Query 033626
Match_columns 115
No_of_seqs 34 out of 36
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 04:26:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033626.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033626hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10280 Med11: Mediator compl 99.9 7.5E-27 1.6E-31 167.9 6.0 105 7-111 2-115 (117)
2 KOG4057 Uncharacterized conser 99.8 1.7E-17 3.8E-22 128.0 12.1 106 6-112 7-115 (180)
3 cd07624 BAR_SNX7_30 The Bin/Am 78.6 16 0.00035 28.0 7.7 77 8-88 56-138 (200)
4 PF15605 Toxin_52: Putative to 75.2 30 0.00065 25.4 8.9 100 1-108 1-101 (103)
5 cd07628 BAR_Atg24p The Bin/Amp 73.0 11 0.00024 28.7 5.5 89 8-100 46-141 (185)
6 TIGR02959 SigZ RNA polymerase 72.4 5.4 0.00012 28.9 3.4 67 9-84 97-168 (170)
7 PF14712 Snapin_Pallidin: Snap 69.1 31 0.00067 22.9 7.4 79 26-110 4-89 (92)
8 PF11598 COMP: Cartilage oligo 58.3 40 0.00086 21.1 4.9 29 43-71 4-32 (45)
9 PF13412 HTH_24: Winged helix- 56.8 12 0.00025 22.0 2.3 41 13-53 1-42 (48)
10 PF04210 MtrG: Tetrahydrometha 52.6 13 0.00027 25.6 2.1 21 1-21 9-29 (70)
11 PF03623 Focal_AT: Focal adhes 49.2 1.2E+02 0.0025 23.2 7.3 49 49-99 34-82 (139)
12 PF08580 KAR9: Yeast cortical 49.2 1.7E+02 0.0038 27.2 9.5 35 81-115 112-146 (683)
13 cd07622 BAR_SNX4 The Bin/Amphi 47.4 1.3E+02 0.0029 23.4 8.2 61 9-74 57-117 (201)
14 PF07464 ApoLp-III: Apolipopho 47.2 1.3E+02 0.0028 23.0 7.7 55 16-70 1-57 (155)
15 PHA02986 hypothetical protein; 46.9 92 0.002 23.9 6.2 84 16-111 3-104 (141)
16 PF07445 priB_priC: Primosomal 43.5 1.2E+02 0.0027 23.0 6.6 58 40-109 30-87 (173)
17 PF02954 HTH_8: Bacterial regu 41.2 23 0.00051 20.7 1.8 33 13-45 2-35 (42)
18 PF04545 Sigma70_r4: Sigma-70, 40.6 26 0.00057 20.6 2.0 46 10-55 2-47 (50)
19 PF00570 HRDC: HRDC domain Blo 39.1 58 0.0013 20.0 3.5 32 25-56 37-68 (68)
20 smart00502 BBC B-Box C-termina 37.6 1.2E+02 0.0026 20.0 9.6 52 19-70 18-69 (127)
21 PRK01203 prefoldin subunit alp 37.1 32 0.0007 25.8 2.4 30 78-110 76-105 (130)
22 cd07642 BAR_ASAP2 The Bin/Amph 36.6 1.8E+02 0.004 23.6 6.8 58 7-69 15-88 (215)
23 cd07627 BAR_Vps5p The Bin/Amph 36.0 2E+02 0.0044 22.1 8.1 17 21-37 38-54 (216)
24 COG4064 MtrG Tetrahydromethano 35.6 35 0.00076 23.7 2.2 21 1-21 12-32 (75)
25 PF07889 DUF1664: Protein of u 34.0 1.9E+02 0.0042 21.4 6.1 52 9-61 66-117 (126)
26 PRK11924 RNA polymerase sigma 33.3 76 0.0016 22.1 3.7 44 8-51 121-164 (179)
27 smart00806 AIP3 Actin interact 32.9 2.2E+02 0.0047 25.5 7.2 60 50-110 172-235 (426)
28 PRK09652 RNA polymerase sigma 32.6 67 0.0015 22.4 3.4 42 9-50 125-166 (182)
29 smart00397 t_SNARE Helical reg 31.9 1.1E+02 0.0024 18.0 5.7 57 6-63 7-63 (66)
30 PF00435 Spectrin: Spectrin re 31.9 1.3E+02 0.0027 18.6 10.8 90 12-111 2-99 (105)
31 COG3165 Uncharacterized protei 31.8 2.5E+02 0.0055 22.8 6.9 79 30-111 119-198 (204)
32 smart00421 HTH_LUXR helix_turn 31.6 37 0.0008 19.1 1.6 44 12-56 3-46 (58)
33 PF06013 WXG100: Proteins of 1 31.1 1.3E+02 0.0027 18.3 8.6 63 8-70 11-74 (86)
34 cd07609 BAR_SIP3_fungi The Bin 30.0 2.8E+02 0.0062 22.0 8.3 56 12-68 9-84 (214)
35 PRK00304 hypothetical protein; 29.4 87 0.0019 21.6 3.4 36 62-103 12-47 (75)
36 PF12994 DUF3878: Domain of un 29.3 2.8E+02 0.0062 23.7 7.1 62 27-90 171-247 (299)
37 KOG1401 Acetylornithine aminot 29.1 1.1E+02 0.0025 27.3 4.8 45 24-81 315-359 (433)
38 smart00344 HTH_ASNC helix_turn 28.7 52 0.0011 21.9 2.2 42 13-54 1-43 (108)
39 cd06171 Sigma70_r4 Sigma70, re 28.3 47 0.001 18.1 1.6 43 9-51 7-49 (55)
40 TIGR02449 conserved hypothetic 27.9 59 0.0013 21.8 2.3 20 86-105 43-62 (65)
41 TIGR02948 SigW_bacill RNA poly 27.9 55 0.0012 23.3 2.3 51 8-58 132-182 (187)
42 PF09325 Vps5: Vps5 C terminal 27.4 2.4E+02 0.0052 21.1 5.8 27 11-37 48-74 (236)
43 COG1344 FlgL Flagellin and rel 27.4 2.2E+02 0.0047 23.7 6.0 66 8-74 57-128 (360)
44 PF01519 DUF16: Protein of unk 27.3 2.5E+02 0.0054 20.5 7.6 21 91-111 80-100 (102)
45 PF02828 L27: L27 domain; Int 27.3 1.6E+02 0.0034 18.1 4.6 45 23-67 1-49 (56)
46 TIGR01149 mtrG N5-methyltetrah 26.9 60 0.0013 22.3 2.2 20 2-21 10-29 (70)
47 KOG4403 Cell surface glycoprot 26.8 2.3E+02 0.0049 26.1 6.4 46 29-74 379-430 (575)
48 PRK01026 tetrahydromethanopter 26.0 62 0.0013 22.6 2.2 20 2-21 13-32 (77)
49 PF03915 AIP3: Actin interacti 26.0 1.2E+02 0.0027 26.7 4.5 61 50-111 168-232 (424)
50 TIGR02937 sigma70-ECF RNA poly 25.9 84 0.0018 20.5 2.8 49 9-57 107-155 (158)
51 PF14476 Chloroplast_duf: Peta 25.9 3.5E+02 0.0075 23.4 7.0 42 22-63 63-106 (313)
52 PF10455 BAR_2: Bin/amphiphysi 25.8 4E+02 0.0087 22.4 8.0 50 11-60 229-281 (289)
53 KOG2196 Nuclear porin [Nuclear 25.0 1.4E+02 0.0031 25.0 4.5 64 45-112 87-154 (254)
54 PRK09641 RNA polymerase sigma 24.7 96 0.0021 22.0 3.1 49 9-57 133-181 (187)
55 TIGR02984 Sig-70_plancto1 RNA 24.0 90 0.0019 22.2 2.8 48 10-57 138-185 (189)
56 TIGR02952 Sig70_famx2 RNA poly 23.4 1.1E+02 0.0024 21.3 3.1 49 9-57 119-167 (170)
57 PRK10093 primosomal replicatio 23.2 1.6E+02 0.0034 23.2 4.2 70 13-83 3-72 (171)
58 KOG4127 Renal dipeptidase [Pos 23.0 1.1E+02 0.0023 27.3 3.6 43 31-77 363-405 (419)
59 PRK12543 RNA polymerase sigma 23.0 2.4E+02 0.0052 20.2 5.0 60 9-68 114-173 (179)
60 PF11593 Med3: Mediator comple 22.8 4.3E+02 0.0092 23.4 7.1 61 41-110 23-83 (379)
61 KOG2631 Class II aldolase/addu 22.7 56 0.0012 27.1 1.7 15 101-115 170-184 (238)
62 PF14643 DUF4455: Domain of un 22.6 5.2E+02 0.011 22.5 12.0 74 31-115 192-265 (473)
63 PF08700 Vps51: Vps51/Vps67; 22.5 2.2E+02 0.0048 18.2 6.6 46 6-61 17-62 (87)
64 PRK04966 hypothetical protein; 22.2 1.4E+02 0.0031 20.4 3.3 35 62-102 12-47 (72)
65 PF04439 Adenyl_transf: Strept 21.8 3.5E+02 0.0075 22.2 6.2 25 39-63 146-170 (282)
66 PF02947 Flt3_lig: flt3 ligand 21.7 81 0.0018 24.1 2.3 45 63-110 75-121 (135)
67 PF15205 PLAC9: Placenta-speci 21.6 1.7E+02 0.0038 20.2 3.7 21 9-29 23-43 (74)
68 PF13805 Pil1: Eisosome compon 21.5 4.9E+02 0.011 21.8 7.3 66 6-74 55-127 (271)
69 COG1671 Uncharacterized protei 21.2 1.6E+02 0.0034 22.8 3.8 63 24-87 75-137 (150)
70 smart00550 Zalpha Z-DNA-bindin 20.8 80 0.0017 20.2 1.8 36 14-49 5-43 (68)
71 KOG3156 Uncharacterized membra 20.7 4.8E+02 0.011 21.5 8.8 94 13-109 79-203 (220)
72 PF10224 DUF2205: Predicted co 20.6 3E+02 0.0065 19.0 5.7 37 1-37 1-38 (80)
73 KOG3366 Mitochondrial F1F0-ATP 20.6 2.8E+02 0.006 22.0 5.1 39 41-80 95-134 (172)
74 PRK12512 RNA polymerase sigma 20.6 1.6E+02 0.0034 21.1 3.6 48 9-56 128-175 (184)
75 PRK13919 putative RNA polymera 20.3 1.4E+02 0.003 21.4 3.2 49 8-56 131-179 (186)
76 PRK10929 putative mechanosensi 20.2 4.8E+02 0.01 26.0 7.6 88 17-113 43-130 (1109)
No 1
>PF10280 Med11: Mediator complex protein ; InterPro: IPR019404 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med11 of the Mediator complex []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 3R84_S 3RJ1_O.
Probab=99.93 E-value=7.5e-27 Score=167.89 Aligned_cols=105 Identities=30% Similarity=0.471 Sum_probs=78.5
Q ss_pred hhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCC------CHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc---CCCC
Q 033626 7 TTSLQRLQNVEKRVVRVLELAGGVMDELANPMGP------RKEIINNHCREFMQLIKDIQVTLRDEIKSACEY---RPFE 77 (115)
Q Consensus 7 ~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gp------r~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~ey---rPfe 77 (115)
.++|++|++||++||.+|++||+||.+|+++.+| ++++|..||++|+..+++|+++|+.||+++++| +||+
T Consensus 2 ~eRL~~L~~Idk~I~~lL~~A~~ai~~Ls~~~~~~~~~~~~k~~f~~~~~~f~~~L~~V~~~Lr~qI~~L~e~~~~~~~~ 81 (117)
T PF10280_consen 2 AERLQQLNEIDKKIVSLLQHAGQAIQELSNPKSPDQDPESSKEAFESATSEFFSTLSSVEVELRRQIKYLEEVSIIQPHE 81 (117)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT---TGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCBTT----
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccc
Confidence 4799999999999999999999999999999777 899999999999999999999999999999999 9999
Q ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033626 78 KCDYSTRILNEICCKKLEYVLSQLDAMKQTIDEC 111 (115)
Q Consensus 78 ~s~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i~~~ 111 (115)
+|+|++.+.++++.+++.+.+++|+++-..++++
T Consensus 82 ~s~~~~l~v~~ln~~~~~~~~~~l~el~~~~~~~ 115 (117)
T PF10280_consen 82 GSSYGALDVGWLNSKKTEVGRDKLAELWATLREF 115 (117)
T ss_dssp ----TBS---------------GGGTTTHHHHHH
T ss_pred cccccccchHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999998876
No 2
>KOG4057 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.75 E-value=1.7e-17 Score=127.95 Aligned_cols=106 Identities=21% Similarity=0.359 Sum_probs=98.6
Q ss_pred hhhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh---hhccCCCCCcchh
Q 033626 6 QTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKS---ACEYRPFEKCDYS 82 (115)
Q Consensus 6 q~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s---~~eyrPfe~s~Y~ 82 (115)
=+.++++|..+||.|..+|+.||.++-||++. +......+.++..|..+|..|+.+|+++|.| ||.+.|+|+|+|+
T Consensus 7 ~~dri~Al~~iEkeI~~~mq~Ag~iiqeLgKE-K~~~kn~e~qa~~F~ksit~VE~eLSaQi~YLtqV~tGqpHeGS~y~ 85 (180)
T KOG4057|consen 7 LTDRIQALVTIEKEIDEMMQCAGEIIQELGKE-KQIGKNMEDQANNFKKSITQVENELSAQIQYLTQVCTGQPHEGSTYG 85 (180)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH-hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchH
Confidence 36899999999999999999999999999999 6666669999999999999999999999999 6999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033626 83 TRILNEICCKKLEYVLSQLDAMKQTIDECN 112 (115)
Q Consensus 83 ~r~~~Ei~~~k~e~v~~qL~~l~~~i~~~~ 112 (115)
.++++.++.+++.+.++.|-.+-++++--.
T Consensus 86 s~k~~qmA~~r~~~ars~l~~i~rt~~~~s 115 (180)
T KOG4057|consen 86 SLKNSQMAQSRLSSARSELFQIVRTLDPTS 115 (180)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 999999999999999999999988876433
No 3
>cd07624 BAR_SNX7_30 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 7 and 30. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX7, SNX30, and similar proteins. The specific functions of SNX7 and SNX30 have not been elucidated. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=78.58 E-value=16 Score=28.01 Aligned_cols=77 Identities=14% Similarity=0.218 Sum_probs=46.1
Q ss_pred hhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC-----CCC-cch
Q 033626 8 TSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRP-----FEK-CDY 81 (115)
Q Consensus 8 ~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrP-----fe~-s~Y 81 (115)
.+++.|-+.|..+...|+..|.+++.++.. ..+..+.....|...+||... +.+-||.+..+|- |+. ++|
T Consensus 56 ~~~~~ls~~E~~L~~~L~~~~~~~~~~~~~---~~~l~~~~~~~f~e~Lkey~~-y~~svk~~l~~R~~~q~~~e~~~e~ 131 (200)
T cd07624 56 PIFQLWSASETELAPLLEGVSSAVERCTAA---LEVLLSDHEFVFLPPLREYLL-YSDAVKDVLKRRDQFQIEYELSVEE 131 (200)
T ss_pred HHHHHHHhcchhHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHhhHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677788888888888888888877765 334444444556666666544 4444554444332 333 555
Q ss_pred hhHHHHH
Q 033626 82 STRILNE 88 (115)
Q Consensus 82 ~~r~~~E 88 (115)
..++..+
T Consensus 132 L~~k~~~ 138 (200)
T cd07624 132 LNKKRLE 138 (200)
T ss_pred HHHHHHH
Confidence 5555554
No 4
>PF15605 Toxin_52: Putative toxin 52
Probab=75.23 E-value=30 Score=25.37 Aligned_cols=100 Identities=19% Similarity=0.230 Sum_probs=56.2
Q ss_pred CCchhhhhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCc
Q 033626 1 MDSQSQTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKE-IINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKC 79 (115)
Q Consensus 1 m~~~~q~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~-~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s 79 (115)
|.+++|.+++.+++|+=+.=....-+-|+-=|-=++++ |.++ .-=.| ++-|.+-+.+|++.++.+=--.+=+.-
T Consensus 1 ~L~~~q~~~i~k~dn~I~~hltd~D~sgt~Rdl~G~pV-pKp~GgywdH----lqEm~da~~GL~n~~~~le~~L~np~l 75 (103)
T PF15605_consen 1 GLSQAQRSAINKIDNIINSHLTDMDFSGTLRDLQGNPV-PKPDGGYWDH----LQEMQDAYRGLVNRKRTLEGSLKNPNL 75 (103)
T ss_pred CCCHHHHHHHHHHHHHHHhhccccchHHHHHHHcCCcc-cCCCCCccHH----HHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 57899999999998873332334444555444445554 4442 22233 344666677888888876433444443
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033626 80 DYSTRILNEICCKKLEYVLSQLDAMKQTI 108 (115)
Q Consensus 80 ~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i 108 (115)
+=.. .+...+|+.=+..+|+....++
T Consensus 76 ~~~~---r~~lq~~l~ea~~~l~kiE~~~ 101 (103)
T PF15605_consen 76 SGRT---RELLQSKLNEANNYLDKIEDFF 101 (103)
T ss_pred chHH---HHHHHHHHHHHHHHHHHHHHHh
Confidence 3333 3444555555555555554444
No 5
>cd07628 BAR_Atg24p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Atg24p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Atg24p is involved in membrane fusion events at the vacuolar surface during pexophagy. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=72.96 E-value=11 Score=28.72 Aligned_cols=89 Identities=12% Similarity=0.172 Sum_probs=48.3
Q ss_pred hhhHHHHHHHHH-HHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCC------Ccc
Q 033626 8 TSLQRLQNVEKR-VVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFE------KCD 80 (115)
Q Consensus 8 ~sLqrL~~VEkk-IV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe------~s~ 80 (115)
.+++.|.+.|.. +...|+-.|..|+.+|... .+.....-..|...+||-.. ...-++.+..+|-=- -++
T Consensus 46 ~~~~~L~~~E~~~L~~~l~~~~~~~~~~s~~~---~~l~~~~~~~f~~~Lkd~~~-y~~s~k~~lk~R~~kq~d~e~l~e 121 (185)
T cd07628 46 TQFQKLGSLESGEITEPFKIFSESLSQFSTSL---RVLNKYTDENYLTSLKDLLH-YILSLKNLIKLRDQKQLDYEELSD 121 (185)
T ss_pred HHHHHHHhhCchhhhHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhHHHHHH
Confidence 456777777877 8888888888888877652 22223333456666666544 333333333332111 123
Q ss_pred hhhHHHHHHHHHHHHHHHHH
Q 033626 81 YSTRILNEICCKKLEYVLSQ 100 (115)
Q Consensus 81 Y~~r~~~Ei~~~k~e~v~~q 100 (115)
|.-..+.|-|.++.+.+-..
T Consensus 122 ~ll~~~ve~a~~~~e~f~~~ 141 (185)
T cd07628 122 YLLTDEVENAKETSDAFNKE 141 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33555556566555544433
No 6
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=72.41 E-value=5.4 Score=28.89 Aligned_cols=67 Identities=18% Similarity=0.405 Sum_probs=45.3
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC-----CCCCcchhh
Q 033626 9 SLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYR-----PFEKCDYST 83 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyr-----Pfe~s~Y~~ 83 (115)
.|..|..-++.|+..--+=|-.++|+|...|-+...|.++ +.-+...|+..++..|+|. |+ |+|.+
T Consensus 97 ~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~-------l~Rar~~Lr~~l~~~~~~~~~~~~~~--~~~~~ 167 (170)
T TIGR02959 97 MIKELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSR-------VQRGRKKLKELLETCCHFEFDRVGNL--IDYEP 167 (170)
T ss_pred HHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHH-------HHHHHHHHHHHHHHhCCeeecCCCCe--ecCCC
Confidence 3556666677777666678888888888888777766654 3445556666777666665 33 66665
Q ss_pred H
Q 033626 84 R 84 (115)
Q Consensus 84 r 84 (115)
+
T Consensus 168 ~ 168 (170)
T TIGR02959 168 K 168 (170)
T ss_pred C
Confidence 4
No 7
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=69.15 E-value=31 Score=22.94 Aligned_cols=79 Identities=18% Similarity=0.303 Sum_probs=44.8
Q ss_pred HhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh-------hhccCCCCCcchhhHHHHHHHHHHHHHHH
Q 033626 26 LAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKS-------ACEYRPFEKCDYSTRILNEICCKKLEYVL 98 (115)
Q Consensus 26 ~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s-------~~eyrPfe~s~Y~~r~~~Ei~~~k~e~v~ 98 (115)
+|.|.+..|.|+ -+.++.+-.+-.+.=.++...+..+... -..+-||+...|..+..+ +-+++..+.
T Consensus 4 La~Gl~~~l~P~----l~~~~~~l~el~~sQ~~L~~~i~~~~~~L~~~~~~~~~~~~~~~~~y~~KL~~--ikkrm~~l~ 77 (92)
T PF14712_consen 4 LAEGLLSLLEPD----LDRLDQQLQELRQSQEELLQQIDRLNEKLKELNEVEQINEPFDLDPYVKKLVN--IKKRMSNLH 77 (92)
T ss_pred HHHHHHHHHhhh----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHH--HHHHHHHHH
Confidence 455566665544 4455544444433322222222222222 233447877778888776 567788888
Q ss_pred HHHHHHHHHHHh
Q 033626 99 SQLDAMKQTIDE 110 (115)
Q Consensus 99 ~qL~~l~~~i~~ 110 (115)
..++.++..+.+
T Consensus 78 ~~l~~lk~R~~~ 89 (92)
T PF14712_consen 78 ERLQKLKKRADK 89 (92)
T ss_pred HHHHHHHHHHHh
Confidence 888888877764
No 8
>PF11598 COMP: Cartilage oligomeric matrix protein; InterPro: IPR024665 Thrombospondins are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. Cartilage oligomeric matrix protein may play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as collagen and fibronectin [, ]. Thrombospondin 3 and 4 and cartilage oligomeric matrix proteins contain a five-stranded coiled-coil domain represented by this entry. This domain has a binding site between two internal rings formed by Leu37 and Thr40 [].; PDB: 1MZ9_D 1FBM_A 1VDF_E.
Probab=58.33 E-value=40 Score=21.14 Aligned_cols=29 Identities=21% Similarity=0.377 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 033626 43 EIINNHCREFMQLIKDIQVTLRDEIKSAC 71 (115)
Q Consensus 43 ~~v~~~c~eFm~~vKeI~~~L~~~I~s~~ 71 (115)
..+..+-.+|.+++++++..|+.+|+-++
T Consensus 4 ~~l~~ql~~l~~~l~elk~~l~~Q~kE~~ 32 (45)
T PF11598_consen 4 SQLIKQLSELNQMLQELKELLRQQIKETR 32 (45)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567788999999999999999998753
No 9
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=56.84 E-value=12 Score=21.97 Aligned_cols=41 Identities=17% Similarity=0.313 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHhH-HHHHhhcCCCCCCHHHHHHHHHHHH
Q 033626 13 LQNVEKRVVRVLELAG-GVMDELANPMGPRKEIINNHCREFM 53 (115)
Q Consensus 13 L~~VEkkIV~~le~Ag-~vMeELs~~~gpr~~~v~~~c~eFm 53 (115)
|++.+++|+..|..-+ ....+||...|-+...|+.+.+++.
T Consensus 1 l~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 1 LDETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLE 42 (48)
T ss_dssp --HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 5788899999888754 7788999888888888888777654
No 10
>PF04210 MtrG: Tetrahydromethanopterin S-methyltransferase, subunit G ; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=52.63 E-value=13 Score=25.64 Aligned_cols=21 Identities=24% Similarity=0.493 Sum_probs=17.9
Q ss_pred CCchhhhhhhHHHHHHHHHHH
Q 033626 1 MDSQSQTTSLQRLQNVEKRVV 21 (115)
Q Consensus 1 m~~~~q~~sLqrL~~VEkkIV 21 (115)
++|...+.-..||+.+|+||=
T Consensus 9 v~~~~~~~i~~rLd~iEeKvE 29 (70)
T PF04210_consen 9 VDPDDFNEIMKRLDEIEEKVE 29 (70)
T ss_pred eCHHHHHHHHHHHHHHHHHHH
Confidence 467778889999999999974
No 11
>PF03623 Focal_AT: Focal adhesion targeting region; InterPro: IPR005189 Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signalling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal "focal adhesion targeting" (FAT) region is necessary and sufficient for localizing FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin []. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.; GO: 0004713 protein tyrosine kinase activity, 0004871 signal transducer activity, 0006468 protein phosphorylation, 0007172 signal complex assembly, 0005925 focal adhesion; PDB: 1K05_C 1OW8_C 1OW7_C 3S9O_C 3B71_B 1K04_A 1OW6_C 3GM1_B 3GM3_A 3GM2_A ....
Probab=49.23 E-value=1.2e+02 Score=23.17 Aligned_cols=49 Identities=24% Similarity=0.305 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhccCCCCCcchhhHHHHHHHHHHHHHHHH
Q 033626 49 CREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLS 99 (115)
Q Consensus 49 c~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~~~k~e~v~~ 99 (115)
..+|..+||.|=..|++-+.++-+..|+=.++. +.+.|++++=+.-=+.
T Consensus 34 ~~~y~~~VK~VG~~Lr~Ll~sVd~~~~~l~~s~--~~EVema~klL~~DM~ 82 (139)
T PF03623_consen 34 PEEYVDLVKNVGLALRDLLTSVDQILPSLPSSV--RREVEMAHKLLSKDMA 82 (139)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHGGGSHTTS--HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhccCCHHH--HHHHHHHHHHHHHHHH
Confidence 567999999999999999999988888766665 6666777654443333
No 12
>PF08580 KAR9: Yeast cortical protein KAR9; InterPro: IPR013889 The KAR9 protein in Saccharomyces cerevisiae (Baker's yeast) is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules []. KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase [].
Probab=49.15 E-value=1.7e+02 Score=27.18 Aligned_cols=35 Identities=23% Similarity=0.216 Sum_probs=29.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 033626 81 YSTRILNEICCKKLEYVLSQLDAMKQTIDECNDTC 115 (115)
Q Consensus 81 Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i~~~~~~~ 115 (115)
.+-+.-+||+.+.-|+--..|.++..-||++...|
T Consensus 112 ~~vK~qveiAmE~~EL~~~vlg~l~~EIe~~~~~v 146 (683)
T PF08580_consen 112 ISVKKQVEIAMEWEELWNDVLGDLDNEIEECIRLV 146 (683)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677889999999999999999999999876543
No 13
>cd07622 BAR_SNX4 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 4. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX4 is involved in recycling traffic from the sorting endosome (post-Golgi endosome) back to the late Golgi. It is also implicated in the regulation of plasma membrane receptor trafficking and interacts with receptors for EGF, insulin, platelet-derived growth factor and leptin. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and
Probab=47.41 E-value=1.3e+02 Score=23.36 Aligned_cols=61 Identities=20% Similarity=0.280 Sum_probs=35.4
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC
Q 033626 9 SLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYR 74 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyr 74 (115)
.++.|-..|..+...|+-+|..+|.++.+.....+. -..|...+||--. ..+-++.++.+|
T Consensus 57 ~f~~ls~~E~~l~~~le~~g~~~d~~~~~~~~~~~~----~~~f~e~LkEy~~-ya~slk~vlk~r 117 (201)
T cd07622 57 VFSEWSAIEKEMGDGLQKAGHYMDSYAASIDNGLED----EELIADQLKEYLF-FADSLRAVCKKH 117 (201)
T ss_pred HHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHHHHh----hhhhHHHHHHHHH-HHHHHHHHHHHH
Confidence 456677778888888888888888877764432221 2335555544433 333444444433
No 14
>PF07464 ApoLp-III: Apolipophorin-III precursor (apoLp-III); InterPro: IPR010009 This family consists of several insect apolipoprotein-III sequences. Exchangeable apolipoproteins constitute a functionally important family of proteins that play critical roles in lipid transport and lipoprotein metabolism. Apolipophorin III (apoLp-III) is a prototypical exchangeable apolipoprotein found in many insect species that functions in transport of diacylglycerol (DAG) from the fat body lipid storage depot to flight muscles in the adult life stage [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0005576 extracellular region; PDB: 1EQ1_A.
Probab=47.21 E-value=1.3e+02 Score=23.02 Aligned_cols=55 Identities=15% Similarity=0.252 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHhHHHHHhhcCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033626 16 VEKRVVRVLELAGGVMDELANPMGP--RKEIINNHCREFMQLIKDIQVTLRDEIKSA 70 (115)
Q Consensus 16 VEkkIV~~le~Ag~vMeELs~~~gp--r~~~v~~~c~eFm~~vKeI~~~L~~~I~s~ 70 (115)
||+.|-.+...=+..+..|-+..+. =...+...+..|.+-|+.+...|.++|+-.
T Consensus 1 ~~~~~~e~~~~~~~~~~~~~~~~~~~Ev~~aik~~sd~~~~~l~~~~~~l~eeik~~ 57 (155)
T PF07464_consen 1 IQQHAQEFQKEFQEQVNKLLGSQNQQEVVKAIKEQSDSVAQQLQNVSSSLQEEIKDA 57 (155)
T ss_dssp HHHHHHHHHHHHHHHHHHHTSS--SS-SSHHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred CchHHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhc
Confidence 5777777887778888888766332 228899999999999999999999999863
No 15
>PHA02986 hypothetical protein; Provisional
Probab=46.90 E-value=92 Score=23.93 Aligned_cols=84 Identities=18% Similarity=0.381 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHH------H-HHHHHH-------HHHH----HHhhhccCCCC
Q 033626 16 VEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQL------I-KDIQVT-------LRDE----IKSACEYRPFE 77 (115)
Q Consensus 16 VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~------v-KeI~~~-------L~~~----I~s~~eyrPfe 77 (115)
.|..|..+|-.+-+.-.-..+.---+-+-|.+.|+||... + ++|.+- |..+ |-.+||.-.|-
T Consensus 3 ~~~ei~~ILi~~Hgt~~~~~~~nei~~k~FsNLCkefi~~~k~~~~ik~~IK~ill~iP~sm~~~~W~PIanlcD~VTY~ 82 (141)
T PHA02986 3 LEEEIINILINNHGTSYLDFNDNEISFKYFSNLCKEFISNKKKTTLIKEEIKKILLEIPDSMISQVWYPIANLCDCVTYY 82 (141)
T ss_pred hHHHHHHHHHHhcCccccccccchhhHHHHHHHHHHHHhcCCCchhHHHHHHHHHHhCChhHHHHHHHHHHhhcceeeec
Confidence 4666776665554442222222123448899999999853 3 233332 2233 22369999998
Q ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033626 78 KCDYSTRILNEICCKKLEYVLSQLDAMKQTIDEC 111 (115)
Q Consensus 78 ~s~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i~~~ 111 (115)
+|. -.+.+.+||..+....-++
T Consensus 83 nc~------------n~~Wi~~QL~~i~~~n~~~ 104 (141)
T PHA02986 83 NCS------------NEKWINDQLNDIDESLSNY 104 (141)
T ss_pred Ccc------------cHHHHHHHHHHHHHhhhhh
Confidence 875 3457778888877655543
No 16
>PF07445 priB_priC: Primosomal replication protein priB and priC; InterPro: IPR010890 This family contains the bacterial primosomal replication proteins priB and priC (approximately 180 residues long). In Escherichia coli, these function in the assembly of the primosome [].
Probab=43.53 E-value=1.2e+02 Score=23.04 Aligned_cols=58 Identities=12% Similarity=0.299 Sum_probs=43.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033626 40 PRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTID 109 (115)
Q Consensus 40 pr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i~ 109 (115)
=+...|..++..+.-.|++|+.+|..=.+...+.++ +...|. ++-+..|+.+++.-+.
T Consensus 30 Fd~~LF~~~~~~L~~yl~Ei~~~l~~L~~~~~~~~~-~~~~~l-----------aEkL~~Q~~AL~r~l~ 87 (173)
T PF07445_consen 30 FDRQLFSCRSQRLSDYLQEIEQTLAQLQQQVEQNRL-QQVAFL-----------AEKLVAQIEALQRELA 87 (173)
T ss_pred ccHHHHhccCchHHHHHHHHHHHHHHHHHHHhcChH-HHHHHH-----------HHHHHHHHHHHHHHHH
Confidence 355889999999999999999999887777777666 443433 2345677778877665
No 17
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=41.20 E-value=23 Score=20.71 Aligned_cols=33 Identities=27% Similarity=0.459 Sum_probs=22.9
Q ss_pred HHHHHH-HHHHHHHHhHHHHHhhcCCCCCCHHHH
Q 033626 13 LQNVEK-RVVRVLELAGGVMDELANPMGPRKEII 45 (115)
Q Consensus 13 L~~VEk-kIV~~le~Ag~vMeELs~~~gpr~~~v 45 (115)
|+.+|+ -|..+|+..++.+.+-|...|-+...+
T Consensus 2 l~~~E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL 35 (42)
T PF02954_consen 2 LEEFEKQLIRQALERCGGNVSKAARLLGISRRTL 35 (42)
T ss_dssp HHHHHHHHHHHHHHHTTT-HHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHH
Confidence 678999 566789988888888777777444433
No 18
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. 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. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=40.63 E-value=26 Score=20.65 Aligned_cols=46 Identities=20% Similarity=0.382 Sum_probs=35.1
Q ss_pred hHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHH
Q 033626 10 LQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQL 55 (115)
Q Consensus 10 LqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~ 55 (115)
|..|..-|+.|+...=..|-...|.|...|-+...|...-+.=+.-
T Consensus 2 l~~L~~~er~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 2 LDQLPPREREVIRLRYFEGLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp HCTS-HHHHHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hhhCCHHHHHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 5678888999998888899999999999998887777665544433
No 19
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability [].; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 3SAG_B 3SAH_B 2CPR_A 3SAF_B 3CYM_A 1WUD_A 2HBK_A 2HBJ_A 2HBM_A 2HBL_A ....
Probab=39.09 E-value=58 Score=19.99 Aligned_cols=32 Identities=19% Similarity=0.228 Sum_probs=24.7
Q ss_pred HHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHH
Q 033626 25 ELAGGVMDELANPMGPRKEIINNHCREFMQLI 56 (115)
Q Consensus 25 e~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~v 56 (115)
+..=+..++|..-.|.+...+..+..+|+++|
T Consensus 37 ~~~P~s~~~L~~i~g~~~~~~~~~g~~il~~I 68 (68)
T PF00570_consen 37 KRLPTSIEELLQIPGMGKRKVRKYGDEILEII 68 (68)
T ss_dssp HH--SSHHHHHTSTTCGHHHHHHCHHHHHHHH
T ss_pred HhCCCCHHHHHHccCCCHHHHHHHHHHHHhhC
Confidence 33345678888877899999999999999875
No 20
>smart00502 BBC B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains
Probab=37.55 E-value=1.2e+02 Score=19.96 Aligned_cols=52 Identities=10% Similarity=0.165 Sum_probs=30.4
Q ss_pred HHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033626 19 RVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSA 70 (115)
Q Consensus 19 kIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~ 70 (115)
.+...+..-...+..|-.....-...|...+......+.+-...|-++|+..
T Consensus 18 ~~~~~~~~l~~~~~~l~~~~~~~~~~I~~~f~~l~~~L~~~e~~ll~~l~~~ 69 (127)
T smart00502 18 ELEDALKQLISIIQEVEENAADVEAQIKAAFDELRNALNKRKKQLLEDLEEQ 69 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444444444444333446666777777777777777887777764
No 21
>PRK01203 prefoldin subunit alpha; Provisional
Probab=37.12 E-value=32 Score=25.78 Aligned_cols=30 Identities=17% Similarity=0.248 Sum_probs=24.8
Q ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033626 78 KCDYSTRILNEICCKKLEYVLSQLDAMKQTIDE 110 (115)
Q Consensus 78 ~s~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i~~ 110 (115)
|+.|...++.+ +|++++.+++++|+..|..
T Consensus 76 GTGy~VEK~~e---~kie~L~~~ie~Le~~i~~ 105 (130)
T PRK01203 76 GSGVYIAEERE---RTIERLKENLEDLKDSIQK 105 (130)
T ss_pred CCCeEEEecHH---HHHHHHHHHHHHHHHHHHH
Confidence 46677777877 6999999999999988874
No 22
>cd07642 BAR_ASAP2 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP2 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2) is also known as DDEF2 (Development and Differentiation Enhancing Factor 2), AMAP2, centaurin beta-3, or PAG3. ASAP2 mediates the functions of Arf GTPases vial dual mechanisms: it exhibits GTPase activating protein (GAP) activity towards class I (Arf1) and II (Arf5) Arfs; and binds class III Arfs (GTP-Arf6) stably without GAP activity. It binds paxillin and is implicated in Fcgamma receptor-mediated phagocytosis in macrophages and in cell migration. ASAP2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, i
Probab=36.64 E-value=1.8e+02 Score=23.57 Aligned_cols=58 Identities=14% Similarity=0.279 Sum_probs=34.9
Q ss_pred hhhhHHHHHHHHHHHHHHHHhHH-----------HHHhhcCC--CCCCHHHHHHHHHHHHHHHHH---HHHHHHHHHHh
Q 033626 7 TTSLQRLQNVEKRVVRVLELAGG-----------VMDELANP--MGPRKEIINNHCREFMQLIKD---IQVTLRDEIKS 69 (115)
Q Consensus 7 ~~sLqrL~~VEkkIV~~le~Ag~-----------vMeELs~~--~gpr~~~v~~~c~eFm~~vKe---I~~~L~~~I~s 69 (115)
++.|+++ ||.|+++..||. ++++||+. ..+ ...+.+.=-.|-...+| .+++|.++|..
T Consensus 15 ~~~l~~~----kk~~k~~~~sG~~yv~~~~~f~~~L~~LG~~~l~~d-d~~~~~~l~kf~~~~~El~~l~~~L~~~~~~ 88 (215)
T cd07642 15 RTVLYKM----KKSVKAIHTSGLAHVENEEQYTQALEKFGSNCVCRD-DPDLGSAFLKFSVFTKELTALFKNLVQNMNN 88 (215)
T ss_pred HHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCC-cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666 678888888875 69999994 332 23344444444444444 34566666654
No 23
>cd07627 BAR_Vps5p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in
Probab=36.00 E-value=2e+02 Score=22.12 Aligned_cols=17 Identities=12% Similarity=0.122 Sum_probs=7.3
Q ss_pred HHHHHHhHHHHHhhcCC
Q 033626 21 VRVLELAGGVMDELANP 37 (115)
Q Consensus 21 V~~le~Ag~vMeELs~~ 37 (115)
+.++.-=|.++..||+.
T Consensus 38 a~~~~efa~~~~~L~~~ 54 (216)
T cd07627 38 ASATEEFAETLEALSSL 54 (216)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 33333334444445443
No 24
>COG4064 MtrG Tetrahydromethanopterin S-methyltransferase, subunit G [Coenzyme metabolism]
Probab=35.60 E-value=35 Score=23.72 Aligned_cols=21 Identities=24% Similarity=0.419 Sum_probs=17.2
Q ss_pred CCchhhhhhhHHHHHHHHHHH
Q 033626 1 MDSQSQTTSLQRLQNVEKRVV 21 (115)
Q Consensus 1 m~~~~q~~sLqrL~~VEkkIV 21 (115)
|+|..=|..-.||+++|+|+-
T Consensus 12 v~~~dfne~~kRLdeieekve 32 (75)
T COG4064 12 VDPDDFNEIHKRLDEIEEKVE 32 (75)
T ss_pred cCHHHHHHHHHHHHHHHHHHH
Confidence 567777888899999999874
No 25
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=33.97 E-value=1.9e+02 Score=21.45 Aligned_cols=52 Identities=15% Similarity=0.265 Sum_probs=34.1
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033626 9 SLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQV 61 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~ 61 (115)
.-+||++|.+|+=+..+..+..-+++..- +.+.+.+..--..+-..|...+.
T Consensus 66 LsqRId~vd~klDe~~ei~~~i~~eV~~v-~~dv~~i~~dv~~v~~~V~~Le~ 117 (126)
T PF07889_consen 66 LSQRIDRVDDKLDEQKEISKQIKDEVTEV-REDVSQIGDDVDSVQQMVEGLEG 117 (126)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHH-HhhHHHHHHHHHHHHHHHHHHHH
Confidence 34799999999999999998888888554 34444444444444444444333
No 26
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=33.34 E-value=76 Score=22.06 Aligned_cols=44 Identities=18% Similarity=0.224 Sum_probs=34.7
Q ss_pred hhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHH
Q 033626 8 TSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCRE 51 (115)
Q Consensus 8 ~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~e 51 (115)
..|++|..-++.|+...-.-|-..+|+|...|-+...|.++=+.
T Consensus 121 ~~l~~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~r 164 (179)
T PRK11924 121 RCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRR 164 (179)
T ss_pred HHHHhCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45777778888888777788889999999999888777766444
No 27
>smart00806 AIP3 Actin interacting protein 3. Aip3p/Bud6p is a regulator of cell and cytoskeletal polarity in Saccharomyces cerevisiae that was previously identified as an actin-interacting protein. Actin-interacting protein 3 (Aip3p) localizes at the cell cortex where cytoskeleton assembly must be achieved to execute polarized cell growth, and deletion of AIP3 causes gross defects in cell and cytoskeletal polarity. Aip3p localization is mediated by the secretory pathway, mutations in early- or late-acting components of the secretory apparatus lead to Aip3p mislocalization PUBMED:10679021.
Probab=32.87 E-value=2.2e+02 Score=25.49 Aligned_cols=60 Identities=22% Similarity=0.305 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccCCCCCcchhhHHHHHHHHHHH----HHHHHHHHHHHHHHHh
Q 033626 50 REFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKL----EYVLSQLDAMKQTIDE 110 (115)
Q Consensus 50 ~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~~~k~----e~v~~qL~~l~~~i~~ 110 (115)
..|...++..-+.++++|+.+-+. .++-+.=+.|--.|-|.+|| +-+++++|+||..||-
T Consensus 172 ~~~~~~~~~sm~~i~~k~~~~k~~-~~~~~~~s~R~y~e~~k~kL~~~Sd~lltkVDDLQD~vE~ 235 (426)
T smart00806 172 NSFFTEIKESIKDILEKIDKFKSS-SLSASGSSNRAYVESSKKKLSEDSDSLLTKVDDLQDIIEA 235 (426)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh-hhccCCCcchHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467777777778888888887554 23444447788888899986 4678889999999985
No 28
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=32.56 E-value=67 Score=22.40 Aligned_cols=42 Identities=17% Similarity=0.253 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHH
Q 033626 9 SLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCR 50 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~ 50 (115)
.|..|...++.|+...-.-|-.+.|.|...|-+...|.++=+
T Consensus 125 ~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 125 AIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred HHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 466777888999987778899999999999988877766544
No 29
>smart00397 t_SNARE Helical region found in SNAREs. All alpha-helical motifs that form twisted and parallel four-helix bundles in target soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor proteins. This motif found in "Q-SNAREs".
Probab=31.90 E-value=1.1e+02 Score=17.95 Aligned_cols=57 Identities=14% Similarity=0.142 Sum_probs=39.8
Q ss_pred hhhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 033626 6 QTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTL 63 (115)
Q Consensus 6 q~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L 63 (115)
-..+.+.|..+++.|..+-+++ .-|..+...+++--+.+..+....-..++.-...|
T Consensus 7 ~~~~~~~l~~l~~~i~~l~~l~-~~i~~~v~~Q~~~ld~i~~~~d~~~~~~~~~~~~l 63 (66)
T smart00397 7 EEERDEELEQLEKSIGELKQIF-LDMGTELEEQGEQLDRIEDNVDDADVNLKKANKRL 63 (66)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 3567788899999998777764 45555555567777777777777766666555444
No 30
>PF00435 Spectrin: Spectrin repeat; InterPro: IPR002017 Spectrin repeats [] are found in several proteins involved in cytoskeletal structure. These include spectrin alpha and beta subunits [, ], alpha-actinin [] and dystrophin. The spectrin repeat forms a three-helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C.; GO: 0005515 protein binding; PDB: 1HCI_A 1QUU_A 3FB2_B 1S35_A 1U5P_A 1U4Q_A 1CUN_B 1YDI_B 3EDV_A 1AJ3_A ....
Probab=31.89 E-value=1.3e+02 Score=18.55 Aligned_cols=90 Identities=17% Similarity=0.274 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHHHHhHHHHHhhcCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-------hccCCCCCcchhh
Q 033626 12 RLQNVEKRVVRVLELAGGVMDELANP-MGPRKEIINNHCREFMQLIKDIQVTLRDEIKSA-------CEYRPFEKCDYST 83 (115)
Q Consensus 12 rL~~VEkkIV~~le~Ag~vMeELs~~-~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~-------~eyrPfe~s~Y~~ 83 (115)
+++...+.+-.+..--+.+...|... .+.+.+.+...-.++-.+-++|.. ....++.+ .+..|.+.
T Consensus 2 ~~~~f~~~~~~l~~Wl~~~e~~l~~~~~~~~~~~~~~~~~~~~~~~~ei~~-~~~~l~~l~~~~~~L~~~~~~~~----- 75 (105)
T PF00435_consen 2 QLQQFQQEADELLDWLQETEAKLSSSEPGSDLEELEEQLKKHKELQEEIES-RQERLESLNEQAQQLIDSGPEDS----- 75 (105)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCSCTHSSSHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHTTHTTH-----
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHhhhhhHHHH-HHHHHHHHHHHHHHHHHcCCCcH-----
Confidence 35566666777777777777777333 245556666666555555555554 33334333 22222221
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033626 84 RILNEICCKKLEYVLSQLDAMKQTIDEC 111 (115)
Q Consensus 84 r~~~Ei~~~k~e~v~~qL~~l~~~i~~~ 111 (115)
....++++-+....+.+...+..+
T Consensus 76 ----~~i~~~~~~l~~~w~~l~~~~~~r 99 (105)
T PF00435_consen 76 ----DEIQEKLEELNQRWEALCELVEER 99 (105)
T ss_dssp ----HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333455566666666666655543
No 31
>COG3165 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.85 E-value=2.5e+02 Score=22.79 Aligned_cols=79 Identities=6% Similarity=-0.014 Sum_probs=59.8
Q ss_pred HHHhhcCCCCCCHHHHHHHHHHHHHHH-HHHHHHHHHHHHhhhccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033626 30 VMDELANPMGPRKEIINNHCREFMQLI-KDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTI 108 (115)
Q Consensus 30 vMeELs~~~gpr~~~v~~~c~eFm~~v-KeI~~~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i 108 (115)
.=++||.-.|+-.-. .--.|+... +.++-.++..-+++++|-.=|-++-....+.+-+++-|.-++..++.|...|
T Consensus 119 ~ae~Lsr~~Gdv~A~---~~~~~l~~~~~~l~~~~~~~q~~~Ae~iTEE~r~~v~~~ela~f~~evd~lr~~~~rL~~RL 195 (204)
T COG3165 119 PAELLSRYFGDVAAQ---SVVRALRSGSRFLKHGLKQLQRNLAEAITEEWRMAVGPLELADFAEEVDALRDAVERLEARL 195 (204)
T ss_pred HHHHHHHHhcchHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhhccCChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346666666643321 122233333 6666677888888999999999999999999999999999999999999999
Q ss_pred Hhh
Q 033626 109 DEC 111 (115)
Q Consensus 109 ~~~ 111 (115)
+.-
T Consensus 196 ~rL 198 (204)
T COG3165 196 ERL 198 (204)
T ss_pred HHH
Confidence 864
No 32
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=31.62 E-value=37 Score=19.07 Aligned_cols=44 Identities=25% Similarity=0.432 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHH
Q 033626 12 RLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLI 56 (115)
Q Consensus 12 rL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~v 56 (115)
.|..-|++|...+ ..|....++|...|-+...|..+-.+.+.-+
T Consensus 3 ~l~~~e~~i~~~~-~~g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRLL-AEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3556777877554 6888999999998988888887776655443
No 33
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=31.10 E-value=1.3e+02 Score=18.26 Aligned_cols=63 Identities=16% Similarity=0.262 Sum_probs=44.1
Q ss_pred hhhHHHHHHHHHHHHHHHHhHHHHHhhcCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 033626 8 TSLQRLQNVEKRVVRVLELAGGVMDELANP-MGPRKEIINNHCREFMQLIKDIQVTLRDEIKSA 70 (115)
Q Consensus 8 ~sLqrL~~VEkkIV~~le~Ag~vMeELs~~-~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~ 70 (115)
..-.+|...-..|-..++.--..|+.|... .|+....|...-.+|...+..+...|.+..+.+
T Consensus 11 ~~a~~~~~~~~~l~~~~~~l~~~~~~l~~~W~G~a~~af~~~~~~~~~~~~~~~~~L~~~~~~l 74 (86)
T PF06013_consen 11 AAAQQLQAQADELQSQLQQLESSIDSLQASWQGEAADAFQDKFEEWNQAFRQLNEALEELSQAL 74 (86)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHGGGBTSSTSHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334566666677777777777777777432 357778888888888888888888777766654
No 34
>cd07609 BAR_SIP3_fungi The Bin/Amphiphysin/Rvs (BAR) domain of fungal Snf1p-interacting protein 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of mostly uncharacterized fungal proteins with similarity to Saccharomyces cerevisiae Snf1p-interacting protein 3 (SIP3). These proteins contain an N-terminal BAR domain followed by a Pleckstrin Homology (PH) domain. SIP3 interacts with SNF1 protein kinase and activates transcription when anchored to DNA. It may function in the SNF1 pathway. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=30.00 E-value=2.8e+02 Score=22.01 Aligned_cols=56 Identities=14% Similarity=0.165 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHhHHH--------------HHhhcCCCCCCHHHHHH------HHHHHHHHHHHHHHHHHHHHH
Q 033626 12 RLQNVEKRVVRVLELAGGV--------------MDELANPMGPRKEIINN------HCREFMQLIKDIQVTLRDEIK 68 (115)
Q Consensus 12 rL~~VEkkIV~~le~Ag~v--------------MeELs~~~gpr~~~v~~------~c~eFm~~vKeI~~~L~~~I~ 68 (115)
+++.+|+-|=..+..++.- ++.+.|+..++ ++|-. .-++|-..++++-+++-+.++
T Consensus 9 Qi~~iE~Wl~~~~~~~~k~~~~~~~~e~~~nsfl~~~~p~~~~s-~~vidqdYT~~al~~f~~~l~e~~~~ll~~~~ 84 (214)
T cd07609 9 QVDAIEKWLDGYVSSTKKLYSSLDELERVINSFLSHLLPPLLVS-GGVIDQDYTPLALKRFGDGLKDFWGGVLSALK 84 (214)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccc-cchhCchhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5677777666655555444 33344422333 44443 468899999999998888886
No 35
>PRK00304 hypothetical protein; Provisional
Probab=29.39 E-value=87 Score=21.64 Aligned_cols=36 Identities=17% Similarity=0.043 Sum_probs=23.1
Q ss_pred HHHHHHHhhhccCCCCCcchhhHHHHHHHHHHHHHHHHHHHH
Q 033626 62 TLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDA 103 (115)
Q Consensus 62 ~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~~~k~e~v~~qL~~ 103 (115)
||++-|+.... =||+|||....+ -.|++-|+.||+.
T Consensus 12 TL~nLIeefv~---ReGTDyg~E~sL---~~kv~qv~~qL~~ 47 (75)
T PRK00304 12 TLTRLIEDFVT---RDGTDNGDETPL---ETRVLRVRQALTK 47 (75)
T ss_pred HHHHHHHHHHh---ccCccCcccccH---HHHHHHHHHHHHc
Confidence 45555555332 578899985554 4577777777753
No 36
>PF12994 DUF3878: Domain of unknown function, E. rectale Gene description (DUF3878); InterPro: IPR024538 This entry represents proteins of unknown function found primarily in Firmicutes. The Eubacterium rectale gene appears to be upregulated in the presence of Bacteroides thetaiotaomicron compared to growth in pure culture [].
Probab=29.30 E-value=2.8e+02 Score=23.73 Aligned_cols=62 Identities=23% Similarity=0.368 Sum_probs=35.8
Q ss_pred hHHHHHhhcCCCCCCH-----HHHHHHHH----HHHHHH--HHHH----HHHHHHHHhhhccCCCCCcchhhHHHHHHH
Q 033626 27 AGGVMDELANPMGPRK-----EIINNHCR----EFMQLI--KDIQ----VTLRDEIKSACEYRPFEKCDYSTRILNEIC 90 (115)
Q Consensus 27 Ag~vMeELs~~~gpr~-----~~v~~~c~----eFm~~v--KeI~----~~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~ 90 (115)
|=.+|.|||...|.+. .....+-. +++..+ ..-| ..|.+.|+-++ .||+.-+||.+++..|-
T Consensus 171 ai~~M~elA~ea~D~~~~~~L~~Yrk~p~k~~~~~la~mL~~~kh~~~~~~l~e~l~~As--~~Yp~R~fg~~~~~~~q 247 (299)
T PF12994_consen 171 AIDVMEELAREAGDKSYLKMLRLYRKHPSKRMARKLARMLHRKKHQKVYDLLIEKLQEAS--SPYPRRDFGEDIDERIQ 247 (299)
T ss_pred HHHHHHHHHHHhCcHHHHHHHHHHHhCCcHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHh--ccCCcccccHHHHHHHH
Confidence 5678999999888554 11111111 111111 1112 23555555555 49999999999987665
No 37
>KOG1401 consensus Acetylornithine aminotransferase [Amino acid transport and metabolism]
Probab=29.06 E-value=1.1e+02 Score=27.34 Aligned_cols=45 Identities=24% Similarity=0.321 Sum_probs=36.8
Q ss_pred HHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcch
Q 033626 24 LELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDY 81 (115)
Q Consensus 24 le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y 81 (115)
.-.|.-+|++|..+ +|++-|.-+.++|++.|...+--.|...|.|
T Consensus 315 csa~~~~l~~l~~~-------------e~~k~vs~~~k~L~~~l~e~~~~~~~~i~g~ 359 (433)
T KOG1401|consen 315 CSAGIKVLDELKDP-------------ETLKNVSKIGKELRKLLDEYLKKTPNSICGG 359 (433)
T ss_pred hhHHHHHHHHHcCH-------------HHHHHHHHHHHHHHHHHHHHhccCCCceeee
Confidence 44566677777777 8999999999999999999888888888773
No 38
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=28.73 E-value=52 Score=21.90 Aligned_cols=42 Identities=17% Similarity=0.395 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHhH-HHHHhhcCCCCCCHHHHHHHHHHHHH
Q 033626 13 LQNVEKRVVRVLELAG-GVMDELANPMGPRKEIINNHCREFMQ 54 (115)
Q Consensus 13 L~~VEkkIV~~le~Ag-~vMeELs~~~gpr~~~v~~~c~eFm~ 54 (115)
|++.+++|+.+|+--| ....+||...|-+...+..+-..+..
T Consensus 1 ld~~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 1 LDEIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred CCHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3567899999998754 57889999888888777766665544
No 39
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=28.33 E-value=47 Score=18.11 Aligned_cols=43 Identities=19% Similarity=0.293 Sum_probs=29.2
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHH
Q 033626 9 SLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCRE 51 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~e 51 (115)
.+..|..-+++++...-.-|....++|...|-+...|...-..
T Consensus 7 ~~~~l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 7 ALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred HHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4566777788888777667777777777777655555544433
No 40
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=27.94 E-value=59 Score=21.78 Aligned_cols=20 Identities=30% Similarity=0.466 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 033626 86 LNEICCKKLEYVLSQLDAMK 105 (115)
Q Consensus 86 ~~Ei~~~k~e~v~~qL~~l~ 105 (115)
-||.+..||+-.+++|.+|.
T Consensus 43 kne~Ar~rvEamI~RLk~le 62 (65)
T TIGR02449 43 KNEQARQKVEAMITRLKALE 62 (65)
T ss_pred HHHHHHHHHHHHHHhhhhhc
Confidence 46778888888888887764
No 41
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=27.90 E-value=55 Score=23.32 Aligned_cols=51 Identities=8% Similarity=0.092 Sum_probs=38.3
Q ss_pred hhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHH
Q 033626 8 TSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKD 58 (115)
Q Consensus 8 ~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKe 58 (115)
..|++|..-++.|+...-.-|...+|.|...|-+...|.+.-..-+..++.
T Consensus 132 ~~l~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 132 QEIQALPPKYRMVIVLKYMEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred HHHHhCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345566777778886667789999999999998888888777666655543
No 42
>PF09325 Vps5: Vps5 C terminal like; InterPro: IPR015404 Vps5 is a sorting nexin that functions in membrane trafficking. This is the C-terminal dimerisation domain [].
Probab=27.45 E-value=2.4e+02 Score=21.10 Aligned_cols=27 Identities=22% Similarity=0.348 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHhhcCC
Q 033626 11 QRLQNVEKRVVRVLELAGGVMDELANP 37 (115)
Q Consensus 11 qrL~~VEkkIV~~le~Ag~vMeELs~~ 37 (115)
++|..=.+.++.++.-=|.++..||+.
T Consensus 48 ~~l~~~~~~l~~~~~e~~~~~~~la~~ 74 (236)
T PF09325_consen 48 ERLVKRRQELASALAEFGSSFSQLAKS 74 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 344444445555555556666666665
No 43
>COG1344 FlgL Flagellin and related hook-associated proteins [Cell motility and secretion]
Probab=27.43 E-value=2.2e+02 Score=23.68 Aligned_cols=66 Identities=15% Similarity=0.250 Sum_probs=36.8
Q ss_pred hhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCC-CCHHHHHHHH-----HHHHHHHHHHHHHHHHHHHhhhccC
Q 033626 8 TSLQRLQNVEKRVVRVLELAGGVMDELANPMG-PRKEIINNHC-----REFMQLIKDIQVTLRDEIKSACEYR 74 (115)
Q Consensus 8 ~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~g-pr~~~v~~~c-----~eFm~~vKeI~~~L~~~I~s~~eyr 74 (115)
..|.....-=......|++|-++|++..+-.. =+..+|++.- ...-.+-+||.. |.++|..++.=.
T Consensus 57 ~~L~q~~~n~~~g~s~lqtae~aL~~~~~~lqrirelavqaan~t~s~~dr~~iq~Ei~~-l~~el~~iantt 128 (360)
T COG1344 57 RGLSQAKDNAQDGISKLQTAEGALSEISKILQRIKELAVQAANGTLSDADRAAIQKEIEQ-LLDELDNIANTT 128 (360)
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHH-HHHHHHHHHhcc
Confidence 33333333333445578888888888877644 3334444331 233333366665 778888765444
No 44
>PF01519 DUF16: Protein of unknown function DUF16; InterPro: IPR002862 Proteins that contain this domain are of unknown function. It appears to be confined to proteins from Mycoplasma pneumoniae [].; PDB: 2BA2_C.
Probab=27.32 E-value=2.5e+02 Score=20.50 Aligned_cols=21 Identities=24% Similarity=0.518 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 033626 91 CKKLEYVLSQLDAMKQTIDEC 111 (115)
Q Consensus 91 ~~k~e~v~~qL~~l~~~i~~~ 111 (115)
-+-++.|...|+.|+++|+.-
T Consensus 80 gktL~~I~~~L~~inkRLD~~ 100 (102)
T PF01519_consen 80 GKTLQLILKTLQSINKRLDKM 100 (102)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhhc
Confidence 567789999999999999864
No 45
>PF02828 L27: L27 domain; InterPro: IPR014775 The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7, as well as some protein kinases and human MPP2 protein.; PDB: 1ZL8_B 1VA8_A 3LRA_A 3UIT_A 1Y74_D 1RSO_B.
Probab=27.32 E-value=1.6e+02 Score=18.13 Aligned_cols=45 Identities=9% Similarity=0.161 Sum_probs=29.7
Q ss_pred HHHHhHHHHHhhcCCCCCC-H---HHHHHHHHHHHHHHHHHHHHHHHHH
Q 033626 23 VLELAGGVMDELANPMGPR-K---EIINNHCREFMQLIKDIQVTLRDEI 67 (115)
Q Consensus 23 ~le~Ag~vMeELs~~~gpr-~---~~v~~~c~eFm~~vKeI~~~L~~~I 67 (115)
+++.+-.++++|....+.+ . +...--..-|++.+-++|-.+....
T Consensus 1 av~~~~e~L~~L~~~~~~~~~~~~eL~~lL~~p~~~aLl~~hD~va~~~ 49 (56)
T PF02828_consen 1 AVQRVLELLEELQSLSSASQEDAQELQQLLQSPHFQALLEVHDKVAQKV 49 (56)
T ss_dssp HHHHHHHHHHHHHHHTSSTHHHHHHHHHHHHSHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHhccCCChHHHHHHHHHHcCHHHHHHHHHHHHHHhhc
Confidence 4567788889998877765 2 3344455667777777777665543
No 46
>TIGR01149 mtrG N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G. coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.
Probab=26.93 E-value=60 Score=22.34 Aligned_cols=20 Identities=20% Similarity=0.466 Sum_probs=15.7
Q ss_pred CchhhhhhhHHHHHHHHHHH
Q 033626 2 DSQSQTTSLQRLQNVEKRVV 21 (115)
Q Consensus 2 ~~~~q~~sLqrL~~VEkkIV 21 (115)
+|..=+..+.|||.+|+||=
T Consensus 10 ~~~d~~~i~~rLd~iEeKVE 29 (70)
T TIGR01149 10 EPDEFNEVMKRLDEIEEKVE 29 (70)
T ss_pred CHHHHHHHHHHHHHHHHHHH
Confidence 44556778899999999974
No 47
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=26.81 E-value=2.3e+02 Score=26.12 Aligned_cols=46 Identities=20% Similarity=0.405 Sum_probs=35.9
Q ss_pred HHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH------HHHhhhccC
Q 033626 29 GVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRD------EIKSACEYR 74 (115)
Q Consensus 29 ~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~------~I~s~~eyr 74 (115)
++..-|--.-|.+.+.|+..--+--+.+.+|++.||+ +|.++|-+.
T Consensus 379 sv~gtl~vahgsslDdVD~kIleak~al~evtt~lrErl~RWqQIE~lcGf~ 430 (575)
T KOG4403|consen 379 SVFGTLHVAHGSSLDDVDHKILEAKSALSEVTTLLRERLHRWQQIESLCGFQ 430 (575)
T ss_pred chheeeeeccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCce
Confidence 4444454555677899999999999999999999998 677777654
No 48
>PRK01026 tetrahydromethanopterin S-methyltransferase subunit G; Provisional
Probab=25.97 E-value=62 Score=22.60 Aligned_cols=20 Identities=25% Similarity=0.421 Sum_probs=15.5
Q ss_pred CchhhhhhhHHHHHHHHHHH
Q 033626 2 DSQSQTTSLQRLQNVEKRVV 21 (115)
Q Consensus 2 ~~~~q~~sLqrL~~VEkkIV 21 (115)
+|-.=+....|||.+|.||=
T Consensus 13 ~~~d~~~i~~rLD~iEeKVE 32 (77)
T PRK01026 13 DPKDFKEIQKRLDEIEEKVE 32 (77)
T ss_pred CHHHHHHHHHHHHHHHHHHH
Confidence 44455778899999999974
No 49
>PF03915 AIP3: Actin interacting protein 3; InterPro: IPR022782 This entry represents a domain found in yeast actin interacting protein 3 and bud site selection protein 6. In these proteins it is typically found towards the C terminus. It is also found in metazoan proteins, such as the mouse enhancer trap locus 4 protein. ; PDB: 3ONX_B 3OKQ_A.
Probab=25.95 E-value=1.2e+02 Score=26.66 Aligned_cols=61 Identities=23% Similarity=0.345 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccCCCCCcchhhHHHHHHHHHHH----HHHHHHHHHHHHHHHhh
Q 033626 50 REFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKL----EYVLSQLDAMKQTIDEC 111 (115)
Q Consensus 50 ~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~~~k~----e~v~~qL~~l~~~i~~~ 111 (115)
..|...+++.-.+++++|+.+-. ..++.+.=+.|.-.+-|.+|+ +-+.+++|+|+..||.-
T Consensus 168 ~~~~~~~~~~i~~i~~ki~~~k~-~s~~~~~~~~R~~~~~~k~~L~~~sd~Ll~kVdDLQD~VE~L 232 (424)
T PF03915_consen 168 SEFQSEVKESISSIREKIKKVKS-ASTNASGDSNRAYMESGKKKLSEESDRLLTKVDDLQDLVEDL 232 (424)
T ss_dssp ---------------------------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-hhccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46777777766778888887766 556666667788788888777 46788999999999863
No 50
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=25.91 E-value=84 Score=20.51 Aligned_cols=49 Identities=18% Similarity=0.290 Sum_probs=34.9
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHH
Q 033626 9 SLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIK 57 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vK 57 (115)
.|..|..-|+.|+...-.-|..+.++|...|-+...|...-..-...++
T Consensus 107 ~l~~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 107 ALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred HHHhCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3445667788888666567888999999989777777776665544443
No 51
>PF14476 Chloroplast_duf: Petal formation-expressed
Probab=25.88 E-value=3.5e+02 Score=23.37 Aligned_cols=42 Identities=33% Similarity=0.328 Sum_probs=28.5
Q ss_pred HHHHHhHHHHHhhcCCCCCCH--HHHHHHHHHHHHHHHHHHHHH
Q 033626 22 RVLELAGGVMDELANPMGPRK--EIINNHCREFMQLIKDIQVTL 63 (115)
Q Consensus 22 ~~le~Ag~vMeELs~~~gpr~--~~v~~~c~eFm~~vKeI~~~L 63 (115)
.+|-.|++.|--..|.--|+. +-=.+.+|=|-|+-.+|+++|
T Consensus 63 tlL~~aAtg~l~~mNkiQPSQLAEEQRNAtRLfkqL~~~I~t~l 106 (313)
T PF14476_consen 63 TLLFSAATGMLAIMNKIQPSQLAEEQRNATRLFKQLHSQIETTL 106 (313)
T ss_pred HHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355566666666666656665 344566788888888888887
No 52
>PF10455 BAR_2: Bin/amphiphysin/Rvs domain for vesicular trafficking; InterPro: IPR018859 Endocytosis and intracellular transport involve several mechanistic steps: (1) for the internalisation of cargo molecules, the membrane needs to bend to form a vesicular structure, which requires membrane curvature and a rearrangement of the cytoskeleton; (2) following its formation, the vesicle has to be pinched off the membrane; (3) the cargo has to be subsequently transported through the cell and the vesicle must fuse with the correct cellular compartment. Members of the Amphiphysin protein family are key regulators in the early steps of endocytosis, involved in the formation of clathrin-coated vesicles by promoting the assembly of a protein complex at the plasma membrane and directly assist in the induction of the high curvature of the membrane at the neck of the vesicle. Amphiphysins contain a characteristic domain, known as the BAR (Bin-Amphiphysin-Rvs)-domain, which is required for their in vivo function and their ability to tubulate membranes []. The crystal structure of these proteins suggest the domain forms a crescent-shaped dimer of a three-helix coiled coil with a characteristic set of conserved hydrophobic, aromatic and hydrophilic amino acids. Proteins containing this domain have been shown to homodimerise, heterodimerise or, in a few cases, interact with small GTPases. This entry identifies several fungal BAR domain proteins, such as Gvp36, that are not found by IPR004148 from INTERPRO [].
Probab=25.83 E-value=4e+02 Score=22.38 Aligned_cols=50 Identities=20% Similarity=0.268 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCH---HHHHHHHHHHHHHHHHHH
Q 033626 11 QRLQNVEKRVVRVLELAGGVMDELANPMGPRK---EIINNHCREFMQLIKDIQ 60 (115)
Q Consensus 11 qrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~---~~v~~~c~eFm~~vKeI~ 60 (115)
..|++.|...|.+-+.|=.+|.++-...+|-. +++++|--=|-++.+.+.
T Consensus 229 ~~lE~aEDeFv~aTeeAv~~Mk~vl~~~e~l~~Lk~lv~AQl~Yhk~aae~L~ 281 (289)
T PF10455_consen 229 VELEQAEDEFVSATEEAVEVMKEVLDNSEPLRLLKELVKAQLEYHKKAAEALS 281 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45899999999999999999999988866554 555555444444444433
No 53
>KOG2196 consensus Nuclear porin [Nuclear structure]
Probab=25.00 E-value=1.4e+02 Score=24.98 Aligned_cols=64 Identities=20% Similarity=0.252 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcchhhHHHHHHHHHHH----HHHHHHHHHHHHHHHhhh
Q 033626 45 INNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKL----EYVLSQLDAMKQTIDECN 112 (115)
Q Consensus 45 v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~~~k~----e~v~~qL~~l~~~i~~~~ 112 (115)
+..+.+=|.+..+.|-.-=|. +-+.-|-=..-|+.-.+.+..++|+ +||.+|.++|...|..|.
T Consensus 87 l~~Qe~vF~~q~~qvNaWDr~----LI~ngekI~~Ly~e~~~vk~~qkrLdq~L~~I~sqQ~ELE~~L~~lE 154 (254)
T KOG2196|consen 87 LEEQERVFLQQATQVNAWDRT----LIENGEKISGLYNEVVKVKLDQKRLDQELEFILSQQQELEDLLDPLE 154 (254)
T ss_pred HHHHHHHHHHHHHHHhHHHHH----HHhCcHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555565555555431111 1122222234588888888888885 699999999999998875
No 54
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=24.73 E-value=96 Score=22.05 Aligned_cols=49 Identities=6% Similarity=0.106 Sum_probs=38.9
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHH
Q 033626 9 SLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIK 57 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vK 57 (115)
.|.+|..-++.|+..--.-|...+|.|...|-+...|.++.+.-+.-++
T Consensus 133 ~l~~L~~~~r~il~l~~~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 133 AILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred HHHhCCHHHHHHhhhHHhhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4666777788888766788999999999999889888888776666554
No 55
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=24.03 E-value=90 Score=22.17 Aligned_cols=48 Identities=17% Similarity=0.198 Sum_probs=35.2
Q ss_pred hHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHH
Q 033626 10 LQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIK 57 (115)
Q Consensus 10 LqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vK 57 (115)
|..|..-++.|+...-.-|-..+|+|...|-+...|..+-+.=+.-++
T Consensus 138 l~~L~~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr 185 (189)
T TIGR02984 138 LAKLPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGLARLR 185 (189)
T ss_pred HHcCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 456667778888776788888999999888888777776555444443
No 56
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=23.44 E-value=1.1e+02 Score=21.35 Aligned_cols=49 Identities=12% Similarity=0.087 Sum_probs=37.0
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHH
Q 033626 9 SLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIK 57 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vK 57 (115)
.|..|..-++.|+...-.-|....|.|...|-+...|.++-+.-...+|
T Consensus 119 ~l~~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 119 ALKILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred HHHhCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4556666777888776788999999999999888888877666555554
No 57
>PRK10093 primosomal replication protein N''; Provisional
Probab=23.25 E-value=1.6e+02 Score=23.19 Aligned_cols=70 Identities=4% Similarity=0.067 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcchhh
Q 033626 13 LQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYST 83 (115)
Q Consensus 13 L~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y~~ 83 (115)
|+.++++|-..-+-++...+.=.....=+.-.|..+.+.+--.++||+.+|..=++.+.++++ +...|.+
T Consensus 3 L~~L~~qi~~L~~~~~p~~~~~~~~~rFD~~LF~~~s~~L~~yl~Ei~~~l~qL~~~~~~~~~-~~~~fla 72 (171)
T PRK10093 3 LEKLEGQLATLRQRCAPLAQHATLSARFDRHLFQTRSTLLQAYLDEAGDNLAALRHAVEQQQL-PQVAWLA 72 (171)
T ss_pred HHHHHHHHHHHHHHhhhhccccccccchhHHHHccCCcchHHHHHHHHHHHHHHHHHHhcCcH-HHHHHHH
Confidence 455666666444444333221111112334678888899999999999999887777788877 4555544
No 58
>KOG4127 consensus Renal dipeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=23.00 E-value=1.1e+02 Score=27.35 Aligned_cols=43 Identities=21% Similarity=0.370 Sum_probs=33.5
Q ss_pred HHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCC
Q 033626 31 MDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFE 77 (115)
Q Consensus 31 MeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe 77 (115)
+.||........+...-.-++|+-.+|+|++ ++++++... |+|
T Consensus 363 iaeLl~r~~~~~E~~~l~g~N~LRV~~~vE~-~~~~~~~~~---P~E 405 (419)
T KOG4127|consen 363 IAELLERGWWEEELIGLAGGNLLRVFRQVEK-VRDELLAQA---PIE 405 (419)
T ss_pred HHHHHhcCCcHHHHHHHhcchHHHHHHHHHH-HhhhhcccC---Ccc
Confidence 4566666445667777788999999999998 888877765 877
No 59
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=22.97 E-value=2.4e+02 Score=20.25 Aligned_cols=60 Identities=8% Similarity=0.058 Sum_probs=44.3
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033626 9 SLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIK 68 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~ 68 (115)
.|.+|-.-++.|+..--.-|....|.|...|-+...|.++=+.=++-++..-.-+..+-+
T Consensus 114 ~l~~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~~~~ 173 (179)
T PRK12543 114 LIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEIFLG 173 (179)
T ss_pred HHHhCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455566667788877778899999999999988888888877777777665555554443
No 60
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=22.80 E-value=4.3e+02 Score=23.43 Aligned_cols=61 Identities=16% Similarity=0.201 Sum_probs=34.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033626 41 RKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDE 110 (115)
Q Consensus 41 r~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i~~ 110 (115)
.++.|..+-.|=-..|-=|.--+.|+|.-|+-. |+- .+.=.-+|--.||.+|-+|...|++
T Consensus 23 ~Kd~V~~~I~ea~~sILPlRL~FNeFi~tma~I---e~~------~~~s~qeKFl~IR~KlleL~~~lQ~ 83 (379)
T PF11593_consen 23 SKDSVMDKISEAQDSILPLRLQFNEFIQTMANI---EEM------NNKSPQEKFLLIRSKLLELYNKLQE 83 (379)
T ss_pred hHHHHHHHHHHHHhccccHHHHHHHHHHHHHHh---hcc------cccCHHHHHHHHHHHHHHHHHHHHH
Confidence 666776666666666655666677777777655 111 1111245555666666666665554
No 61
>KOG2631 consensus Class II aldolase/adducin N-terminal domain protein [Carbohydrate transport and metabolism]
Probab=22.73 E-value=56 Score=27.09 Aligned_cols=15 Identities=40% Similarity=0.733 Sum_probs=13.9
Q ss_pred HHHHHHHHHhhhhcC
Q 033626 101 LDAMKQTIDECNDTC 115 (115)
Q Consensus 101 L~~l~~~i~~~~~~~ 115 (115)
-|.|.+.|++|+++|
T Consensus 170 ~D~l~~aie~YP~tc 184 (238)
T KOG2631|consen 170 KDSLKKAIELYPDTC 184 (238)
T ss_pred HHHHHHHHHhCCcce
Confidence 399999999999998
No 62
>PF14643 DUF4455: Domain of unknown function (DUF4455)
Probab=22.58 E-value=5.2e+02 Score=22.50 Aligned_cols=74 Identities=16% Similarity=0.234 Sum_probs=51.4
Q ss_pred HHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033626 31 MDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDE 110 (115)
Q Consensus 31 MeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i~~ 110 (115)
.+.|.++.=-+|..+..--.+|..--+.|+....+.+..+++-.| ..|++.. |.=..+.|..+++.++.
T Consensus 192 ~~~~~s~~~~~P~~~~~~~e~~~~~Q~~l~~~r~~~L~~l~~l~P---p~~t~~~--------v~eW~~~l~~l~~~~d~ 260 (473)
T PF14643_consen 192 REFMASEEFQNPPERKQLLEQMRKEQVDLHEKRLELLQSLCDLLP---PNLTKEK--------VEEWYASLNALNEQIDE 260 (473)
T ss_pred HHHhCccccCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCC---CCCCHHH--------HHHHHHHHHHHHHHHHH
Confidence 344444433555667777778888889999999999999999998 3333332 55566677777777777
Q ss_pred hhhcC
Q 033626 111 CNDTC 115 (115)
Q Consensus 111 ~~~~~ 115 (115)
|+..|
T Consensus 261 ~~~~~ 265 (473)
T PF14643_consen 261 YHQQC 265 (473)
T ss_pred HHHHH
Confidence 66554
No 63
>PF08700 Vps51: Vps51/Vps67; InterPro: IPR014812 The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved in recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1 [].
Probab=22.47 E-value=2.2e+02 Score=18.23 Aligned_cols=46 Identities=15% Similarity=0.395 Sum_probs=34.3
Q ss_pred hhhhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 033626 6 QTTSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQV 61 (115)
Q Consensus 6 q~~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~ 61 (115)
++.++..+.++++++...++...+-|-.+. -.+-++|+.+-++|..
T Consensus 17 ~~~s~~~i~~~~~~L~~~i~~~~~eLr~~V----------~~nY~~fI~as~~I~~ 62 (87)
T PF08700_consen 17 KNSSIKEIRQLENKLRQEIEEKDEELRKLV----------YENYRDFIEASDEISS 62 (87)
T ss_pred hhCCHHHHHHHHHHHHHHHHHHHHHHHHHH----------HhhHHHHHHHHHHHHH
Confidence 466788889999999888888777776654 4467777777776665
No 64
>PRK04966 hypothetical protein; Provisional
Probab=22.25 E-value=1.4e+02 Score=20.39 Aligned_cols=35 Identities=31% Similarity=0.221 Sum_probs=21.0
Q ss_pred HHHHHHHhhhccCCCCCcchhh-HHHHHHHHHHHHHHHHHHH
Q 033626 62 TLRDEIKSACEYRPFEKCDYST-RILNEICCKKLEYVLSQLD 102 (115)
Q Consensus 62 ~L~~~I~s~~eyrPfe~s~Y~~-r~~~Ei~~~k~e~v~~qL~ 102 (115)
||++-|+..- -=||+|||. ...+ -.|++-|+.||+
T Consensus 12 TL~nLIeefv---~ReGTdyG~~E~sl---~~kv~qv~~qL~ 47 (72)
T PRK04966 12 TLENLIESFV---LREGTDYGEHERSL---EQKVADVKRQLQ 47 (72)
T ss_pred HHHHHHHHHH---hccCccCCcccccH---HHHHHHHHHHHH
Confidence 4555555421 118999986 4444 357777777775
No 65
>PF04439 Adenyl_transf: Streptomycin adenylyltransferase; InterPro: IPR007530 Also known as aminoglycoside 6-adenylyltransferase (2.7.7 from EC), this protein confers resistance to aminoglycoside antibiotics.; PDB: 2PBE_A.
Probab=21.82 E-value=3.5e+02 Score=22.17 Aligned_cols=25 Identities=20% Similarity=0.411 Sum_probs=20.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH
Q 033626 39 GPRKEIINNHCREFMQLIKDIQVTL 63 (115)
Q Consensus 39 gpr~~~v~~~c~eFm~~vKeI~~~L 63 (115)
.|+...|..+|.||.-..-.|-++|
T Consensus 146 ~Ps~~eF~~~cNeFw~~~~~VaKgL 170 (282)
T PF04439_consen 146 KPSEQEFDDCCNEFWWVSTYVAKGL 170 (282)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3899999999999999988888866
No 66
>PF02947 Flt3_lig: flt3 ligand ; InterPro: IPR004213 The flt3 (fms-related tyrosine kinase 3) ligand is a short chain cytokine with a 4 helical bundle fold. It is a type I membrane protein which stimulates the proliferation of of early hematopoeitic cells, and synergises well with other colony stimulating factors and interleukins.; GO: 0005125 cytokine activity, 0016020 membrane; PDB: 3QS7_A 1ETE_C 3QS9_A.
Probab=21.68 E-value=81 Score=24.11 Aligned_cols=45 Identities=27% Similarity=0.428 Sum_probs=22.7
Q ss_pred HHHHHHhh--hccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033626 63 LRDEIKSA--CEYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTIDE 110 (115)
Q Consensus 63 L~~~I~s~--~eyrPfe~s~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i~~ 110 (115)
+.-||+-+ |+++|++.|----..+ |+ ..+.=+..||.+|+.-|..
T Consensus 75 V~tei~FVt~C~fq~~psClrFvqtN--IS-hlL~d~s~~L~aLkp~it~ 121 (135)
T PF02947_consen 75 VNTEIHFVTSCAFQPLPSCLRFVQTN--IS-HLLQDTSQQLEALKPWITS 121 (135)
T ss_dssp HHHHHGGGGGS--B---TT--EEEEE--HH-HHHHHHHHHHHHHTTTTTT
T ss_pred HhhheehhhhhccCCChHHHHHHHHh--HH-HHHHhHHHHHHHhhHHHHH
Confidence 45578875 9999999985322221 11 2355567788888766654
No 67
>PF15205 PLAC9: Placenta-specific protein 9
Probab=21.57 E-value=1.7e+02 Score=20.24 Aligned_cols=21 Identities=24% Similarity=0.297 Sum_probs=16.6
Q ss_pred hhHHHHHHHHHHHHHHHHhHH
Q 033626 9 SLQRLQNVEKRVVRVLELAGG 29 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~ 29 (115)
.-.||+.||++|-+.+|+-++
T Consensus 23 v~~RLdviEe~veKTVEhLea 43 (74)
T PF15205_consen 23 VHSRLDVIEETVEKTVEHLEA 43 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999888876553
No 68
>PF13805 Pil1: Eisosome component PIL1; PDB: 3PLT_B.
Probab=21.49 E-value=4.9e+02 Score=21.82 Aligned_cols=66 Identities=24% Similarity=0.277 Sum_probs=38.0
Q ss_pred hhhhhHHHHHHHHHHHHHHHHhHH-------HHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccC
Q 033626 6 QTTSLQRLQNVEKRVVRVLELAGG-------VMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYR 74 (115)
Q Consensus 6 q~~sLqrL~~VEkkIV~~le~Ag~-------vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyr 74 (115)
.+..|++|=..||-++..++.||. .+-+-|...+ +.+..-+++.-.++-++-.-...++...-+||
T Consensus 55 ~sr~L~~LIk~EK~vi~s~e~~are~~~~A~~L~~WG~~ed---ddl~DIsDklgvLl~e~ge~e~~~a~~~d~yR 127 (271)
T PF13805_consen 55 LSRKLQRLIKAEKSVIRSLESAARERKAAAKQLSEWGEQED---DDLSDISDKLGVLLYEIGELEDQYADRLDQYR 127 (271)
T ss_dssp TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHhcCCC---chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355688899999999999988764 4445554433 33444444444444444443334444444443
No 69
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.17 E-value=1.6e+02 Score=22.84 Aligned_cols=63 Identities=19% Similarity=0.167 Sum_probs=48.0
Q ss_pred HHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcchhhHHHH
Q 033626 24 LELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILN 87 (115)
Q Consensus 24 le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y~~r~~~ 87 (115)
+=+|..+++.=+...+||.+.+....=.++..+.++...||.+.++. .|-++-.+-+-.+..+
T Consensus 75 i~LA~~ll~kg~~v~~prGr~y~~~nI~~~L~~R~~~~~lR~~G~~~-~gp~~~~~rDr~~F~~ 137 (150)
T COG1671 75 IPLASLLLDKGAAVLNPRGRLYTEENIGERLAMRDFMAKLRRQGKKT-GGPAAFSSRDRSRFAN 137 (150)
T ss_pred hHHHHHHHhcCCEEECCCCcccCHhHHHHHHHHHHHHHHHHHhcccc-CCCCccChHHHHHHHH
Confidence 45788888888888889999999999999999999999999999983 3333333344444333
No 70
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=20.79 E-value=80 Score=20.23 Aligned_cols=36 Identities=25% Similarity=0.407 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHhHH---HHHhhcCCCCCCHHHHHHHH
Q 033626 14 QNVEKRVVRVLELAGG---VMDELANPMGPRKEIINNHC 49 (115)
Q Consensus 14 ~~VEkkIV~~le~Ag~---vMeELs~~~gpr~~~v~~~c 49 (115)
+.+|.+|...|...|. ...+||...|-+...|+.+-
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L 43 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVL 43 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence 4578899999998754 67889998886666776553
No 71
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=20.69 E-value=4.8e+02 Score=21.46 Aligned_cols=94 Identities=20% Similarity=0.209 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHH----------HHHHHHHHHhh-h----------
Q 033626 13 LQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDI----------QVTLRDEIKSA-C---------- 71 (115)
Q Consensus 13 L~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI----------~~~L~~~I~s~-~---------- 71 (115)
|++|+|-+|.==+.--.+|---++=..-|++.+...=.||-.+=++. ..-||++|+-+ +
T Consensus 79 l~~vsk~~vtkaqq~~v~~QQ~~~f~kiRsel~S~e~sEF~~lr~e~EklkndlEk~ks~lr~ei~~~~a~~rLdLNLEk 158 (220)
T KOG3156|consen 79 LETVSKELVTKAQQEKVSYQQKVDFAKIRSELVSIERSEFANLRAENEKLKNDLEKLKSSLRHEISKTTAEFRLDLNLEK 158 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhceeecchhh
Confidence 45555555544443333433333333345566666666776654433 34577777653 1
Q ss_pred ----------ccCCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 033626 72 ----------EYRPFEKCDYSTRILNEICCKKLEYVLSQLDAMKQTID 109 (115)
Q Consensus 72 ----------eyrPfe~s~Y~~r~~~Ei~~~k~e~v~~qL~~l~~~i~ 109 (115)
+-+-+|-| .+||.||.-=|..+-.-+++.++|.+-
T Consensus 159 gr~~d~~~~~~l~~~e~s---~kId~Ev~~lk~qi~s~K~qt~qw~~g 203 (220)
T KOG3156|consen 159 GRIKDESSSHDLQIKEIS---TKIDQEVTNLKTQIESVKTQTIQWLIG 203 (220)
T ss_pred ccccchhhhcchhHhHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 12223333 889999998888888888888888764
No 72
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=20.56 E-value=3e+02 Score=18.99 Aligned_cols=37 Identities=14% Similarity=0.349 Sum_probs=19.8
Q ss_pred CCchhhhhhhHHHHHHHH-HHHHHHHHhHHHHHhhcCC
Q 033626 1 MDSQSQTTSLQRLQNVEK-RVVRVLELAGGVMDELANP 37 (115)
Q Consensus 1 m~~~~q~~sLqrL~~VEk-kIV~~le~Ag~vMeELs~~ 37 (115)
|+|..-+.-+.++...++ ++.+=+-..-..++.|.+.
T Consensus 1 msp~~~~~d~e~~~~e~k~~Li~ei~~LQ~sL~~L~~R 38 (80)
T PF10224_consen 1 MSPRRNSEDIEKLEKEEKEELIQEILELQDSLEALSDR 38 (80)
T ss_pred CCCCCchHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666666666666766665 3333333334455555544
No 73
>KOG3366 consensus Mitochondrial F1F0-ATP synthase, subunit d/ATP7 [Energy production and conversion]
Probab=20.56 E-value=2.8e+02 Score=22.00 Aligned_cols=39 Identities=26% Similarity=0.418 Sum_probs=31.0
Q ss_pred CHHHHHHHHHHHHHHH-HHHHHHHHHHHHhhhccCCCCCcc
Q 033626 41 RKEIINNHCREFMQLI-KDIQVTLRDEIKSACEYRPFEKCD 80 (115)
Q Consensus 41 r~~~v~~~c~eFm~~v-KeI~~~L~~~I~s~~eyrPfe~s~ 80 (115)
-.......|.|..+++ |+||. |..+|.-+-.-|||+.-|
T Consensus 95 ~~k~~~~~~ke~~~~s~~~iq~-l~k~le~v~~~~P~demT 134 (172)
T KOG3366|consen 95 EEKAAVKEIKEYESLSKKRIQE-LEKELEKVKSARPFDEMT 134 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhcCCccccc
Confidence 3366778899999999 67765 888988888888887644
No 74
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=20.56 E-value=1.6e+02 Score=21.11 Aligned_cols=48 Identities=15% Similarity=0.241 Sum_probs=37.6
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHH
Q 033626 9 SLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLI 56 (115)
Q Consensus 9 sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~v 56 (115)
.|..|-.-++.|+.....-|-..+|+|...|.+...|.+..+.=+..+
T Consensus 128 ~l~~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 128 HLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAAL 175 (184)
T ss_pred HHHhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 466677778888877778899999999999988888887766544444
No 75
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=20.33 E-value=1.4e+02 Score=21.37 Aligned_cols=49 Identities=24% Similarity=0.329 Sum_probs=38.5
Q ss_pred hhhHHHHHHHHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHH
Q 033626 8 TSLQRLQNVEKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLI 56 (115)
Q Consensus 8 ~sLqrL~~VEkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~v 56 (115)
..|++|..-++.|+..--.-|-...|.|...|-+...|.++-+.=+..+
T Consensus 131 ~~l~~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~L 179 (186)
T PRK13919 131 RALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRL 179 (186)
T ss_pred HHHHhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4567777888888877778999999999999988888887766544433
No 76
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=20.20 E-value=4.8e+02 Score=25.97 Aligned_cols=88 Identities=16% Similarity=0.149 Sum_probs=61.5
Q ss_pred HHHHHHHHHHhHHHHHhhcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCCcchhhHHHHHHHHHHHHH
Q 033626 17 EKRVVRVLELAGGVMDELANPMGPRKEIINNHCREFMQLIKDIQVTLRDEIKSACEYRPFEKCDYSTRILNEICCKKLEY 96 (115)
Q Consensus 17 EkkIV~~le~Ag~vMeELs~~~gpr~~~v~~~c~eFm~~vKeI~~~L~~~I~s~~eyrPfe~s~Y~~r~~~Ei~~~k~e~ 96 (115)
.|.+++.++-|-..+++.-.. .-+.+..+..-..|-+.+++++..|...-+. . -+|.+.....---.++.-
T Consensus 43 ~k~~~~~l~~tl~~l~~~~~~-~~~~~~~~~~i~~ap~~~~~~~~~l~~~~~~---~-----~~~~~~~s~~~Leq~l~~ 113 (1109)
T PRK10929 43 QAEIVEALQSALNWLEERKGS-LERAKQYQQVIDNFPKLSAELRQQLNNERDE---P-----RSVPPNMSTDALEQEILQ 113 (1109)
T ss_pred hHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHhHHHHHHHHHHHHhhhcc---c-----ccccccCCHHHHHHHHHH
Confidence 678899999999988888776 5677888888888888888888877653222 2 334333333333455556
Q ss_pred HHHHHHHHHHHHHhhhh
Q 033626 97 VLSQLDAMKQTIDECND 113 (115)
Q Consensus 97 v~~qL~~l~~~i~~~~~ 113 (115)
+..+|.+++..+.++++
T Consensus 114 ~~~~L~~~q~~l~~~~~ 130 (1109)
T PRK10929 114 VSSQLLEKSRQAQQEQD 130 (1109)
T ss_pred HHHHHHHHHHHHHHHhh
Confidence 77788888888776643
Done!