Query 032804
Match_columns 133
No_of_seqs 39 out of 41
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 06:10:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032804.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032804hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13991 BssS: BssS protein fa 85.2 1.1 2.5E-05 31.8 3.2 43 50-105 2-55 (73)
2 cd08915 V_Alix_like Protein-in 47.0 22 0.00047 29.5 3.1 32 91-122 10-41 (342)
3 KOG3389 NADH:ubiquinone oxidor 43.4 11 0.00025 30.7 0.9 18 45-62 106-123 (178)
4 KOG1610 Corticosteroid 11-beta 41.4 9.9 0.00021 33.4 0.3 21 85-105 54-74 (322)
5 PF15361 RIC3: Resistance to i 38.6 21 0.00046 27.6 1.7 21 90-110 126-146 (152)
6 PRK15441 peptidyl-prolyl cis-t 37.5 35 0.00075 23.3 2.5 23 91-113 12-34 (93)
7 PLN03052 acetate--CoA ligase; 35.6 34 0.00073 31.2 2.8 10 109-118 63-72 (728)
8 cd09237 V_ScBro1_like Protein- 34.5 45 0.00098 28.1 3.2 30 91-121 10-39 (356)
9 PF10925 DUF2680: Protein of u 33.2 46 0.00099 22.3 2.5 22 90-111 31-52 (59)
10 PRK12301 bssS biofilm formatio 33.0 39 0.00085 24.9 2.3 20 85-106 47-66 (84)
11 PF04800 ETC_C1_NDUFA4: ETC co 32.3 20 0.00044 26.4 0.7 18 46-63 32-49 (101)
12 PLN02917 CMP-KDO synthetase 31.8 23 0.0005 29.2 1.0 14 34-47 4-17 (293)
13 PF02217 T_Ag_DNA_bind: Origin 31.6 31 0.00067 25.6 1.6 16 91-106 27-42 (94)
14 KOG3894 SNARE protein Syntaxin 31.0 38 0.00082 29.9 2.2 22 94-115 231-252 (316)
15 cd00483 HPPK 7,8-dihydro-6-hyd 30.5 20 0.00043 26.4 0.4 24 44-67 35-58 (128)
16 KOG1268 Glucosamine 6-phosphat 30.0 25 0.00054 33.7 1.0 21 111-131 363-397 (670)
17 PRK13658 hypothetical protein; 29.9 25 0.00054 24.4 0.8 21 97-120 6-30 (59)
18 PRK13666 hypothetical protein; 29.9 19 0.0004 26.9 0.1 27 90-116 64-91 (92)
19 PF00771 FHIPEP: FHIPEP family 29.7 18 0.00038 34.0 0.0 31 85-115 137-167 (658)
20 COG4831 Roadblock/LC7 domain [ 28.2 24 0.00051 27.0 0.5 21 43-64 63-84 (109)
21 PF01756 ACOX: Acyl-CoA oxidas 27.9 33 0.00071 26.0 1.2 32 90-121 104-149 (187)
22 PF08153 NGP1NT: NGP1NT (NUC09 27.7 8.4 0.00018 29.9 -2.1 31 84-114 70-100 (130)
23 PRK10239 2-amino-4-hydroxy-6-h 27.4 30 0.00065 26.9 0.9 23 44-66 38-60 (159)
24 PF12513 SUV3_C: Mitochondrial 26.7 58 0.0013 20.4 2.0 20 86-106 20-40 (49)
25 cd00307 RuBisCO_small_like Rib 26.5 26 0.00056 25.1 0.4 12 45-56 30-41 (84)
26 cd02679 MIT_spastin MIT: domai 25.0 51 0.0011 23.2 1.6 17 92-108 53-69 (79)
27 PRK15337 type III secretion sy 24.0 48 0.001 31.8 1.7 29 86-114 158-186 (686)
28 PF14048 MBD_C: C-terminal dom 23.4 63 0.0014 23.5 1.9 45 50-106 42-94 (96)
29 TIGR01498 folK 2-amino-4-hydro 23.2 37 0.00081 25.2 0.7 22 44-65 34-55 (127)
30 PF12209 SAC3: Leucine permeas 21.9 99 0.0021 21.7 2.6 33 90-122 24-63 (79)
31 PHA02417 hypothetical protein 21.4 75 0.0016 23.3 2.0 15 112-126 51-66 (83)
32 PF11365 DUF3166: Protein of u 21.1 93 0.002 23.0 2.4 26 91-116 11-36 (96)
33 PF10231 DUF2315: Uncharacteri 20.9 1.2E+02 0.0026 23.1 3.1 20 95-114 27-46 (126)
34 cd09236 V_AnPalA_UmRIM20_like 20.9 1.1E+02 0.0023 26.0 3.1 32 91-122 10-41 (353)
35 TIGR01398 FlhA flagellar biosy 20.9 60 0.0013 31.1 1.7 28 87-114 153-180 (678)
36 PF15060 PPDFL: Differentiatio 20.9 61 0.0013 24.9 1.5 10 44-53 51-60 (110)
37 TIGR01399 hrcV type III secret 20.6 60 0.0013 31.1 1.6 29 86-114 148-176 (677)
No 1
>PF13991 BssS: BssS protein family
Probab=85.22 E-value=1.1 Score=31.76 Aligned_cols=43 Identities=26% Similarity=0.366 Sum_probs=29.9
Q ss_pred cccCCCCC-----------CCccCCCccccchhccccCCCCCCCCCCCCCCCcccHHHHHHHHHHhh
Q 032804 50 PLFGWSSD-----------PGYLNNNNRKKNQLEMAGTDNNSGRPGSRFSPGCFTEEKAKQLRKKTA 105 (133)
Q Consensus 50 PLFGWSs~-----------pDYIda~~~~~~~~~~~~~e~~~~~~rsrf~~G~lTEEKAkqLR~~~~ 105 (133)
|+.||-=. -+|++....... .+-..||. +||.|-||||...+-
T Consensus 2 Pv~GW~i~pv~~~dal~lrl~yls~~~q~~e-----------~a~~~~~~--~lT~e~Ar~Li~~L~ 55 (73)
T PF13991_consen 2 PVTGWDIGPVDSYDALMLRLHYLSSPDQPPE-----------EAQVGRTY--WLTTEMARQLISILE 55 (73)
T ss_pred CcccceeccccccceeEEEecccCCCCCCcc-----------ccccCcee--EecHHHHHHHHHHHH
Confidence 78888544 388887754421 11246777 799999999988764
No 2
>cd08915 V_Alix_like Protein-interacting V-domain of mammalian Alix and related domains. This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains
Probab=47.04 E-value=22 Score=29.50 Aligned_cols=32 Identities=22% Similarity=0.333 Sum_probs=27.1
Q ss_pred cccHHHHHHHHHHhhhcchhHHHHHHHHHHHH
Q 032804 91 CFTEEKAKQLRKKTAESSSFHDVMYHSALASR 122 (133)
Q Consensus 91 ~lTEEKAkqLR~~~~etesFHD~MYHSAIASR 122 (133)
.++|+||+.||..+++---.++.++|+.+++.
T Consensus 10 ~Y~E~k~~lvr~e~~~~~e~~~~~l~~~L~sl 41 (342)
T cd08915 10 AYNERQDDYVREHIVEPIEALNKLLNSFLAER 41 (342)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 47899999999998555667899999999875
No 3
>KOG3389 consensus NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion]
Probab=43.35 E-value=11 Score=30.67 Aligned_cols=18 Identities=39% Similarity=0.898 Sum_probs=13.8
Q ss_pred CcccccccCCCCCCCccC
Q 032804 45 TNWWAPLFGWSSDPGYLN 62 (133)
Q Consensus 45 ~~WWAPLFGWSs~pDYId 62 (133)
-+|=.||.||++.+|=+.
T Consensus 106 ~rWENPLMGWtsTaDPls 123 (178)
T KOG3389|consen 106 LRWENPLMGWTSTADPLS 123 (178)
T ss_pred hhccCccccccccCCccc
Confidence 356679999999987543
No 4
>KOG1610 consensus Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism; General function prediction only]
Probab=41.42 E-value=9.9 Score=33.42 Aligned_cols=21 Identities=48% Similarity=0.681 Sum_probs=17.6
Q ss_pred CCCCCCcccHHHHHHHHHHhh
Q 032804 85 SRFSPGCFTEEKAKQLRKKTA 105 (133)
Q Consensus 85 srf~~G~lTEEKAkqLR~~~~ 105 (133)
=+-+.||||||.|++||..+.
T Consensus 54 f~V~Agcl~~~gae~L~~~~~ 74 (322)
T KOG1610|consen 54 FRVFAGCLTEEGAESLRGETK 74 (322)
T ss_pred CEEEEEeecCchHHHHhhhhc
Confidence 344559999999999999985
No 5
>PF15361 RIC3: Resistance to inhibitors of cholinesterase homologue 3
Probab=38.58 E-value=21 Score=27.64 Aligned_cols=21 Identities=19% Similarity=0.215 Sum_probs=18.6
Q ss_pred CcccHHHHHHHHHHhhhcchh
Q 032804 90 GCFTEEKAKQLRKKTAESSSF 110 (133)
Q Consensus 90 G~lTEEKAkqLR~~~~etesF 110 (133)
..+|+.+-.||++|+.|||.-
T Consensus 126 ~~~~~~eL~qLq~rL~qTE~~ 146 (152)
T PF15361_consen 126 RKITDYELAQLQERLAQTERA 146 (152)
T ss_pred ccchHHHHHHHHHHHHHHHHH
Confidence 469999999999999999953
No 6
>PRK15441 peptidyl-prolyl cis-trans isomerase C; Provisional
Probab=37.54 E-value=35 Score=23.30 Aligned_cols=23 Identities=17% Similarity=0.216 Sum_probs=19.6
Q ss_pred cccHHHHHHHHHHhhhcchhHHH
Q 032804 91 CFTEEKAKQLRKKTAESSSFHDV 113 (133)
Q Consensus 91 ~lTEEKAkqLR~~~~etesFHD~ 113 (133)
+-+|++|++|+.++.+.++|=++
T Consensus 12 ~~~~~~A~~i~~~l~~g~~F~~l 34 (93)
T PRK15441 12 VKEEKLALDLLEQIKNGADFGKL 34 (93)
T ss_pred ECCHHHHHHHHHHHHCCCCHHHH
Confidence 35899999999999988898654
No 7
>PLN03052 acetate--CoA ligase; Provisional
Probab=35.62 E-value=34 Score=31.23 Aligned_cols=10 Identities=40% Similarity=0.813 Sum_probs=8.7
Q ss_pred hhHHHHHHHH
Q 032804 109 SFHDVMYHSA 118 (133)
Q Consensus 109 sFHD~MYHSA 118 (133)
+||+.|||+-
T Consensus 63 ~~~~~~~~~~ 72 (728)
T PLN03052 63 ALHQLMYYSC 72 (728)
T ss_pred cHHHHhhhhc
Confidence 6899999984
No 8
>cd09237 V_ScBro1_like Protein-interacting V-domain of Saccharomyces cerevisiae Bro1 and related domains. This family contains the V-shaped (V) domain of Saccharomyces cerevisiae Bro1, and related domains. It belongs to the V_Alix_like superfamily which also includes the V-domain of Saccharomyces cerevisiae Rim20 (also known as PalA), mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Bro1 interacts with the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in endosomal trafficking. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Bro1 also has an N-terminal Bro1-like domain, which binds Snf7, a component of the ESCRT-III complex, and a C-terminal proline-rich
Probab=34.47 E-value=45 Score=28.08 Aligned_cols=30 Identities=33% Similarity=0.392 Sum_probs=24.3
Q ss_pred cccHHHHHHHHHHhhhcchhHHHHHHHHHHH
Q 032804 91 CFTEEKAKQLRKKTAESSSFHDVMYHSALAS 121 (133)
Q Consensus 91 ~lTEEKAkqLR~~~~etesFHD~MYHSAIAS 121 (133)
..+||||+.+|..+.+ --.++..+|+.+++
T Consensus 10 ~YsE~ka~lvr~e~~~-~e~a~~~~~~~L~~ 39 (356)
T cd09237 10 LYSEEKAKLLRAEVER-VEVANEEYASFLEY 39 (356)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHH
Confidence 4689999999999755 45678888988876
No 9
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=33.23 E-value=46 Score=22.29 Aligned_cols=22 Identities=23% Similarity=0.511 Sum_probs=18.1
Q ss_pred CcccHHHHHHHHHHhhhcchhH
Q 032804 90 GCFTEEKAKQLRKKTAESSSFH 111 (133)
Q Consensus 90 G~lTEEKAkqLR~~~~etesFH 111 (133)
|.+|.|+|..+...|-+-..+|
T Consensus 31 G~iTqeqAd~ik~~id~~~~~~ 52 (59)
T PF10925_consen 31 GVITQEQADAIKKHIDQRQEYM 52 (59)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH
Confidence 8999999999999987654444
No 10
>PRK12301 bssS biofilm formation regulatory protein BssS; Reviewed
Probab=33.05 E-value=39 Score=24.88 Aligned_cols=20 Identities=15% Similarity=0.104 Sum_probs=15.2
Q ss_pred CCCCCCcccHHHHHHHHHHhhh
Q 032804 85 SRFSPGCFTEEKAKQLRKKTAE 106 (133)
Q Consensus 85 srf~~G~lTEEKAkqLR~~~~e 106 (133)
.|+. .||.+-||||=..+-+
T Consensus 47 ~~tl--wLTtdvArqlI~iLea 66 (84)
T PRK12301 47 GQTL--WLTTDVARQFISILEA 66 (84)
T ss_pred cceE--EecHHHHHHHHHHHHH
Confidence 4555 5999999999776643
No 11
>PF04800 ETC_C1_NDUFA4: ETC complex I subunit conserved region; InterPro: IPR006885 This entry represents prokaryotic NADH-ubiquinone oxidoreductase subunits (1.6.5.3 from EC, 1.6.99.3 from EC) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein [].; GO: 0016651 oxidoreductase activity, acting on NADH or NADPH, 0022900 electron transport chain, 0005743 mitochondrial inner membrane; PDB: 2JYA_A 2LJU_A.
Probab=32.27 E-value=20 Score=26.43 Aligned_cols=18 Identities=39% Similarity=0.909 Sum_probs=10.8
Q ss_pred cccccccCCCCCCCccCC
Q 032804 46 NWWAPLFGWSSDPGYLNN 63 (133)
Q Consensus 46 ~WWAPLFGWSs~pDYIda 63 (133)
+|=-||.||.+..|.+..
T Consensus 32 ~~~~PLMGWtss~D~~~q 49 (101)
T PF04800_consen 32 RWENPLMGWTSSGDPLSQ 49 (101)
T ss_dssp S---TTT-SSSS--SEEE
T ss_pred CcCCCccCCCCCCChhhC
Confidence 667799999999999886
No 12
>PLN02917 CMP-KDO synthetase
Probab=31.77 E-value=23 Score=29.22 Aligned_cols=14 Identities=79% Similarity=0.921 Sum_probs=6.0
Q ss_pred CCCCCCCCCCCCcc
Q 032804 34 SSSSSSSSSSSTNW 47 (133)
Q Consensus 34 s~~~~~~~~~s~~W 47 (133)
|+++++++++...|
T Consensus 4 ~~~~~~~~~~~~~~ 17 (293)
T PLN02917 4 SSSSSSSSSSTKSW 17 (293)
T ss_pred ccCCccccccchhH
Confidence 33344444444445
No 13
>PF02217 T_Ag_DNA_bind: Origin of replication binding protein; InterPro: IPR003133 The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses []. Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA []. T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see PDOC00553 from PROSITEDOC, IPR001623 from INTERPRO), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see PDOC51206 from PROSITEDOC, IPR010932 from INTERPRO) []. This entry represents the central origin-binding domain (OBD). The overall fold of the ~130-residue T-ag OBD can be described as a central five-stranded antiparallel beta-sheet flanked by two alpha-helices on one side and one alpha-helix and one 3(10)-helix on the other. Both faces of the central beta-sheet are largely hydrophobic and are protected from solvent by the helices, thus forming two hydrophobic cores []. The T-ag OBD molecules are arranged as a spiral with a left-handed twist having six T-ag OBD's per turn. The spiral surrounds a central channel, the inner wall of which consists of alpha helices []. ; GO: 0003688 DNA replication origin binding, 0006260 DNA replication; PDB: 2IPR_B 2ITL_B 1Z1D_B 2FUF_A 2TBD_A 3QK2_A 2ITJ_A 2IF9_A 2NL8_A 2NTC_A ....
Probab=31.57 E-value=31 Score=25.63 Aligned_cols=16 Identities=56% Similarity=0.497 Sum_probs=13.6
Q ss_pred cccHHHHHHHHHHhhh
Q 032804 91 CFTEEKAKQLRKKTAE 106 (133)
Q Consensus 91 ~lTEEKAkqLR~~~~e 106 (133)
.=|-||+++|++++.|
T Consensus 27 yTT~eK~~~Ly~kl~~ 42 (94)
T PF02217_consen 27 YTTKEKAEQLYKKLLE 42 (94)
T ss_dssp EEEHHHHHHHHHHCHH
T ss_pred EEcHHHHHHHHHHHHH
Confidence 4589999999999964
No 14
>KOG3894 consensus SNARE protein Syntaxin 18/UFE1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=31.03 E-value=38 Score=29.90 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=20.3
Q ss_pred HHHHHHHHHHhhhcchhHHHHH
Q 032804 94 EEKAKQLRKKTAESSSFHDVMY 115 (133)
Q Consensus 94 EEKAkqLR~~~~etesFHD~MY 115 (133)
-|+++|++++|+|-+..||+|-
T Consensus 231 ~devrqie~~lvEI~~Lq~ifs 252 (316)
T KOG3894|consen 231 LDEVRQIEKRLVEISALQDIFS 252 (316)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 5889999999999999999984
No 15
>cd00483 HPPK 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is HPPK which catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The functional enzyme is a monomer. Mammals lack many of the enzymes in the folate pathway including, HPPK.
Probab=30.48 E-value=20 Score=26.42 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=20.1
Q ss_pred CCcccccccCCCCCCCccCCCccc
Q 032804 44 STNWWAPLFGWSSDPGYLNNNNRK 67 (133)
Q Consensus 44 s~~WWAPLFGWSs~pDYIda~~~~ 67 (133)
|.-||+|-+|..+++||+|+-..-
T Consensus 35 S~~y~T~p~g~~~~~~FlN~v~~~ 58 (128)
T cd00483 35 SPLYETAPVGFTDQPDFLNAVVEL 58 (128)
T ss_pred CCCEEeCCCCCCCChHHHheEEEE
Confidence 447999999999999999987543
No 16
>KOG1268 consensus Glucosamine 6-phosphate synthetases, contain amidotransferase and phosphosugar isomerase domains [Cell wall/membrane/envelope biogenesis]
Probab=29.96 E-value=25 Score=33.71 Aligned_cols=21 Identities=52% Similarity=0.559 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHH--------------HhhhcCCCC
Q 032804 111 HDVMYHSALASR--------------LASDMSVLP 131 (133)
Q Consensus 111 HD~MYHSAIASR--------------LAsd~~~~~ 131 (133)
+-+-||||+|.| |||||-+|.
T Consensus 363 cgtSyhs~~A~R~ilEEL~eiPV~vElAsDflDR~ 397 (670)
T KOG1268|consen 363 CGTSYHSALATRPILEELSEIPVSVELASDFLDRN 397 (670)
T ss_pred ecchHHHHHHHHHHHHHHhcCCeeeehhhhhHhcC
Confidence 556699999999 788886653
No 17
>PRK13658 hypothetical protein; Provisional
Probab=29.94 E-value=25 Score=24.43 Aligned_cols=21 Identities=29% Similarity=0.653 Sum_probs=13.7
Q ss_pred HHHHHHHhhhcchhHHHH----HHHHHH
Q 032804 97 AKQLRKKTAESSSFHDVM----YHSALA 120 (133)
Q Consensus 97 AkqLR~~~~etesFHD~M----YHSAIA 120 (133)
|.+|-.|+ .+.-|++ |||||-
T Consensus 6 aq~~A~RI---DTVLDILVAGdyHSAI~ 30 (59)
T PRK13658 6 AQRVAERI---DTVLDILVAGDYHSAIH 30 (59)
T ss_pred HHHHHHHH---hHHHHHHhcccHHHHHH
Confidence 44555554 5666776 999994
No 18
>PRK13666 hypothetical protein; Provisional
Probab=29.86 E-value=19 Score=26.91 Aligned_cols=27 Identities=33% Similarity=0.503 Sum_probs=22.4
Q ss_pred CcccHHHHHHHHHHhh-hcchhHHHHHH
Q 032804 90 GCFTEEKAKQLRKKTA-ESSSFHDVMYH 116 (133)
Q Consensus 90 G~lTEEKAkqLR~~~~-etesFHD~MYH 116 (133)
|+.+++.-|||=.++- +-+..|+++|-
T Consensus 64 gli~~~~Gk~ll~~LE~~Ls~L~~a~~~ 91 (92)
T PRK13666 64 GLIDEEEGKQLLSRLERELSALHEAFTN 91 (92)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 8999999999887775 77788888873
No 19
>PF00771 FHIPEP: FHIPEP family; InterPro: IPR001712 The Flagellar/Hr/Invasion Proteins Export Pore (FHIPEP) family [, ] consists of a number of proteins that constitute the type III secretion (or signal peptide-independent) pathway apparatus [, ]. This mechanism translocates proteins lacking an N-terminal signal peptide across the cell membrane in one step, as it does not require an intermediate periplasmic process to cleave the signal peptide. It is a common pathway amongst Gram-negative bacteria for secreting toxic and flagellar proteins. The pathway apparatus comprises three components: two within the inner membrane and one within the outer []. An FHIPEP protein is located within the inner membrane, although it is unknown which component it constitutes. FHIPEP proteins have all about 700 amino-acid residues. Within the sequence, the N terminus is highly conserved and hydrophobic, suggesting that this terminus is embedded within the membrane, with 6-8 transmembrane (TM) domains, while the C terminus is less conserved and appears to be devoid of TM regions. It is possible that members of the FHIPEP family serve as pores for the export of specific proteins.; GO: 0009306 protein secretion, 0016020 membrane; PDB: 3MIX_A 2X4A_A 3LW9_A 2X49_A 3MYD_A 3A5I_A.
Probab=29.67 E-value=18 Score=33.99 Aligned_cols=31 Identities=23% Similarity=0.403 Sum_probs=0.0
Q ss_pred CCCCCCcccHHHHHHHHHHhhhcchhHHHHH
Q 032804 85 SRFSPGCFTEEKAKQLRKKTAESSSFHDVMY 115 (133)
Q Consensus 85 srf~~G~lTEEKAkqLR~~~~etesFHD~MY 115 (133)
..+-.|..|||-||..|+++..-..||-+|=
T Consensus 137 aDl~aG~I~~~eA~~rR~~l~~E~~fyGaMD 167 (658)
T PF00771_consen 137 ADLNAGLIDEEEARRRREELEREADFYGAMD 167 (658)
T ss_dssp -------------------------------
T ss_pred hHhhcCCCCHHHHHHHHHHHHHHhhhhhhcc
Confidence 3455699999999999999998889999883
No 20
>COG4831 Roadblock/LC7 domain [Function unknown]
Probab=28.21 E-value=24 Score=27.04 Aligned_cols=21 Identities=33% Similarity=0.654 Sum_probs=15.9
Q ss_pred CCCcccccccCCCCC-CCccCCC
Q 032804 43 SSTNWWAPLFGWSSD-PGYLNNN 64 (133)
Q Consensus 43 ~s~~WWAPLFGWSs~-pDYIda~ 64 (133)
++.+ |.|+.||--. ++|+-+-
T Consensus 63 sg~~-w~P~~gwa~agg~yavci 84 (109)
T COG4831 63 SGMN-WTPQNGWAVAGGKYAVCI 84 (109)
T ss_pred hcCc-cccccceEEecCceEEEE
Confidence 3556 9999999765 6887664
No 21
>PF01756 ACOX: Acyl-CoA oxidase; InterPro: IPR002655 Acyl-CoA oxidase (ACO) acts on CoA derivatives of fatty acids with chain lengths from 8 to 18. It catalyses the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids []. Acyl-CoA oxidase is a homodimer and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain []. Functional differences between the peroxisomal acyl-CoA oxidases and the mitochondrial acyl-CoA dehydrogenases are attributed to structural differences in the FAD environments []. Experimental data indicate that, in the pumpkin, the expression pattern of ACOX is very similar to that of the glyoxysomal enzyme 3-ketoacyl-CoA thiolase []. In humans, defects in ACOX1 are the cause of pseudoneonatal adrenoleukodystrophy, also known as peroxisomal acyl-CoA oxidase deficiency. Pseudo-NALD is a peroxisomal single-enzyme disorder. Clinical features include mental retardation, leukodystrophy, seizures, mild hepatomegaly and hearing deficit. Pseudo-NALD is characterised by increased plasma levels of very-long chain fatty acids due to a decrease in, or absence of, peroxisome acyl-CoA oxidase activity, despite the peroxisomes being intact and functioning. This entry represents the Acyl-CoA oxidase C-terminal.; GO: 0003997 acyl-CoA oxidase activity, 0006635 fatty acid beta-oxidation, 0055114 oxidation-reduction process, 0005777 peroxisome; PDB: 2FON_A 1IS2_B 2DDH_A 1W07_B.
Probab=27.92 E-value=33 Score=26.01 Aligned_cols=32 Identities=28% Similarity=0.501 Sum_probs=21.7
Q ss_pred CcccHHHHHHHHHHh--------------hhcchhHHHHHHHHHHH
Q 032804 90 GCFTEEKAKQLRKKT--------------AESSSFHDVMYHSALAS 121 (133)
Q Consensus 90 G~lTEEKAkqLR~~~--------------~etesFHD~MYHSAIAS 121 (133)
|.+|.++++.||... +++=-|+|.+.+|+|++
T Consensus 104 g~ls~~~~~~l~~~i~~l~~~lrp~av~LVDAF~~~D~~L~S~iG~ 149 (187)
T PF01756_consen 104 GYLSPEQIKALRKAIEELCAELRPNAVALVDAFDFPDFFLNSPIGR 149 (187)
T ss_dssp TSS-HHHHHHHHHHHHHHHHHHGGGHHHHHHTT---HHHHT-STT-
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHhHHHHHHHhcCCCHHHHcChhcc
Confidence 789999999999864 45667899999999975
No 22
>PF08153 NGP1NT: NGP1NT (NUC091) domain; InterPro: IPR012971 This N-terminal domain is found in a subfamily of hypothetical nucleolar GTP-binding proteins similar to human NGP1 [].
Probab=27.72 E-value=8.4 Score=29.89 Aligned_cols=31 Identities=23% Similarity=0.348 Sum_probs=25.8
Q ss_pred CCCCCCCcccHHHHHHHHHHhhhcchhHHHH
Q 032804 84 GSRFSPGCFTEEKAKQLRKKTAESSSFHDVM 114 (133)
Q Consensus 84 rsrf~~G~lTEEKAkqLR~~~~etesFHD~M 114 (133)
+++.=++.|++.+.|+-|..+.+||+|+|+.
T Consensus 70 ~~KLPmsLL~d~~~k~~~~~il~te~F~~tF 100 (130)
T PF08153_consen 70 RSKLPMSLLQDSGTKQKRVHILETEPFEDTF 100 (130)
T ss_pred CCcCCHHHhcccccccCCcceeecCCHHHHh
Confidence 3566667788777999999999999999974
No 23
>PRK10239 2-amino-4-hydroxy-6-hydroxymethyldihyropteridine pyrophosphokinase; Provisional
Probab=27.45 E-value=30 Score=26.93 Aligned_cols=23 Identities=30% Similarity=0.495 Sum_probs=19.6
Q ss_pred CCcccccccCCCCCCCccCCCcc
Q 032804 44 STNWWAPLFGWSSDPGYLNNNNR 66 (133)
Q Consensus 44 s~~WWAPLFGWSs~pDYIda~~~ 66 (133)
|.-|+++-+|..+++||+|+-..
T Consensus 38 S~~y~T~P~g~~~q~~FlN~v~~ 60 (159)
T PRK10239 38 SSFYRTPPLGPQDQPDYLNAAVA 60 (159)
T ss_pred CCCEEeCCCCCCCCCCceEEEEE
Confidence 44799999999999999998753
No 24
>PF12513 SUV3_C: Mitochondrial degradasome RNA helicase subunit C terminal; InterPro: IPR022192 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00271 from PFAM. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 3RC8_A 3RC3_A.
Probab=26.71 E-value=58 Score=20.38 Aligned_cols=20 Identities=45% Similarity=0.870 Sum_probs=14.9
Q ss_pred CCCCCcccH-HHHHHHHHHhhh
Q 032804 86 RFSPGCFTE-EKAKQLRKKTAE 106 (133)
Q Consensus 86 rf~~G~lTE-EKAkqLR~~~~e 106 (133)
|| ++.|++ |+|.++|.++.+
T Consensus 20 Rf-p~~F~d~e~a~~~k~~~~~ 40 (49)
T PF12513_consen 20 RF-PDVFPDRELAEELKKRVEE 40 (49)
T ss_dssp C--TTTSTTHHHHHHHHHHHHH
T ss_pred Hc-ccccCCHHHHHHHHHHHHH
Confidence 56 567776 999999998854
No 25
>cd00307 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome t
Probab=26.47 E-value=26 Score=25.08 Aligned_cols=12 Identities=17% Similarity=0.141 Sum_probs=9.8
Q ss_pred CcccccccCCCC
Q 032804 45 TNWWAPLFGWSS 56 (133)
Q Consensus 45 ~~WWAPLFGWSs 56 (133)
..||.|+||-.+
T Consensus 30 t~w~lp~f~~~~ 41 (84)
T cd00307 30 TSSWQSCGPIEG 41 (84)
T ss_pred hhhcCCCCCCCC
Confidence 479999999843
No 26
>cd02679 MIT_spastin MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be involved in microtubule dynamics. The molecular function of the MIT domain is unclear.
Probab=25.01 E-value=51 Score=23.20 Aligned_cols=17 Identities=24% Similarity=0.270 Sum_probs=13.8
Q ss_pred ccHHHHHHHHHHhhhcc
Q 032804 92 FTEEKAKQLRKKTAESS 108 (133)
Q Consensus 92 lTEEKAkqLR~~~~ete 108 (133)
-.=|+|++|+.||.++-
T Consensus 53 ~~w~~ar~~~~Km~~~~ 69 (79)
T cd02679 53 SQWERARRLQQKMKTNL 69 (79)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45689999999998753
No 27
>PRK15337 type III secretion system protein InvA; Provisional
Probab=23.99 E-value=48 Score=31.80 Aligned_cols=29 Identities=14% Similarity=0.212 Sum_probs=25.2
Q ss_pred CCCCCcccHHHHHHHHHHhhhcchhHHHH
Q 032804 86 RFSPGCFTEEKAKQLRKKTAESSSFHDVM 114 (133)
Q Consensus 86 rf~~G~lTEEKAkqLR~~~~etesFHD~M 114 (133)
....|..||+-||+-|+++.+-+.|+-+|
T Consensus 158 DLnAG~Ide~eAr~RR~~l~~EadFyGAM 186 (686)
T PRK15337 158 DLKAGIIDADGVKERRSVLERESQLYGSF 186 (686)
T ss_pred HhhcCCCCHHHHHHHHHHHHHHHHhccCc
Confidence 34559999999999999999888898877
No 28
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=23.40 E-value=63 Score=23.55 Aligned_cols=45 Identities=33% Similarity=0.434 Sum_probs=11.5
Q ss_pred cccCCCCCCCccCCCccccchhccccCCCCCCCCC-CCCCCCccc-------HHHHHHHHHHhhh
Q 032804 50 PLFGWSSDPGYLNNNNRKKNQLEMAGTDNNSGRPG-SRFSPGCFT-------EEKAKQLRKKTAE 106 (133)
Q Consensus 50 PLFGWSs~pDYIda~~~~~~~~~~~~~e~~~~~~r-srf~~G~lT-------EEKAkqLR~~~~e 106 (133)
|.+|=.+..+-++..+-.-. ....|= ..|. .| |+|.|..|+|+.|
T Consensus 42 Pi~gQ~~~~~~~e~~P~~~~---------~~~QPLc~~~~---VT~eDIr~QE~rVk~aR~RLae 94 (96)
T PF14048_consen 42 PITGQTSSKDALEKNPGVGL---------NPPQPLCKQFV---VTEEDIRRQERRVKKARKRLAE 94 (96)
T ss_dssp ------------------------------------T--------HHHHHHHHHHHHHHHHHHHH
T ss_pred CCcCCccchhhhccCccccc---------CCCcccccCCc---cCHHHHHHHHHHHHHHHHHHHH
Confidence 88887777677666643211 111111 2232 45 5799999999976
No 29
>TIGR01498 folK 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase. This model describes the folate biosynthesis enzyme 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase. Alternate names include 6-hydroxymethyl-7,8-dihydropterin diphosphokinase and 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase (HPPK). The extreme C-terminal region, of typically eight to thirty residues, is not included in the model. This enzyme may be found as a fusion protein with other enzymes of folate biosynthesis.
Probab=23.16 E-value=37 Score=25.20 Aligned_cols=22 Identities=27% Similarity=0.595 Sum_probs=18.6
Q ss_pred CCcccccccCCCCCCCccCCCc
Q 032804 44 STNWWAPLFGWSSDPGYLNNNN 65 (133)
Q Consensus 44 s~~WWAPLFGWSs~pDYIda~~ 65 (133)
|.-+|+|-+|...++||+|+-.
T Consensus 34 S~~y~T~p~g~~~q~~FlN~v~ 55 (127)
T TIGR01498 34 SSIYETPPWGFTDQPDFLNAVV 55 (127)
T ss_pred ccCEEEcCCCCCCCchhheEEE
Confidence 3478999999999999999764
No 30
>PF12209 SAC3: Leucine permease transcriptional regulator helical domain; InterPro: IPR024293 This domain is found in fungal proteins, including the nuclear mRNA export protein SAC3. It has been suggested this domain provides a scaffold within the yeast Sac3:Cdc31:Sus1:Thp1 (TREX-2) complex to integrate interactions between protein complexes to facilitate the coupling of transcription and mRNA export during gene expression [].; PDB: 3FWC_N 3FWB_B.
Probab=21.93 E-value=99 Score=21.69 Aligned_cols=33 Identities=27% Similarity=0.459 Sum_probs=21.7
Q ss_pred CcccHHHHHHHHHHhhhcch-------hHHHHHHHHHHHH
Q 032804 90 GCFTEEKAKQLRKKTAESSS-------FHDVMYHSALASR 122 (133)
Q Consensus 90 G~lTEEKAkqLR~~~~etes-------FHD~MYHSAIASR 122 (133)
-+|.++.+++.|+++.++=+ +|++||.-..-++
T Consensus 24 ~~l~~~n~~~~R~~iI~sLs~ELy~AFi~E~~Y~~~lesk 63 (79)
T PF12209_consen 24 NLLRRQNARKERKQIIDSLSEELYDAFIHEQLYQIYLESK 63 (79)
T ss_dssp HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36788899999988866533 5888888776654
No 31
>PHA02417 hypothetical protein
Probab=21.36 E-value=75 Score=23.27 Aligned_cols=15 Identities=27% Similarity=0.251 Sum_probs=11.8
Q ss_pred HHHHHHH-HHHHHhhh
Q 032804 112 DVMYHSA-LASRLASD 126 (133)
Q Consensus 112 D~MYHSA-IASRLAsd 126 (133)
.+|.|+| ||.||||-
T Consensus 51 s~~l~aAv~ARR~A~L 66 (83)
T PHA02417 51 EAAIRAAVIARRRARL 66 (83)
T ss_pred HHHHHHHHHHHHHhcc
Confidence 4788876 78999984
No 32
>PF11365 DUF3166: Protein of unknown function (DUF3166); InterPro: IPR021507 This eukaryotic family of proteins has no known function.
Probab=21.09 E-value=93 Score=23.02 Aligned_cols=26 Identities=31% Similarity=0.376 Sum_probs=23.9
Q ss_pred cccHHHHHHHHHHhhhcchhHHHHHH
Q 032804 91 CFTEEKAKQLRKKTAESSSFHDVMYH 116 (133)
Q Consensus 91 ~lTEEKAkqLR~~~~etesFHD~MYH 116 (133)
-|-||-|-.||+++.+-+.--|.|-|
T Consensus 11 qFvEEEa~LlRRkl~ele~eN~~l~~ 36 (96)
T PF11365_consen 11 QFVEEEAELLRRKLSELEDENKQLTE 36 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 37799999999999999999999987
No 33
>PF10231 DUF2315: Uncharacterised conserved protein (DUF2315); InterPro: IPR018796 This entry consists of small conserved proteins found from worms to humans. Their function is not known.
Probab=20.95 E-value=1.2e+02 Score=23.12 Aligned_cols=20 Identities=15% Similarity=0.278 Sum_probs=15.0
Q ss_pred HHHHHHHHHhhhcchhHHHH
Q 032804 95 EKAKQLRKKTAESSSFHDVM 114 (133)
Q Consensus 95 EKAkqLR~~~~etesFHD~M 114 (133)
+-.++||..-.||..||..-
T Consensus 27 ~lE~klR~~Rqe~~~wNq~F 46 (126)
T PF10231_consen 27 PLERKLRLLRQETQEWNQEF 46 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 55678888888888887654
No 34
>cd09236 V_AnPalA_UmRIM20_like Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins. This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas PalA/RIM20 and Ustilago maydis RIM20, like Saccharomyces cerevisiae Rim20, participate in the response to the external pH via the Pal/Rim101 pathway; however, Saccharomyces cerevisiae Rim20 does not belong to this family. This pathway is a signaling cascade resulting in the activation of the transcription factor PacC/Rim101. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. Aspergillus nidulas Pa
Probab=20.93 E-value=1.1e+02 Score=26.00 Aligned_cols=32 Identities=16% Similarity=0.152 Sum_probs=26.0
Q ss_pred cccHHHHHHHHHHhhhcchhHHHHHHHHHHHH
Q 032804 91 CFTEEKAKQLRKKTAESSSFHDVMYHSALASR 122 (133)
Q Consensus 91 ~lTEEKAkqLR~~~~etesFHD~MYHSAIASR 122 (133)
.++|+|++.+|....+---.++.+.|+.++|.
T Consensus 10 ~Y~erk~~lVr~~~~~~le~~~~~l~~~L~sl 41 (353)
T cd09236 10 IYDDRKDRLVNESIIDELEELTNRAHSTLRSL 41 (353)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHhC
Confidence 47899999999997555666788888888874
No 35
>TIGR01398 FlhA flagellar biosynthesis protein FlhA. This model describes flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. A separate model describes InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc., all of which score below the noise cutoff for this model.
Probab=20.88 E-value=60 Score=31.08 Aligned_cols=28 Identities=32% Similarity=0.521 Sum_probs=24.7
Q ss_pred CCCCcccHHHHHHHHHHhhhcchhHHHH
Q 032804 87 FSPGCFTEEKAKQLRKKTAESSSFHDVM 114 (133)
Q Consensus 87 f~~G~lTEEKAkqLR~~~~etesFHD~M 114 (133)
...|..||+-||+-|+++.+-..|+-+|
T Consensus 153 LnAG~I~~~eAr~RR~~l~~Ea~FyGAM 180 (678)
T TIGR01398 153 LNAGLITEEEAKKRREELEQEADFYGAM 180 (678)
T ss_pred HhCCCCCHHHHHHHHHHHHHHHHhcccc
Confidence 4459999999999999999888898777
No 36
>PF15060 PPDFL: Differentiation and proliferation regulator
Probab=20.86 E-value=61 Score=24.89 Aligned_cols=10 Identities=40% Similarity=1.182 Sum_probs=7.2
Q ss_pred CCcccccccC
Q 032804 44 STNWWAPLFG 53 (133)
Q Consensus 44 s~~WWAPLFG 53 (133)
.+.||+-.|=
T Consensus 51 ~g~WW~sfFF 60 (110)
T PF15060_consen 51 PGHWWASFFF 60 (110)
T ss_pred CCcceEEeEe
Confidence 4789996654
No 37
>TIGR01399 hrcV type III secretion protein, HrcV family. Members of this family are closely homologous to the flagellar biosynthesis protein FlhA (TIGR01398) and should all participate in type III secretion systems. Examples include InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc. Type III secretion systems resemble flagellar biogenesis systems, and may share the property of translocating special classes of peptides through the membrane.
Probab=20.61 E-value=60 Score=31.11 Aligned_cols=29 Identities=17% Similarity=0.339 Sum_probs=25.1
Q ss_pred CCCCCcccHHHHHHHHHHhhhcchhHHHH
Q 032804 86 RFSPGCFTEEKAKQLRKKTAESSSFHDVM 114 (133)
Q Consensus 86 rf~~G~lTEEKAkqLR~~~~etesFHD~M 114 (133)
..-.|..||+-||+-|+++.+-..|+-+|
T Consensus 148 DLnAGlI~~~eAr~RR~~l~~Ea~FyGAM 176 (677)
T TIGR01399 148 DLRAGVIDADEARRRRSTLEKESQLYGAM 176 (677)
T ss_pred HhhcCCCCHHHHHHHHHHHHHHHHhccCc
Confidence 34559999999999999999888898777
Done!