Query psy4741
Match_columns 62
No_of_seqs 186 out of 1193
Neff 8.9
Searched_HMMs 46136
Date Sat Aug 17 00:49:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4741.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4741hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00698 Acyl_transf_1: Acyl t 99.7 1.7E-18 3.7E-23 104.9 1.1 62 1-62 7-71 (318)
2 smart00827 PKS_AT Acyl transfe 99.6 5.7E-16 1.2E-20 92.6 5.6 62 1-62 4-69 (298)
3 TIGR00128 fabD malonyl CoA-acy 99.6 4.2E-16 9.1E-21 92.8 4.4 59 1-62 10-69 (290)
4 PLN02752 [acyl-carrier protein 99.6 3.6E-15 7.8E-20 91.3 4.7 58 1-62 47-105 (343)
5 COG0331 FabD (acyl-carrier-pro 99.5 5.1E-15 1.1E-19 90.2 4.1 58 1-61 11-69 (310)
6 KOG1202|consensus 99.5 1.1E-14 2.3E-19 99.9 4.8 62 1-62 508-569 (2376)
7 TIGR03131 malonate_mdcH malona 99.4 1.4E-13 3.1E-18 82.5 4.4 56 1-62 8-63 (295)
8 TIGR02813 omega_3_PfaA polyket 99.4 5.1E-13 1.1E-17 96.2 5.1 62 1-62 588-661 (2582)
9 KOG2926|consensus 99.3 3.7E-13 7.9E-18 82.8 2.0 57 1-60 71-127 (386)
10 TIGR02816 pfaB_fam PfaB family 99.1 2.9E-11 6.3E-16 78.2 2.9 52 1-60 190-247 (538)
11 COG3321 Polyketide synthase mo 99.1 1.2E-10 2.5E-15 79.8 3.5 62 1-62 534-597 (1061)
12 PLN03219 uncharacterized prote 69.6 8.5 0.00018 20.7 2.8 22 11-35 62-83 (108)
13 PLN03220 uncharacterized prote 68.9 9.2 0.0002 20.4 2.9 21 12-35 61-81 (105)
14 PLN03090 auxin-responsive fami 68.9 8.8 0.00019 20.5 2.8 18 12-29 62-79 (104)
15 PF04070 DUF378: Domain of unk 68.0 4.8 0.0001 19.5 1.6 29 33-61 26-54 (62)
16 COG3036 Uncharacterized protei 67.0 10 0.00022 18.5 2.6 26 2-27 10-35 (66)
17 PF13556 HTH_30: PucR C-termin 57.3 19 0.00042 16.6 2.9 32 3-37 13-45 (59)
18 PF02519 Auxin_inducible: Auxi 56.7 16 0.00034 19.2 2.4 19 11-29 57-75 (100)
19 COG0103 RpsI Ribosomal protein 49.6 16 0.00035 20.3 1.8 25 2-26 77-102 (130)
20 PF08837 DUF1810: Protein of u 47.3 14 0.00031 20.7 1.4 32 10-41 62-94 (139)
21 PF08066 PMC2NT: PMC2NT (NUC01 46.2 31 0.00066 17.5 2.5 20 10-29 16-37 (91)
22 PF03889 DUF331: Domain of unk 44.2 20 0.00044 15.7 1.4 21 6-26 5-25 (39)
23 PF09585 Lin0512_fam: Conserve 41.8 18 0.00039 19.6 1.2 34 6-39 7-41 (113)
24 TIGR02617 tnaA_trp_ase tryptop 38.8 27 0.00059 23.4 1.9 27 3-29 58-87 (467)
25 TIGR02058 lin0512_fam conserve 38.2 22 0.00047 19.4 1.2 33 7-40 8-42 (116)
26 TIGR01411 tatAE twin arginine- 38.0 30 0.00064 15.6 1.5 18 6-23 24-42 (47)
27 PF05303 DUF727: Protein of un 36.9 41 0.00088 17.9 2.1 15 11-25 83-99 (108)
28 PF13910 DUF4209: Domain of un 34.5 70 0.0015 16.4 5.4 42 2-43 23-70 (93)
29 PF15469 Sec5: Exocyst complex 34.1 55 0.0012 18.5 2.5 38 7-44 110-152 (182)
30 PF02416 MttA_Hcf106: mttA/Hcf 34.1 55 0.0012 15.0 2.8 26 4-29 21-47 (53)
31 PHA02754 hypothetical protein; 34.1 36 0.00079 16.4 1.5 22 15-36 13-34 (67)
32 PF12785 VESA1_N: Variant eryt 34.0 24 0.00052 23.6 1.1 28 15-42 52-80 (462)
33 PF15457 HopW1-1: Type III T3S 33.4 31 0.00067 21.5 1.4 28 1-32 97-124 (320)
34 PF09959 DUF2193: Uncharacteri 33.4 73 0.0016 21.3 3.1 26 4-29 90-116 (499)
35 PF12292 DUF3624: Protein of u 29.0 43 0.00092 16.9 1.3 40 13-52 6-51 (77)
36 cd06150 YjgF_YER057c_UK114_lik 28.2 69 0.0015 16.3 2.1 26 16-41 29-54 (105)
37 PRK14985 maltodextrin phosphor 28.2 58 0.0013 23.4 2.2 41 8-48 70-110 (798)
38 PF03592 Terminase_2: Terminas 28.2 1.1E+02 0.0023 16.6 4.4 34 7-40 34-68 (144)
39 PF02526 GBP_repeat: Glycophor 27.7 63 0.0014 13.8 2.4 18 12-29 12-30 (38)
40 PRK13237 tyrosine phenol-lyase 26.8 67 0.0015 21.5 2.2 27 3-29 62-91 (460)
41 KOG0064|consensus 26.6 67 0.0015 22.5 2.2 35 3-41 618-652 (728)
42 cd06155 eu_AANH_C_1 A group of 26.5 78 0.0017 16.1 2.1 26 16-41 26-51 (101)
43 PF01042 Ribonuc_L-PSP: Endori 26.1 61 0.0013 17.0 1.7 25 17-41 44-68 (121)
44 COG1850 RbcL Ribulose 1,5-bisp 25.9 83 0.0018 20.9 2.5 34 2-40 353-410 (429)
45 COG3726 AhpA Uncharacterized m 25.7 61 0.0013 19.4 1.7 38 1-42 29-67 (214)
46 PF10397 ADSL_C: Adenylosuccin 25.5 97 0.0021 15.1 2.8 11 33-43 38-48 (81)
47 PRK00182 tatB sec-independent 25.0 1.2E+02 0.0026 17.5 2.8 24 6-29 27-51 (160)
48 PRK14986 glycogen phosphorylas 24.2 79 0.0017 22.8 2.3 41 8-48 81-121 (815)
49 cd05838 WHSC1_related The PWWP 23.9 98 0.0021 15.8 2.2 16 15-30 78-93 (95)
50 cd05836 N_Pac_NP60 The PWWP do 23.9 85 0.0018 15.8 1.9 14 15-28 72-85 (86)
51 PF03514 GRAS: GRAS domain fam 23.9 54 0.0012 21.0 1.4 14 1-14 121-134 (374)
52 PF09772 Tmem26: Transmembrane 23.8 31 0.00068 21.5 0.3 26 5-30 158-184 (283)
53 PF02153 PDH: Prephenate dehyd 23.5 1.2E+02 0.0026 18.2 2.8 38 3-44 209-248 (258)
54 PRK01371 sec-independent trans 23.4 1.2E+02 0.0027 16.9 2.6 28 4-31 24-52 (137)
55 PRK14861 tatA twin arginine tr 22.3 1.1E+02 0.0024 14.6 2.7 22 6-27 27-49 (61)
56 KOG1369|consensus 22.3 40 0.00086 22.7 0.6 21 7-27 417-438 (474)
57 PRK15279 type III secretion pr 21.6 2E+02 0.0043 17.3 3.4 39 2-40 100-141 (240)
58 PF00210 Ferritin: Ferritin-li 21.4 1.4E+02 0.003 15.4 3.5 31 2-32 27-58 (142)
59 TIGR01037 pyrD_sub1_fam dihydr 21.4 1.2E+02 0.0025 18.5 2.5 34 2-35 256-290 (300)
60 PF07487 SopE_GEF: SopE GEF do 21.2 1.5E+02 0.0032 17.1 2.6 38 3-40 26-66 (165)
61 PF07624 PSD2: Protein of unkn 21.2 1.2E+02 0.0026 14.7 2.6 17 23-39 49-65 (76)
62 TIGR03610 RutC pyrimidine util 20.9 1.1E+02 0.0024 16.3 2.1 25 17-41 51-75 (127)
63 TIGR02093 P_ylase glycogen/sta 20.8 85 0.0018 22.6 1.9 28 21-48 74-101 (794)
64 TIGR03793 TOMM_pelo TOMM prope 20.6 95 0.0021 15.5 1.7 22 15-36 16-38 (77)
65 cd03397 PAP2_acid_phosphatase 20.5 2.1E+02 0.0045 17.1 3.5 20 10-29 212-231 (232)
66 COG2155 Uncharacterized conser 20.5 97 0.0021 15.7 1.7 27 33-60 28-54 (79)
67 cd04300 GT1_Glycogen_Phosphory 20.3 91 0.002 22.5 2.0 28 21-48 77-104 (797)
68 PRK07259 dihydroorotate dehydr 20.0 1.1E+02 0.0024 18.6 2.2 38 2-39 256-295 (301)
No 1
>PF00698 Acyl_transf_1: Acyl transferase domain; InterPro: IPR014043 Enzymes like bacterial malonyl CoA-acly carrier protein transacylase (2.3.1.39 from EC) and eukaryotic fatty acid synthase (2.3.1.85 from EC) that are involved in fatty acid biosynthesis belong to this group. Also included are the polyketide synthases 6-methylsalicylic acid synthase (2.3.1 from EC), a multifunctional enzyme that involved in the biosynthesis of patulin and conidial green pigment synthase (2.3.1 from EC).; PDB: 3HHD_C 2JFD_D 2JFK_A 3G87_A 3IM9_A 2QO3_B 3IM8_A 3EZO_A 2QJ3_A 2QC3_A ....
Probab=99.71 E-value=1.7e-18 Score=104.85 Aligned_cols=62 Identities=29% Similarity=0.544 Sum_probs=53.1
Q ss_pred CCchHHHHHHHHhc-CHHHHHHHHHHHHhhccC-CCCHHHhhcCCCC-CCchhhHHHHHHHHhcC
Q psy4741 1 MGSQWPGMARELMW-FAPFRQAIFECDRVYRPL-GLDIVKIITSDDP-TTFDDILNSFVAIVTCH 62 (62)
Q Consensus 1 QGsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~-g~~l~~~l~~~~~-~~~~~~~~~q~~i~~~q 62 (62)
||+||+|||++||+ +|.||+.+++|+++++.. |+++.+.+.+++. +.+++|.++||+||++|
T Consensus 7 QGsq~~gMg~~L~~~~p~f~~~~~~~~~~l~~~~g~~l~~~l~~~~~~~~l~~~~~~qpai~~~~ 71 (318)
T PF00698_consen 7 QGSQYPGMGRDLYENNPVFRETIDRCDEILKELLGFSLLELLFEGPESEDLNDTEYAQPAIFAIQ 71 (318)
T ss_dssp TTS--TTTTHHHHHH-HHHHHHHHHHHHHHTSHHTS-HHHHHHHTTHCHHHTSHHHHHHHHHHHH
T ss_pred cchhhHhHHHHHHHcChhhHHHHHhhhhhhhcccccchhhhhhcccccccccchheecchhhhhh
Confidence 89999999999999 999999999999999986 9999999987664 56899999999999875
No 2
>smart00827 PKS_AT Acyl transferase domain in polyketide synthase (PKS) enzymes.
Probab=99.63 E-value=5.7e-16 Score=92.59 Aligned_cols=62 Identities=34% Similarity=0.602 Sum_probs=55.6
Q ss_pred CCchHHHHHHHHhc-CHHHHHHHHHHHHhhccC-CCCHHHhhcCCCC--CCchhhHHHHHHHHhcC
Q psy4741 1 MGSQWPGMARELMW-FAPFRQAIFECDRVYRPL-GLDIVKIITSDDP--TTFDDILNSFVAIVTCH 62 (62)
Q Consensus 1 QGsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~-g~~l~~~l~~~~~--~~~~~~~~~q~~i~~~q 62 (62)
||+||+|||++||+ +|.||+.+++|+++++.. |+++.+.+.+.+. ..++++.++||+|+++|
T Consensus 4 QG~q~~~m~~~l~~~~~~~~~~~~~~~~~l~~~~g~~~~~~l~~~~~~~~~l~~~~~~q~~i~~~~ 69 (298)
T smart00827 4 QGSQWPGMGRELYETEPVFRAALDECDAALQPLLGWSLLDVLFGEDGAASLLRRTEVAQPALFAVQ 69 (298)
T ss_pred CchhHHHHHHHHHHcCHHHHHHHHHHHHHHHHhcCCCHHHHHcCCCCchhhhcccchhHHHHHHHH
Confidence 89999999999998 999999999999999887 9999999987543 34788999999999865
No 3
>TIGR00128 fabD malonyl CoA-acyl carrier protein transacylase. The seed alignment for this family of proteins contains a single member each from a number of bacterial species but also an additional pair of closely related, uncharacterized proteins from B. subtilis, one of which has a long C-terminal extension.
Probab=99.63 E-value=4.2e-16 Score=92.78 Aligned_cols=59 Identities=17% Similarity=0.250 Sum_probs=54.1
Q ss_pred CCchHHHHHHHHhc-CHHHHHHHHHHHHhhccCCCCHHHhhcCCCCCCchhhHHHHHHHHhcC
Q psy4741 1 MGSQWPGMARELMW-FAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTFDDILNSFVAIVTCH 62 (62)
Q Consensus 1 QGsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~g~~l~~~l~~~~~~~~~~~~~~q~~i~~~q 62 (62)
||+||+|||++||+ +|.||+.+++|++++ |+++.+.+++++.+.++++.++||+||++|
T Consensus 10 qg~~~~~m~~~l~~~~p~~~~~~~~~~~~l---g~~~~~~~~~~~~~~~~~~~~~q~~i~~~~ 69 (290)
T TIGR00128 10 QGSQTVGMGKDLYEQYPIAKELFDQASEAL---GYDLKKLCQEGPAEELNKTQYTQPALYVVS 69 (290)
T ss_pred CCcchhhhHHHHHHcCHHHHHHHHHHHHHh---CcCHHHHHhCCCHHHhccccchhHHHHHHH
Confidence 89999999999998 999999999999999 999999998766666788999999999875
No 4
>PLN02752 [acyl-carrier protein] S-malonyltransferase
Probab=99.57 E-value=3.6e-15 Score=91.32 Aligned_cols=58 Identities=19% Similarity=0.272 Sum_probs=53.2
Q ss_pred CCchHHHHHHHHhc-CHHHHHHHHHHHHhhccCCCCHHHhhcCCCCCCchhhHHHHHHHHhcC
Q psy4741 1 MGSQWPGMARELMW-FAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTFDDILNSFVAIVTCH 62 (62)
Q Consensus 1 QGsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~g~~l~~~l~~~~~~~~~~~~~~q~~i~~~q 62 (62)
||+||+|||++ |. +|.|++.+++|++++ |+++.+++.+++.+.+++|.++||+||++|
T Consensus 47 QGsq~~gm~~~-~~~~p~~~~~~~~~~~~l---g~~l~~~~~~~~~~~l~~~~~~qp~i~~~~ 105 (343)
T PLN02752 47 QGAQAVGMGKE-AAEVPAAKALFDKASEIL---GYDLLDVCVNGPKEKLDSTVVSQPAIYVAS 105 (343)
T ss_pred CCcchhhHHHH-HHhCHHHHHHHHHHHHHh---CCCHHHHHhcCCHHHHhcchhhhHHHHHHH
Confidence 89999999999 77 999999999999998 999999998776666889999999999875
No 5
>COG0331 FabD (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]
Probab=99.55 E-value=5.1e-15 Score=90.24 Aligned_cols=58 Identities=21% Similarity=0.272 Sum_probs=55.0
Q ss_pred CCchHHHHHHHHhc-CHHHHHHHHHHHHhhccCCCCHHHhhcCCCCCCchhhHHHHHHHHhc
Q psy4741 1 MGSQWPGMARELMW-FAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTFDDILNSFVAIVTC 61 (62)
Q Consensus 1 QGsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~g~~l~~~l~~~~~~~~~~~~~~q~~i~~~ 61 (62)
|||||.|||++||+ +|.+++.++++++.+ ++++.+++++++++.+..|.++||+|.++
T Consensus 11 QGsQ~~gMg~~l~~~~~~a~~~~~~a~~~l---~~~l~~i~~~~p~~~L~~T~~tQPal~~~ 69 (310)
T COG0331 11 QGSQSLGMGKDLYENSPEAKETFDEADEAL---GFDLWALVFEGPEEELNLTQNTQPALLLV 69 (310)
T ss_pred chHHHHHhHHHHHhccHHHHHHHHHHHHHh---cccHHHHhcCCCHHHhcccchhhHHHHHH
Confidence 89999999999999 999999999999999 99999999988888899999999999875
No 6
>KOG1202|consensus
Probab=99.53 E-value=1.1e-14 Score=99.90 Aligned_cols=62 Identities=48% Similarity=0.910 Sum_probs=60.0
Q ss_pred CCchHHHHHHHHhcCHHHHHHHHHHHHhhccCCCCHHHhhcCCCCCCchhhHHHHHHHHhcC
Q psy4741 1 MGSQWPGMARELMWFAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTFDDILNSFVAIVTCH 62 (62)
Q Consensus 1 QGsq~~gMg~~L~~~p~f~~~~~~~~~~l~~~g~~l~~~l~~~~~~~~~~~~~~q~~i~~~q 62 (62)
+||||+||+++|++.+.||+.|.+|++.|++.|+++.++|.+.+++.++++.+++++|+|+|
T Consensus 508 MGsQW~~Ma~~LMkl~~F~dsi~~~ae~l~~~gldv~~vL~~s~~~tfdn~l~sfvsitAiQ 569 (2376)
T KOG1202|consen 508 MGSQWAGMAKDLMKLERFRDSIQRSAEVLKPFGLDVIDVLTRSDESTFDNILNSFVSITAIQ 569 (2376)
T ss_pred CcchhhHHHHHHhhhHHHHHHHHHHHhhhcccCcchhhhhcCCChHHHHHHHHHHHHHHHHH
Confidence 59999999999999999999999999999999999999999999999999999999999987
No 7
>TIGR03131 malonate_mdcH malonate decarboxylase, epsilon subunit. Members of this protein family are the epsilon subunit of malonate decarboxylase. This subunit has malonyl-CoA/dephospho-CoA acyltransferase activity. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. The epsilon subunit is closely related to the malonyl CoA-acyl carrier protein (ACP) transacylase family described by TIGR00128, but acts on an ACP subunit of malonate decarboxylase that has an unusual coenzyme A derivative as its prothetic group.
Probab=99.44 E-value=1.4e-13 Score=82.53 Aligned_cols=56 Identities=23% Similarity=0.311 Sum_probs=48.4
Q ss_pred CCchHHHHHHHHhcCHHHHHHHHHHHHhhccCCCCHHHhhcCCCCCCchhhHHHHHHHHhcC
Q psy4741 1 MGSQWPGMARELMWFAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTFDDILNSFVAIVTCH 62 (62)
Q Consensus 1 QGsq~~gMg~~L~~~p~f~~~~~~~~~~l~~~g~~l~~~l~~~~~~~~~~~~~~q~~i~~~q 62 (62)
||+||+|||++|+++|+||+.+++|++++ ++++.+ +. +.+.++++.++||+|+++|
T Consensus 8 qG~q~~~m~~~l~~~p~~~~~~~~~~~~l---~~~~~~-~~--~~~~l~~~~~~qp~i~~~q 63 (295)
T TIGR03131 8 QGSQRAGMLAELPDHPAVAAVLAEASDVL---GIDPRE-LD--DAEALASTRSAQLCILAAG 63 (295)
T ss_pred cchhhhhHHHHHHhCHHHHHHHHHHHHHh---CcCHHH-cC--CHhhhccchhhhHHHHHHH
Confidence 89999999999955999999999999999 889887 32 2345788999999999875
No 8
>TIGR02813 omega_3_PfaA polyketide-type polyunsaturated fatty acid synthase PfaA. Members of the seed for this alignment are involved in omega-3 polyunsaturated fatty acid biosynthesis, such as the protein PfaA from the eicosapentaenoic acid biosynthesis operon in Photobacterium profundum strain SS9. PfaA is encoded together with PfaB, PfaC, and PfaD, and the functions of the individual polypeptides have not yet been described. More distant homologs of PfaA, also included with the reach of this model, appear to be involved in polyketide-like biosynthetic mechanisms of polyunsaturated fatty acid biosynthesis, an alternative to the more familiar iterated mechanism of chain extension and desaturation, and in most cases are encoded near genes for homologs of PfaB, PfaC, and/or PfaD.
Probab=99.39 E-value=5.1e-13 Score=96.21 Aligned_cols=62 Identities=26% Similarity=0.305 Sum_probs=52.4
Q ss_pred CCchHHHHHHHHhc-CHHHHHHHHHHHHhhccC-CCCHHHhhcCC----------CCCCchhhHHHHHHHHhcC
Q psy4741 1 MGSQWPGMARELMW-FAPFRQAIFECDRVYRPL-GLDIVKIITSD----------DPTTFDDILNSFVAIVTCH 62 (62)
Q Consensus 1 QGsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~-g~~l~~~l~~~----------~~~~~~~~~~~q~~i~~~q 62 (62)
||+||+|||++||+ +|.||+.+++|++++... ++++.++++.. ..+.+++|.++||+|+++|
T Consensus 588 QGSQy~gMgreL~~~~P~fr~~ld~~d~~l~~~~~~~L~~~l~p~~~~~~~~~~~~~~~L~~t~~aQPaI~a~q 661 (2582)
T TIGR02813 588 QGSQYLNMGRELACNFPEVRQAAADMDSVFTQAGKGALSPVLYPIPVFNDESRKAQEEALTNTQHAQSAIGTLS 661 (2582)
T ss_pred CCchhHHHHHHHHhcCHHHHHHHHHHHHHhhhhcCCcHHHHhccccccccccccchhhhhccchhHHHHHHHHH
Confidence 89999999999999 999999999999999776 67888876521 1234788999999999875
No 9
>KOG2926|consensus
Probab=99.35 E-value=3.7e-13 Score=82.82 Aligned_cols=57 Identities=26% Similarity=0.308 Sum_probs=54.7
Q ss_pred CCchHHHHHHHHhcCHHHHHHHHHHHHhhccCCCCHHHhhcCCCCCCchhhHHHHHHHHh
Q psy4741 1 MGSQWPGMARELMWFAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTFDDILNSFVAIVT 60 (62)
Q Consensus 1 QGsq~~gMg~~L~~~p~f~~~~~~~~~~l~~~g~~l~~~l~~~~~~~~~~~~~~q~~i~~ 60 (62)
||+||.|||+.++++|..|+.+++|+++| |++|.+++.+++.+.+++|.++||+|.+
T Consensus 71 QG~q~vgm~q~~l~~p~a~~~~~~A~~vl---~YdLlki~~~gP~e~ldrT~~~QpAI~~ 127 (386)
T KOG2926|consen 71 QGAQSVGMGQYLLQNPAARRLFAEASNVL---GYDLLKICVNGPKEKLDRTVIAQPAIDV 127 (386)
T ss_pred CChhhhhhhHHHHhCcchhHHHHHHHHHh---hHHHHHHHhcCccchhhcccccccceec
Confidence 89999999999999999999999999999 9999999999999999999999999864
No 10
>TIGR02816 pfaB_fam PfaB family protein. The protein PfaB is part of four gene locus, similar to polyketide biosynthesis systems, responsible for omega-3 polyunsaturated fatty acid biosynthesis in several high pressure and/or cold-adapted bacteria. The fairly permissive trusted cutoff set for this model allows detection of homologs encoded near homologs to other proteins of the locus: PfaA, PfaC, and/or PfaD. The likely role in every case is either polyunsaturated fatty acid or polyketide biosynthesis.
Probab=99.14 E-value=2.9e-11 Score=78.18 Aligned_cols=52 Identities=15% Similarity=0.291 Sum_probs=38.5
Q ss_pred CCchHHHHHHHHhc-CHHHHHHHHHHHHhhccCCCCHHHhhcC-----CCCCCchhhHHHHHHHHh
Q psy4741 1 MGSQWPGMARELMW-FAPFRQAIFECDRVYRPLGLDIVKIITS-----DDPTTFDDILNSFVAIVT 60 (62)
Q Consensus 1 QGsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~g~~l~~~l~~-----~~~~~~~~~~~~q~~i~~ 60 (62)
||+||+|||++||. +|+||+.+++|. ++.+.+.. .+.....++...||++|+
T Consensus 190 qGsqy~gMGr~L~~~~P~fr~~ld~~~--------~L~~~L~~~~~~~~~~~~~~~~~l~q~alfa 247 (538)
T TIGR02816 190 VGTVYADMFNDFHQYFPALFAKLEREG--------DLKAMLQAEDIYGEDPKHAAEMSLGDLAIAG 247 (538)
T ss_pred CchHHHHHHHHHHhhCHHHHHHHHhcC--------CHHHHhccccccccchhhhhhhhhHhHHHHH
Confidence 89999999999999 999999999875 33444432 222334566678888874
No 11
>COG3321 Polyketide synthase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=99.07 E-value=1.2e-10 Score=79.84 Aligned_cols=62 Identities=27% Similarity=0.387 Sum_probs=55.2
Q ss_pred CCchHHHHHHHHhc-CHHHHHHHHHHHHhhccC-CCCHHHhhcCCCCCCchhhHHHHHHHHhcC
Q psy4741 1 MGSQWPGMARELMW-FAPFRQAIFECDRVYRPL-GLDIVKIITSDDPTTFDDILNSFVAIVTCH 62 (62)
Q Consensus 1 QGsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~-g~~l~~~l~~~~~~~~~~~~~~q~~i~~~q 62 (62)
||+||.+||++||+ +|+|++.+++|+..+... ++++.+.+...+.+.+..+.++||++|++|
T Consensus 534 qgsq~~~mg~el~~~~p~f~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~l~~~~~~Qp~lfai~ 597 (1061)
T COG3321 534 QGSQWAGMGRELYALEPVFASAFDALEALLHRLLGFSLPEVIFAPDYPFLESIDFAQPALFAVS 597 (1061)
T ss_pred hHHHHHHHHHHHhhccHHHHHHHHHHHHHHHHHcCCcccceecCCCCccccCcchhhhHHHHHH
Confidence 79999999999999 999999999999999887 999999998865433777889999999875
No 12
>PLN03219 uncharacterized protein; Provisional
Probab=69.55 E-value=8.5 Score=20.68 Aligned_cols=22 Identities=14% Similarity=0.285 Sum_probs=17.9
Q ss_pred HHhcCHHHHHHHHHHHHhhccCCCC
Q psy4741 11 ELMWFAPFRQAIFECDRVYRPLGLD 35 (62)
Q Consensus 11 ~L~~~p~f~~~~~~~~~~l~~~g~~ 35 (62)
.++.+|.|++.++++.+-+ |++
T Consensus 62 ~yL~hP~F~~LL~~AeEEf---Gf~ 83 (108)
T PLN03219 62 SYLNHPLFREFLNRAEEEC---GFH 83 (108)
T ss_pred HHcCChHHHHHHHHHHHHh---CCC
Confidence 3455899999999999988 664
No 13
>PLN03220 uncharacterized protein; Provisional
Probab=68.90 E-value=9.2 Score=20.44 Aligned_cols=21 Identities=10% Similarity=0.460 Sum_probs=17.7
Q ss_pred HhcCHHHHHHHHHHHHhhccCCCC
Q psy4741 12 LMWFAPFRQAIFECDRVYRPLGLD 35 (62)
Q Consensus 12 L~~~p~f~~~~~~~~~~l~~~g~~ 35 (62)
++.+|.|++.++++.+-+ |++
T Consensus 61 yL~hP~F~~LL~~AeEEf---Gf~ 81 (105)
T PLN03220 61 FLNHPSFKEFLSRAEEEF---GFN 81 (105)
T ss_pred HcCChHHHHHHHHHHHHh---CCC
Confidence 455899999999999988 664
No 14
>PLN03090 auxin-responsive family protein; Provisional
Probab=68.88 E-value=8.8 Score=20.45 Aligned_cols=18 Identities=6% Similarity=0.320 Sum_probs=15.7
Q ss_pred HhcCHHHHHHHHHHHHhh
Q psy4741 12 LMWFAPFRQAIFECDRVY 29 (62)
Q Consensus 12 L~~~p~f~~~~~~~~~~l 29 (62)
.+.+|.|++.++++.+-+
T Consensus 62 ~L~hP~F~~LL~~aeeEf 79 (104)
T PLN03090 62 FLTHPEFQSLLQQAEEEF 79 (104)
T ss_pred HcCCHHHHHHHHHHHHHh
Confidence 445899999999999888
No 15
>PF04070 DUF378: Domain of unknown function (DUF378); InterPro: IPR007211 These are predicted membrane proteins of unknown function. The majority of the proteins have two predicted transmembrane regions.
Probab=67.96 E-value=4.8 Score=19.51 Aligned_cols=29 Identities=10% Similarity=0.249 Sum_probs=24.0
Q ss_pred CCCHHHhhcCCCCCCchhhHHHHHHHHhc
Q psy4741 33 GLDIVKIITSDDPTTFDDILNSFVAIVTC 61 (62)
Q Consensus 33 g~~l~~~l~~~~~~~~~~~~~~q~~i~~~ 61 (62)
++|+.+.+++++.+.+.++.+.-+++.++
T Consensus 26 ~~nlV~~lfgG~~s~l~RiiY~lVGlagl 54 (62)
T PF04070_consen 26 NFNLVAALFGGSASWLSRIIYILVGLAGL 54 (62)
T ss_pred hccHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 68999999977777788899998888764
No 16
>COG3036 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.99 E-value=10 Score=18.47 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=19.6
Q ss_pred CchHHHHHHHHhcCHHHHHHHHHHHH
Q psy4741 2 GSQWPGMARELMWFAPFRQAIFECDR 27 (62)
Q Consensus 2 Gsq~~gMg~~L~~~p~f~~~~~~~~~ 27 (62)
|.-.+.-.+.|+..|.||..+++...
T Consensus 10 g~ikdNalkALv~~pLFR~RvEk~kK 35 (66)
T COG3036 10 GVIKDNALKALVHDPLFRQRVEKKKK 35 (66)
T ss_pred cccchhHHHHHHcCHHHHHHHHHhhc
Confidence 34445667788889999999988763
No 17
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=57.30 E-value=19 Score=16.61 Aligned_cols=32 Identities=22% Similarity=0.280 Sum_probs=22.1
Q ss_pred chHHHHHHHHhc-CHHHHHHHHHHHHhhccCCCCHH
Q psy4741 3 SQWPGMARELMW-FAPFRQAIFECDRVYRPLGLDIV 37 (62)
Q Consensus 3 sq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~g~~l~ 37 (62)
......++.|+= -..++..++++.+++ |.|+.
T Consensus 13 ~n~~~tA~~L~iHrNTl~yRl~ki~~l~---g~dl~ 45 (59)
T PF13556_consen 13 GNISKTARALHIHRNTLRYRLKKIEELL---GLDLD 45 (59)
T ss_dssp T-HHHHHHHHTS-HHHHHHHHHHHHHHH---S--TT
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHH---CcCCC
Confidence 345566777776 667889999999999 77653
No 18
>PF02519 Auxin_inducible: Auxin responsive protein; InterPro: IPR003676 This family consists of the protein products of a gene cluster that encodes a group of auxin-regulated RNAs (small auxin up RNAs, SAURs) []. Proteins from this ARG7 auxin responsive genes family have no identified functional role [].
Probab=56.68 E-value=16 Score=19.18 Aligned_cols=19 Identities=5% Similarity=0.242 Sum_probs=15.9
Q ss_pred HHhcCHHHHHHHHHHHHhh
Q psy4741 11 ELMWFAPFRQAIFECDRVY 29 (62)
Q Consensus 11 ~L~~~p~f~~~~~~~~~~l 29 (62)
..+.+|.|++.++++.+-+
T Consensus 57 ~~L~hp~f~~LL~~aeeEf 75 (100)
T PF02519_consen 57 SYLNHPLFQELLEQAEEEF 75 (100)
T ss_pred HHcCchhHHHHHHHHhhhc
Confidence 3455899999999999877
No 19
>COG0103 RpsI Ribosomal protein S9 [Translation, ribosomal structure and biogenesis]
Probab=49.58 E-value=16 Score=20.28 Aligned_cols=25 Identities=28% Similarity=0.350 Sum_probs=20.3
Q ss_pred CchHHHHHHHHhc-CHHHHHHHHHHH
Q psy4741 2 GSQWPGMARELMW-FAPFRQAIFECD 26 (62)
Q Consensus 2 Gsq~~gMg~~L~~-~p~f~~~~~~~~ 26 (62)
|+-..|+.+.|.+ +|.+|..+.+.+
T Consensus 77 ~AiR~gIaRAL~~~~~~lr~~lk~~g 102 (130)
T COG0103 77 GAIRHGIARALVEYDPELRPALKKAG 102 (130)
T ss_pred HHHHHHHHHHHHHHCHHHHHHHHHCC
Confidence 3456789999999 999998887776
No 20
>PF08837 DUF1810: Protein of unknown function (DUF1810); InterPro: IPR014937 This is a family of uncharacterised proteins. The structure of one of the members in this family has been solved and it adopts a mainly alpha helical structure. ; PDB: 2JEK_A.
Probab=47.33 E-value=14 Score=20.69 Aligned_cols=32 Identities=19% Similarity=0.284 Sum_probs=22.2
Q ss_pred HHHhcCHHHHHHHHHHHHhhccC-CCCHHHhhc
Q psy4741 10 RELMWFAPFRQAIFECDRVYRPL-GLDIVKIIT 41 (62)
Q Consensus 10 ~~L~~~p~f~~~~~~~~~~l~~~-g~~l~~~l~ 41 (62)
+..+++|+.-..+.+|.+++-.. +-+..+++-
T Consensus 62 ~AYL~HpvLG~RL~e~~~~ll~~~~~s~~~IfG 94 (139)
T PF08837_consen 62 RAYLAHPVLGPRLRECTEALLALEGRSAEEIFG 94 (139)
T ss_dssp HHHHHSTTHHHHHHHHHHHHHH--S--HHHHS-
T ss_pred HHHHcCHHHHHHHHHHHHHHHhcCCCCHHHHCC
Confidence 44555899999999999988776 778777663
No 21
>PF08066 PMC2NT: PMC2NT (NUC016) domain; InterPro: IPR012588 Exosomes are nano-compartments that function in the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA) [, ]. Exosomes occur in both archaea and eukaryotes, and have a similar overall structure to each other and to bacterial/organelle PNPases (polynucleotide phosphorylases; 2.7.7.8 from EC) [], consisting of a barrel structure composed of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. There are two types of exosomes in eukaryotes, cytoplasmic exosomes that are responsible for 3'-5' exoribonuclease degradation of mRNAs, and nuclear exosomes that degrade pre-mRNAs (such as nonsense transcripts) and degrade rRNAs, snRNAs and snoRNAs. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. There are several accessory proteins that help degrade, unwind or polyadenylate RNA substrate before they enter the exosome. This entry represents the N-terminal domain of Rrp6 (exosome component 10 in humans), a nuclear exosome accessory factor that interacts with the bottom of the hexameric PH-ring opposite the cap. Rrp6 functions as a hydrolytic exonuclease, and is homologous to RNase-D in Escherichia coli. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0006396 RNA processing, 0000176 nuclear exosome (RNase complex)
Probab=46.17 E-value=31 Score=17.52 Aligned_cols=20 Identities=15% Similarity=0.278 Sum_probs=16.3
Q ss_pred HHHhc-C-HHHHHHHHHHHHhh
Q psy4741 10 RELMW-F-APFRQAIFECDRVY 29 (62)
Q Consensus 10 ~~L~~-~-p~f~~~~~~~~~~l 29 (62)
-++|. + |.|++.+++..+-+
T Consensus 16 ~~Fy~s~dp~f~~~ld~~s~rl 37 (91)
T PF08066_consen 16 YDFYRSFDPEFAESLDEQSQRL 37 (91)
T ss_pred HHHHHHhhHHHHHHHHHHHHHH
Confidence 36788 6 99999999988766
No 22
>PF03889 DUF331: Domain of unknown function; InterPro: IPR005589 The members of this family are uncharacterised proteins from a number of bacterial species. They range in size from 50-100 residues.
Probab=44.16 E-value=20 Score=15.71 Aligned_cols=21 Identities=19% Similarity=0.208 Sum_probs=14.3
Q ss_pred HHHHHHHhcCHHHHHHHHHHH
Q psy4741 6 PGMARELMWFAPFRQAIFECD 26 (62)
Q Consensus 6 ~gMg~~L~~~p~f~~~~~~~~ 26 (62)
..-.+.|..+|.||..+++..
T Consensus 5 dNalkAlv~~~LFr~rvek~k 25 (39)
T PF03889_consen 5 DNALKALVTSPLFRQRVEKAK 25 (39)
T ss_pred hhHHHHHHhCcchhhhhhccc
Confidence 344567777888888776543
No 23
>PF09585 Lin0512_fam: Conserved hypothetical protein (Lin0512_fam); InterPro: IPR011719 This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N terminus.
Probab=41.77 E-value=18 Score=19.57 Aligned_cols=34 Identities=18% Similarity=0.143 Sum_probs=20.6
Q ss_pred HHHHHHHhcCHHHHHHHHHHHHhhccCCC-CHHHh
Q psy4741 6 PGMARELMWFAPFRQAIFECDRVYRPLGL-DIVKI 39 (62)
Q Consensus 6 ~gMg~~L~~~p~f~~~~~~~~~~l~~~g~-~l~~~ 39 (62)
-|||-+|+.-..-+.+.+.|.+++...-. ++.+.
T Consensus 7 ~GmG~DlhGqD~TkAA~RAv~DAI~~nslp~l~~~ 41 (113)
T PF09585_consen 7 MGMGNDLHGQDYTKAAVRAVRDAISHNSLPGLFEI 41 (113)
T ss_pred ecccccccCCcHHHHHHHHHHHHHhhcchHHHHHH
Confidence 38999999833345666777777744323 34443
No 24
>TIGR02617 tnaA_trp_ase tryptophanase, leader peptide-associated. Members of this family belong to the beta-eliminating lyase family (pfam01212) and act as tryptophanase (L-tryptophan indole-lyase). The tryptophanases of this family, as a rule, are found with a tryptophanase leader peptide (TnaC) encoded upstream. Both tryptophanases (4.1.99.1) and tyrosine phenol-lyases (EC 4.1.99.2) are found between trusted and noise cutoffs, but this model captures nearly all tryptophanases for which the leader peptide gene tnaC can be found upstream.
Probab=38.77 E-value=27 Score=23.38 Aligned_cols=27 Identities=11% Similarity=0.077 Sum_probs=22.8
Q ss_pred chHHHH--HHHHhc-CHHHHHHHHHHHHhh
Q psy4741 3 SQWPGM--ARELMW-FAPFRQAIFECDRVY 29 (62)
Q Consensus 3 sq~~gM--g~~L~~-~p~f~~~~~~~~~~l 29 (62)
.||.+| |.+-|. +|.|.+.-+.+.+++
T Consensus 58 ~m~aAM~~GDD~Y~gdpSv~~Lee~vael~ 87 (467)
T TIGR02617 58 SMQAAMMRGDEAYSGSRSYYALAESVKNIF 87 (467)
T ss_pred HHHHHHHcCCcccccCchHHHHHHHHHHHh
Confidence 478888 567898 999999888888888
No 25
>TIGR02058 lin0512_fam conserved hypothetical protein. This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N-terminus.
Probab=38.21 E-value=22 Score=19.38 Aligned_cols=33 Identities=12% Similarity=0.059 Sum_probs=21.1
Q ss_pred HHHHHHhc-CHHHHHHHHHHHHhhccCCCC-HHHhh
Q psy4741 7 GMARELMW-FAPFRQAIFECDRVYRPLGLD-IVKII 40 (62)
Q Consensus 7 gMg~~L~~-~p~f~~~~~~~~~~l~~~g~~-l~~~l 40 (62)
|||-+|+. .+ -+.+.+.|.+++.....+ +.+.+
T Consensus 8 GmG~DlhGqD~-TkAA~RAvrDAI~hnsipg~~~~~ 42 (116)
T TIGR02058 8 GMGVDQHGQNI-TKAAMRAVRNAIASNSMPGIWESL 42 (116)
T ss_pred cccccccCccH-HHHHHHHHHHHHhhccchhHHHhc
Confidence 79999998 54 455667777777543333 55544
No 26
>TIGR01411 tatAE twin arginine-targeting protein translocase, TatA/E family. This model distinguishes TatA/E from the related TatB, but does not distinguish TatA from TatE. The Tat (twin-arginine translocation) system is a Sec-independent exporter for folded proteins, often with a redox cofactor already bound, across the bacterial inner membrane. Functionally equivalent systems are found in the chloroplast and some in archaeal species. The signal peptide recognized by the Tat system is modeled by TIGR01409.
Probab=38.02 E-value=30 Score=15.61 Aligned_cols=18 Identities=28% Similarity=0.514 Sum_probs=9.9
Q ss_pred HHHHHHHhc-CHHHHHHHH
Q psy4741 6 PGMARELMW-FAPFRQAIF 23 (62)
Q Consensus 6 ~gMg~~L~~-~p~f~~~~~ 23 (62)
|.+++++=+ -..||+.+.
T Consensus 24 P~~~r~lG~~i~~fk~~~~ 42 (47)
T TIGR01411 24 PELGRDLGKAIKEFKKALK 42 (47)
T ss_pred HHHHHHHHHHHHHHHHHhh
Confidence 556666555 455555544
No 27
>PF05303 DUF727: Protein of unknown function (DUF727); InterPro: IPR007967 This family consists of several uncharacterised eukaryotic proteins of unknown function.; PDB: 1SGO_A.
Probab=36.92 E-value=41 Score=17.86 Aligned_cols=15 Identities=27% Similarity=0.135 Sum_probs=10.3
Q ss_pred HHhc--CHHHHHHHHHH
Q psy4741 11 ELMW--FAPFRQAIFEC 25 (62)
Q Consensus 11 ~L~~--~p~f~~~~~~~ 25 (62)
+|+. +|.||+.|.+.
T Consensus 83 ~LL~~iSP~fr~~F~~~ 99 (108)
T PF05303_consen 83 ALLDSISPLFRKRFGEK 99 (108)
T ss_dssp HHHHHH-HHHHHHHHHH
T ss_pred HHHHHHCHHHHHHHHHH
Confidence 4555 89999988754
No 28
>PF13910 DUF4209: Domain of unknown function (DUF4209)
Probab=34.53 E-value=70 Score=16.37 Aligned_cols=42 Identities=14% Similarity=0.241 Sum_probs=26.5
Q ss_pred CchHHHHHHHHhcCHHHHHHHHH-----HHHhhccC-CCCHHHhhcCC
Q psy4741 2 GSQWPGMARELMWFAPFRQAIFE-----CDRVYRPL-GLDIVKIITSD 43 (62)
Q Consensus 2 Gsq~~gMg~~L~~~p~f~~~~~~-----~~~~l~~~-g~~l~~~l~~~ 43 (62)
|.+.+-+.++|+..+..++.+.+ ...++.+. |++++..+.-+
T Consensus 23 ~~~~e~~L~dLL~~~~i~~~~g~~~~~~lr~l~~~p~GlNLRN~v~HG 70 (93)
T PF13910_consen 23 GIEQEKLLSDLLASEEIKEIFGEDLIFLLRALFGPPRGLNLRNNVWHG 70 (93)
T ss_pred cchhhhhHHHHHcChHHHHHcChHHHHHHHHHHCCCCCccHHHHHHHh
Confidence 33445667788887777776433 33444444 89998887643
No 29
>PF15469 Sec5: Exocyst complex component Sec5
Probab=34.14 E-value=55 Score=18.45 Aligned_cols=38 Identities=13% Similarity=0.219 Sum_probs=26.9
Q ss_pred HHHHHHhc-C----HHHHHHHHHHHHhhccCCCCHHHhhcCCC
Q psy4741 7 GMARELMW-F----APFRQAIFECDRVYRPLGLDIVKIITSDD 44 (62)
Q Consensus 7 gMg~~L~~-~----p~f~~~~~~~~~~l~~~g~~l~~~l~~~~ 44 (62)
..++.+|+ . ++|.+.+.+|+.+...+.-.+++.|.+.+
T Consensus 110 ~kak~l~~~~~~~~~vf~~v~~eve~ii~~~r~~l~~~L~~~~ 152 (182)
T PF15469_consen 110 KKAKSLFEKYKQQVPVFQKVWSEVEKIIEEFREKLWEKLLSPP 152 (182)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 45677776 4 69999999999988655445666665543
No 30
>PF02416 MttA_Hcf106: mttA/Hcf106 family; InterPro: IPR003369 Members of this protein family are involved in a sec-independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts []. Members of this family in Escherichia coli are involved in export of redox proteins with a "twin arginine" leader motif (S/T-R-R-X-F-L-K) []. This sec-independent pathway is termed TAT for twin-arginine translocation system. This system mainly transports proteins with bound cofactors that require folding prior to export.; GO: 0008565 protein transporter activity, 0015031 protein transport; PDB: 2L16_A.
Probab=34.13 E-value=55 Score=15.03 Aligned_cols=26 Identities=31% Similarity=0.405 Sum_probs=17.4
Q ss_pred hHHHHHHHHhc-CHHHHHHHHHHHHhh
Q psy4741 4 QWPGMARELMW-FAPFRQAIFECDRVY 29 (62)
Q Consensus 4 q~~gMg~~L~~-~p~f~~~~~~~~~~l 29 (62)
--|++++.+=+ ...||+.+.+..+-.
T Consensus 21 kLP~~~r~lG~~ir~fk~~~~~~~~~~ 47 (53)
T PF02416_consen 21 KLPELARSLGKAIREFKKAINEAKEEI 47 (53)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 35777777766 677888877776543
No 31
>PHA02754 hypothetical protein; Provisional
Probab=34.12 E-value=36 Score=16.38 Aligned_cols=22 Identities=23% Similarity=0.338 Sum_probs=17.7
Q ss_pred CHHHHHHHHHHHHhhccCCCCH
Q psy4741 15 FAPFRQAIFECDRVYRPLGLDI 36 (62)
Q Consensus 15 ~p~f~~~~~~~~~~l~~~g~~l 36 (62)
+..|.+.+++..++|...|..+
T Consensus 13 eK~Fke~MRelkD~LSe~GiYi 34 (67)
T PHA02754 13 EKDFKEAMRELKDILSEAGIYI 34 (67)
T ss_pred HhHHHHHHHHHHHHHhhCceEE
Confidence 5678999999999998777544
No 32
>PF12785 VESA1_N: Variant erythrocyte surface antigen-1; InterPro: IPR024751 This entry represents variant erythrocyte surface antigen 1, versions a and b, of Babesia. Babesia bovis is a tick-borne, intra-erythrocytic, protozoal parasite of cattle that shares many lifestyle parallels with the most virulent of the human malarial parasites, Plasmodium falciparum. Babesia uses antigenic variation to establish consistent infections of long duration. The two variants of VESA1, a and b, are expressed from different but closely related genes, and variation is achieved through the involvement of a segmental gene conversion mechanism and low-frequency epigenetic in situ switching of transcriptional activity from the VESA1 gene-pair to a possible other gene pair [].
Probab=34.03 E-value=24 Score=23.56 Aligned_cols=28 Identities=21% Similarity=0.147 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHHhhccC-CCCHHHhhcC
Q psy4741 15 FAPFRQAIFECDRVYRPL-GLDIVKIITS 42 (62)
Q Consensus 15 ~p~f~~~~~~~~~~l~~~-g~~l~~~l~~ 42 (62)
..|+|..||....+|... |||=++.+.+
T Consensus 52 tavvrtyidqlaqvLsalvGWS~i~kc~~ 80 (462)
T PF12785_consen 52 TAVVRTYIDQLAQVLSALVGWSKIEKCWN 80 (462)
T ss_pred ceeHHHHHHHHHHHHHHHhCccccccccc
Confidence 479999999999999998 9998888874
No 33
>PF15457 HopW1-1: Type III T3SS secreted effector HopW1-1/HopPmaA
Probab=33.39 E-value=31 Score=21.55 Aligned_cols=28 Identities=7% Similarity=0.046 Sum_probs=19.2
Q ss_pred CCchHHHHHHHHhcCHHHHHHHHHHHHhhccC
Q psy4741 1 MGSQWPGMARELMWFAPFRQAIFECDRVYRPL 32 (62)
Q Consensus 1 QGsq~~gMg~~L~~~p~f~~~~~~~~~~l~~~ 32 (62)
||.+|.+-.. -|+.+..||+|-.-|...
T Consensus 97 QG~H~la~ed----Q~~Lk~~ldrC~~qLadt 124 (320)
T PF15457_consen 97 QGWHQLASED----QQALKGMLDRCTSQLADT 124 (320)
T ss_pred cccccccccc----HHHHHHHHHHHHHHhccC
Confidence 4445544433 388999999999888653
No 34
>PF09959 DUF2193: Uncharacterized protein conserved in archaea (DUF2193); InterPro: IPR018694 This family of various hypothetical archaeal proteins has no known function
Probab=33.36 E-value=73 Score=21.31 Aligned_cols=26 Identities=19% Similarity=0.153 Sum_probs=20.8
Q ss_pred hHHHHHHHHhc-CHHHHHHHHHHHHhh
Q psy4741 4 QWPGMARELMW-FAPFRQAIFECDRVY 29 (62)
Q Consensus 4 q~~gMg~~L~~-~p~f~~~~~~~~~~l 29 (62)
|-|-...=||+ .|.||+.+++.-+..
T Consensus 90 QTP~ilEILy~eD~~F~ks~~kfi~~I 116 (499)
T PF09959_consen 90 QTPAILEILYEEDPAFRKSVEKFIEAI 116 (499)
T ss_pred cccHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 55667778999 999999988877655
No 35
>PF12292 DUF3624: Protein of unknown function (DUF3624); InterPro: IPR022072 This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved GRC sequence motif.
Probab=29.00 E-value=43 Score=16.95 Aligned_cols=40 Identities=28% Similarity=0.288 Sum_probs=25.9
Q ss_pred hcCHHHHHHHHHHHHhhccC------CCCHHHhhcCCCCCCchhhH
Q psy4741 13 MWFAPFRQAIFECDRVYRPL------GLDIVKIITSDDPTTFDDIL 52 (62)
Q Consensus 13 ~~~p~f~~~~~~~~~~l~~~------g~~l~~~l~~~~~~~~~~~~ 52 (62)
.+...|++.+.+|...+... +|.+.-..+.+++...+.+.
T Consensus 6 C~~~~F~~KiGRC~rCM~QLtvLs~~~w~iWw~~f~d~P~sieSIA 51 (77)
T PF12292_consen 6 CQESWFWQKIGRCQRCMWQLTVLSVLSWPIWWFFFRDTPTSIESIA 51 (77)
T ss_pred HHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHcCCcchHHHHH
Confidence 34678999999999777542 45555555666655555443
No 36
>cd06150 YjgF_YER057c_UK114_like_2 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=28.20 E-value=69 Score=16.34 Aligned_cols=26 Identities=23% Similarity=0.346 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHhhccCCCCHHHhhc
Q psy4741 16 APFRQAIFECDRVYRPLGLDIVKIIT 41 (62)
Q Consensus 16 p~f~~~~~~~~~~l~~~g~~l~~~l~ 41 (62)
.-.+.+++.+.++|+..|.++.++..
T Consensus 29 ~Q~~~~~~nl~~~L~~~G~~~~dvvk 54 (105)
T cd06150 29 GQTRQVLAKIDALLAEAGSDKSRILS 54 (105)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHEEE
Confidence 34677888888888877888777653
No 37
>PRK14985 maltodextrin phosphorylase; Provisional
Probab=28.18 E-value=58 Score=23.39 Aligned_cols=41 Identities=5% Similarity=0.029 Sum_probs=24.0
Q ss_pred HHHHHhcCHHHHHHHHHHHHhhccCCCCHHHhhcCCCCCCc
Q psy4741 8 MARELMWFAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTF 48 (62)
Q Consensus 8 Mg~~L~~~p~f~~~~~~~~~~l~~~g~~l~~~l~~~~~~~~ 48 (62)
||+.|-.+-.=-...+++.++|+..|+++.++....++..+
T Consensus 70 ~Gr~l~nnl~nlgl~~~~~~al~~lg~~l~~i~~~E~Da~L 110 (798)
T PRK14985 70 IGRLTGNNLLNLGWYDDVQDVLKAYDINLTDLLEEETDPAL 110 (798)
T ss_pred ccHHHHHHHHhcCCHHHHHHHHHHcCCCHHHHhccCCCCCC
Confidence 45544332122233466777777779999888765544444
No 38
>PF03592 Terminase_2: Terminase small subunit ; InterPro: IPR005335 Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].; GO: 0006323 DNA packaging; PDB: 3ZQP_B 2CMP_A 3ZQO_C 3ZQN_B 3ZQQ_B 3ZQM_D.
Probab=28.15 E-value=1.1e+02 Score=16.56 Aligned_cols=34 Identities=12% Similarity=0.009 Sum_probs=24.0
Q ss_pred HHHHHHhcCHHHHHHHHHHHHhhccC-CCCHHHhh
Q psy4741 7 GMARELMWFAPFRQAIFECDRVYRPL-GLDIVKII 40 (62)
Q Consensus 7 gMg~~L~~~p~f~~~~~~~~~~l~~~-g~~l~~~l 40 (62)
..|..|+.+|.+++.|++.-...... .++..+++
T Consensus 34 ~~asrLL~n~~V~~~I~~~~~e~~~~~~~t~~~vl 68 (144)
T PF03592_consen 34 ANASRLLRNPKVKAYIEELMKEREERAIITADEVL 68 (144)
T ss_dssp HHHHHHTTSHHHHHHHHHHHHHHSSS-S--HHHHH
T ss_pred HHHHHHHcCCchHHHHHHHHHHHHHHHhhhHHHHH
Confidence 46788999999999999998777554 45544443
No 39
>PF02526 GBP_repeat: Glycophorin-binding protein; InterPro: IPR003681 The glycophorin-binding protein contains a tandem repeat. The repeated sequence determines the binding domain for an erythrocyte receptor binding protein of Plasmodium falciparum, the malarial parasite []. Erythrocyte invasion by the malarial merozoite is a receptor-mediated process, an obligatory step in the development of the parasite. The P. falciparum protein binds to the erythrocyte receptor glycophorin.
Probab=27.73 E-value=63 Score=13.77 Aligned_cols=18 Identities=6% Similarity=-0.018 Sum_probs=13.9
Q ss_pred Hhc-CHHHHHHHHHHHHhh
Q psy4741 12 LMW-FAPFRQAIFECDRVY 29 (62)
Q Consensus 12 L~~-~p~f~~~~~~~~~~l 29 (62)
-|. .|++|+.++-.-.+|
T Consensus 12 ~yaadpeyrkh~~v~yqil 30 (38)
T PF02526_consen 12 AYAADPEYRKHLNVLYQIL 30 (38)
T ss_pred HHhcCHHHHHHHHHHHHHH
Confidence 345 899999988777766
No 40
>PRK13237 tyrosine phenol-lyase; Provisional
Probab=26.79 E-value=67 Score=21.50 Aligned_cols=27 Identities=26% Similarity=0.358 Sum_probs=20.8
Q ss_pred chHHHH--HHHHhc-CHHHHHHHHHHHHhh
Q psy4741 3 SQWPGM--ARELMW-FAPFRQAIFECDRVY 29 (62)
Q Consensus 3 sq~~gM--g~~L~~-~p~f~~~~~~~~~~l 29 (62)
.||.+| |.+-|. +|.|.+.=+++.+++
T Consensus 62 ~q~a~~~vGDd~Yagd~s~~~LE~~vAe~l 91 (460)
T PRK13237 62 RQWAGMMIGDEAYAGSRNFYHLEETVQEYY 91 (460)
T ss_pred HHHHHHhhcchhhcCCCcHHHHHHHHHHHH
Confidence 378887 668898 998887766677776
No 41
>KOG0064|consensus
Probab=26.59 E-value=67 Score=22.55 Aligned_cols=35 Identities=26% Similarity=0.343 Sum_probs=24.7
Q ss_pred chHHHHHHHHhcCHHHHHHHHHHHHhhccCCCCHHHhhc
Q psy4741 3 SQWPGMARELMWFAPFRQAIFECDRVYRPLGLDIVKIIT 41 (62)
Q Consensus 3 sq~~gMg~~L~~~p~f~~~~~~~~~~l~~~g~~l~~~l~ 41 (62)
-|+.||++-+|.-|.| ..+|+|-.+. ..|+...++
T Consensus 618 kQR~~mARm~yHrPky-alLDEcTsAv---sidvE~~i~ 652 (728)
T KOG0064|consen 618 KQRMGMARMFYHRPKY-ALLDECTSAV---SIDVEGKIF 652 (728)
T ss_pred HHHHHHHHHHhcCcch-hhhhhhhccc---ccchHHHHH
Confidence 3788999999987766 4689998777 444444443
No 42
>cd06155 eu_AANH_C_1 A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the first of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=26.48 E-value=78 Score=16.07 Aligned_cols=26 Identities=12% Similarity=0.252 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHhhccCCCCHHHhhc
Q psy4741 16 APFRQAIFECDRVYRPLGLDIVKIIT 41 (62)
Q Consensus 16 p~f~~~~~~~~~~l~~~g~~l~~~l~ 41 (62)
.-.+..++...++|+..|.++.+++.
T Consensus 26 ~Q~~~v~~ni~~~L~~aG~~~~dVv~ 51 (101)
T cd06155 26 EQMESIFSKLREILQSNGLSLSDILY 51 (101)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHEEE
Confidence 35677888888888877888777653
No 43
>PF01042 Ribonuc_L-PSP: Endoribonuclease L-PSP; InterPro: IPR006175 This domain is found in endoribonuclease, that is active on single-stranded mRNA and inhibits protein synthesis by cleavage of mRNA []. Previously it was thought to inhibit protein synthesis initiation []. This endoribonuclease may also be involved in the regulation of purine biosynthesis []. ; PDB: 3GTZ_B 3V4D_E 1J7H_A 3R0P_D 2IG8_A 1QD9_B 3L7Q_E 3VCZ_A 3QUW_A 2EWC_K ....
Probab=26.15 E-value=61 Score=16.96 Aligned_cols=25 Identities=20% Similarity=0.363 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHhhccCCCCHHHhhc
Q psy4741 17 PFRQAIFECDRVYRPLGLDIVKIIT 41 (62)
Q Consensus 17 ~f~~~~~~~~~~l~~~g~~l~~~l~ 41 (62)
-.+..++.+..+|+..|.++.+++.
T Consensus 44 Q~~~~l~ni~~~L~~~G~~~~dvv~ 68 (121)
T PF01042_consen 44 QTRQALDNIERILAAAGASLDDVVK 68 (121)
T ss_dssp HHHHHHHHHHHHHHHTTS-GGGEEE
T ss_pred HHHHHHHhhhhhhhcCCCcceeEee
Confidence 4677888888888888877777653
No 44
>COG1850 RbcL Ribulose 1,5-bisphosphate carboxylase, large subunit [Carbohydrate transport and metabolism]
Probab=25.94 E-value=83 Score=20.94 Aligned_cols=34 Identities=35% Similarity=0.518 Sum_probs=22.4
Q ss_pred CchHHHHHHHHhc-C-----------------------HHHHHHHHHHHHhhccCCCCHHHhh
Q psy4741 2 GSQWPGMARELMW-F-----------------------APFRQAIFECDRVYRPLGLDIVKII 40 (62)
Q Consensus 2 Gsq~~gMg~~L~~-~-----------------------p~f~~~~~~~~~~l~~~g~~l~~~l 40 (62)
|.+||||.-.|++ + .++|++++.|-+ |.+|.+.-
T Consensus 353 gGihpg~~P~l~~~fG~D~viq~GGGv~gHP~G~~aGarA~RqAieA~v~-----g~~L~e~A 410 (429)
T COG1850 353 GGIHPGMMPELVRIFGKDLVIQAGGGVHGHPDGPAAGARAVRQAIEAAVE-----GIPLREYA 410 (429)
T ss_pred CCcCcccchHHHHHhCchheEecCCceecCCCCcchhHHHHHHHHHHHHh-----CCCHHHHH
Confidence 5677888777776 4 467777777665 55665543
No 45
>COG3726 AhpA Uncharacterized membrane protein affecting hemolysin expression [General function prediction only]
Probab=25.73 E-value=61 Score=19.44 Aligned_cols=38 Identities=13% Similarity=0.167 Sum_probs=22.0
Q ss_pred CCchHHHHHHHHhcCHHHHHHHHHHHHhhccC-CCCHHHhhcC
Q psy4741 1 MGSQWPGMARELMWFAPFRQAIFECDRVYRPL-GLDIVKIITS 42 (62)
Q Consensus 1 QGsq~~gMg~~L~~~p~f~~~~~~~~~~l~~~-g~~l~~~l~~ 42 (62)
||++|..||.++.+.+- +++....|... ..++..++.+
T Consensus 29 qg~~~fs~g~Q~~qa~Q----~e~L~~~Li~Q~A~s~s~ll~s 67 (214)
T COG3726 29 QGASWFSQGHQRAQANQ----LEELAQTLIRQVALSASPLLVS 67 (214)
T ss_pred HHHHHHHhhhHHHHHhH----HHHHHHHHHHHHHhhhhhHhhc
Confidence 68888888888866221 34444444333 4455555544
No 46
>PF10397 ADSL_C: Adenylosuccinate lyase C-terminus; InterPro: IPR019468 Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide (the fifth step of de novo IMP biosynthesis); the formation of adenosine monophosphate (AMP) from adenylosuccinate (the final step in the synthesis of AMP from IMP) []. This entry represents the C-terminal, seven alpha-helical, domain of adenylosuccinate lyase [].; PDB: 1YIS_A 1C3U_B 1C3C_A 3C8T_A 2PFM_B 1RE5_D 1Q5N_A 2VD6_D 2J91_B 2X75_A.
Probab=25.46 E-value=97 Score=15.15 Aligned_cols=11 Identities=27% Similarity=0.652 Sum_probs=7.2
Q ss_pred CCCHHHhhcCC
Q psy4741 33 GLDIVKIITSD 43 (62)
Q Consensus 33 g~~l~~~l~~~ 43 (62)
+.++.+.+..+
T Consensus 38 ~~~l~e~l~~d 48 (81)
T PF10397_consen 38 GRDLREVLLAD 48 (81)
T ss_dssp TS-HHHHHCTT
T ss_pred CCCHHHHHHCC
Confidence 67888888753
No 47
>PRK00182 tatB sec-independent translocase; Provisional
Probab=25.05 E-value=1.2e+02 Score=17.46 Aligned_cols=24 Identities=17% Similarity=0.236 Sum_probs=13.8
Q ss_pred HHHHHHHhc-CHHHHHHHHHHHHhh
Q psy4741 6 PGMARELMW-FAPFRQAIFECDRVY 29 (62)
Q Consensus 6 ~gMg~~L~~-~p~f~~~~~~~~~~l 29 (62)
|++++.+-. ...||+.+....+-+
T Consensus 27 P~~~r~lg~~ir~~R~~~~~~k~el 51 (160)
T PRK00182 27 PRLIEDVRAALLAARTAINNAKQQL 51 (160)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556666655 556666555555444
No 48
>PRK14986 glycogen phosphorylase; Provisional
Probab=24.18 E-value=79 Score=22.82 Aligned_cols=41 Identities=15% Similarity=0.202 Sum_probs=24.0
Q ss_pred HHHHHhcCHHHHHHHHHHHHhhccCCCCHHHhhcCCCCCCc
Q psy4741 8 MARELMWFAPFRQAIFECDRVYRPLGLDIVKIITSDDPTTF 48 (62)
Q Consensus 8 Mg~~L~~~p~f~~~~~~~~~~l~~~g~~l~~~l~~~~~~~~ 48 (62)
||+.|-.+-.=-...+.+.++|...|+++.++....++..+
T Consensus 81 ~Gr~l~nnl~nlg~~~~~~~al~~lg~~l~~l~~~E~Da~L 121 (815)
T PRK14986 81 IGRTLSNALLSLGIYDDVQGALEAMGLDLEELIDEENDPGL 121 (815)
T ss_pred ccHHHHHHHHhcCcHHHHHHHHHHcCCCHHHHHhcCCCCCC
Confidence 45544332122233566777777779999888765544444
No 49
>cd05838 WHSC1_related The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as plasmacytoma. WHCS1 proteins typically contain two copies of the PWWP domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=23.93 E-value=98 Score=15.84 Aligned_cols=16 Identities=25% Similarity=0.443 Sum_probs=13.3
Q ss_pred CHHHHHHHHHHHHhhc
Q psy4741 15 FAPFRQAIFECDRVYR 30 (62)
Q Consensus 15 ~p~f~~~~~~~~~~l~ 30 (62)
...|+++++++.++++
T Consensus 78 ~~~f~~AleEA~~~~~ 93 (95)
T cd05838 78 AKRFRKALEEASLAFK 93 (95)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 4789999999998773
No 50
>cd05836 N_Pac_NP60 The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the nucleus. In addition to the PWWP domain, NP60 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
Probab=23.92 E-value=85 Score=15.78 Aligned_cols=14 Identities=29% Similarity=0.226 Sum_probs=11.2
Q ss_pred CHHHHHHHHHHHHh
Q psy4741 15 FAPFRQAIFECDRV 28 (62)
Q Consensus 15 ~p~f~~~~~~~~~~ 28 (62)
.+.|++++++++..
T Consensus 72 ~~~F~~Av~~ie~~ 85 (86)
T cd05836 72 GARFQQAVDAIEEY 85 (86)
T ss_pred hHHHHHHHHHHHHh
Confidence 57799999988765
No 51
>PF03514 GRAS: GRAS domain family; InterPro: IPR005202 Sequence analysis of the products of the GRAS (GAI, RGA, SCR) gene family indicates that they share a variable N terminus and a highly conserved C terminus that contains five recognizable motifs []. Proteins in the GRAS family are transcription factors that seem to be involved in development and other processes. Mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. The PAT1 protein is involved in phytochrome A signal transduction []. GRAS proteins contain a conserved region of about 350 amino acids that can be divided in 5 motifs, found in the following order: leucine heptad repeat I, the VHIID motif, leucine heptad repeat II, the PFYRE motif and the SAW motif [, ]. Plant specific GRAS proteins have parallels in their motif structure to the animal Signal Transducers and Activators of Transcription (STAT) family of proteins [] which suggests also some parallels in their functions.
Probab=23.87 E-value=54 Score=20.99 Aligned_cols=14 Identities=36% Similarity=0.847 Sum_probs=10.9
Q ss_pred CCchHHHHHHHHhc
Q psy4741 1 MGSQWPGMARELMW 14 (62)
Q Consensus 1 QGsq~~gMg~~L~~ 14 (62)
+|.|||.+.+.|-.
T Consensus 121 ~G~QW~~LiqaLa~ 134 (374)
T PF03514_consen 121 FGVQWPSLIQALAS 134 (374)
T ss_pred cchHHHHHHHHHhc
Confidence 57888888888765
No 52
>PF09772 Tmem26: Transmembrane protein 26; InterPro: IPR019169 The function of this family of transmembrane proteins has not, as yet, been determined.
Probab=23.83 E-value=31 Score=21.54 Aligned_cols=26 Identities=27% Similarity=0.644 Sum_probs=20.0
Q ss_pred HHHHHHHHhc-CHHHHHHHHHHHHhhc
Q psy4741 5 WPGMARELMW-FAPFRQAIFECDRVYR 30 (62)
Q Consensus 5 ~~gMg~~L~~-~p~f~~~~~~~~~~l~ 30 (62)
|.|||.|+++ +..|++.--+|+..+.
T Consensus 158 yvg~aADIlEf~e~~~e~~v~~n~~lv 184 (283)
T PF09772_consen 158 YVGTAADILEFFETFKEEEVRCNRVLV 184 (283)
T ss_pred HHHhHHHHHHHHHhcchHHhhcCceEE
Confidence 6799999999 8778876666766553
No 53
>PF02153 PDH: Prephenate dehydrogenase; InterPro: IPR003099 Members of this family are prephenate dehydrogenases 1.3.1.12 from EC involved in tyrosine biosynthesis. ; GO: 0004665 prephenate dehydrogenase (NADP+) activity, 0008977 prephenate dehydrogenase activity, 0006571 tyrosine biosynthetic process, 0055114 oxidation-reduction process; PDB: 2F1K_B 2PV7_A 3DZB_B 3KTD_B 3B1F_A 2G5C_D 3GGP_C 3GGG_C 3GGO_D.
Probab=23.50 E-value=1.2e+02 Score=18.18 Aligned_cols=38 Identities=13% Similarity=0.182 Sum_probs=23.7
Q ss_pred chHHHHHHHHhc-CHH-HHHHHHHHHHhhccCCCCHHHhhcCCC
Q psy4741 3 SQWPGMARELMW-FAP-FRQAIFECDRVYRPLGLDIVKIITSDD 44 (62)
Q Consensus 3 sq~~gMg~~L~~-~p~-f~~~~~~~~~~l~~~g~~l~~~l~~~~ 44 (62)
++-|.|-.+++. ++. ..+.+++..+.|. .+.+.|.+++
T Consensus 209 ~~~p~l~~~I~~~N~~~~~~~l~~~~~~L~----~l~~~l~~~d 248 (258)
T PF02153_consen 209 SSDPELWADIFLSNPENLLEALDEFIKELN----ELREALEAGD 248 (258)
T ss_dssp GS-HHHHHHHHHHTHHHHHHHHHHHHHHHH----HHHHHHHTTS
T ss_pred cCChHHHHHHHHHCHHHHHHHHHHHHHHHH----HHHHHHHcCC
Confidence 355778888887 776 7777777766663 3445555444
No 54
>PRK01371 sec-independent translocase; Provisional
Probab=23.38 E-value=1.2e+02 Score=16.94 Aligned_cols=28 Identities=18% Similarity=0.225 Sum_probs=19.8
Q ss_pred hHHHHHHHHhc-CHHHHHHHHHHHHhhcc
Q psy4741 4 QWPGMARELMW-FAPFRQAIFECDRVYRP 31 (62)
Q Consensus 4 q~~gMg~~L~~-~p~f~~~~~~~~~~l~~ 31 (62)
..|++++.+-+ ...||+....+.+-++.
T Consensus 24 KLP~~ar~lg~~ir~~R~~~~~ak~~i~~ 52 (137)
T PRK01371 24 KLPKAARDAGRTLRQLREMANNARNDLRS 52 (137)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788888877 77788877666655544
No 55
>PRK14861 tatA twin arginine translocase protein A; Provisional
Probab=22.30 E-value=1.1e+02 Score=14.60 Aligned_cols=22 Identities=23% Similarity=0.338 Sum_probs=12.6
Q ss_pred HHHHHHHhc-CHHHHHHHHHHHH
Q psy4741 6 PGMARELMW-FAPFRQAIFECDR 27 (62)
Q Consensus 6 ~gMg~~L~~-~p~f~~~~~~~~~ 27 (62)
|.+++.+=+ ...||+.+....+
T Consensus 27 P~l~r~~G~~~~~fk~~~~~~~~ 49 (61)
T PRK14861 27 PELGKALGKTLREFKKATKELTD 49 (61)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 556666655 5566665555443
No 56
>KOG1369|consensus
Probab=22.29 E-value=40 Score=22.67 Aligned_cols=21 Identities=29% Similarity=0.308 Sum_probs=17.6
Q ss_pred HHHHHHhc-CHHHHHHHHHHHH
Q psy4741 7 GMARELMW-FAPFRQAIFECDR 27 (62)
Q Consensus 7 gMg~~L~~-~p~f~~~~~~~~~ 27 (62)
||.-.||+ +|.|++.+.+.-.
T Consensus 417 gvdGsly~~yP~f~~~m~~~l~ 438 (474)
T KOG1369|consen 417 GVDGSLYKNHPFFREYLKEALR 438 (474)
T ss_pred EeccchhHcCchHHHHHHHHHH
Confidence 56678999 9999999887765
No 57
>PRK15279 type III secretion protein SopE; Provisional
Probab=21.62 E-value=2e+02 Score=17.31 Aligned_cols=39 Identities=18% Similarity=0.239 Sum_probs=26.1
Q ss_pred CchHHHHHHHHhc---CHHHHHHHHHHHHhhccCCCCHHHhh
Q psy4741 2 GSQWPGMARELMW---FAPFRQAIFECDRVYRPLGLDIVKII 40 (62)
Q Consensus 2 Gsq~~gMg~~L~~---~p~f~~~~~~~~~~l~~~g~~l~~~l 40 (62)
|++-|.-+++-++ ..+|-+.-++|...+...|.++...|
T Consensus 100 askDp~yarQt~EA~lsavyS~~Kd~~c~ll~skg~~i~pfL 141 (240)
T PRK15279 100 ASKDPAYASQTREAILSAVYSKNKDQCCNLLISKGINIAPFL 141 (240)
T ss_pred cccChHHHHHHHHHHHHHHHHHhHHHHHHHHHhcCCCchHHH
Confidence 4555566666665 56777888888888776666665544
No 58
>PF00210 Ferritin: Ferritin-like domain; InterPro: IPR008331 Ferritin is one of the major non-haem iron storage proteins in animals, plants, and microorganisms []. It consists of a mineral core of hydrated ferric oxide, and a multi-subunit protein shell that encloses the former and assures its solubility in an aqueous environment. In animals the protein is mainly cytoplasmic and there are generally two or more genes that encode closely related subunits - in mammals there are two subunits which are known as H(eavy) and L(ight). In plants ferritin is found in the chloroplast []. This entry represents the main structural domain of ferritin. The domain is also found in other ferritin-like proteins such as members of the DNA protection during starvation (DPS) family and bacterioferritins.; GO: 0008199 ferric iron binding, 0006879 cellular iron ion homeostasis; PDB: 1N1Q_C 4DYU_E 2YJJ_D 2YJK_B 2VXX_B 3FVB_A 2WLU_A 2XGW_A 2WLA_A 1Z4A_D ....
Probab=21.41 E-value=1.4e+02 Score=15.37 Aligned_cols=31 Identities=23% Similarity=0.193 Sum_probs=22.1
Q ss_pred CchHHHHHHHHhc-CHHHHHHHHHHHHhhccC
Q psy4741 2 GSQWPGMARELMW-FAPFRQAIFECDRVYRPL 32 (62)
Q Consensus 2 Gsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~ 32 (62)
|..++|+.+-+.+ ...-++..+.+.+.+...
T Consensus 27 ~~~~~~l~~~~~~~a~e~~~h~~~l~e~i~~l 58 (142)
T PF00210_consen 27 GPNFPGLAKFFQDQAEEEREHADELAERILML 58 (142)
T ss_dssp STTHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCCchhhHHHhHHHHHHHHHHHHHHHHHHhcC
Confidence 5567788777766 666667777777777666
No 59
>TIGR01037 pyrD_sub1_fam dihydroorotate dehydrogenase (subfamily 1) family protein. This family includes subfamily 1 dihydroorotate dehydrogenases while excluding the closely related subfamily 2 (TIGR01036). This family also includes a number of uncharacterized proteins and a domain of dihydropyrimidine dehydrogenase. The uncharacterized proteins might all be dihydroorotate dehydrogenase.
Probab=21.35 E-value=1.2e+02 Score=18.54 Aligned_cols=34 Identities=12% Similarity=0.145 Sum_probs=25.3
Q ss_pred CchHHHHHHHHhc-CHHHHHHHHHHHHhhccCCCC
Q psy4741 2 GSQWPGMARELMW-FAPFRQAIFECDRVYRPLGLD 35 (62)
Q Consensus 2 Gsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~g~~ 35 (62)
|+--..+|+.++. -..|++..++..+.+...|++
T Consensus 256 GAd~V~igr~~l~~p~~~~~i~~~l~~~~~~~g~~ 290 (300)
T TIGR01037 256 GASAVQVGTAVYYRGFAFKKIIEGLIAFLKAEGFT 290 (300)
T ss_pred CCCceeecHHHhcCchHHHHHHHHHHHHHHHcCCC
Confidence 4444568888887 667888888888888777764
No 60
>PF07487 SopE_GEF: SopE GEF domain; InterPro: IPR016019 The type III secretion system of Gram-negative bacteria is used to transport virulence factors from the pathogen directly into the host cell [] and is only triggered when the bacterium comes into close contact with the host. Effector proteins secreted by the type III system do not possess a secretion signal, and are considered unique because of this. Salmonella spp. secrete an effector protein called SopE that is responsible for stimulating the reorganisation of the host cell actin cytoskeleton, and ruffling of the cellular membrane []. It acts as a guanyl-nucleotide-exchange factor on Rho-GTPase proteins such as Cdc42 and Rac. As it is imperative for the bacterium to revert the cell back to its "normal" state as quickly as possible, another tyrosine phosphatase effector called SptP reverses the actions brought about by SopE []. Recently, it has been found that SopE and its protein homologue SopE2 can activate different sets of Rho-GTPases in the host cell []. Far from being a redundant set of two similar type III effectors, they both act in unison to specifically activate different Rho-GTPase signalling cascades in the host cell during infection. This entry represents the guanine nucleotide exchange factor domain of SopE. This domain has an alpha-helical structure consisting of two three-helix bundles arranged in a lamdba shape [, ].; GO: 0005085 guanyl-nucleotide exchange factor activity, 0009405 pathogenesis, 0031532 actin cytoskeleton reorganization, 0032862 activation of Rho GTPase activity, 0005576 extracellular region; PDB: 1GZS_B 1R9K_A 1R6E_A 2JOL_A 2JOK_A.
Probab=21.24 E-value=1.5e+02 Score=17.06 Aligned_cols=38 Identities=16% Similarity=0.105 Sum_probs=24.9
Q ss_pred chHHHHHHHHhc---CHHHHHHHHHHHHhhccCCCCHHHhh
Q psy4741 3 SQWPGMARELMW---FAPFRQAIFECDRVYRPLGLDIVKII 40 (62)
Q Consensus 3 sq~~gMg~~L~~---~p~f~~~~~~~~~~l~~~g~~l~~~l 40 (62)
++-+.-++++++ ..+|.+..++|...+...|.++...+
T Consensus 26 ~~D~~y~rQ~~EA~LsavYS~~kd~fc~~l~~~g~ni~pFL 66 (165)
T PF07487_consen 26 SKDPAYRRQTCEATLSAVYSENKDRFCKLLISKGENIQPFL 66 (165)
T ss_dssp HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSHHHH
T ss_pred ccChHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccHHH
Confidence 344556667766 57788888888888755555544433
No 61
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=21.23 E-value=1.2e+02 Score=14.73 Aligned_cols=17 Identities=6% Similarity=0.157 Sum_probs=6.3
Q ss_pred HHHHHhhccCCCCHHHh
Q psy4741 23 FECDRVYRPLGLDIVKI 39 (62)
Q Consensus 23 ~~~~~~l~~~g~~l~~~ 39 (62)
++..+.++..|+.+.++
T Consensus 49 ~~i~~~~~~~~y~~~~L 65 (76)
T PF07624_consen 49 DRIVEAFKANGYRLRDL 65 (76)
T ss_pred HHHHHHHHHcCCCHHHH
Confidence 33333333334444433
No 62
>TIGR03610 RutC pyrimidine utilization protein C. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the endoribonuclease L-PSP family defined by pfam01042.
Probab=20.90 E-value=1.1e+02 Score=16.35 Aligned_cols=25 Identities=12% Similarity=0.085 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHhhccCCCCHHHhhc
Q psy4741 17 PFRQAIFECDRVYRPLGLDIVKIIT 41 (62)
Q Consensus 17 ~f~~~~~~~~~~l~~~g~~l~~~l~ 41 (62)
-.+..++....+|+..|.++.+++.
T Consensus 51 Q~~~~l~ni~~iL~~aG~~~~dvv~ 75 (127)
T TIGR03610 51 QTRHVLETIKSVIETAGGTMDDVTF 75 (127)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHEEE
Confidence 4677888888888877888777654
No 63
>TIGR02093 P_ylase glycogen/starch/alpha-glucan phosphorylases. This family consists of phosphorylases. Members use phosphate to break alpha 1,4 linkages between pairs of glucose residues at the end of long glucose polymers, releasing alpha-D-glucose 1-phosphate. The nomenclature convention is to preface the name according to the natural substrate, as in glycogen phosphorylase, starch phosphorylase, maltodextrin phosphorylase, etc. Name differences among these substrates reflect differences in patterns of branching with alpha 1,6 linkages. Members include allosterically regulated and unregulated forms. A related family, TIGR02094, contains examples known to act well on particularly small alpha 1,4 glucans, as may be found after import from exogenous sources.
Probab=20.77 E-value=85 Score=22.62 Aligned_cols=28 Identities=25% Similarity=0.411 Sum_probs=19.1
Q ss_pred HHHHHHHhhccCCCCHHHhhcCCCCCCc
Q psy4741 21 AIFECDRVYRPLGLDIVKIITSDDPTTF 48 (62)
Q Consensus 21 ~~~~~~~~l~~~g~~l~~~l~~~~~~~~ 48 (62)
..+.+.++|+..|+++.++..-.+++.+
T Consensus 74 l~~~~~~~l~~lg~~l~~i~~~E~Da~L 101 (794)
T TIGR02093 74 LYDEVKEALRELGLDLEEILEIENDAGL 101 (794)
T ss_pred CHHHHHHHHHHhCCCHHHHHhcCCCCCC
Confidence 3466777777779999888765544444
No 64
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=20.56 E-value=95 Score=15.49 Aligned_cols=22 Identities=18% Similarity=0.291 Sum_probs=14.5
Q ss_pred CHHHHHHH-HHHHHhhccCCCCH
Q psy4741 15 FAPFRQAI-FECDRVYRPLGLDI 36 (62)
Q Consensus 15 ~p~f~~~~-~~~~~~l~~~g~~l 36 (62)
.|.||+.+ .....+|..+|+++
T Consensus 16 Dp~Fr~~Ll~DPraaL~e~G~~~ 38 (77)
T TIGR03793 16 DEAFKQALLTNPKEALEREGVQV 38 (77)
T ss_pred CHHHHHHHHHCHHHHHHHhCCCC
Confidence 79999865 55555665556654
No 65
>cd03397 PAP2_acid_phosphatase PAP2, bacterial acid phosphatase or class A non-specific acid phosphatases. These enzymes catalyze phosphomonoester hydrolysis, with optimal activity in low pH conditions. They are secreted into the periplasmic space, and their physiological role remains to be determined.
Probab=20.50 E-value=2.1e+02 Score=17.08 Aligned_cols=20 Identities=10% Similarity=0.049 Sum_probs=15.2
Q ss_pred HHHhcCHHHHHHHHHHHHhh
Q psy4741 10 RELMWFAPFRQAIFECDRVY 29 (62)
Q Consensus 10 ~~L~~~p~f~~~~~~~~~~l 29 (62)
..++.+|.|++.++++...+
T Consensus 212 a~l~~~~~f~~~~~~A~~El 231 (232)
T cd03397 212 AALLADPAFAADLAAARAEL 231 (232)
T ss_pred HHHhcCHHHHHHHHHHHHHh
Confidence 34555899999999988655
No 66
>COG2155 Uncharacterized conserved protein [Function unknown]
Probab=20.49 E-value=97 Score=15.74 Aligned_cols=27 Identities=19% Similarity=0.343 Sum_probs=19.1
Q ss_pred CCCHHHhhcCCCCCCchhhHHHHHHHHh
Q psy4741 33 GLDIVKIITSDDPTTFDDILNSFVAIVT 60 (62)
Q Consensus 33 g~~l~~~l~~~~~~~~~~~~~~q~~i~~ 60 (62)
++|+...+++ ....+.+..|..+++.+
T Consensus 28 ~fdLvaalfG-~gs~lsri~YiivGlag 54 (79)
T COG2155 28 GFDLVAALFG-VGSMLTRIIYIIVGLAG 54 (79)
T ss_pred hhhHHHHHHc-CchHHHHHHHHHHHHHH
Confidence 5788888887 44556777777777654
No 67
>cd04300 GT1_Glycogen_Phosphorylase This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of oligosaccharides into glucose-1-phosphate units. They are important allosteric enzymes in carbohydrate metabolism. The allosteric control mechanisms of yeast and mammalian members of this family are different from that of bacterial members. The members of this family belong to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility.
Probab=20.26 E-value=91 Score=22.47 Aligned_cols=28 Identities=14% Similarity=0.214 Sum_probs=18.9
Q ss_pred HHHHHHHhhccCCCCHHHhhcCCCCCCc
Q psy4741 21 AIFECDRVYRPLGLDIVKIITSDDPTTF 48 (62)
Q Consensus 21 ~~~~~~~~l~~~g~~l~~~l~~~~~~~~ 48 (62)
..+++.++|+..|+++.++....+++.+
T Consensus 77 l~~~~~~~L~~lg~~l~~i~~~E~Da~L 104 (797)
T cd04300 77 LYDEVREALAELGVDLEDLEEQEPDAGL 104 (797)
T ss_pred cHHHHHHHHHHhCCCHHHHHhcCCCCCC
Confidence 3466777777779999888765444433
No 68
>PRK07259 dihydroorotate dehydrogenase 1B; Reviewed
Probab=20.04 E-value=1.1e+02 Score=18.62 Aligned_cols=38 Identities=16% Similarity=0.197 Sum_probs=27.0
Q ss_pred CchHHHHHHHHhc-CHHHHHHHHHHHHhhccCCC-CHHHh
Q psy4741 2 GSQWPGMARELMW-FAPFRQAIFECDRVYRPLGL-DIVKI 39 (62)
Q Consensus 2 Gsq~~gMg~~L~~-~p~f~~~~~~~~~~l~~~g~-~l~~~ 39 (62)
|+--..||+.++. ...+++..+...+.+...|+ ++.+.
T Consensus 256 GAd~V~igr~ll~~P~~~~~i~~~l~~~~~~~g~~~i~~~ 295 (301)
T PRK07259 256 GASAVQVGTANFYDPYAFPKIIEGLEAYLDKYGIKSIEEI 295 (301)
T ss_pred CCCceeEcHHHhcCcHHHHHHHHHHHHHHHHcCCCCHHHH
Confidence 4445678888888 66788888888888877776 34443
Done!