 23 ARTGGQRESLKCIYNLYVESIDKN 46 (53)
Q Consensus 23 ~~~~~~~~~L~~iY~~YvdyV~KN 46 (53)
|++-...+.||++| -|.||.=||
T Consensus 361 psvMT~nDA~RELY-rYSdyLPK~ 383 (624)
T PF05819_consen 361 PSVMTENDAMRELY-RYSDYLPKN 383 (624)
T ss_pred CcccchhHHHHHHH-Hhhhccccc
Confidence 34456689999999 799999887
No 43
>PF03164 Mon1: Trafficking protein Mon1; InterPro: IPR004353 Members of this family have been called SAND proteins [] although these proteins do not contain a SAND domain. In Saccharomyces cerevisiae a protein complex of Mon1 and Ccz1 functions with the small GTPase Ypt7 to mediate vesicle trafficking to the vacuole [, ]. The Mon1/Ccz1 complex is conserved in eukaryotic evolution and members of this family (previously known as DUF254) are distant homologues to domains of known structure that assemble into cargo vesicle adapter (AP) complexes [, ].
Probab=26.83 E-value=2.4e+02 Score=20.09 Aligned_cols=35 Identities=17% Similarity=0.430 Sum_probs=27.1
Q ss_pred eeEEEeCCeEEEEE------EEEeeCCCCc--cHHHHHHHHHH
Q 035942 3 FHSSHTHTYKLCFM------IILVTHARTG--GQRESLKCIYN 37 (53)
Q Consensus 3 f~s~~T~~yklh~~------Fvl~td~~~~--~~~~~L~~iY~ 37 (53)
++++.++.-++.++ +|.+|..+.+ -++..|+.+|.
T Consensus 55 l~~i~~~~~~ivfl~r~pl~lv~vS~~~e~~~~l~~qL~~ly~ 97 (415)
T PF03164_consen 55 LRSIRAGDHRIVFLNRGPLILVAVSKTGESESQLRKQLDYLYS 97 (415)
T ss_pred EEEEEeCCEEEEEEecCCEEEEEEcCCcCCHHHHHHHHHHHHH
Confidence 57888999999988 7778877655 46777777776
No 44
>KOG4651 consensus Chondroitin 6-sulfotransferase and related sulfotransferases [Cell wall/membrane/envelope biogenesis; Extracellular structures]
Probab=26.34 E-value=41 Score=23.42 Aligned_cols=18 Identities=28% Similarity=0.305 Sum_probs=14.1
Q ss_pred cHHHHHHHHHHHhHhhhhcC
Q 035942 27 GQRESLKCIYNLYVESIDKN 46 (53)
Q Consensus 27 ~~~~~L~~iY~~YvdyV~KN 46 (53)
-.++.|.+|| |-|||+-|
T Consensus 296 ~~r~~L~kiY--~~Dy~lF~ 313 (324)
T KOG4651|consen 296 LIRQYLHKIY--YFDYLLFG 313 (324)
T ss_pred HHHHHHHHHH--hhheeeeC
Confidence 4577777787 89999876
No 45
>PF09949 DUF2183: Uncharacterized conserved protein (DUF2183); InterPro: IPR019236 This domain, found in various bacterial and fungal proteins, has no known function.
Probab=26.15 E-value=1e+02 Score=17.88 Aligned_cols=13 Identities=15% Similarity=0.268 Sum_probs=11.4
Q ss_pred EEEeeCCCCccHH
Q 035942 17 IILVTHARTGGQR 29 (53)
Q Consensus 17 Fvl~td~~~~~~~ 29 (53)
|||+-|.++.+.+
T Consensus 67 fiLIGDsgq~Dpe 79 (100)
T PF09949_consen 67 FILIGDSGQHDPE 79 (100)
T ss_pred EEEEeeCCCcCHH
Confidence 9999999999854
No 46
>PF07002 Copine: Copine; InterPro: IPR010734 This represents a conserved region approximately 180 residues long within eukaryotic copines. Copines are Ca2+-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth [].
Probab=25.89 E-value=1.2e+02 Score=18.67 Aligned_cols=25 Identities=12% Similarity=0.379 Sum_probs=20.7
Q ss_pred EEEE-EEEeeCCCCccHHHHHHHHHH
Q 035942 13 LCFM-IILVTHARTGGQRESLKCIYN 37 (53)
Q Consensus 13 lh~~-Fvl~td~~~~~~~~~L~~iY~ 37 (53)
.+++ .+++||-...++++..+.|-+
T Consensus 107 ~~Y~iLlIlTDG~i~D~~~T~~aIv~ 132 (146)
T PF07002_consen 107 QQYFILLILTDGQITDMEETIDAIVE 132 (146)
T ss_pred ceEEEEEEecccccccHHHHHHHHHH
Confidence 3455 788999999999999998865
No 47
>cd07022 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases.
Probab=25.80 E-value=27 Score=22.20 Aligned_cols=23 Identities=13% Similarity=0.488 Sum_probs=19.1
Q ss_pred CCccHHHHHHHHHHHhHhhhhcC
Q 035942 24 RTGGQRESLKCIYNLYVESIDKN 46 (53)
Q Consensus 24 ~~~~~~~~L~~iY~~YvdyV~KN 46 (53)
....+++.|..+|+-|++.|.+|
T Consensus 151 ~re~~~~~l~~~~~~f~~~V~~~ 173 (214)
T cd07022 151 ARARLQAEVDALYAMFVAAVARN 173 (214)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 34568999999999999998876
No 48
>PF11530 Pilin_PilX: Minor type IV pilin, PilX; PDB: 2OPE_D 2OPD_A.
Probab=25.45 E-value=59 Score=20.25 Aligned_cols=23 Identities=30% Similarity=0.151 Sum_probs=17.0
Q ss_pred cHHHHHHHHHHHhHhhhhcCCCC
Q 035942 27 GQRESLKCIYNLYVESIDKNPLY 49 (53)
Q Consensus 27 ~~~~~L~~iY~~YvdyV~KNPfy 49 (53)
.+..-|-.|+...=..++|||..
T Consensus 10 qa~aelv~INn~~K~~ivkNP~~ 32 (127)
T PF11530_consen 10 QAYAELVGINNVVKQFIVKNPGD 32 (127)
T ss_dssp HHHHHHHHHHHHHHHHHHH-TTS
T ss_pred HHHHHHHHHHHHHHHHHHhCcch
Confidence 34566778888888889999974
No 49
>PHA02097 hypothetical protein
Probab=25.37 E-value=1.2e+02 Score=16.33 Aligned_cols=22 Identities=23% Similarity=0.472 Sum_probs=16.4
Q ss_pred eEEEeCCeEEEEE--EEEeeCCCC
Q 035942 4 HSSHTHTYKLCFM--IILVTHART 25 (53)
Q Consensus 4 ~s~~T~~yklh~~--Fvl~td~~~ 25 (53)
++|+.++|++.+. .=+++||+-
T Consensus 28 ~tf~~~~f~~~fi~~ikvv~~~n~ 51 (59)
T PHA02097 28 HTFDVSNFKIQFIAGVKVVKDANY 51 (59)
T ss_pred eEEeeccceEEEeCCcEEEecCCC
Confidence 4678889999887 666677664
No 50
>PRK14818 NADH dehydrogenase subunit B; Provisional
Probab=23.35 E-value=1.1e+02 Score=19.85 Aligned_cols=21 Identities=19% Similarity=0.308 Sum_probs=19.2
Q ss_pred EEEeeCCCCccHHHHHHHHHH
Q 035942 17 IILVTHARTGGQRESLKCIYN 37 (53)
Q Consensus 17 Fvl~td~~~~~~~~~L~~iY~ 37 (53)
.+++|.+-+.++.+.|+++|+
T Consensus 73 vLlVtG~vT~km~~~l~~~ye 93 (173)
T PRK14818 73 FMIVAGTLTYKMAERARLLYD 93 (173)
T ss_pred EEEEeCcCccccHHHHHHHHH
Confidence 778888889999999999997
No 51
>PF03607 DCX: Doublecortin; InterPro: IPR003533 X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder []. Doublecortin was found to bind to the microtubule cytoskeleton. In vivo and in vitro assays show that Doublecortin stabilises microtubules and causes bundling []. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s). The detailed sequence analysis of Doublecortin and Doublecortin-like proteins allowed the identification of an evolutionarily conserved Doublecortin (DC) domain. This domain is found in the N terminus of proteins and consists of one or two tandemly repeated copies of an around 80 amino acids region. It has been suggested that the first DC domain of Doublecortin binds tubulin and enhances microtubule polymerisation []. Some proteins known to contain a DC domain are listed below: Doublecortin. It is required for neuronal migration []. A large number of point mutations in the human DCX gene leading to lissencephaly are located within the DC domains []. Human serine/threonine-protein kinase DCAMKL1. It is a probable kinase that may be involved in a calcium-signaling pathway controling neuronal migration in the developing brain []. Retinitis pigmentosa 1 protein. It could play a role in the differentiation of photoreceptor cells. Mutation in the human RP1 gene cause retinitis pigmentosa of type 1 []. ; GO: 0035556 intracellular signal transduction; PDB: 1UF0_A 1MG4_A 1MFW_A 2DNF_A 2XRP_I 2BQQ_A 1MJD_A.
Probab=23.21 E-value=90 Score=16.19 Aligned_cols=20 Identities=15% Similarity=0.179 Sum_probs=15.9
Q ss_pred EEeeCCCCccHHHHHHHHHH
Q 035942 18 ILVTHARTGGQRESLKCIYN 37 (53)
Q Consensus 18 vl~td~~~~~~~~~L~~iY~ 37 (53)
|+++....++++.+|.+|=+
T Consensus 1 ~~i~~r~~~s~e~lL~~it~ 20 (60)
T PF03607_consen 1 VVINPRRFRSFEQLLDEITE 20 (60)
T ss_dssp EEESTTTHSSHHHHHHHHHH
T ss_pred CeEChhhhcCHHHHHHHHHh
Confidence 45677788899999998865
No 52
>PF08701 GN3L_Grn1: GNL3L/Grn1 putative GTPase; InterPro: IPR014813 Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA []. This family contains a potential nuclear localisation signal.
Probab=22.65 E-value=71 Score=18.08 Aligned_cols=15 Identities=27% Similarity=0.131 Sum_probs=11.5
Q ss_pred CCCCccH----HHHHHHHH
Q 035942 22 HARTGGQ----RESLKCIY 36 (53)
Q Consensus 22 d~~~~~~----~~~L~~iY 36 (53)
||++||+ +++|.+|-
T Consensus 34 dpgIPN~~PfKe~iL~eie 52 (79)
T PF08701_consen 34 DPGIPNSFPFKEEILKEIE 52 (79)
T ss_pred CCCCCCCCcCHHHHHHHHH
Confidence 7888877 67887764
No 53
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=22.61 E-value=43 Score=20.57 Aligned_cols=32 Identities=22% Similarity=0.361 Sum_probs=22.4
Q ss_pred EEEeeCCCCcc------HHHHHHHHHHHhHhhhhcCCC
Q 035942 17 IILVTHARTGG------QRESLKCIYNLYVESIDKNPL 48 (53)
Q Consensus 17 Fvl~td~~~~~------~~~~L~~iY~~YvdyV~KNPf 48 (53)
.+++|||+.++ +.+.|...+.+|+|--.+||.
T Consensus 58 VIILTD~D~~Ge~Irk~l~~~l~~~~~~~id~~~~~~~ 95 (127)
T COG1658 58 VIILTDPDRKGERIRKKLKEYLPGAKGAFIDREIRNKL 95 (127)
T ss_pred EEEEeCCCcchHHHHHHHHHHhcccccccccHHHhhhc
Confidence 68899999764 345555555677777777774
No 54
>PF08442 ATP-grasp_2: ATP-grasp domain; InterPro: IPR013650 The ATP-grasp superfamily currently includes 17 groups of enzymes, catalyzing ATP-dependent ligation of a carboxylate containing molecule to an amino or thiol group-containing molecule []. They contribute predominantly to macromolecular synthesis. ATP-hydrolysis is used to activate a substrate. For example, DD-ligase transfers phosphate from ATP to D-alanine on the first step of catalysis. On the second step the resulting acylphosphate is attacked by a second D-alanine to produce a DD dipeptide following phosphate elimination []. The ATP-grasp domain contains three conserved motifs, corresponding to the phosphate binding loop and the Mg(2+) binding site []. The fold is characterised by two alpha-beta subdomains that grasp the ATP molecule between them. Each subdomain provides a variable loop that forms a part of the active site, completed by region of other domains not conserved between the various ATP-grasp enzymes []. The ATP-grasp domain represented by this entry is found primarily in succinyl-CoA synthetases (6.2.1.5 from EC).; PDB: 3PFF_A 3MWD_A 3MWE_A 1CQI_E 1SCU_B 2NU9_G 2NU6_E 1CQJ_E 2NU7_B 1JLL_E ....
Probab=22.60 E-value=70 Score=20.69 Aligned_cols=17 Identities=29% Similarity=0.413 Sum_probs=14.6
Q ss_pred ccHHHHHHHHHHHhHhh
Q 035942 26 GGQRESLKCIYNLYVES 42 (53)
Q Consensus 26 ~~~~~~L~~iY~~Yvdy 42 (53)
..+.++|+++|.+|.++
T Consensus 174 ~~~~~~l~~Ly~~F~~~ 190 (202)
T PF08442_consen 174 EQLADILKKLYRLFREY 190 (202)
T ss_dssp HHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHc
Confidence 45789999999999886
No 55
>PF01004 Flavi_M: Flavivirus envelope glycoprotein M; InterPro: IPR000069 Flaviviruses are small enveloped viruses with virions comprised of three proteins called C, M and E [, , ]. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.; GO: 0019058 viral infectious cycle, 0019028 viral capsid
Probab=22.42 E-value=30 Score=19.57 Aligned_cols=22 Identities=23% Similarity=0.289 Sum_probs=14.4
Q ss_pred CccHHHHHHHHHHHhHhhhhcCCCCC
Q 035942 25 TGGQRESLKCIYNLYVESIDKNPLYS 50 (53)
Q Consensus 25 ~~~~~~~L~~iY~~YvdyV~KNPfy~ 50 (53)
..+.++-|.++= ..|+|||.|.
T Consensus 22 ~~~~~~hl~rvE----~WilrNp~~a 43 (75)
T PF01004_consen 22 SDSAWKHLTRVE----SWILRNPGYA 43 (75)
T ss_pred CccHHHHHHHHH----HHHhcCchHH
Confidence 345566666654 4689999875
No 56
>KOG3120 consensus Predicted haloacid dehalogenase-like hydrolase [General function prediction only]
Probab=22.22 E-value=1.7e+02 Score=20.24 Aligned_cols=32 Identities=34% Similarity=0.415 Sum_probs=25.9
Q ss_pred EEEeeCCCCccHHHHHHH--HHHHhHhhhhcCCCC
Q 035942 17 IILVTHARTGGQRESLKC--IYNLYVESIDKNPLY 49 (53)
Q Consensus 17 Fvl~td~~~~~~~~~L~~--iY~~YvdyV~KNPfy 49 (53)
.++++|.+.--++..|++ |.++|++ |.-||-.
T Consensus 104 liIVSDaNsfFIe~~Lea~~~~d~F~~-IfTNPa~ 137 (256)
T KOG3120|consen 104 LIIVSDANSFFIEEILEAAGIHDLFSE-IFTNPAC 137 (256)
T ss_pred EEEEecCchhHHHHHHHHccHHHHHHH-HhcCCcc
Confidence 688999999999999986 4558885 8888854
No 57
>PF10170 C6_DPF: Cysteine-rich domain; InterPro: IPR018785 This entry represents the N-terminal approximately 100 amino acids of a family of proteins found in a range of organisms, including human, chicken and Drosophila [, , ]. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Probab=22.08 E-value=36 Score=20.23 Aligned_cols=9 Identities=11% Similarity=0.416 Sum_probs=7.4
Q ss_pred hhhcCCCCC
Q 035942 42 SIDKNPLYS 50 (53)
Q Consensus 42 yV~KNPfy~ 50 (53)
||||.||.+
T Consensus 32 yvmrDPF~~ 40 (97)
T PF10170_consen 32 YVMRDPFSP 40 (97)
T ss_pred eEEeCCCCC
Confidence 599999974
No 58
>cd07023 S49_Sppa_N_C Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad
Probab=21.93 E-value=39 Score=21.18 Aligned_cols=22 Identities=14% Similarity=0.300 Sum_probs=17.8
Q ss_pred CccHHHHHHHHHHHhHhhhhcC
Q 035942 25 TGGQRESLKCIYNLYVESIDKN 46 (53)
Q Consensus 25 ~~~~~~~L~~iY~~YvdyV~KN 46 (53)
.+.++++|..+|+-|++-|.+|
T Consensus 145 ~e~~~~~l~~~~~~f~~~Va~~ 166 (208)
T cd07023 145 RAILQALVDDIYDQFVDVVAEG 166 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHhc
Confidence 3456889999999998888765
No 59
>PHA02705 hypothetical protein; Provisional
Probab=21.32 E-value=70 Score=17.72 Aligned_cols=17 Identities=12% Similarity=0.120 Sum_probs=13.6
Q ss_pred eCCCCccHHHHHHHHHH
Q 035942 21 THARTGGQRESLKCIYN 37 (53)
Q Consensus 21 td~~~~~~~~~L~~iY~ 37 (53)
||.++.+.++++.+|=.
T Consensus 1 tdtdvanvedimneidr 17 (72)
T PHA02705 1 TDTDVANVEDIMNEIDR 17 (72)
T ss_pred CccchhhHHHHHHHHHH
Confidence 67888899998888754
No 60
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=20.54 E-value=1e+02 Score=16.03 Aligned_cols=15 Identities=40% Similarity=0.612 Sum_probs=11.7
Q ss_pred CccHHHHHHHHHHHh
Q 035942 25 TGGQRESLKCIYNLY 39 (53)
Q Consensus 25 ~~~~~~~L~~iY~~Y 39 (53)
+++.++.|+.||++-
T Consensus 3 t~~~e~YL~~Iy~l~ 17 (60)
T PF01325_consen 3 TESEEDYLKAIYELS 17 (60)
T ss_dssp SCHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHH
Confidence 456789999999854
No 61
>COG4939 Major membrane immunogen, membrane-anchored lipoprotein [Function unknown]
Probab=20.27 E-value=89 Score=19.83 Aligned_cols=16 Identities=19% Similarity=0.237 Sum_probs=13.5
Q ss_pred Ccee-----EEEeCCeEEEEE
Q 035942 1 CLFH-----SSHTHTYKLCFM 16 (53)
Q Consensus 1 ~~f~-----s~~T~~yklh~~ 16 (53)
|++. ++.-++|+.|+-
T Consensus 19 Cg~sd~s~~t~~dGtY~~~y~ 39 (147)
T COG4939 19 CGKSDFSKMTFNDGTYQGHYE 39 (147)
T ss_pred hcccccccccccCCceeeeec
Confidence 7777 788899999986
No 62
>COG2122 Uncharacterized conserved protein [Function unknown]
Probab=20.07 E-value=2.7e+02 Score=19.29 Aligned_cols=33 Identities=15% Similarity=0.155 Sum_probs=19.0
Q ss_pred EEEeeCCCCcc--HHHHHHHHHHHhHhhhhcCCCC
Q 035942 17 IILVTHARTGG--QRESLKCIYNLYVESIDKNPLY 49 (53)
Q Consensus 17 Fvl~td~~~~~--~~~~L~~iY~~YvdyV~KNPfy 49 (53)
..+-+|..... .++....--+.--|||+|||-.
T Consensus 24 v~i~ad~~~~~~aa~~aV~~~R~~Le~yI~~nP~f 58 (256)
T COG2122 24 VTIRADDEAHEKAAEEAVLRHRSELEDYILKNPEF 58 (256)
T ss_pred EEEEecCHHHHHHHHHHHHHHHHHHHHHHHhCcch
Confidence 44455554332 4444433334778999999954
Done!