Query psy12362
Match_columns 92
No_of_seqs 41 out of 43
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 17:07:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12362.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12362hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2343|consensus 98.1 3E-06 6.5E-11 73.9 4.2 55 8-73 374-428 (689)
2 KOG2343|consensus 97.6 7.3E-05 1.6E-09 65.5 4.2 82 5-91 548-634 (689)
3 PF04091 Sec15: Exocyst comple 62.6 17 0.00037 28.7 4.7 34 20-55 24-57 (311)
4 KOG3039|consensus 57.7 38 0.00083 27.6 5.9 75 2-84 32-111 (303)
5 PTZ00218 40S ribosomal protein 50.3 6.7 0.00015 24.6 0.5 18 46-64 22-39 (54)
6 PF08066 PMC2NT: PMC2NT (NUC01 50.1 54 0.0012 21.4 4.8 60 32-91 23-87 (91)
7 KOG3506|consensus 46.5 13 0.00029 23.6 1.4 15 50-64 27-41 (56)
8 PF05385 Adeno_E4: Mastadenovi 46.2 1.1E+02 0.0023 21.8 6.2 53 23-75 5-57 (109)
9 PF05103 DivIVA: DivIVA protei 41.3 48 0.001 22.0 3.6 31 58-88 17-47 (131)
10 KOG2712|consensus 36.6 18 0.00038 25.7 0.9 26 66-91 79-104 (108)
11 PF10654 DUF2481: Protein of u 36.1 57 0.0012 23.7 3.5 30 59-88 7-42 (126)
12 PF12929 Mid1: Stretch-activat 28.6 82 0.0018 26.7 3.7 38 25-62 250-289 (427)
13 cd01067 globin_like superfamil 27.3 1.1E+02 0.0025 19.8 3.6 10 13-22 11-20 (117)
14 PF09278 MerR-DNA-bind: MerR, 27.3 1.1E+02 0.0025 17.8 3.3 19 50-68 6-24 (65)
15 PRK07920 lipid A biosynthesis 27.1 1.4E+02 0.0031 22.8 4.6 50 31-80 53-102 (298)
16 PRK05766 rps14P 30S ribosomal 26.7 23 0.0005 21.7 0.2 14 52-65 25-38 (52)
17 cd00454 Trunc_globin Truncated 26.4 1.7E+02 0.0038 18.7 4.4 43 30-74 7-51 (116)
18 PRK00300 gmk guanylate kinase; 26.1 1.6E+02 0.0034 20.6 4.3 18 58-75 186-203 (205)
19 PF12352 V-SNARE_C: Snare regi 25.9 91 0.002 18.6 2.7 32 59-90 29-60 (66)
20 PF01152 Bac_globin: Bacterial 25.7 68 0.0015 20.9 2.3 12 35-46 41-52 (120)
21 PF03112 DUF244: Uncharacteriz 24.8 1E+02 0.0022 23.2 3.2 41 48-88 50-92 (158)
22 PRK11702 hypothetical protein; 24.2 48 0.001 23.3 1.4 16 62-79 7-22 (108)
23 PF10168 Nup88: Nuclear pore c 23.7 5.4E+02 0.012 23.1 8.1 33 59-91 572-604 (717)
24 cd03569 VHS_Hrs_Vps27p VHS dom 22.3 2.9E+02 0.0062 19.4 5.4 44 34-77 60-114 (142)
25 TIGR00016 ackA acetate kinase. 22.2 2.4E+02 0.0053 23.8 5.4 46 31-76 298-356 (404)
26 PF11616 EZH2_WD-Binding: WD r 20.8 1.7E+02 0.0038 16.4 3.0 25 56-80 3-27 (30)
27 smart00096 UTG Uteroglobin. 20.3 41 0.00088 21.8 0.4 26 7-41 22-47 (69)
28 PF00790 VHS: VHS domain; Int 20.0 3E+02 0.0065 18.8 5.3 44 34-77 61-118 (140)
No 1
>KOG2343|consensus
Probab=98.10 E-value=3e-06 Score=73.88 Aligned_cols=55 Identities=22% Similarity=0.373 Sum_probs=48.6
Q ss_pred HHHHhhcCCcccCcCCCCCCCCCCCHHHHHHHHHHHHHhhHhHHHHHHHHhchhhHHHHHHHHHHH
Q psy12362 8 SMVRSFIAPPFLHSLYWPSPRAGFTAQGREAVESFLNHCVRPFAGLIQMCGHNRARQRDRLSHLLE 73 (92)
Q Consensus 8 ~svk~F~~pP~L~~~vlp~s~l~~d~q~~~~~d~F~~~~~~pf~~l~~~~g~NRaRQRdkL~h~le 73 (92)
-+++.|++||.|+-. +|+..++-.+..+- ..+..+|++||.|+|||||||..+++
T Consensus 374 ~~iq~~~s~~~l~~~----~pi~~~~i~q~~~~-------~~~~~~~~~c~~n~~r~~~kl~~l~~ 428 (689)
T KOG2343|consen 374 LSIQAQFSPTPLNFD----HPIMMDLIQQSSIS-------NAYGTFYESCGANLARQRDKLERLIN 428 (689)
T ss_pred HhhhhhcCCCccccc----Cchhhhhhhhhhhh-------hhHHHHHHHHhhhhHhHHHHHHhhhc
Confidence 478999999999988 99998877776632 78889999999999999999999988
No 2
>KOG2343|consensus
Probab=97.58 E-value=7.3e-05 Score=65.45 Aligned_cols=82 Identities=28% Similarity=0.331 Sum_probs=72.9
Q ss_pred hhhHHHHhhcCCc----ccCcCCCCCCCCCCC-HHHHHHHHHHHHHhhHhHHHHHHHHhchhhHHHHHHHHHHHHHHHhh
Q psy12362 5 TGASMVRSFIAPP----FLHSLYWPSPRAGFT-AQGREAVESFLNHCVRPFAGLIQMCGHNRARQRDRLSHLLEEFAALQ 79 (92)
Q Consensus 5 ~g~~svk~F~~pP----~L~~~vlp~s~l~~d-~q~~~~~d~F~~~~~~pf~~l~~~~g~NRaRQRdkL~h~lee~~~LQ 79 (92)
+-...+|.|.++| ++.|+ +...+. .+...+++.|.+.++.|++...+.-|+++.+||| +.+..+++...|
T Consensus 548 l~~G~~~~~val~~~G~I~~Pk----~~f~nE~~ry~~rF~PF~sl~~P~~~~Ye~Fk~~~~~~q~~-~~~ieel~~~aq 622 (689)
T KOG2343|consen 548 LCKGMLRLFVALPRDGIILKPK----GKFDNEELRYNRRFEPFNSLGVPPPVSYEQFKGHSDIRQRD-LGSIEELFATAQ 622 (689)
T ss_pred HHHHHHHHhhhcccCCcccCCC----CCcchHHHHHHHhhhhHhhcCCCCCccHHHHhhhhHHhhcc-ccchHHHHHHHH
Confidence 3456789999999 66666 888765 4889999999999999999999999999999999 999999999999
Q ss_pred HHHHhHhhhccC
Q psy12362 80 DEKSKIRAGNSE 91 (92)
Q Consensus 80 ~EAe~vD~~l~~ 91 (92)
.+++++++.|.-
T Consensus 623 k~f~~ak~~L~n 634 (689)
T KOG2343|consen 623 KSFDEAKNGLEN 634 (689)
T ss_pred HHHHHHHHHHhc
Confidence 999999988753
No 3
>PF04091 Sec15: Exocyst complex subunit Sec15-like ; InterPro: IPR007225 Sec15 is a component of the exocyst complex involved in the docking of exocystic vesicles with a fusion site on the plasma membrane. The exocyst complex is composed of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84.; GO: 0006904 vesicle docking involved in exocytosis, 0000145 exocyst; PDB: 2A2F_X.
Probab=62.56 E-value=17 Score=28.70 Aligned_cols=34 Identities=18% Similarity=0.224 Sum_probs=21.5
Q ss_pred CcCCCCCCCCCCCHHHHHHHHHHHHHhhHhHHHHHH
Q psy12362 20 HSLYWPSPRAGFTAQGREAVESFLNHCVRPFAGLIQ 55 (92)
Q Consensus 20 ~~~vlp~s~l~~d~q~~~~~d~F~~~~~~pf~~l~~ 55 (92)
-|..+|+|+.+ |.++..+.+|++.|+.=..++++
T Consensus 24 fP~~lPFS~~v--p~~c~~ir~fi~~~~~F~~~~~~ 57 (311)
T PF04091_consen 24 FPKKLPFSQMV--PMCCRQIRSFIEKCYKFSDDLYQ 57 (311)
T ss_dssp ----SSSBTHH--HHHHHHHHHHHHHHHHHHHHTT-
T ss_pred CCeeCCCchHH--HHHHHHHHHHHHHHHHHHHhccc
Confidence 35788999987 88888888888777654444433
No 4
>KOG3039|consensus
Probab=57.71 E-value=38 Score=27.63 Aligned_cols=75 Identities=16% Similarity=0.066 Sum_probs=41.7
Q ss_pred chhhhhHHHHhhcC-----CcccCcCCCCCCCCCCCHHHHHHHHHHHHHhhHhHHHHHHHHhchhhHHHHHHHHHHHHHH
Q psy12362 2 RIATGASMVRSFIA-----PPFLHSLYWPSPRAGFTAQGREAVESFLNHCVRPFAGLIQMCGHNRARQRDRLSHLLEEFA 76 (92)
Q Consensus 2 ~~~~g~~svk~F~~-----pP~L~~~vlp~s~l~~d~q~~~~~d~F~~~~~~pf~~l~~~~g~NRaRQRdkL~h~lee~~ 76 (92)
|+-||+||||.|=+ .|-.+|-+-|..-|+.-.-+-|++-.=- +-+..=+.. ..+||+.=....++-+
T Consensus 32 ~~RLgrDsiK~FdcCsLtLqPc~dPvit~~GylfdrEaILe~ilaqK----ke~arrlka----yekqrr~eed~e~qra 103 (303)
T KOG3039|consen 32 RERLGRDSIKPFDCCSLTLQPCRDPVITPDGYLFDREAILEYILAQK----KEIARRLKA----YEKQRRAEEDKEEQRA 103 (303)
T ss_pred hhhhcccccCCcceeeeecccccCCccCCCCeeeeHHHHHHHHHHHH----HHHHHHHHH----HHHHHHhhhhHHHHHH
Confidence 57799999999943 2233333333377772223333332222 223222222 2467766667777788
Q ss_pred HhhHHHHh
Q psy12362 77 ALQDEKSK 84 (92)
Q Consensus 77 ~LQ~EAe~ 84 (92)
+.|.+++-
T Consensus 104 ~~q~~~~~ 111 (303)
T KOG3039|consen 104 MSQKARRL 111 (303)
T ss_pred HhhhHHHH
Confidence 88887654
No 5
>PTZ00218 40S ribosomal protein S29; Provisional
Probab=50.35 E-value=6.7 Score=24.59 Aligned_cols=18 Identities=44% Similarity=0.698 Sum_probs=14.3
Q ss_pred hhHhHHHHHHHHhchhhHH
Q psy12362 46 CVRPFAGLIQMCGHNRARQ 64 (92)
Q Consensus 46 ~~~pf~~l~~~~g~NRaRQ 64 (92)
|.++ -.+||.||+|-|||
T Consensus 22 Cg~~-~gliRkygL~~CRq 39 (54)
T PTZ00218 22 CSNR-HGLIRKYGLNVCRQ 39 (54)
T ss_pred CCCc-chhhhhcCcchhhH
Confidence 3344 37999999999998
No 6
>PF08066 PMC2NT: PMC2NT (NUC016) domain; InterPro: IPR012588 Exosomes are nano-compartments that function in the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA) [, ]. Exosomes occur in both archaea and eukaryotes, and have a similar overall structure to each other and to bacterial/organelle PNPases (polynucleotide phosphorylases; 2.7.7.8 from EC) [], consisting of a barrel structure composed of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. There are two types of exosomes in eukaryotes, cytoplasmic exosomes that are responsible for 3'-5' exoribonuclease degradation of mRNAs, and nuclear exosomes that degrade pre-mRNAs (such as nonsense transcripts) and degrade rRNAs, snRNAs and snoRNAs. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. There are several accessory proteins that help degrade, unwind or polyadenylate RNA substrate before they enter the exosome. This entry represents the N-terminal domain of Rrp6 (exosome component 10 in humans), a nuclear exosome accessory factor that interacts with the bottom of the hexameric PH-ring opposite the cap. Rrp6 functions as a hydrolytic exonuclease, and is homologous to RNase-D in Escherichia coli. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0006396 RNA processing, 0000176 nuclear exosome (RNase complex)
Probab=50.11 E-value=54 Score=21.35 Aligned_cols=60 Identities=12% Similarity=0.139 Sum_probs=39.9
Q ss_pred CHHHHHHHHHHHHHhhHhHHHHHHHHhchhhHHHHH-HHHHHHHHHHhhHH----HHhHhhhccC
Q psy12362 32 TAQGREAVESFLNHCVRPFAGLIQMCGHNRARQRDR-LSHLLEEFAALQDE----KSKIRAGNSE 91 (92)
Q Consensus 32 d~q~~~~~d~F~~~~~~pf~~l~~~~g~NRaRQRdk-L~h~lee~~~LQ~E----Ae~vD~~l~~ 91 (92)
||..++.++..=++.......+++..|.+.--.... ..-.=+.|..+.+= -|++|..|+|
T Consensus 23 dp~f~~~ld~~s~rll~l~n~ll~~~~~~~~~~~~~~~~d~d~~~~~vvd~~D~LlEk~D~~LDe 87 (91)
T PF08066_consen 23 DPEFAESLDEQSQRLLSLINSLLKSAGSKSNISSPDDVDDVDERWDSVVDVNDSLLEKADISLDE 87 (91)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhccccccccCCCccccHHHHHHHHHHHHHHHHHHHhHHHHh
Confidence 789999999999999999999999998886554433 11111222222221 3677777765
No 7
>KOG3506|consensus
Probab=46.49 E-value=13 Score=23.57 Aligned_cols=15 Identities=47% Similarity=0.547 Sum_probs=13.5
Q ss_pred HHHHHHHHhchhhHH
Q psy12362 50 FAGLIQMCGHNRARQ 64 (92)
Q Consensus 50 f~~l~~~~g~NRaRQ 64 (92)
+-+|||-||+|-|||
T Consensus 27 ~~gLIrKYGL~vcr~ 41 (56)
T KOG3506|consen 27 RHGLIRKYGLNVCRQ 41 (56)
T ss_pred chhHHHHhhhHHhHH
Confidence 568999999999998
No 8
>PF05385 Adeno_E4: Mastadenovirus early E4 13 kDa protein; InterPro: IPR008680 This family consists of Homo sapiens and simian mastadenovirus early E4 13 kDa proteins. Human adenovirus 9 (HAdV-9) is unique in eliciting exclusively estrogen-dependent mammary tumours in Rattus spp. and in not requiring viral E1 region transforming genes for tumorigenicity. E4 codes for an oncoprotein essential for tumourigenesis by Ad9 [].
Probab=46.21 E-value=1.1e+02 Score=21.81 Aligned_cols=53 Identities=19% Similarity=0.085 Sum_probs=27.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhhHhHHHHHHHHhchhhHHHHHHHHHHHHH
Q psy12362 23 YWPSPRAGFTAQGREAVESFLNHCVRPFAGLIQMCGHNRARQRDRLSHLLEEF 75 (92)
Q Consensus 23 vlp~s~l~~d~q~~~~~d~F~~~~~~pf~~l~~~~g~NRaRQRdkL~h~lee~ 75 (92)
.||.+||..|++++=.+-.+--..+--.+.-++..|.+-+=-=..|=+.|-||
T Consensus 5 ~LPpPPv~rd~~~Ci~WLglA~at~~Dv~r~ir~~g~~ispeAe~lL~~LrEW 57 (109)
T PF05385_consen 5 SLPPPPVCRDQSACIAWLGLAYATVVDVIRAIRRDGVFISPEAERLLTGLREW 57 (109)
T ss_pred CCCCCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHcCeeECHHHHHHHHHHHHH
Confidence 47889999899877665554333333333334444544433333333333333
No 9
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=41.29 E-value=48 Score=21.97 Aligned_cols=31 Identities=29% Similarity=0.427 Sum_probs=15.9
Q ss_pred hchhhHHHHHHHHHHHHHHHhhHHHHhHhhh
Q psy12362 58 GHNRARQRDRLSHLLEEFAALQDEKSKIRAG 88 (92)
Q Consensus 58 g~NRaRQRdkL~h~lee~~~LQ~EAe~vD~~ 88 (92)
|+|+.-.-+-|..+..++..|+.|-..+...
T Consensus 17 GYd~~eVD~fl~~l~~~~~~l~~e~~~L~~~ 47 (131)
T PF05103_consen 17 GYDPDEVDDFLDELAEELERLQRENAELKEE 47 (131)
T ss_dssp EEEHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5555555555555555555555554444443
No 10
>KOG2712|consensus
Probab=36.60 E-value=18 Score=25.65 Aligned_cols=26 Identities=19% Similarity=0.307 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHhhHHHHhHhhhccC
Q psy12362 66 DRLSHLLEEFAALQDEKSKIRAGNSE 91 (92)
Q Consensus 66 dkL~h~lee~~~LQ~EAe~vD~~l~~ 91 (92)
--++-.++.|+.|-..++.||..|+.
T Consensus 79 KGISLs~~qW~~Lk~~~~eId~Al~~ 104 (108)
T KOG2712|consen 79 KGISLSLEQWSKLKEHIEEIDKALRK 104 (108)
T ss_pred cccccCHHHHHHHHHHHHHHHHHHHH
Confidence 34667889999999999999998865
No 11
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=36.07 E-value=57 Score=23.65 Aligned_cols=30 Identities=30% Similarity=0.410 Sum_probs=23.7
Q ss_pred chhhHHHHHHHHHH------HHHHHhhHHHHhHhhh
Q psy12362 59 HNRARQRDRLSHLL------EEFAALQDEKSKIRAG 88 (92)
Q Consensus 59 ~NRaRQRdkL~h~l------ee~~~LQ~EAe~vD~~ 88 (92)
-|.+|||.-+++++ .+.-.||.|-..+-.+
T Consensus 7 ~NKerQreIIsyl~n~dl~~~~~k~LqkeLn~Lm~~ 42 (126)
T PF10654_consen 7 ENKERQREIISYLVNNDLSFSKRKELQKELNQLMNE 42 (126)
T ss_pred hhHHHHHHHHHHHHhCCCChHHHHHHHHHHHHHHhc
Confidence 59999999999985 5677889887666443
No 12
>PF12929 Mid1: Stretch-activated Ca2+-permeable channel component; InterPro: IPR024338 Mid1 is a yeast plasma membrane protein required for Ca2+ influx induced by the mating pheromone alpha-factor during the mating process [, , ]. The protein is composed of 548-amino-acid residues, contains four hydrophobic regions (H1, H2, H3 and H4) and two cysteine-rich regions (C1 and C2) at the C terminus. H1 appears to be a signal sequence necessary for the alpha-factor-induced delivery to the plasma membrane. The region from H1 to H3 is required for the localisation of Mid1 in the plasma and ER membranes. C1 and C2 are thought to be involved in oligomerisation via the formation of disulphide bonds. Trafficking of Mid1-GFP to the plasma membrane is dependent on the N-glycosylation of Mid1 and the transporter protein Sec12. This suggests that the trafficking of Mid1-GFP to the plasma membrane requires a Sec12-dependent pathway from the ER to the Golgi, and that Mid1 is recruited via a Sec6- and Sec7-independent pathway from the Golgi to the plasma membrane.
Probab=28.62 E-value=82 Score=26.68 Aligned_cols=38 Identities=13% Similarity=0.075 Sum_probs=34.0
Q ss_pred CCCCCC--CCHHHHHHHHHHHHHhhHhHHHHHHHHhchhh
Q psy12362 25 PSPRAG--FTAQGREAVESFLNHCVRPFAGLIQMCGHNRA 62 (92)
Q Consensus 25 p~s~l~--~d~q~~~~~d~F~~~~~~pf~~l~~~~g~NRa 62 (92)
|++|-. +....++.+|.....+.+-|...++.+-||+-
T Consensus 250 P~np~~~~n~t~L~~~YD~~A~~~Y~NFs~sL~qi~C~t~ 289 (427)
T PF12929_consen 250 PSNPSFFYNKTELAKFYDDYAKSLYANFSKSLQQIPCNTD 289 (427)
T ss_pred ccCcccccCHHHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 667776 77899999999999999999999999999864
No 13
>cd01067 globin_like superfamily containing globins and truncated hemoglobins
Probab=27.33 E-value=1.1e+02 Score=19.80 Aligned_cols=10 Identities=30% Similarity=0.315 Sum_probs=4.8
Q ss_pred hcCCcccCcC
Q psy12362 13 FIAPPFLHSL 22 (92)
Q Consensus 13 F~~pP~L~~~ 22 (92)
|-.+|.+.+.
T Consensus 11 f~~~P~~~~~ 20 (117)
T cd01067 11 FENYPPLRKY 20 (117)
T ss_pred HHhChhHHHH
Confidence 3344555544
No 14
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=27.32 E-value=1.1e+02 Score=17.79 Aligned_cols=19 Identities=21% Similarity=0.294 Sum_probs=8.7
Q ss_pred HHHHHHHHhchhhHHHHHH
Q psy12362 50 FAGLIQMCGHNRARQRDRL 68 (92)
Q Consensus 50 f~~l~~~~g~NRaRQRdkL 68 (92)
|+.-++..|...+=.|+-+
T Consensus 6 ~I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 6 FIRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 3444455555555555555
No 15
>PRK07920 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=27.08 E-value=1.4e+02 Score=22.81 Aligned_cols=50 Identities=16% Similarity=0.150 Sum_probs=37.9
Q ss_pred CCHHHHHHHHHHHHHhhHhHHHHHHHHhchhhHHHHHHHHHHHHHHHhhH
Q psy12362 31 FTAQGREAVESFLNHCVRPFAGLIQMCGHNRARQRDRLSHLLEEFAALQD 80 (92)
Q Consensus 31 ~d~q~~~~~d~F~~~~~~pf~~l~~~~g~NRaRQRdkL~h~lee~~~LQ~ 80 (92)
+..+.++....++.++.+.+..++.....+..+.++.+...++++.+|+.
T Consensus 53 s~~e~~~i~~~~~~~~~~~~~E~~~~~~~~~~~~~~~v~i~~~g~e~l~~ 102 (298)
T PRK07920 53 PAAVLDALVRAAMRSYARYWREAFRLPSMSRERLAARVRVSIEGLEHLDA 102 (298)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHhhhhhccCCHHHHHH
Confidence 46799999999999999999999999888877666544221266666544
No 16
>PRK05766 rps14P 30S ribosomal protein S14P; Reviewed
Probab=26.66 E-value=23 Score=21.68 Aligned_cols=14 Identities=43% Similarity=0.501 Sum_probs=12.1
Q ss_pred HHHHHHhchhhHHH
Q psy12362 52 GLIQMCGHNRARQR 65 (92)
Q Consensus 52 ~l~~~~g~NRaRQR 65 (92)
++|+.||+|.|||-
T Consensus 25 gvirkf~l~lcR~~ 38 (52)
T PRK05766 25 GLIRKYGLYLCRQC 38 (52)
T ss_pred eeHHhhCCcccHHH
Confidence 68999999999874
No 17
>cd00454 Trunc_globin Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct from the three-over-three pattern found in other globins. A subset of these have been demonstrated to form homodimers.
Probab=26.45 E-value=1.7e+02 Score=18.71 Aligned_cols=43 Identities=19% Similarity=0.310 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHHHHHHhh-HhH-HHHHHHHhchhhHHHHHHHHHHHH
Q psy12362 30 GFTAQGREAVESFLNHCV-RPF-AGLIQMCGHNRARQRDRLSHLLEE 74 (92)
Q Consensus 30 ~~d~q~~~~~d~F~~~~~-~pf-~~l~~~~g~NRaRQRdkL~h~lee 74 (92)
...+.+.+.++.|.+++. .|- ..++ -+.|..+|++++...+..
T Consensus 7 GG~~~i~~lv~~FY~~i~~dp~i~~~F--~~~~~~~~~~~~~~fl~~ 51 (116)
T cd00454 7 GGEEAIRALVDRFYARVAADPRLGPIF--PADDLEEHRAKLADFLTQ 51 (116)
T ss_pred CCHHHHHHHHHHHHHHHhcChHHHHhc--CCcchHHHHHHHHHHHHH
Confidence 344666777777776654 221 1111 134466777666655543
No 18
>PRK00300 gmk guanylate kinase; Provisional
Probab=26.13 E-value=1.6e+02 Score=20.59 Aligned_cols=18 Identities=39% Similarity=0.617 Sum_probs=14.4
Q ss_pred hchhhHHHHHHHHHHHHH
Q psy12362 58 GHNRARQRDRLSHLLEEF 75 (92)
Q Consensus 58 g~NRaRQRdkL~h~lee~ 75 (92)
..+++||-+|...+|+++
T Consensus 186 ~~~~~~~~~~~~~~~~~~ 203 (205)
T PRK00300 186 RLRRSRQQQRHAELIEEL 203 (205)
T ss_pred HhhhhhhHHHHHHHHHHh
Confidence 345889999999888876
No 19
>PF12352 V-SNARE_C: Snare region anchored in the vesicle membrane C-terminus; PDB: 1GL2_C 2NPS_C.
Probab=25.94 E-value=91 Score=18.57 Aligned_cols=32 Identities=13% Similarity=0.207 Sum_probs=24.8
Q ss_pred chhhHHHHHHHHHHHHHHHhhHHHHhHhhhcc
Q psy12362 59 HNRARQRDRLSHLLEEFAALQDEKSKIRAGNS 90 (92)
Q Consensus 59 ~NRaRQRdkL~h~lee~~~LQ~EAe~vD~~l~ 90 (92)
.+...||++|..+=..+..+...-...+.-+.
T Consensus 29 ~~L~~Qre~L~~~~~kl~~i~~~l~~s~~~l~ 60 (66)
T PF12352_consen 29 EDLRSQREQLKRVRDKLDDIDSNLPKSNSLLK 60 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 46788999999998888888877766665543
No 20
>PF01152 Bac_globin: Bacterial-like globin; InterPro: IPR001486 Globins are haem-containing proteins involved in binding and/or transporting oxygen. They belong to a very large and well studied family that is widely distributed in many organisms []. Globins have evolved from a common ancestor and can be divided into three groups: single-domain globins, and two types of chimeric globins, flavohaemoglobins and globin-coupled sensors. Bacteria have all three types of globins, while archaea lack flavohaemoglobins, and eukaryotes lack globin-coupled sensors []. Several functionally different haemoglobins can coexist in the same species. The major types of globins include: Haemoglobin (Hb): trimer of two alpha and two beta chains, although embryonic and foetal forms can substitute the alpha or beta chain for ones with higher oxygen affinity, such as gamma, delta, epsilon or zeta chains. Hb transports oxygen from lungs to other tissues in vertebrates []. Hb proteins are also present in unicellular organisms where they act as enzymes or sensors []. Myoglobin (Mb): monomeric protein responsible for oxygen storage in vertebrate muscle []. Neuroglobin: a myoglobin-like haemprotein expressed in vertebrate brain and retina, where it is involved in neuroprotection from damage due to hypoxia or ischemia []. Neuroglobin belongs to a branch of the globin family that diverged early in evolution. Cytoglobin: an oxygen sensor expressed in multiple tissues. Related to neuroglobin []. Erythrocruorin: highly cooperative extracellular respiratory proteins found in annelids and arthropods that are assembled from as many as 180 subunit into hexagonal bilayers []. Leghaemoglobin (legHb or symbiotic Hb): occurs in the root nodules of leguminous plants, where it facilitates the diffusion of oxygen to symbiotic bacteriods in order to promote nitrogen fixation. Non-symbiotic haemoglobin (NsHb): occurs in non-leguminous plants, and can be over-expressed in stressed plants []. Flavohaemoglobins (FHb): chimeric, with an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD/FAD-binding domain. FHb provides protection against nitric oxide via its C-terminal domain, which transfers electrons to haem in the globin []. Globin-coupled sensors: chimeric, with an N-terminal myoglobin-like domain and a C-terminal domain that resembles the cytoplasmic signalling domain of bacterial chemoreceptors. They bind oxygen, and act to initiate an aerotactic response or regulate gene expression [, ]. Protoglobin: a single domain globin found in archaea that is related to the N-terminal domain of globin-coupled sensors []. Truncated 2/2 globin: lack the first helix, giving them a 2-over-2 instead of the canonical 3-over-3 alpha-helical sandwich fold. Can be divided into three main groups (I, II and II) based on structural features []. This entry represents a group of haemoglobin-like proteins found in eubacteria, cyanobacteria, protozoa, algae and plants, but not in animals or yeast. These proteins have a truncated 2-over-2 rather than the canonical 3-over-3 alpha-helical sandwich fold []. This entry includes: HbN (or GlbN): a truncated haemoglobin-like protein that binds oxygen cooperatively with a very high affinity and a slow dissociation rate, which may exclude it from oxygen transport. It appears to be involved in bacterial nitric oxide detoxification and in nitrosative stress []. Cyanoglobin (or GlbN): a truncated haemoprotein found in cyanobacteria that has high oxygen affinity, and which appears to serve as part of a terminal oxidase, rather than as a respiratory pigment []. HbO (or GlbO): a truncated haemoglobin-like protein with a lower oxygen affinity than HbN. HbO associates with the bacterial cell membrane, where it significantly increases oxygen uptake over membranes lacking this protein. HbO appears to interact with a terminal oxidase, and could participate in an oxygen/electron-transfer process that facilitates oxygen transfer during aerobic metabolism []. Glb3: a nuclear-encoded truncated haemoglobin from plants that appears more closely related to HbO than HbN. Glb3 from Arabidopsis thaliana (Mouse-ear cress) exhibits an unusual concentration-independent binding of oxygen and carbon dioxide []. ; GO: 0019825 oxygen binding, 0015671 oxygen transport; PDB: 2BKM_B 1UVY_A 1DLW_A 2XYK_B 2IG3_A 2GKM_B 1S61_A 1S56_B 1RTE_B 2GLN_A ....
Probab=25.67 E-value=68 Score=20.94 Aligned_cols=12 Identities=25% Similarity=0.412 Sum_probs=5.1
Q ss_pred HHHHHHHHHHHh
Q psy12362 35 GREAVESFLNHC 46 (92)
Q Consensus 35 ~~~~~d~F~~~~ 46 (92)
.++.+-.|+...
T Consensus 41 ~~~~~~~fl~~~ 52 (120)
T PF01152_consen 41 HKEKQAEFLSQL 52 (120)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH
Confidence 344444444433
No 21
>PF03112 DUF244: Uncharacterized protein family (ORF7) DUF; InterPro: IPR004335 Many of the proteins in this entry are Borrelia burgdorferi plasmid proteins of unknown function.
Probab=24.81 E-value=1e+02 Score=23.21 Aligned_cols=41 Identities=24% Similarity=0.276 Sum_probs=31.4
Q ss_pred HhHHHHHHHHhchh-hHHHHH-HHHHHHHHHHhhHHHHhHhhh
Q psy12362 48 RPFAGLIQMCGHNR-ARQRDR-LSHLLEEFAALQDEKSKIRAG 88 (92)
Q Consensus 48 ~pf~~l~~~~g~NR-aRQRdk-L~h~lee~~~LQ~EAe~vD~~ 88 (92)
+-|+..+.+.-++- ..|... |.+.|.|.+.||-|++++...
T Consensus 50 ~eFveyV~cvdLeI~~eq~a~nLe~~L~EI~~lq~ElnKiqnE 92 (158)
T PF03112_consen 50 DEFVEYVDCVDLEIKTEQSAENLECSLMEIDSLQTELNKIQNE 92 (158)
T ss_pred HHHHHHHHHHHhhccchHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 56777777666653 445544 999999999999999998754
No 22
>PRK11702 hypothetical protein; Provisional
Probab=24.19 E-value=48 Score=23.30 Aligned_cols=16 Identities=31% Similarity=0.665 Sum_probs=12.9
Q ss_pred hHHHHHHHHHHHHHHHhh
Q psy12362 62 ARQRDRLSHLLEEFAALQ 79 (92)
Q Consensus 62 aRQRdkL~h~lee~~~LQ 79 (92)
.|||.||. |.||..|=
T Consensus 7 RRlRKKL~--v~EFqeLG 22 (108)
T PRK11702 7 RRLRKKMH--IDEFQELG 22 (108)
T ss_pred HHHHhhhh--hHhhHhhe
Confidence 37999997 88888774
No 23
>PF10168 Nup88: Nuclear pore component; InterPro: IPR019321 Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein have no obvious structural motifs. It is, however, where it binds to Nup98; one of the components of the nuclear pore. The C-terminal end is a predicted coiled-coil domain []. Nup88 is over expressed in tumour cells [].
Probab=23.67 E-value=5.4e+02 Score=23.13 Aligned_cols=33 Identities=24% Similarity=0.347 Sum_probs=24.8
Q ss_pred chhhHHHHHHHHHHHHHHHhhHHHHhHhhhccC
Q psy12362 59 HNRARQRDRLSHLLEEFAALQDEKSKIRAGNSE 91 (92)
Q Consensus 59 ~NRaRQRdkL~h~lee~~~LQ~EAe~vD~~l~~ 91 (92)
.-..+|.++|+.+-++-..|+..|+++...+.+
T Consensus 572 ~~~e~Ql~~L~~l~e~~~~l~~~ae~LaeR~e~ 604 (717)
T PF10168_consen 572 QQKEQQLKELQELQEERKSLRESAEKLAERYEE 604 (717)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344567778888888888888888888776544
No 24
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=22.25 E-value=2.9e+02 Score=19.39 Aligned_cols=44 Identities=16% Similarity=0.263 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHhhHhHHHHHHHHh-----------chhhHHHHHHHHHHHHHHH
Q psy12362 34 QGREAVESFLNHCVRPFAGLIQMCG-----------HNRARQRDRLSHLLEEFAA 77 (92)
Q Consensus 34 q~~~~~d~F~~~~~~pf~~l~~~~g-----------~NRaRQRdkL~h~lee~~~ 77 (92)
.+-.++|.++++|..+|-.-+-+-. .--.+.++|+-.+|.+|+.
T Consensus 60 ~AL~LLe~~vkNCG~~fh~evas~~fl~~l~~l~~~~~~~~Vk~kil~li~~W~~ 114 (142)
T cd03569 60 YALLLLESCVKNCGTHFHDEVASREFMDELKDLIKTTKNEEVRQKILELIQAWAL 114 (142)
T ss_pred HHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHHcccCCHHHHHHHHHHHHHHHH
Confidence 5667788888888776655443322 1223689999999999984
No 25
>TIGR00016 ackA acetate kinase. Acetate kinase is involved in the activation of acetate to acetyl CoA and in the secretion of acetate. It catalyzes the reaction ATP + acetate = ADP + acetyl phosphate. Some members of this family have been shown to act on propionate as well as acetate. An example of a propionate/acetate kinase is TdcD of E. coli, an enzyme of an anaerobic pathway of threonine catabolism. It is not known how many members of this family act on additional substrates besides acetate.
Probab=22.22 E-value=2.4e+02 Score=23.75 Aligned_cols=46 Identities=17% Similarity=0.180 Sum_probs=40.3
Q ss_pred CCHHHHHHHHHHHHHhhHhHHHHHHHHhc-------------hhhHHHHHHHHHHHHHH
Q psy12362 31 FTAQGREAVESFLNHCVRPFAGLIQMCGH-------------NRARQRDRLSHLLEEFA 76 (92)
Q Consensus 31 ~d~q~~~~~d~F~~~~~~pf~~l~~~~g~-------------NRaRQRdkL~h~lee~~ 76 (92)
.|++++..+|.|.-+..+-...+.-..|- |-++.|+++|.-|+=+.
T Consensus 298 gd~~A~lA~~~f~yri~k~Iga~~a~L~G~vDaiVFTGGIGEns~~vr~~i~~~l~~lG 356 (404)
T TIGR00016 298 GNEQAQLAIKMYVHRIAKYIGSYIASLEGNLDAIVFTGGIGENAATVRELVLEALEFLG 356 (404)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCEEEEcCccccCCHHHHHHHHhhhhhcC
Confidence 37899999999999999999998888875 99999999999887543
No 26
>PF11616 EZH2_WD-Binding: WD repeat binding protein EZH2; InterPro: IPR021654 This family of proteins represents Enhancer of zest homologue 2, (EZH2) a 30 residue peptide which binds to a WD-repeat domain of EED by residues 39-68. EED is a component of PRC2 complex which is involved in gene expression []. This interaction is required for the HMTase activity of PCR2 []. ; GO: 0018024 histone-lysine N-methyltransferase activity; PDB: 2QXV_B.
Probab=20.76 E-value=1.7e+02 Score=16.36 Aligned_cols=25 Identities=28% Similarity=0.400 Sum_probs=19.2
Q ss_pred HHhchhhHHHHHHHHHHHHHHHhhH
Q psy12362 56 MCGHNRARQRDRLSHLLEEFAALQD 80 (92)
Q Consensus 56 ~~g~NRaRQRdkL~h~lee~~~LQ~ 80 (92)
.|-.||+..-++--.+=+||..|-.
T Consensus 3 lf~sNr~Ki~e~t~iLN~eWk~lRi 27 (30)
T PF11616_consen 3 LFSSNRQKIQERTDILNEEWKKLRI 27 (30)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH---
T ss_pred hhHhhHHHHHHHHHHHHHHHHHhcc
Confidence 4667999999999999999998743
No 27
>smart00096 UTG Uteroglobin.
Probab=20.31 E-value=41 Score=21.82 Aligned_cols=26 Identities=15% Similarity=0.243 Sum_probs=18.3
Q ss_pred hHHHHhhcCCcccCcCCCCCCCCCCCHHHHHHHHH
Q psy12362 7 ASMVRSFIAPPFLHSLYWPSPRAGFTAQGREAVES 41 (92)
Q Consensus 7 ~~svk~F~~pP~L~~~vlp~s~l~~d~q~~~~~d~ 41 (92)
..+++.|..||.+..- -.|+++|+|+
T Consensus 22 ~~~l~~y~~~~~~~ea---------~~~lK~cvD~ 47 (69)
T smart00096 22 EASLKQFKPDPDMLEA---------GRQLKKLVDT 47 (69)
T ss_pred HHHHHhcCCCHHHHHH---------HHHHHHHHhc
Confidence 3467777777766533 4588999998
No 28
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=20.03 E-value=3e+02 Score=18.80 Aligned_cols=44 Identities=14% Similarity=0.291 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhhHhHHH---------HHHH-----HhchhhHHHHHHHHHHHHHHH
Q psy12362 34 QGREAVESFLNHCVRPFAG---------LIQM-----CGHNRARQRDRLSHLLEEFAA 77 (92)
Q Consensus 34 q~~~~~d~F~~~~~~pf~~---------l~~~-----~g~NRaRQRdkL~h~lee~~~ 77 (92)
.+-..+|..+++|..+|-. .+.. ...+..+.|+|+-.+|.+|+.
T Consensus 61 ~aL~lld~lvkNcg~~f~~ev~~~~fl~~l~~l~~~~~~~~~~~Vk~k~l~ll~~W~~ 118 (140)
T PF00790_consen 61 LALTLLDALVKNCGPRFHREVASKEFLDELVKLIKSKKTDPETPVKEKILELLQEWAE 118 (140)
T ss_dssp HHHHHHHHHHHHSHHHHHHHHTSHHHHHHHHHHHHHTTTHHHSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHhHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHHHHH
Confidence 5667788888888655533 3332 223334489999999999975
Done!