Query psy17963
Match_columns 943
No_of_seqs 3 out of 5
Neff 1.0
Searched_HMMs 46136
Date Fri Aug 16 18:51:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17963.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17963hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03422 CBM_6: Carbohydrate b 76.2 3.1 6.8E-05 34.8 3.4 56 57-112 39-112 (125)
2 COG4067 Uncharacterized protei 71.4 8.2 0.00018 38.1 5.4 109 13-128 22-141 (162)
3 smart00276 GLECT Galectin. Gal 62.7 22 0.00047 31.2 5.9 33 98-136 94-126 (128)
4 cd00025 BPI1 BPI/LBP/CETP N-te 52.9 47 0.001 31.8 6.8 83 88-170 58-145 (223)
5 PF05618 Zn_protease: Putative 52.8 31 0.00067 32.1 5.4 58 75-133 58-128 (138)
6 smart00606 CBD_IV Cellulose Bi 50.5 64 0.0014 27.4 6.6 33 63-95 53-92 (129)
7 KOG3939|consensus 50.2 9.1 0.0002 40.4 1.7 31 90-120 85-115 (312)
8 PF09792 But2: Ubiquitin 3 bin 47.8 80 0.0017 29.6 7.3 21 1-21 3-23 (143)
9 COG0249 MutS Mismatch repair A 45.6 5.5 0.00012 46.0 -0.8 67 63-150 550-616 (843)
10 cd08023 GH16_laminarinase_like 40.7 2.8E+02 0.0061 25.9 9.8 33 135-167 197-231 (235)
11 cd00070 GLECT Galectin/galacto 39.6 78 0.0017 27.6 5.6 31 99-135 96-126 (127)
12 KOG1322|consensus 36.3 21 0.00045 38.8 1.8 94 2-138 252-349 (371)
13 PF03292 Pox_P4B: Poxvirus P4B 35.1 71 0.0015 37.0 5.7 57 93-160 445-502 (666)
14 PF13115 YtkA: YtkA-like 31.5 1.2E+02 0.0027 24.3 5.1 25 86-110 24-48 (86)
15 PF09315 DUF1973: Domain of un 31.3 1.5E+02 0.0032 28.7 6.5 14 144-157 74-87 (179)
16 PF13897 GOLD_2: Golgi-dynamic 30.3 43 0.00092 32.4 2.6 21 76-110 5-25 (136)
17 PLN03103 GDP-L-galactose-hexos 29.3 8 0.00017 41.9 -2.6 36 81-117 6-41 (403)
18 PF01803 LIM_bind: LIM-domain 28.9 56 0.0012 31.6 3.2 66 71-138 69-134 (240)
19 PRK10767 chaperone protein Dna 28.0 3E+02 0.0066 28.4 8.5 63 75-137 210-288 (371)
20 PRK14301 chaperone protein Dna 26.3 3.7E+02 0.0081 28.1 8.8 64 75-138 212-291 (373)
21 KOG0536|consensus 26.2 49 0.0011 32.4 2.3 43 27-69 1-50 (145)
22 PF05326 SVA: Seminal vesicle 26.0 30 0.00066 32.8 0.8 36 117-155 67-103 (124)
23 PF01847 VHL: von Hippel-Linda 25.6 59 0.0013 31.8 2.7 58 77-155 8-65 (156)
24 PRK14285 chaperone protein Dna 24.2 2.8E+02 0.006 28.9 7.4 63 75-137 214-292 (365)
25 cd05722 Ig1_Neogenin First imm 24.0 2.2E+02 0.0048 22.8 5.4 42 102-143 28-77 (95)
26 PRK00892 lpxD UDP-3-O-[3-hydro 23.8 2E+02 0.0044 29.1 6.2 7 123-129 243-249 (343)
27 KOG0517|consensus 23.6 23 0.0005 44.9 -0.5 33 11-47 182-217 (2473)
28 PRK14293 chaperone protein Dna 23.3 3.9E+02 0.0085 27.8 8.3 63 76-138 216-294 (374)
29 PRK10658 putative alpha-glucos 22.8 2.4E+02 0.0053 31.9 7.2 77 21-102 3-81 (665)
30 COG3962 Acetolactate synthase 22.3 32 0.00069 39.1 0.3 71 99-170 461-537 (617)
31 KOG0676|consensus 21.6 69 0.0015 34.5 2.6 31 21-51 12-45 (372)
32 cd00110 LamG Laminin G domain; 21.5 3.2E+02 0.007 22.6 6.1 12 73-84 19-30 (151)
33 PLN03089 hypothetical protein; 21.3 2.8E+02 0.0061 30.1 7.0 54 97-155 101-155 (373)
34 PF04096 Nucleoporin2: Nucleop 21.2 45 0.00096 31.2 1.0 18 138-155 122-139 (141)
35 PRK00409 recombination and DNA 21.2 32 0.0007 39.2 0.1 37 66-106 276-312 (782)
36 cd06191 FNR_iron_sulfur_bindin 21.1 1.7E+02 0.0037 26.8 4.7 31 81-111 9-42 (231)
37 COG4540 gpV Phage P2 baseplate 20.3 1.1E+02 0.0023 31.1 3.4 17 114-130 163-179 (184)
No 1
>PF03422 CBM_6: Carbohydrate binding module (family 6); InterPro: IPR005084 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This entry represents CBM6 from CAZY which was previously known as cellulose-binding domain family VI (CBD VI). CBM6 bind to amorphous cellulose, xylan, mixed beta-(1,3)(1,4)glucan and beta-1,3-glucan[, , ]. CBM6 adopts a classic lectin-like beta-jelly roll fold, predominantly consisting of five antiparallel beta-strands on one face and four antiparallel beta-strands on the other face. It contains two potential ligand binding sites, named respectively cleft A and B. These clefts include aromatic residues which are probably involved in the substrate binding. The cleft B is located on the concave surface of one beta-sheet, and the cleft A on one edge of the protein between the loop that connects the inner and outer beta-sheets of the jellyroll fold []. The multiple binding clefts confer the extensive range of specificities displayed by the domain [, , ].; GO: 0030246 carbohydrate binding; PDB: 1UY1_A 1UY3_A 1UY4_A 1UY2_A 1UYY_A 1UXZ_B 1UYZ_A 1UY0_B 1UYX_A 1UZ0_A ....
Probab=76.23 E-value=3.1 Score=34.78 Aligned_cols=56 Identities=23% Similarity=0.388 Sum_probs=34.5
Q ss_pred cCCCCCCccccccccCCCC--ceeEEeece-----EEEEEeecCCCc-----------CCCCcEEEEEEeecCC
Q psy17963 57 MRYPAKPEKDVMYNFAKPQ--TSIEIRVPT-----VVSVQLENSGSS-----------LTNGRHVIVFWCIAGS 112 (943)
Q Consensus 57 mrypakpekdvmynfakpq--tsieirvpt-----vvsvqlensgss-----------ltngrhvivfwciaGS 112 (943)
+..|......+...++.+. ..|+|||-. +-.|.+.+.|.. |..|+|.|.|++-.|.
T Consensus 39 Vd~~~~g~y~~~~~~a~~~~~~~~~l~id~~~g~~~~~~~~~~tg~w~~~~~~~~~v~l~~G~h~i~l~~~~~~ 112 (125)
T PF03422_consen 39 VDVPEAGTYTLTIRYANGGGGGTIELRIDGPDGTLIGTVSLPPTGGWDTWQTVSVSVKLPAGKHTIYLVFNGGD 112 (125)
T ss_dssp EEESSSEEEEEEEEEEESSSSEEEEEEETTTTSEEEEEEEEE-ESSTTEEEEEEEEEEEESEEEEEEEEESSSS
T ss_pred EeeCCCceEEEEEEEECCCCCcEEEEEECCCCCcEEEEEEEcCCCCccccEEEEEEEeeCCCeeEEEEEEECCC
Confidence 4445555555655666555 478888865 667777665542 3457777777766654
No 2
>COG4067 Uncharacterized protein conserved in archaea [Posttranslational modification, protein turnover, chaperones]
Probab=71.42 E-value=8.2 Score=38.07 Aligned_cols=109 Identities=24% Similarity=0.277 Sum_probs=71.6
Q ss_pred ceEEEEeeccCCCCccccCCCCCCCCCCCCcccCCCCCCCcccccCCCCCCccccccccC----CCCceeEEeeceEEEE
Q psy17963 13 FNVLFHYNFSSVNGLFKNGIGPESKPRPSTISTPRSHGSSKRDRMRYPAKPEKDVMYNFA----KPQTSIEIRVPTVVSV 88 (943)
Q Consensus 13 ~NV~~~~Nfsn~NGm~~NGIG~nsn~RPseIstprshgsskrdrmrypakpekdvmynfa----kpqtsieirvptvvsv 88 (943)
++|.-.+.+. .++|++-..+-+-||.-+.-+- +-+|-.+|-...+.=|-+..+ .-+.++++-.|.+--+
T Consensus 22 ~~v~G~~E~~-----~l~~l~~~~kAkiDTGA~TSsL--~A~dI~~fkRdGe~WVRF~~~~~~~~~~~~~~~e~pvi~~i 94 (162)
T COG4067 22 KMVLGWIEWV-----SLPGLKIQLKAKIDTGAVTSSL--SASDIERFKRDGERWVRFRLADTDNLDQRSEECEAPVIRKI 94 (162)
T ss_pred ceEeeeEEEE-----EcCcccceeeeeecccceeeeE--EeecceeeeeCCceEEEEEeecccCccccceeeccceEEEE
Confidence 4555555554 4555555566666776543321 233444444444444444443 3467888889988888
Q ss_pred EeecCCCcCCCCcEEEEEEeecCC-------ccccccccccceeeCc
Q psy17963 89 QLENSGSSLTNGRHVIVFWCIAGS-------SLTNRRHIKTNVFIGQ 128 (943)
Q Consensus 89 qlensgssltngrhvivfwciaGS-------sLtnrrhikTnVfIgq 128 (943)
.+..+|.+-+.-|.||..|.-.|. .||+|.|+.-.|.+|-
T Consensus 95 kvR~s~~~~~e~RpVV~~~l~lG~~~~~~E~tLtDR~~m~Yp~LlGr 141 (162)
T COG4067 95 KVRSSSGSRAERRPVVRLTLCLGGRILPIEFTLTDRSNMRYPVLLGR 141 (162)
T ss_pred EEecCCCCccccccEEEEEEeeCCeeeeEEEEeecccccccceEecH
Confidence 888888777889999999966665 3789999988888874
No 3
>smart00276 GLECT Galectin. Galectin - galactose-binding lectin
Probab=62.69 E-value=22 Score=31.21 Aligned_cols=33 Identities=24% Similarity=0.267 Sum_probs=23.0
Q ss_pred CCCcEEEEEEeecCCccccccccccceeeCcceEEeccc
Q psy17963 98 TNGRHVIVFWCIAGSSLTNRRHIKTNVFIGQDVEVDMFD 136 (943)
Q Consensus 98 tngrhvivfwciaGSsLtnrrhikTnVfIgqdVeVdmFd 136 (943)
-||.|+.-|..=.+ + .. -+.+.|.|||.|....
T Consensus 94 vng~~~~~f~~R~~--~---~~-i~~l~v~Gdv~l~~v~ 126 (128)
T smart00276 94 VNGVHITTFPHRLP--L---ES-IDYLSINGDVQLTSVS 126 (128)
T ss_pred ECCEeEEEecCCCC--c---cc-EeEEEEeCCEEEEEEE
Confidence 38999988876432 1 22 4568899999987653
No 4
>cd00025 BPI1 BPI/LBP/CETP N-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide.
Probab=52.95 E-value=47 Score=31.78 Aligned_cols=83 Identities=14% Similarity=0.180 Sum_probs=41.7
Q ss_pred EEeecCCCcCCCCcEEEEEEeecCCcccccccccc-ceeeCcceEEecccccceeeeeeee---eccee-eeeccCCCce
Q psy17963 88 VQLENSGSSLTNGRHVIVFWCIAGSSLTNRRHIKT-NVFIGQDVEVDMFDYTAYVCMNVIS---GPWRF-QVECASSQHH 162 (943)
Q Consensus 88 vqlensgssltngrhvivfwciaGSsLtnrrhikT-nVfIgqdVeVdmFdytayvcmNvis---gpWrF-QvEcassqHh 162 (943)
+.+.++--.+..|..+.+.++-+--.|+-..+.+. .+.++|++.++.-+-...+...+.+ |+=.+ -.+|..+.|+
T Consensus 58 ~~lp~s~l~~~~~~gi~~~~s~~si~l~~~w~~~~~~i~~~G~~~l~v~gv~i~~~l~l~~d~~G~p~v~~~~C~~~v~~ 137 (223)
T cd00025 58 LKLPSSSIKLVEVKGLDLSISNVSIGLSGVWKYNYRFILDGGNVELSVEGMNIQADLRLGRDPSGRPKLSLSDCSSTVGS 137 (223)
T ss_pred EecCCCceEEcCCCceEEEEeCCeEEEEEEEEEeeEEEEecEEEEEEEeEEEEEEEEEEeeCCCCCeEEEeCCCCcccCc
Confidence 33333333334444444444433322333333322 2456666666554333333333333 44444 4689999999
Q ss_pred eeeeeccc
Q psy17963 163 LRIKYASQ 170 (943)
Q Consensus 163 lrikyasq 170 (943)
++|+.-.-
T Consensus 138 ~~i~l~gg 145 (223)
T cd00025 138 LRVHLGGS 145 (223)
T ss_pred EEEEEeCC
Confidence 99998654
No 5
>PF05618 Zn_protease: Putative ATP-dependant zinc protease; InterPro: IPR008503 This family consists of several hypothetical proteins from different archaeal and bacterial species.; PDB: 2PMA_B.
Probab=52.83 E-value=31 Score=32.09 Aligned_cols=58 Identities=22% Similarity=0.379 Sum_probs=33.7
Q ss_pred CceeEEeeceEEEEEeecCCCcCCCCcEEEEEEeecCC-------ccccccccccceeeC------cceEEe
Q psy17963 75 QTSIEIRVPTVVSVQLENSGSSLTNGRHVIVFWCIAGS-------SLTNRRHIKTNVFIG------QDVEVD 133 (943)
Q Consensus 75 qtsieirvptvvsvqlensgssltngrhvivfwciaGS-------sLtnrrhikTnVfIg------qdVeVd 133 (943)
...+++..|.+--+.+-|++.. +.-|.||-.++..|. .|++|.+++-.+-|| +++.||
T Consensus 58 ~~~~~~e~p~~~~~~Ik~s~g~-~e~R~VV~~~~~lg~~~~~~e~tL~dR~~m~yp~LlGrR~~l~~~~lVD 128 (138)
T PF05618_consen 58 KEGVTFEAPVVRRRKIKSSNGE-SERRPVVETTLCLGGKTWKIEFTLTDRSNMKYPMLLGRRNFLRGRFLVD 128 (138)
T ss_dssp TEEEEEEEEEECEEE----------CCEEEEEEEEETTEEEEEEEEEE-S--SS-SEEE-HHHHHHTTEEEE
T ss_pred cceEEEEEEeEeEEEEEcCCCc-eeEeeEEEEEEEECCEEEEEEEEEcCCCcCcCCEEEEehHHhcCCEEEC
Confidence 4456677777777777777766 788999988876665 699999999999999 566666
No 6
>smart00606 CBD_IV Cellulose Binding Domain Type IV.
Probab=50.50 E-value=64 Score=27.39 Aligned_cols=33 Identities=24% Similarity=0.269 Sum_probs=18.9
Q ss_pred CccccccccCCC--CceeEEeec-----eEEEEEeecCCC
Q psy17963 63 PEKDVMYNFAKP--QTSIEIRVP-----TVVSVQLENSGS 95 (943)
Q Consensus 63 pekdvmynfakp--qtsieirvp-----tvvsvqlensgs 95 (943)
....+....+.| ...|+|||. ++-.+.+.+.|.
T Consensus 53 g~~~i~~~~as~~~~~~i~v~~d~~~G~~~~~~~~p~tg~ 92 (129)
T smart00606 53 GAYTFTARVASGNAGGSIELRLDSPTGTLVGTVDVPSTGG 92 (129)
T ss_pred CceEEEEEEeCCCCCceEEEEECCCCCcEEEEEEeCCCCC
Confidence 334444444443 347888883 556677766654
No 7
>KOG3939|consensus
Probab=50.25 E-value=9.1 Score=40.44 Aligned_cols=31 Identities=35% Similarity=0.627 Sum_probs=26.6
Q ss_pred eecCCCcCCCCcEEEEEEeecCCcccccccc
Q psy17963 90 LENSGSSLTNGRHVIVFWCIAGSSLTNRRHI 120 (943)
Q Consensus 90 lensgssltngrhvivfwciaGSsLtnrrhi 120 (943)
.+..|.++|.|..|+..|||.|.+-|+-.+-
T Consensus 85 a~e~gt~v~ggqtv~npw~~igGVatsVcq~ 115 (312)
T KOG3939|consen 85 AEEAGTPVTGGQTVINPWCIIGGVATSVCQP 115 (312)
T ss_pred HHhcCCceecCeeecCcceeeccccccccCc
Confidence 4667899999999999999999998876553
No 8
>PF09792 But2: Ubiquitin 3 binding protein But2 C-terminal domain; InterPro: IPR018620 This entry represents a presumed C-terminal domain of ubiquitin 3 binding proteins (But2). But2 is conserved in yeasts. It binds to Uba3 and is involved in the NEDD8 signalling pathway [].
Probab=47.85 E-value=80 Score=29.55 Aligned_cols=21 Identities=38% Similarity=0.564 Sum_probs=16.6
Q ss_pred CCCceeeccCCCceEEEEeec
Q psy17963 1 MPPMIVSADKSNFNVLFHYNF 21 (943)
Q Consensus 1 mppmivsadksn~NV~~~~Nf 21 (943)
.|-+||..|+++||-.+...|
T Consensus 3 fPhlIvpi~~s~P~~a~gt~~ 23 (143)
T PF09792_consen 3 FPHLIVPIDSSNPNKAFGTSY 23 (143)
T ss_pred CCcEEEecCccCCCCcCCCcc
Confidence 488999999999998764433
No 9
>COG0249 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=45.57 E-value=5.5 Score=45.96 Aligned_cols=67 Identities=22% Similarity=0.386 Sum_probs=46.5
Q ss_pred CccccccccCCCCceeEEeeceEEEEEeecCCCcCCCCcEEEEEEeecCCccccccccccceeeCcceEEecccccceee
Q psy17963 63 PEKDVMYNFAKPQTSIEIRVPTVVSVQLENSGSSLTNGRHVIVFWCIAGSSLTNRRHIKTNVFIGQDVEVDMFDYTAYVC 142 (943)
Q Consensus 63 pekdvmynfakpqtsieirvptvvsvqlensgssltngrhvivfwciaGSsLtnrrhikTnVfIgqdVeVdmFdytayvc 142 (943)
-+-||..+||..-+......|+++ ++.|-.+.+|||.+|= +.+.+. ||-.||..+. =.-
T Consensus 550 a~lD~l~slA~~a~~~~y~rP~~~----~~~~l~i~~gRHPvvE-----------~~~~~~-fVpNd~~L~~-----~~~ 608 (843)
T COG0249 550 AELDVLSSLAEIAAEQNYVRPEFV----DSNDLEIKEGRHPVVE-----------AVLDNG-FVPNDIDLSG-----NRR 608 (843)
T ss_pred HHHHHHHHHHHHHhhCCCCCceec----CCCCEEEEecCcchhh-----------hhccCC-cccCceeeCC-----Cce
Confidence 355888899888877777788776 3445678899998873 222222 7888888777 225
Q ss_pred eeeeeecc
Q psy17963 143 MNVISGPW 150 (943)
Q Consensus 143 mNvisgpW 150 (943)
|-+||||=
T Consensus 609 i~lITGPN 616 (843)
T COG0249 609 IILITGPN 616 (843)
T ss_pred EEEEECCC
Confidence 66888883
No 10
>cd08023 GH16_laminarinase_like Laminarinase, member of the glycosyl hydrolase family 16. Laminarinase, also known as glucan endo-1,3-beta-D-glucosidase, is a glycosyl hydrolase family 16 member that hydrolyzes 1,3-beta-D-glucosidic linkages in 1,3-beta-D-glucans such as laminarins, curdlans, paramylons, and pachymans, with very limited action on mixed-link (1,3-1,4-)-beta-D-glucans.
Probab=40.70 E-value=2.8e+02 Score=25.92 Aligned_cols=33 Identities=21% Similarity=0.451 Sum_probs=22.3
Q ss_pred ccccceeeeeeeee-cceee-eeccCCCceeeeee
Q psy17963 135 FDYTAYVCMNVISG-PWRFQ-VECASSQHHLRIKY 167 (943)
Q Consensus 135 FdytayvcmNvisg-pWrFQ-vEcassqHhlriky 167 (943)
|+.-.+++.|+..| -|.+. ...+..|.++.|.|
T Consensus 197 ~~~p~~liln~~~gg~w~g~~~~~~~~p~~~~VDy 231 (235)
T cd08023 197 FDQPFYLILNLAVGGNWPGPPDDDTPFPATMEVDY 231 (235)
T ss_pred CCCCcEEEEEEEEcCCCCCCCCCCCCCCCEEEEEE
Confidence 56666888887664 47776 34556677777766
No 11
>cd00070 GLECT Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation.
Probab=39.62 E-value=78 Score=27.57 Aligned_cols=31 Identities=29% Similarity=0.337 Sum_probs=19.6
Q ss_pred CCcEEEEEEeecCCccccccccccceeeCcceEEecc
Q psy17963 99 NGRHVIVFWCIAGSSLTNRRHIKTNVFIGQDVEVDMF 135 (943)
Q Consensus 99 ngrhvivfwciaGSsLtnrrhikTnVfIgqdVeVdmF 135 (943)
||.|+.-|=.- + |...| +.|.|.|||.|+.+
T Consensus 96 ng~~~~~F~~R----~-~~~~i-~~l~v~Gdv~i~~v 126 (127)
T cd00070 96 NGQHFFSFPHR----L-PLESI-DYLSINGDVSLTSV 126 (127)
T ss_pred CCEeEEEecCc----C-ChhhE-EEEEEeCCEEEEEe
Confidence 78887666332 1 22333 56889999998754
No 12
>KOG1322|consensus
Probab=36.35 E-value=21 Score=38.84 Aligned_cols=94 Identities=23% Similarity=0.338 Sum_probs=52.2
Q ss_pred CCceeeccCCCceEEEEeeccCCCCccccCCCCCCCCCCCCcccCCCCCCCcccccCCCCCCccccccccCCCCceeEEe
Q psy17963 2 PPMIVSADKSNFNVLFHYNFSSVNGLFKNGIGPESKPRPSTISTPRSHGSSKRDRMRYPAKPEKDVMYNFAKPQTSIEIR 81 (943)
Q Consensus 2 ppmivsadksn~NV~~~~Nfsn~NGm~~NGIG~nsn~RPseIstprshgsskrdrmrypakpekdvmynfakpqtsieir 81 (943)
||-.....+---||++|--. +||-|-..+|+-|--||+.=.+. ++|+
T Consensus 252 ~~r~~p~~~i~~nvlvd~~~---------~iG~~C~Ig~~vvIG~r~~i~~g------------------------V~l~ 298 (371)
T KOG1322|consen 252 SPRLLPGSKIVGNVLVDSIA---------SIGENCSIGPNVVIGPRVRIEDG------------------------VRLQ 298 (371)
T ss_pred CccccCCccccccEeecccc---------ccCCccEECCCceECCCcEecCc------------------------eEEE
Confidence 44455556666678877543 55666666776676676532110 1111
Q ss_pred eceEE---EEEeecC-CCcCCCCcEEEEEEeecCCccccccccccceeeCcceEEeccccc
Q psy17963 82 VPTVV---SVQLENS-GSSLTNGRHVIVFWCIAGSSLTNRRHIKTNVFIGQDVEVDMFDYT 138 (943)
Q Consensus 82 vptvv---svqlens-gssltngrhvivfwciaGSsLtnrrhikTnVfIgqdVeVdmFdyt 138 (943)
=-||+ .++-+-- .+++..|+--|--|+ -|..|..||.||+|-++||.
T Consensus 299 ~s~il~~~~~~~~s~i~s~ivg~~~~IG~~~----------~id~~a~lG~nV~V~d~~~v 349 (371)
T KOG1322|consen 299 DSTILGADYYETHSEISSSIVGWNVPIGIWA----------RIDKNAVLGKNVIVADEDYV 349 (371)
T ss_pred eeEEEccceechhHHHHhhhccccccccCce----------EEecccEeccceEEeccccc
Confidence 11111 1111111 233444444455676 57788999999999999874
No 13
>PF03292 Pox_P4B: Poxvirus P4B major core protein; InterPro: IPR004972 This family is the Poxvirus P4B major core protein. It is a precursor for one of the two most abundant structural components of the virion (major core proteins 4A and 4B).
Probab=35.07 E-value=71 Score=36.97 Aligned_cols=57 Identities=19% Similarity=0.275 Sum_probs=38.0
Q ss_pred CCCcCCC-CcEEEEEEeecCCccccccccccceeeCcceEEecccccceeeeeeeeecceeeeeccCCC
Q psy17963 93 SGSSLTN-GRHVIVFWCIAGSSLTNRRHIKTNVFIGQDVEVDMFDYTAYVCMNVISGPWRFQVECASSQ 160 (943)
Q Consensus 93 sgssltn-grhvivfwciaGSsLtnrrhikTnVfIgqdVeVdmFdytayvcmNvisgpWrFQvEcassq 160 (943)
.|..-+. -+++=.|||++|...- ++..++|.+- .|=+| ..|-.-++--|-|||...-
T Consensus 445 ~~~~~~~~~~~~~~~~~~~n~~~~--~~~~SpVivn---GvLIf------yVeRRq~k~~~~Gec~tg~ 502 (666)
T PF03292_consen 445 IGYAGPIGNRTVQQFPCLNNKTIQ--PKENSPVIVN---GVLIF------YVERRQNKNTFSGECYTGF 502 (666)
T ss_pred cCcccccCCccccceeeccCcccc--cCCCCceEec---ceEEE------EEeehhccceeccccccch
Confidence 3444333 3789999999776554 4455666655 35556 6677778888999996543
No 14
>PF13115 YtkA: YtkA-like
Probab=31.47 E-value=1.2e+02 Score=24.34 Aligned_cols=25 Identities=16% Similarity=0.460 Sum_probs=20.5
Q ss_pred EEEEeecCCCcCCCCcEEEEEEeec
Q psy17963 86 VSVQLENSGSSLTNGRHVIVFWCIA 110 (943)
Q Consensus 86 vsvqlensgssltngrhvivfwcia 110 (943)
+.|.+...|..+++.+--+.+|.-.
T Consensus 24 i~v~~~~~g~pv~~a~V~~~~~m~~ 48 (86)
T PF13115_consen 24 ITVTVDQGGKPVTDADVQFEIWMPD 48 (86)
T ss_pred EEEEECCCCCCCCCCEEEEEEEeCC
Confidence 3445778899999999888999886
No 15
>PF09315 DUF1973: Domain of unknown function (DUF1973); InterPro: IPR015394 These functionally uncharacterised domains are found in various eukaryotic calcium-dependent chloride channels.
Probab=31.34 E-value=1.5e+02 Score=28.68 Aligned_cols=14 Identities=14% Similarity=0.589 Sum_probs=11.6
Q ss_pred eeeeecceeeeecc
Q psy17963 144 NVISGPWRFQVECA 157 (943)
Q Consensus 144 NvisgpWrFQvEca 157 (943)
.++.|.|+|.++..
T Consensus 74 ~ae~G~W~y~i~~~ 87 (179)
T PF09315_consen 74 TAEVGTWTYSITNT 87 (179)
T ss_pred CcccccEEEEEecC
Confidence 48999999999644
No 16
>PF13897 GOLD_2: Golgi-dynamics membrane-trafficking
Probab=30.30 E-value=43 Score=32.38 Aligned_cols=21 Identities=38% Similarity=0.893 Sum_probs=15.5
Q ss_pred ceeEEeeceEEEEEeecCCCcCCCCcEEEEEEeec
Q psy17963 76 TSIEIRVPTVVSVQLENSGSSLTNGRHVIVFWCIA 110 (943)
Q Consensus 76 tsieirvptvvsvqlensgssltngrhvivfwcia 110 (943)
..+.|||||. .+|+ .+|||+|
T Consensus 5 e~~tvrVpt~------------~~G~--~l~WeFa 25 (136)
T PF13897_consen 5 ETVTVRVPTH------------PEGK--CLFWEFA 25 (136)
T ss_pred cEEEEEcccC------------CCCC--EEEEEEe
Confidence 3578999984 3453 7899987
No 17
>PLN03103 GDP-L-galactose-hexose-1-phosphate guanyltransferase; Provisional
Probab=29.26 E-value=8 Score=41.93 Aligned_cols=36 Identities=33% Similarity=0.439 Sum_probs=26.3
Q ss_pred eeceEEEEEeecCCCcCCCCcEEEEEEeecCCccccc
Q psy17963 81 RVPTVVSVQLENSGSSLTNGRHVIVFWCIAGSSLTNR 117 (943)
Q Consensus 81 rvptvvsvqlensgssltngrhvivfwciaGSsLtnr 117 (943)
|||||||..-+.. ....-||...--.||.|+.|.--
T Consensus 6 ~~~~~~~~~~~~~-~~~~~~~~~~~~c~~~~~~~pl~ 41 (403)
T PLN03103 6 RVPTVVSNYQDDD-ELGGCGRNCLGKCCLPGAKLPLY 41 (403)
T ss_pred ecchhhhhhhhhc-cccCcchhhhhhcCCCCccCchh
Confidence 9999999754333 33556788888899999887543
No 18
>PF01803 LIM_bind: LIM-domain binding protein; InterPro: IPR002691 The LIM-domain binding protein, binds to the LIM domain IPR001781 from INTERPRO of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) P70662 from SWISSPROT is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons []. It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development []. The Drosophila melanogaster protein Chip O18353 from SWISSPROT is required for segmentation and activity of a remote wing margin enhancer []. Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development []. It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions [].; GO: 0003712 transcription cofactor activity, 0005634 nucleus
Probab=28.91 E-value=56 Score=31.59 Aligned_cols=66 Identities=14% Similarity=0.374 Sum_probs=46.8
Q ss_pred cCCCCceeEEeeceEEEEEeecCCCcCCCCcEEEEEEeecCCccccccccccceeeCcceEEeccccc
Q psy17963 71 FAKPQTSIEIRVPTVVSVQLENSGSSLTNGRHVIVFWCIAGSSLTNRRHIKTNVFIGQDVEVDMFDYT 138 (943)
Q Consensus 71 fakpqtsieirvptvvsvqlensgssltngrhvivfwciaGSsLtnrrhikTnVfIgqdVeVdmFdyt 138 (943)
|.-.-+.|+|-++....-.|.|.+--+...|-++++|---|+.++...+|+.-. +.+..|+.||++
T Consensus 69 ~~sGv~~~~~~l~~~~e~~l~ng~i~ie~~~~~~~~~y~~gs~v~~~G~lr~~f--~~~lKIe~~df~ 134 (240)
T PF01803_consen 69 FESGVKRMQLVLDGPREQVLPNGSIFIECPRATFIYWYEDGSQVVHEGQLRAQF--DPDLKIEWWDFC 134 (240)
T ss_pred hcCCceEEEEEecCCceEEcCCCeEEEEECCEEEEEEECCceEEEEEeEEEEEE--CccccEEEEEEE
Confidence 444556666666555555566666666788888999999999998877776443 777777777654
No 19
>PRK10767 chaperone protein DnaJ; Provisional
Probab=28.04 E-value=3e+02 Score=28.41 Aligned_cols=63 Identities=17% Similarity=0.333 Sum_probs=34.2
Q ss_pred CceeEEeeceEE----EEEeecCCCcC----CCCcEEEEEEeecCCcccc-ccccccceee-------CcceEEecccc
Q psy17963 75 QTSIEIRVPTVV----SVQLENSGSSL----TNGRHVIVFWCIAGSSLTN-RRHIKTNVFI-------GQDVEVDMFDY 137 (943)
Q Consensus 75 qtsieirvptvv----svqlensgssl----tngrhvivfwciaGSsLtn-rrhikTnVfI-------gqdVeVdmFdy 137 (943)
...|+|.||..+ .+.+.+-|... ..|..+|++=..--..+.- -.+|++.+.| |..|.|..+|-
T Consensus 210 ~~~l~V~Ip~G~~~G~~i~~~g~G~~~~~~~~~GDL~v~i~v~~h~~F~R~G~DL~~~~~Isl~eAl~G~~~~i~~ldG 288 (371)
T PRK10767 210 EKTLSVKIPAGVDTGDRIRLSGEGEAGERGGPAGDLYVQIHVKEHPIFERDGNDLYCEVPISFTTAALGGEIEVPTLDG 288 (371)
T ss_pred eeeEEEecCCCCCCCcEEEEecCccCCCCCCCCcCEEEEEEEeeCCCEEEecCCEEEEEEeCHHHHhCCCeEEEecCCC
Confidence 357888888543 25566666542 3455666654332222221 1356666655 56677766655
No 20
>PRK14301 chaperone protein DnaJ; Provisional
Probab=26.28 E-value=3.7e+02 Score=28.06 Aligned_cols=64 Identities=19% Similarity=0.314 Sum_probs=40.3
Q ss_pred CceeEEeeceEEE----EEeecCCCcCC----CCcEEEEEEeecCCcccc-ccccccceee-------CcceEEeccccc
Q psy17963 75 QTSIEIRVPTVVS----VQLENSGSSLT----NGRHVIVFWCIAGSSLTN-RRHIKTNVFI-------GQDVEVDMFDYT 138 (943)
Q Consensus 75 qtsieirvptvvs----vqlensgsslt----ngrhvivfwciaGSsLtn-rrhikTnVfI-------gqdVeVdmFdyt 138 (943)
...|+|.||..+. +.+.+-|-... .|..+|+|=..--..+.- -.+|++++.| |+.|.|..+|-+
T Consensus 212 ~~~l~V~Ip~G~~~G~~i~~~g~G~~~~~~~~~GDLiv~i~v~~h~~f~r~G~DL~~~~~Isl~eAl~G~~~~v~tldG~ 291 (373)
T PRK14301 212 TRELKVRIPAGVDTGSRLRLRGEGEPGVHGGPPGDLYVVITVEDDKIFQRQGQDLVVTQEISFVQAALGDRIEVPTLDDP 291 (373)
T ss_pred ceEEEEEeCCCCcCCCEEEEeccccCCCCCCCCcCEEEEEEEEECCCceeecCcEEEEEEecHHHHhCCCeEEEecCCcc
Confidence 3578888887765 77777776433 356666654443333332 2467777766 588888888755
No 21
>KOG0536|consensus
Probab=26.22 E-value=49 Score=32.39 Aligned_cols=43 Identities=21% Similarity=0.410 Sum_probs=29.9
Q ss_pred ccccCCCCCC-CCCCCCcccCCCCC----C--CcccccCCCCCCcccccc
Q psy17963 27 LFKNGIGPES-KPRPSTISTPRSHG----S--SKRDRMRYPAKPEKDVMY 69 (943)
Q Consensus 27 m~~NGIG~ns-n~RPseIstprshg----s--skrdrmrypakpekdvmy 69 (943)
|+++|+|... |-+|...-.|+.-| . ..|+|..++-.|..+.|-
T Consensus 1 ~~k~~l~~~~sn~~~~~~~~~~~s~~~~~~s~~~r~R~K~~l~PG~s~md 50 (145)
T KOG0536|consen 1 MSKDGLNRPESNGTPQFAAPPATSGAHMPRSKKQRKRTKVALAPGHSQMD 50 (145)
T ss_pred CcccccCChhhcCCcccccCCCcccccCcccchhcccceeecCCCcchhh
Confidence 5777777654 66777776676666 3 345578888889888773
No 22
>PF05326 SVA: Seminal vesicle autoantigen (SVA); InterPro: IPR007990 This family consists of seminal vesicle autoantigen and prolactin-inducible (PIP) proteins. Seminal vesicle autoantigen (SVA) is specifically present in the seminal plasma of mice. This 19 kDa secretory glycoprotein suppresses the motility of spermatozoa by interacting with phospholipid. PIP has several known functions. In saliva, this protein plays a role in host defence by binding to microorganisms such as Streptococcus. PIP is an aspartyl proteinase and it acts as a factor capable of suppressing T-cell apoptosis through its interaction with CD4 [].; GO: 0005576 extracellular region; PDB: 3ES6_B.
Probab=26.00 E-value=30 Score=32.84 Aligned_cols=36 Identities=25% Similarity=0.380 Sum_probs=21.6
Q ss_pred ccccccceeeCcceEEecccccceeee-eeeeecceeeee
Q psy17963 117 RRHIKTNVFIGQDVEVDMFDYTAYVCM-NVISGPWRFQVE 155 (943)
Q Consensus 117 rrhikTnVfIgqdVeVdmFdytayvcm-NvisgpWrFQvE 155 (943)
+.++.+|+.|++.- ||-|||-+|. +..+==||||+-
T Consensus 67 k~yl~sn~~i~~~f---ny~YTaCLC~d~~r~FyWDi~~~ 103 (124)
T PF05326_consen 67 KIYLESNPPIDGSF---NYKYTACLCDDYPRTFYWDIQVN 103 (124)
T ss_dssp EEEEEESS---SGG---G-EEEEEE-SSS-EEEEEEE--S
T ss_pred EEEeccCCCccccc---cceEEEEeCCCCCccEEEEEEEC
Confidence 45666777777654 8999999999 567888999974
No 23
>PF01847 VHL: von Hippel-Lindau disease tumour suppressor protein; InterPro: IPR022772 Von Hippel-Lindau disease tumor suppressor (VHL) has two domains: a roughly 100-residue N-terminal domain rich in beta sheet (beta domain) and a smaller alpha-helical domain (alpha domain), held together by two linkers and a polar interface. A large portion of the alpha domain surface, and a small portion of the beta domain, interact with ElonginC. About half of the tumorigenic mutations map to the alpha domain and its residues that contact ElonginC. The remaining mutations map to the beta domain, and significantly, to a beta domain surface patch uninvolved in ElonginC binding. This suggests that two intact macromolecular binding sites may be required for the tumor suppressor effects of VHL []. This entry represents both beta and alpha domains of VHL.; PDB: 3ZRF_L 3ZRC_C 1LM8_V 1LQB_C 1VCB_F.
Probab=25.56 E-value=59 Score=31.77 Aligned_cols=58 Identities=24% Similarity=0.426 Sum_probs=26.2
Q ss_pred eeEEeeceEEEEEeecCCCcCCCCcEEEEEEeecCCccccccccccceeeCcceEEecccccceeeeeeeeecceeeee
Q psy17963 77 SIEIRVPTVVSVQLENSGSSLTNGRHVIVFWCIAGSSLTNRRHIKTNVFIGQDVEVDMFDYTAYVCMNVISGPWRFQVE 155 (943)
Q Consensus 77 sieirvptvvsvqlensgssltngrhvivfwciaGSsLtnrrhikTnVfIgqdVeVdmFdytayvcmNvisgpWrFQvE 155 (943)
|..=+.|+.|. +-|. .+|.|-|||.=--+-..+= ..+-=|+.+.|+.| .+|||.|-..
T Consensus 8 S~~S~~~s~V~--F~N~-----s~r~V~v~Wldy~G~~~~Y----~~L~Pg~~~~~~TY----------~tHpW~frDa 65 (156)
T PF01847_consen 8 SLNSREPSFVR--FVNR-----SPRTVDVYWLDYDGKPVPY----GTLKPGQGRRQNTY----------VTHPWVFRDA 65 (156)
T ss_dssp -----SEEEEE--EEE------SSS-EEEEEE-TTS-EEE-------B-TTEEEEEEEE----------TT-EEEEEET
T ss_pred cCCCCCceEEE--EEEC-----CCCEEEEEEEcCCCcEeec----cccCCCCeEEcccc----------cCCcEEEEeC
Confidence 33344554443 4453 4688888886433322222 22333556666666 6899999754
No 24
>PRK14285 chaperone protein DnaJ; Provisional
Probab=24.24 E-value=2.8e+02 Score=28.92 Aligned_cols=63 Identities=14% Similarity=0.364 Sum_probs=37.9
Q ss_pred CceeEEeeceEEE----EEeecCCCcCCC----CcEEEEEEeecCCcccc-ccccccceee-------CcceEEecccc
Q psy17963 75 QTSIEIRVPTVVS----VQLENSGSSLTN----GRHVIVFWCIAGSSLTN-RRHIKTNVFI-------GQDVEVDMFDY 137 (943)
Q Consensus 75 qtsieirvptvvs----vqlensgssltn----grhvivfwciaGSsLtn-rrhikTnVfI-------gqdVeVdmFdy 137 (943)
...|+|+||--+. +.+.+-|..-.+ |..+|++=..--..++. -.+|++++.| |..|.|..+|-
T Consensus 214 ~~~~~V~Ip~G~~~G~~i~~~g~G~~~~~~~~~GDL~v~i~v~~h~~f~R~G~dL~~~~~Isl~eAl~G~~~~i~tldG 292 (365)
T PRK14285 214 KETIELKIPAGIDDNQQIKMRGKGSVNPDNQQYGDLYIKILIKPHKIFKRNGKDLYATLPISFTQAALGKEIKIQTIAS 292 (365)
T ss_pred cEEEEEEECCCCCCCCEEEEeeccccCCCCCCCCCEEEEEEEecCCCeEEeccceEEEEecCHHHHhCCCEEEEECCCC
Confidence 3578888886553 777887765443 44455543332222221 2467777766 57888887764
No 25
>cd05722 Ig1_Neogenin First immunoglobulin (Ig)-like domain in neogenin and similar proteins. Ig1_Neogenin: first immunoglobulin (Ig)-like domain in neogenin and related proteins. Neogenin is a cell surface protein which is expressed in the developing nervous system of vertebrate embryos in the growing nerve cells. It is also expressed in other embryonic tissues, and may play a general role in developmental processes such as cell migration, cell-cell recognition, and tissue growth regulation. Included in this group is the tumor suppressor protein DCC, which is deleted in colorectal carcinoma . DCC and neogenin each have four Ig-like domains followed by six fibronectin type III domains, a transmembrane domain, and an intracellular domain.
Probab=23.98 E-value=2.2e+02 Score=22.82 Aligned_cols=42 Identities=14% Similarity=0.188 Sum_probs=24.6
Q ss_pred EEEEEEeecCCccccccccccceeeCcceEEecc--------cccceeee
Q psy17963 102 HVIVFWCIAGSSLTNRRHIKTNVFIGQDVEVDMF--------DYTAYVCM 143 (943)
Q Consensus 102 hvivfwciaGSsLtnrrhikTnVfIgqdVeVdmF--------dytayvcm 143 (943)
...|.|.--|..|.+....+-.++-++.+.+.++ |...|-|.
T Consensus 28 ~p~i~W~k~g~~l~~~~~~~~~~~~~~~l~i~~v~~~~~~~~D~G~Y~C~ 77 (95)
T cd05722 28 PPKIEWKKDGVLLNLVSDERRQQLPNGSLLITSVVHSKHNKPDEGFYQCV 77 (95)
T ss_pred CCEEEEEECCeECccccCcceEEccCCeEEEeeeeccCCCCCcCEEEEEE
Confidence 4567787777777655433333444555555444 66677773
No 26
>PRK00892 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional
Probab=23.83 E-value=2e+02 Score=29.07 Aligned_cols=7 Identities=57% Similarity=0.942 Sum_probs=2.6
Q ss_pred ceeeCcc
Q psy17963 123 NVFIGQD 129 (943)
Q Consensus 123 nVfIgqd 129 (943)
||.||.+
T Consensus 243 ~~~IG~~ 249 (343)
T PRK00892 243 NVVIGRH 249 (343)
T ss_pred CCEECCC
Confidence 3333333
No 27
>KOG0517|consensus
Probab=23.64 E-value=23 Score=44.89 Aligned_cols=33 Identities=24% Similarity=0.471 Sum_probs=23.7
Q ss_pred CCceEEEEeeccCCCCccccCCCCCC---CCCCCCcccCC
Q psy17963 11 SNFNVLFHYNFSSVNGLFKNGIGPES---KPRPSTISTPR 47 (943)
Q Consensus 11 sn~NV~~~~Nfsn~NGm~~NGIG~ns---n~RPseIstpr 47 (943)
.-|||.|+ ||.+. ..+|+|||+ +-|||-|--.+
T Consensus 182 GYpnVNI~-nFTtS---WRdGLaFNALIHkHRPDLvDf~~ 217 (2473)
T KOG0517|consen 182 GYPNVNIT-NFTTS---WRDGLAFNALIHKHRPDLVDFDK 217 (2473)
T ss_pred CCCCcccc-cCccc---hhcchhHHHHHHhcCcchhhhcc
Confidence 45777765 66553 568899998 88999886543
No 28
>PRK14293 chaperone protein DnaJ; Provisional
Probab=23.33 E-value=3.9e+02 Score=27.78 Aligned_cols=63 Identities=19% Similarity=0.356 Sum_probs=37.5
Q ss_pred ceeEEeeceEE----EEEeecCCCcC----CCCcEEEEEEeecCCcccc-ccccccceee-------CcceEEeccccc
Q psy17963 76 TSIEIRVPTVV----SVQLENSGSSL----TNGRHVIVFWCIAGSSLTN-RRHIKTNVFI-------GQDVEVDMFDYT 138 (943)
Q Consensus 76 tsieirvptvv----svqlensgssl----tngrhvivfwciaGSsLtn-rrhikTnVfI-------gqdVeVdmFdyt 138 (943)
..++|+||.-+ .+.|.|.|-.- ..|..+|+|=...-..++. -.+|++++.| |+.|.|...|=+
T Consensus 216 ~~~~V~IppG~~~G~~i~l~g~G~~~~~~~~~GDL~v~v~v~~~~~f~r~g~DL~~~~~Isl~eAl~G~~~~i~~ldG~ 294 (374)
T PRK14293 216 KKLKINIPAGVDTGTRLRVSGEGDAGLRGGPPGDLYVYLFVKNDPEFRRDGINILSEIKISYLQAILGDTLEVDTVDGP 294 (374)
T ss_pred eEEEEEeCCCCCCCCEEEEccCccCCCCCCCCcCEEEEEEEeCCCccChhhhceEEEeccCHHHHhCCCEEEecCCCCC
Confidence 45677777532 35677766532 2466666655444434432 2467777766 688888887754
No 29
>PRK10658 putative alpha-glucosidase; Provisional
Probab=22.79 E-value=2.4e+02 Score=31.91 Aligned_cols=77 Identities=22% Similarity=0.343 Sum_probs=41.5
Q ss_pred ccCCCCccccCCCCCCCCCCCCcccCCCCCCCcccccCCCCCCccccccccCCCCceeEEeec--eEEEEEeecCCCcCC
Q psy17963 21 FSSVNGLFKNGIGPESKPRPSTISTPRSHGSSKRDRMRYPAKPEKDVMYNFAKPQTSIEIRVP--TVVSVQLENSGSSLT 98 (943)
Q Consensus 21 fsn~NGm~~NGIG~nsn~RPseIstprshgsskrdrmrypakpekdvmynfakpqtsieirvp--tvvsvqlensgsslt 98 (943)
|.+|+=|...|+-.+ +|.+|-.-+-.+.+ -+.--|.++-..---..-.|+..|+|.+| -||.|.+...+..+.
T Consensus 3 ~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~iirV~~~~~~~~~~ 77 (665)
T PRK10658 3 FSDGNWLIRPGLNLI---HPVQVYDVEQQDNE--LVVYAPPRDVRERGDTLDTPLFTIRFSSPQEGVIGVRIEHFQGALD 77 (665)
T ss_pred ccCceeecCCCcccc---ChhheeEEEEcCCE--EEEEecceEcCCcccccCCCeEEEEEEeccCCeEEEEEECCCCccC
Confidence 556666666665432 34444433333311 11222223222222234568888999998 799999985555555
Q ss_pred CCcE
Q psy17963 99 NGRH 102 (943)
Q Consensus 99 ngrh 102 (943)
++.+
T Consensus 78 ~~~~ 81 (665)
T PRK10658 78 NGPH 81 (665)
T ss_pred CCCC
Confidence 5554
No 30
>COG3962 Acetolactate synthase [Amino acid transport and metabolism]
Probab=22.30 E-value=32 Score=39.08 Aligned_cols=71 Identities=25% Similarity=0.446 Sum_probs=56.5
Q ss_pred CCcEEEEEEeecCCccccccccccceeeCcceEEecccccceeeee---eeeecceeeeeccCCCc---eeeeeeccc
Q psy17963 99 NGRHVIVFWCIAGSSLTNRRHIKTNVFIGQDVEVDMFDYTAYVCMN---VISGPWRFQVECASSQH---HLRIKYASQ 170 (943)
Q Consensus 99 ngrhvivfwciaGSsLtnrrhikTnVfIgqdVeVdmFdytayvcmN---visgpWrFQvEcassqH---hlrikyasq 170 (943)
++|.|||+- --||-|--...|.|.|-.|.-|+|-.||-..|-|.| ..+|-=.|--+-..+.| -+.|.||--
T Consensus 461 pdreV~vmV-GDGSymMlnSEL~Tsv~~g~Ki~Vvl~DN~GyGCIn~LQm~~Gg~sf~~~~r~~~~e~~~~~vDfA~~ 537 (617)
T COG3962 461 PDREVYVMV-GDGSYMMLNSELATSVMLGKKIIVVLLDNRGYGCINRLQMATGGASFNNLLRDTDHEEEILQVDFAAH 537 (617)
T ss_pred CCCeEEEEE-cccchhhhhHHHHHHHHcCCeEEEEEECCCCcchhhhhhhhcCcchhhhhhhhhcccCCCCcccHHHH
Confidence 457777653 357888778889999999999999999999999998 46788888888888888 355666543
No 31
>KOG0676|consensus
Probab=21.63 E-value=69 Score=34.45 Aligned_cols=31 Identities=32% Similarity=0.695 Sum_probs=22.2
Q ss_pred ccCCCCccccCCCCCCCCC---CCCcccCCCCCC
Q psy17963 21 FSSVNGLFKNGIGPESKPR---PSTISTPRSHGS 51 (943)
Q Consensus 21 fsn~NGm~~NGIG~nsn~R---PseIstprshgs 51 (943)
+|||+||+|-|...+.-|| |+.|-+||.+|.
T Consensus 12 iDnGsg~~KaGfag~~~P~~v~ps~vg~~~~~~~ 45 (372)
T KOG0676|consen 12 IDNGSGFVKAGFAGDDAPRAVFPSIVGRPRHQGV 45 (372)
T ss_pred EECCCceeecccCCCCCCceecceeccccccccc
Confidence 6899999999988555443 666766665543
No 32
>cd00110 LamG Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules.
Probab=21.54 E-value=3.2e+02 Score=22.57 Aligned_cols=12 Identities=25% Similarity=0.332 Sum_probs=6.8
Q ss_pred CCCceeEEeece
Q psy17963 73 KPQTSIEIRVPT 84 (943)
Q Consensus 73 kpqtsieirvpt 84 (943)
....+|.+++-|
T Consensus 19 ~~~~~i~~~frt 30 (151)
T cd00110 19 RTRLSISFSFRT 30 (151)
T ss_pred cceeEEEEEEEe
Confidence 344566666655
No 33
>PLN03089 hypothetical protein; Provisional
Probab=21.29 E-value=2.8e+02 Score=30.11 Aligned_cols=54 Identities=20% Similarity=0.268 Sum_probs=31.6
Q ss_pred CCCCcEEEEEEeecCCccccccccccceeeCcceEEecccccc-eeeeeeeeecceeeee
Q psy17963 97 LTNGRHVIVFWCIAGSSLTNRRHIKTNVFIGQDVEVDMFDYTA-YVCMNVISGPWRFQVE 155 (943)
Q Consensus 97 ltngrhvivfwciaGSsLtnrrhikTnVfIgqdVeVdmFdyta-yvcmNvisgpWrFQvE 155 (943)
.+.|+.-.+-+..+. ++.....-+|+++.. -..|++.. |-.+--.+.-|.|...
T Consensus 101 t~~G~~Y~LTFs~ar---~c~~~~~v~vsv~~~--~~~~~~qt~~~~~gw~~~s~~F~A~ 155 (373)
T PLN03089 101 VTKGSYYSLTFSAAR---TCAQDESLNVSVPPE--SGVLPLQTLYSSSGWDSYAWAFKAE 155 (373)
T ss_pred ccCCCEEEEEEEecC---CCCCCceEEEEecCC--CcEEeeEEeccCCCcEEEEEEEEEe
Confidence 456776655444442 344444556666654 34455543 5556678889999864
No 34
>PF04096 Nucleoporin2: Nucleoporin autopeptidase; InterPro: IPR007230 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of autocatalytic serine endopeptidases belong to MEROPS peptidase family S59 (clan SP). The nuclear pore complex protein plays a role in bidirectional transport across the nucleoporin complex in nucleocytoplasmic transport. The mammalian nuclear pore complex (NPC) is comprised of approximately 50 unique proteins, collectively known as nucleoporins. A number of the peptides are synthesised as precursors and undergo self-catalyzed cleavage. The proteolytic cleavage site of yeast Nup145p has been mapped upstream of an evolutionary conserved serine residue. Cleavage occurs at the same site when a precursor is artificially expressed in Escherichia coli. A hydroxyl-containing residue is critical for the reaction, although a thiol-containing residue offers an acceptable replacement. In vitro kinetics experiments using a purified precursor molecule demonstrate that the cleavage is self-catalyzed and that the catalytic domain lies within the N-terminal moiety. Taken altogether, the data are consistent with a proteolytic mechanism involving an N>O acyl rearrangement and a subsequent ester intermediate uncovered in other self-processing proteins []. Nup98 is a component of the nuclear pore that plays its primary role in the export of RNAs. Nup98 is expressed in two forms, derived from alternate mRNA splicing. Both forms are processed into two peptides through autoproteolysis mediated by the C-terminal domain of hNup98. The three-dimensional structure of the C-terminal domain reveals a novel protein fold, and thus a new class of autocatalytic proteases. The structure further reveals that the suggested nucleoporin RNA binding motif is unlikely to bind to RNA []. The following nucleoporins share an ~150-residue C-terminal domain responsible for NPC targeting [, ]: Vertebrate Nup98, a component of the nuclear pore that plays its primary role in the export of RNAs. Yeast Nup100, plays an important role in several nuclear export and import pathways including poly(A)+ RNA and protein transport. Yeast Nup116, involved in mRNA export and protein transport. Yeast Nup145, involved in nuclear poly(A)+ RNA and tRNA export. The NUP C-terminal domains of Nup98 and Nup145 possess peptidase S59 autoproteolytic activity. The autoproteolytic sites of Nup98 and Nup145 each occur immediately C-terminal to the NUP C-terminal domain. Thus, although this domain occurs in the middle of each precursor polypeptide, it winds up at the C-terminal end of the N-terminal cleavage product. Cleavage of the peptide chains are necessary for the proper targeting to the nuclear pore [, ]. The NUP C-terminal domain adopts a predominantly beta-strand structure. The molecule consists of a six-stranded beta-sheet sandwiched against a two-stranded beta-sheet and flanked by alpha-helical regions. The N-terminal helical region consists of two short helices, whereas the stretch on the opposite side of molecule consists of a single, longer helix [, ].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 3PBP_E 2AIV_A 1KO6_A 2Q5X_A 2Q5Y_C 3KEP_A 3KES_A 3NF5_B 3TKN_I.
Probab=21.24 E-value=45 Score=31.15 Aligned_cols=18 Identities=33% Similarity=0.789 Sum_probs=15.1
Q ss_pred cceeeeeeeeecceeeee
Q psy17963 138 TAYVCMNVISGPWRFQVE 155 (943)
Q Consensus 138 tayvcmNvisgpWrFQvE 155 (943)
+-+|+-|++||-|.|.|+
T Consensus 122 ~~FvsYd~~tG~W~F~V~ 139 (141)
T PF04096_consen 122 AEFVSYDPETGTWVFRVE 139 (141)
T ss_dssp SEEEEEETTTTEEEEEES
T ss_pred CEEEEEeCCCcEEEEEEe
Confidence 446777999999999986
No 35
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=21.19 E-value=32 Score=39.16 Aligned_cols=37 Identities=16% Similarity=0.315 Sum_probs=23.5
Q ss_pred ccccccCCCCceeEEeeceEEEEEeecCCCcCCCCcEEEEE
Q psy17963 66 DVMYNFAKPQTSIEIRVPTVVSVQLENSGSSLTNGRHVIVF 106 (943)
Q Consensus 66 dvmynfakpqtsieirvptvvsvqlensgssltngrhvivf 106 (943)
|++..||.-........|+++ ++..-.+.+|||.++-
T Consensus 276 D~l~a~a~~a~~~~~~~P~~~----~~~~i~l~~~rHPll~ 312 (782)
T PRK00409 276 DFIFARARYAKALKATFPLFN----DEGKIDLRQARHPLLD 312 (782)
T ss_pred HHHHHHHHHHHHCCCccceEc----CCCcEEEcCcCCceec
Confidence 566555554444555667775 3344567899999873
No 36
>cd06191 FNR_iron_sulfur_binding Iron-sulfur binding Ferredoxin Reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with a C-terminal iron-sulfur binding cluster domain. FNR was intially identified as a chloroplast reductase activity catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methnae assimilation in a variety of organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in
Probab=21.07 E-value=1.7e+02 Score=26.82 Aligned_cols=31 Identities=23% Similarity=0.452 Sum_probs=15.6
Q ss_pred eeceEEEEEeecCCC---cCCCCcEEEEEEeecC
Q psy17963 81 RVPTVVSVQLENSGS---SLTNGRHVIVFWCIAG 111 (943)
Q Consensus 81 rvptvvsvqlensgs---sltngrhvivfwciaG 111 (943)
.-|.|++|.++-.+. ...-|.||.|.+...|
T Consensus 9 ~t~~~~~~~l~~~~~~~~~~~pGQ~v~l~~~~~~ 42 (231)
T cd06191 9 ETPDAVTIVFAVPGPLQYGFRPGQHVTLKLDFDG 42 (231)
T ss_pred cCCCcEEEEEeCCCCCCCCCCCCCeEEEEEecCC
Confidence 345555555553332 3455666666554444
No 37
>COG4540 gpV Phage P2 baseplate assembly protein gpV [General function prediction only]
Probab=20.32 E-value=1.1e+02 Score=31.09 Aligned_cols=17 Identities=29% Similarity=0.306 Sum_probs=14.3
Q ss_pred cccccccccceeeCcce
Q psy17963 114 LTNRRHIKTNVFIGQDV 130 (943)
Q Consensus 114 LtnrrhikTnVfIgqdV 130 (943)
.-+-+|+||+|+.++|.
T Consensus 163 v~ldkh~ht~v~~~g~t 179 (184)
T COG4540 163 VGLDKHIHTAVNSNGDT 179 (184)
T ss_pred eeEeeecccccccCCCC
Confidence 34579999999999985
Done!