Query psy17939
Match_columns 81
No_of_seqs 106 out of 220
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 18:10:48 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17939.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17939hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1058|consensus 100.0 1E-32 2.2E-37 228.9 5.8 79 3-81 23-101 (948)
2 COG5096 Vesicle coat complex, 99.8 3.7E-19 8E-24 148.1 4.2 70 4-79 22-92 (757)
3 KOG1060|consensus 99.7 3.9E-17 8.4E-22 137.0 6.0 72 3-75 38-109 (968)
4 PTZ00429 beta-adaptin; Provisi 99.6 2.7E-15 5.9E-20 124.8 7.0 67 3-70 35-101 (746)
5 KOG1061|consensus 99.3 3.6E-12 7.7E-17 106.3 3.8 70 3-73 16-85 (734)
6 PF01602 Adaptin_N: Adaptin N 99.2 1.4E-11 3E-16 94.4 4.8 68 2-70 6-75 (526)
7 PRK13431 F0F1 ATP synthase sub 66.3 22 0.00048 25.5 5.5 61 3-66 43-103 (180)
8 cd03561 VHS VHS domain family; 61.2 45 0.00097 22.0 6.1 63 2-64 39-110 (133)
9 PF10274 ParcG: Parkin co-regu 60.5 15 0.00032 26.7 3.7 45 4-48 84-128 (183)
10 PF07923 N1221: N1221-like pro 58.1 30 0.00065 25.9 5.1 49 12-64 171-224 (293)
11 smart00288 VHS Domain present 53.9 41 0.00088 22.4 4.8 61 3-63 40-108 (133)
12 KOG1078|consensus 53.7 36 0.00079 30.1 5.5 55 15-70 38-97 (865)
13 cd03569 VHS_Hrs_Vps27p VHS dom 51.2 45 0.00098 22.6 4.7 61 3-63 44-111 (142)
14 PF05542 DUF760: Protein of un 49.9 28 0.00061 21.8 3.3 40 3-42 12-51 (86)
15 cd06907 M14_AGBL2-3_like Pepti 49.3 5.5 0.00012 30.2 -0.1 39 34-73 61-101 (261)
16 KOG3961|consensus 49.3 33 0.00071 26.4 4.1 44 4-47 159-202 (262)
17 PF12717 Cnd1: non-SMC mitotic 48.4 86 0.0019 21.4 6.2 64 3-67 28-93 (178)
18 cd06238 Peptidase_M14-like_1_1 48.3 19 0.00041 27.1 2.7 62 12-73 18-104 (271)
19 cd06908 M14_AGBL4_like Peptida 45.3 9.4 0.0002 28.7 0.7 42 31-73 55-98 (261)
20 PF01602 Adaptin_N: Adaptin N 44.8 16 0.00035 28.2 1.9 52 3-56 82-133 (526)
21 PF14805 THDPS_N_2: Tetrahydro 44.6 36 0.00077 21.0 3.1 48 7-63 15-69 (70)
22 COG5240 SEC21 Vesicle coat com 43.1 68 0.0015 28.2 5.4 68 3-71 25-99 (898)
23 PF11761 CbiG_mid: Cobalamin b 36.8 29 0.00062 20.8 1.8 17 18-34 18-34 (93)
24 cd06236 M14_AGBL5_like Peptida 34.8 15 0.00032 28.5 0.3 39 35-73 84-123 (304)
25 COG0225 MsrA Peptide methionin 33.6 31 0.00067 25.0 1.8 20 52-71 70-89 (174)
26 PF12348 CLASP_N: CLASP N term 31.5 52 0.0011 22.7 2.6 40 4-43 7-52 (228)
27 PF06918 DUF1280: Protein of u 30.9 64 0.0014 23.9 3.1 36 16-51 10-45 (224)
28 cd06235 M14_Nna1_like_2 Subgro 30.9 23 0.00049 26.3 0.7 38 35-73 62-100 (258)
29 PF11640 TAN: Telomere-length 27.7 81 0.0018 21.3 3.0 44 3-46 7-58 (155)
30 PF03392 OS-D: Insect pheromon 26.8 1.7E+02 0.0036 18.8 4.2 60 8-74 27-92 (95)
31 PF00246 Peptidase_M14: Zinc c 26.6 10 0.00023 27.5 -1.7 38 35-72 63-102 (279)
32 PF14711 Nitr_red_bet_C: Respi 26.5 1E+02 0.0022 19.7 3.1 23 5-27 35-57 (83)
33 PF04031 Las1: Las1-like ; In 25.2 1.6E+02 0.0034 20.3 4.1 32 4-35 12-45 (154)
34 PF01625 PMSR: Peptide methion 24.6 65 0.0014 22.4 2.1 23 49-71 61-83 (155)
35 PF12719 Cnd3: Nuclear condens 24.3 3E+02 0.0064 20.3 6.5 65 5-69 119-188 (298)
36 PF08097 Toxin_26: Conotoxin T 23.7 21 0.00046 14.9 -0.3 6 40-45 4-9 (11)
37 smart00755 Grip golgin-97, Ran 23.5 1.5E+02 0.0033 16.7 3.4 40 17-56 3-43 (46)
38 PF15658 Latrotoxin_C: Latroto 23.2 61 0.0013 22.5 1.7 41 33-76 68-108 (127)
39 KOG1062|consensus 23.0 1.8E+02 0.0038 26.1 4.8 65 4-70 354-419 (866)
40 cd03858 M14_CP_N-E_like Carbox 22.7 32 0.0007 26.4 0.3 39 35-73 69-111 (374)
41 cd06905 Peptidase_M14-like_8 A 22.1 29 0.00064 27.2 -0.0 39 35-73 72-113 (360)
42 PF10508 Proteasom_PSMB: Prote 21.7 3.7E+02 0.008 21.7 6.1 65 3-68 80-150 (503)
43 PF08713 DNA_alkylation: DNA a 21.5 1.1E+02 0.0024 20.8 2.7 39 5-46 1-39 (213)
44 PF12078 DUF3557: Domain of un 21.5 79 0.0017 20.6 2.0 16 19-34 4-19 (154)
45 PHA02650 hypothetical protein; 21.3 96 0.0021 20.0 2.2 11 56-66 65-75 (81)
46 COG3067 NhaB Na+/H+ antiporter 20.9 67 0.0015 26.4 1.8 27 35-61 373-399 (516)
47 PF05997 Nop52: Nucleolar prot 20.9 3E+02 0.0066 19.8 5.1 46 4-62 4-53 (217)
48 cd03863 M14_CPD_II The second 20.2 33 0.00071 27.1 -0.1 39 35-73 74-115 (375)
No 1
>KOG1058|consensus
Probab=99.97 E-value=1e-32 Score=228.89 Aligned_cols=79 Identities=52% Similarity=0.913 Sum_probs=77.4
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCChhhHHHHHHHHHhccCCCCCCCcccceeecC
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPDGKLLQDRCKTT 81 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~~dGkL~~EmiL~~ 81 (81)
.||++.||+|+++.|+||||++|.+|+||+++|+|+|+|||||+||+||+||||+|+|||++||+++||+++|||||+.
T Consensus 23 ~~ik~~Lek~~~~~KIeamK~ii~~mlnGe~~p~Llm~IiRfvlps~~~elKKLly~ywE~vPKt~~dgkl~~EMILvc 101 (948)
T KOG1058|consen 23 DEIKEKLEKGDDEVKIEAMKKIIALMLNGEDLPSLLMTIIRFVLPSRNHELKKLLYYYWELVPKTDSDGKLLHEMILVC 101 (948)
T ss_pred HHHHHHHhcCChHHHHHHHHHHHHHHHcCCCchHHHHHHhheeeccCchHHHHHHHHHHHHccccCCCcccHHHHHHHH
Confidence 5899999999999999999999999999999999999999999999999999999999999999999999999999973
No 2
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=99.76 E-value=3.7e-19 Score=148.06 Aligned_cols=70 Identities=27% Similarity=0.410 Sum_probs=65.4
Q ss_pred HHHhh-hhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCChhhHHHHHHHHHhccCCCCCCCcccceee
Q psy17939 4 CVSHH-IEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPDGKLLQDRCK 79 (81)
Q Consensus 4 elk~~-Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~~dGkL~~EmiL 79 (81)
.++.. |+|+++..|++|||++|+.|..|+|+|.|||+||||++ |.|.|+|||+|+||++||+++| +||||
T Consensus 22 ~~~sg~l~s~n~~~kidAmK~iIa~M~~G~dmssLf~dViK~~~-trd~ElKrL~ylYl~~yak~~P-----~~~lL 92 (757)
T COG5096 22 ALSSGRLESSNDYKKIDAMKKIIAQMSLGEDMSSLFPDVIKNVA-TRDVELKRLLYLYLERYAKLKP-----ELALL 92 (757)
T ss_pred hhccccccccChHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHH-hcCHHHHHHHHHHHHHHhccCH-----HHHHH
Confidence 44555 89999999999999999999999999999999999999 9999999999999999999999 57776
No 3
>KOG1060|consensus
Probab=99.68 E-value=3.9e-17 Score=137.00 Aligned_cols=72 Identities=22% Similarity=0.422 Sum_probs=69.2
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCChhhHHHHHHHHHhccCCCCCCCccc
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPDGKLLQ 75 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~~dGkL~~ 75 (81)
++|+..|+|+++..|+||||+||++|.+|++++.+|++|||||+ |+|.|+|||+|+|+..|+--+||-.|+.
T Consensus 38 ~dL~~lLdSnkd~~KleAmKRIia~iA~G~dvS~~Fp~VVKNVa-skn~EVKkLVyvYLlrYAEeqpdLALLS 109 (968)
T KOG1060|consen 38 DDLKQLLDSNKDSLKLEAMKRIIALIAKGKDVSLLFPAVVKNVA-SKNIEVKKLVYVYLLRYAEEQPDLALLS 109 (968)
T ss_pred HHHHHHHhccccHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHhh-ccCHHHHHHHHHHHHHHhhcCCCceeee
Confidence 48999999999999999999999999999999999999999999 9999999999999999999999988763
No 4
>PTZ00429 beta-adaptin; Provisional
Probab=99.58 E-value=2.7e-15 Score=124.79 Aligned_cols=67 Identities=18% Similarity=0.363 Sum_probs=63.0
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCChhhHHHHHHHHHhccCCCCC
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPD 70 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~~d 70 (81)
+|||+.|+++++++|++|||++|++|+.|+|++.+||+||+ +++|+|+++|||+|+||.++.+.+||
T Consensus 35 ~ELr~~L~s~~~~~kk~alKkvIa~mt~G~DvS~LF~dVvk-~~~S~d~elKKLvYLYL~~ya~~~pe 101 (746)
T PTZ00429 35 AELQNDLNGTDSYRKKAAVKRIIANMTMGRDVSYLFVDVVK-LAPSTDLELKKLVYLYVLSTARLQPE 101 (746)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCchHHHHHHHH-HhCCCCHHHHHHHHHHHHHHcccChH
Confidence 68999999999999999999999999999999999999999 56699999999999999999777664
No 5
>KOG1061|consensus
Probab=99.26 E-value=3.6e-12 Score=106.28 Aligned_cols=70 Identities=20% Similarity=0.395 Sum_probs=65.0
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCChhhHHHHHHHHHhccCCCCCCCc
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPDGKL 73 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~~dGkL 73 (81)
.|+|..|.|...+.+++|.|++|+.|.-|.|+|++|++||+ ++.+.|.++|||+|+|+.+|.+..||+.+
T Consensus 16 ~elks~l~s~~~~kr~~a~kkvIa~Mt~G~DvSslF~dvvk-~~~T~dlelKKlvyLYl~nYa~~~P~~a~ 85 (734)
T KOG1061|consen 16 PELKSQLNSQSKEKRKDAVKKVIAYMTVGKDVSSLFPDVVK-CMQTRDLELKKLVYLYLMNYAKGKPDLAI 85 (734)
T ss_pred hHHHHHhhhhhhhhHHHHHHHHHhcCccCcchHhhhHHHHh-hcccCCchHHHHHHHHHHHhhccCchHHH
Confidence 47889998888899999999999999999999999999998 67799999999999999999999999765
No 6
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=99.21 E-value=1.4e-11 Score=94.38 Aligned_cols=68 Identities=22% Similarity=0.348 Sum_probs=60.9
Q ss_pred hhHHHhhhhcC--ChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCChhhHHHHHHHHHhccCCCCC
Q psy17939 2 APCVSHHIEKG--DTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPD 70 (81)
Q Consensus 2 ~~elk~~Les~--~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~~d 70 (81)
.+|+++.+++. +.+.|++||+++|.++..|.+++.+|++||+++. |+|+++||+.|+||+.+...++|
T Consensus 6 ~~el~~~~~~~~~~~~~~~~~l~kli~~~~~G~~~~~~~~~vi~l~~-s~~~~~Krl~yl~l~~~~~~~~~ 75 (526)
T PF01602_consen 6 SQELAKILNSFKIDISKKKEALKKLIYLMMLGYDISFLFMEVIKLIS-SKDLELKRLGYLYLSLYLHEDPE 75 (526)
T ss_dssp HHHHHHHHHCSSTHHHHHHHHHHHHHHHHHTT---GSTHHHHHCTCS-SSSHHHHHHHHHHHHHHTTTSHH
T ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHhC-CCCHHHHHHHHHHHHHHhhcchh
Confidence 36899999999 9999999999999999999999999999999777 99999999999999999888775
No 7
>PRK13431 F0F1 ATP synthase subunit delta; Provisional
Probab=66.31 E-value=22 Score=25.45 Aligned_cols=61 Identities=18% Similarity=0.231 Sum_probs=51.0
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCChhhHHHHHHHHHhccC
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPK 66 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k 66 (81)
.+++..|+++..+.|.+-+.+++.... |..++..+...++-++ +|+++.-|-+++.+.+..
T Consensus 43 ~el~~il~~P~~~~Kkk~l~~l~~~a~-~~~~~~~~~NFl~LL~--en~Rl~~LpeIa~~L~~~ 103 (180)
T PRK13431 43 HKLNQVLAHVSLKVKKEVVFEILEKIT-SIKACSVLKPVMEVVL--KNNRLDMLELITEELSFD 103 (180)
T ss_pred HHHHHHHhCccHHHHHHHHHHHHhhhc-cccccHHHHHHHHHHH--HcChHHHHHHHHHHHHHH
Confidence 478899999999999999999997665 5588999999998666 999999999998876543
No 8
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=61.18 E-value=45 Score=22.01 Aligned_cols=63 Identities=14% Similarity=0.239 Sum_probs=48.8
Q ss_pred hhHHHhhhhcCChHHHHHHHHHHHHHHHcCCC-C-----C-cchHHHHHhhcc--CCChhhHHHHHHHHHhc
Q psy17939 2 APCVSHHIEKGDTKIKIEALKKVIQMIANGER-L-----P-GILMIIIRFVLP--MQDHMIKKLLLIFWEIV 64 (81)
Q Consensus 2 ~~elk~~Les~~~~~K~ealKkiI~~~~~G~~-~-----~-~L~m~VIr~v~p--s~n~~lKKLl~lY~e~~ 64 (81)
++-|++.|.+++.....-||.=+=..+.|+.+ + + .++-..++.+.+ ..+.++|+-+.-++..+
T Consensus 39 ~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~fl~~l~~l~~~~~~~~~~Vk~kil~ll~~W 110 (133)
T cd03561 39 ARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNSPKYDPKVREKALELILAW 110 (133)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhhHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHH
Confidence 35689999999999999999999999999866 3 2 566677777765 56778888777666554
No 9
>PF10274 ParcG: Parkin co-regulated protein; InterPro: IPR019399 This family of proteins is transcribed anti-sense along the DNA to the Parkin gene product and the two appear to be transcribed under the same promoter. The protein has predicted alpha-helical and beta-sheet domains which suggest its function is in the ubiquitin/proteasome system []. Mutations in parkin are the genetic cause of early-onset and autosomal recessive juvenile parkinsonism.
Probab=60.47 E-value=15 Score=26.67 Aligned_cols=45 Identities=18% Similarity=0.314 Sum_probs=35.7
Q ss_pred HHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccC
Q psy17939 4 CVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPM 48 (81)
Q Consensus 4 elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps 48 (81)
=||++|.+++.+..+.+|+-+-.+...++-+.+-+.+=-|..+|.
T Consensus 84 plk~AL~tr~~~V~~~~L~~Lq~Lv~~~~~vG~aLvPyyrqLLp~ 128 (183)
T PF10274_consen 84 PLKRALNTRDPEVFCATLKALQQLVTSSDMVGEALVPYYRQLLPV 128 (183)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHH
Confidence 478999999999999999988888777777766665556666663
No 10
>PF07923 N1221: N1221-like protein; InterPro: IPR012486 The sequences featured in this family are similar to a hypothetical protein product of ORF N1221 in the CPT1-SPC98 intergenic region of the yeast genome (P53917 from SWISSPROT). This encodes an acidic polypeptide with several possible transmembrane regions [].
Probab=58.13 E-value=30 Score=25.93 Aligned_cols=49 Identities=18% Similarity=0.474 Sum_probs=31.9
Q ss_pred CChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhc-----cCCChhhHHHHHHHHHhc
Q psy17939 12 GDTKIKIEALKKVIQMIANGERLPGILMIIIRFVL-----PMQDHMIKKLLLIFWEIV 64 (81)
Q Consensus 12 ~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~-----ps~n~~lKKLl~lY~e~~ 64 (81)
.+......+.+..|..+.+- .|+...++++. ++.+..+||+++++|..+
T Consensus 171 ~~~~~~~~~~~~~~~~L~~p----~ll~~L~~~i~~~rw~~~~~~pikkvlLLlwK~l 224 (293)
T PF07923_consen 171 RDSPEWMAIVREFIMELEEP----NLLVFLFKMIEKLRWDSAPHFPIKKVLLLLWKLL 224 (293)
T ss_pred cccchhhHHHHHHHHHhcCC----cHHHHHHHHHHHhcCCCCCCccHHHHHHHHHHHH
Confidence 34445566677777765332 45555554443 467778999999999864
No 11
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=53.94 E-value=41 Score=22.36 Aligned_cols=61 Identities=15% Similarity=0.275 Sum_probs=42.7
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHc-CCCC-----Cc-chHHHHHhhccCCChh-hHHHHHHHHHh
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIAN-GERL-----PG-ILMIIIRFVLPMQDHM-IKKLLLIFWEI 63 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~-G~~~-----~~-L~m~VIr~v~ps~n~~-lKKLl~lY~e~ 63 (81)
.-|++.|.+++.....-||.=+=..+.| |.++ +. ++-..++-+.+..++. +|+-+.-+...
T Consensus 40 r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~s~~fl~~L~~l~~~~~~~~~Vk~kil~li~~ 108 (133)
T smart00288 40 RLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKYPLPLVKKRILELIQE 108 (133)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHHHHHHHHcCCCCcHHHHHHHHHHHHH
Confidence 4688999999999999999998889999 6555 32 3444445455555655 77755555444
No 12
>KOG1078|consensus
Probab=53.66 E-value=36 Score=30.15 Aligned_cols=55 Identities=15% Similarity=0.358 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHHHcCCCCC-----cchHHHHHhhccCCChhhHHHHHHHHHhccCCCCC
Q psy17939 15 KIKIEALKKVIQMIANGERLP-----GILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPD 70 (81)
Q Consensus 15 ~~K~ealKkiI~~~~~G~~~~-----~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~~d 70 (81)
++=+..+-+++.++.+||.++ ++|..+-| ..+|+|.-+|+.+|+=..-.++...|
T Consensus 38 r~c~~~lskllyll~qge~~~~~eate~ff~~tK-lfQskd~~LRr~vYl~Ikels~ised 97 (865)
T KOG1078|consen 38 RKCRHILSKLLYLLNQGEHFGETEATELFFAITK-LFQSKDVSLRRMVYLAIKELSKISED 97 (865)
T ss_pred HHHHHHHHHHHHHHhcccccchhhHHHHHHHHHH-HHhhcCHHHHHHHHHHHhhccccchh
Confidence 333568999999999999885 58999998 66799999999999887766655443
No 13
>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=51.19 E-value=45 Score=22.61 Aligned_cols=61 Identities=8% Similarity=0.214 Sum_probs=42.4
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHc-CCCC-----C-cchHHHHHhhccCCChhhHHHHHHHHHh
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIAN-GERL-----P-GILMIIIRFVLPMQDHMIKKLLLIFWEI 63 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~-G~~~-----~-~L~m~VIr~v~ps~n~~lKKLl~lY~e~ 63 (81)
.-|++.|.+++...-.-||.=+=..+.| |.++ + +++-..++-+.+..+.++|+-++-+...
T Consensus 44 ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~~fl~~l~~l~~~~~~~~Vk~kil~li~~ 111 (142)
T cd03569 44 RALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASREFMDELKDLIKTTKNEEVRQKILELIQA 111 (142)
T ss_pred HHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHHcccCCHHHHHHHHHHHHH
Confidence 4688999999999999999988889999 5544 2 3444445544446677788655544433
No 14
>PF05542 DUF760: Protein of unknown function (DUF760); InterPro: IPR008479 This entry contains uncharacterised proteins.
Probab=49.89 E-value=28 Score=21.83 Aligned_cols=40 Identities=13% Similarity=0.153 Sum_probs=31.0
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHH
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIII 42 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VI 42 (81)
.|....|+++...+-.|+||+.|..++.+-..+..|-.+|
T Consensus 12 pe~~~~l~~~~s~ev~e~m~~~v~~llG~l~p~~~~~~~i 51 (86)
T PF05542_consen 12 PERIQQLSEPASPEVLEAMKQHVSGLLGNLSPSDQFNVTI 51 (86)
T ss_pred HHHHHHhhccCCHHHHHHHHHHHHHHHcCCCCcccCccee
Confidence 3667788888888999999999999999985344444444
No 15
>cd06907 M14_AGBL2-3_like Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-2, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This subgroup includes the human AGBL-2, and -3, and the mouse cytosolic carboxypeptidase (CCPs)-2, and -3. ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however does not belong to this subgroup. AGTPBP-1/Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N
Probab=49.34 E-value=5.5 Score=30.21 Aligned_cols=39 Identities=23% Similarity=0.397 Sum_probs=27.4
Q ss_pred CCcchHH-HHHhhccCCChhhHHHH-HHHHHhccCCCCCCCc
Q psy17939 34 LPGILMI-IIRFVLPMQDHMIKKLL-LIFWEIVPKTTPDGKL 73 (81)
Q Consensus 34 ~~~L~m~-VIr~v~ps~n~~lKKLl-~lY~e~~~k~~~dGkL 73 (81)
....+|. .+.+.+ +++.+.++|. .+=|-++|..+|||--
T Consensus 61 ~~s~~~~gll~~L~-~~~~~a~~Lr~~~~f~IvPmlNPDGv~ 101 (261)
T cd06907 61 NASWMMKGFLDFLT-SNSPDAQLLRDTFIFKIVPMLNPDGVI 101 (261)
T ss_pred HHHHHHHHHHHHHh-cCCHHHHHHHhcCCEEEEEeecCcccc
Confidence 3334444 777776 6788888886 3345689999999853
No 16
>KOG3961|consensus
Probab=49.31 E-value=33 Score=26.35 Aligned_cols=44 Identities=18% Similarity=0.240 Sum_probs=31.8
Q ss_pred HHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhcc
Q psy17939 4 CVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLP 47 (81)
Q Consensus 4 elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~p 47 (81)
-||++|.+.|++.++.+||-+-.+...+.=+..-+-+--|..+|
T Consensus 159 plK~al~trd~ev~~~~Lkvlq~lv~~~~~vG~aLVPfYRQlLp 202 (262)
T KOG3961|consen 159 PLKAALVTRDDEVICRTLKVLQQLVVSVGCVGAALVPFYRQLLP 202 (262)
T ss_pred HHHHHHhhccHHHHHHHHHHHHHHHHhccccchhhhhHHHHhhh
Confidence 47899999999999999998887777776454444444444443
No 17
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=48.36 E-value=86 Score=21.41 Aligned_cols=64 Identities=17% Similarity=0.279 Sum_probs=51.2
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHcCC-CC-CcchHHHHHhhccCCChhhHHHHHHHHHhccCC
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIANGE-RL-PGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKT 67 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~G~-~~-~~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~ 67 (81)
..+.+.|.+.+...+..|+.-+-.++++|- .+ +++|..+.+ ++--+|.+++.+.-.|+.-+-+.
T Consensus 28 ~~l~~~L~D~~~~VR~~al~~Ls~Li~~d~ik~k~~l~~~~l~-~l~D~~~~Ir~~A~~~~~e~~~~ 93 (178)
T PF12717_consen 28 PNLYKCLRDEDPLVRKTALLVLSHLILEDMIKVKGQLFSRILK-LLVDENPEIRSLARSFFSELLKK 93 (178)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHcCceeehhhhhHHHHH-HHcCCCHHHHHHHHHHHHHHHHh
Confidence 357788999999999999999988988876 23 567788887 55688999999988887765443
No 18
>cd06238 Peptidase_M14-like_1_1 Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. T
Probab=48.32 E-value=19 Score=27.14 Aligned_cols=62 Identities=16% Similarity=0.203 Sum_probs=42.3
Q ss_pred CChHHHHHHHHHHHHHHHcCC-----------------------CC-CcchHHHHHhhccCCChhhHHHH-HHHHHhccC
Q psy17939 12 GDTKIKIEALKKVIQMIANGE-----------------------RL-PGILMIIIRFVLPMQDHMIKKLL-LIFWEIVPK 66 (81)
Q Consensus 12 ~~~~~K~ealKkiI~~~~~G~-----------------------~~-~~L~m~VIr~v~ps~n~~lKKLl-~lY~e~~~k 66 (81)
.....+++.+|+....++..+ .. +...+.+++.++.+++.++++++ -.-|-++|-
T Consensus 18 ~~n~~~l~~~~~~~~~la~p~~~~~~~~~~~~~v~i~~~iH~~E~~g~~~~l~l~~~L~~~~~~~~~~ll~~~~i~i~P~ 97 (271)
T cd06238 18 PENIARLDQIREDHLALADPAATSSLISDQPVVVWLGYSVHGNEISGTEAALLTAYHLAAAQGDEIEALLDNAVVLIDPM 97 (271)
T ss_pred HHHHHhHHHHHHHHHHhcCccccccccccCCcEEEEECCcCCCChHHHHHHHHHHHHHHHcCCHHHHHHHhcCEEEEEec
Confidence 334566777777776554442 12 23567788888777888888887 444557899
Q ss_pred CCCCCCc
Q psy17939 67 TTPDGKL 73 (81)
Q Consensus 67 ~~~dGkL 73 (81)
.+|||--
T Consensus 98 ~NPDG~~ 104 (271)
T cd06238 98 QNPDGRD 104 (271)
T ss_pred cCCCHHH
Confidence 9999965
No 19
>cd06908 M14_AGBL4_like Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-4, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This eukaryotic subgroup includes the human AGBL4 and the mouse cytosolic carboxypeptidase (CCP)-6. ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however does not belong to this subgroup. AGTPBP-1/Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal
Probab=45.33 E-value=9.4 Score=28.72 Aligned_cols=42 Identities=29% Similarity=0.467 Sum_probs=29.4
Q ss_pred CCCCC-cchHHHHHhhccCCChhhHHHH-HHHHHhccCCCCCCCc
Q psy17939 31 GERLP-GILMIIIRFVLPMQDHMIKKLL-LIFWEIVPKTTPDGKL 73 (81)
Q Consensus 31 G~~~~-~L~m~VIr~v~ps~n~~lKKLl-~lY~e~~~k~~~dGkL 73 (81)
||..+ .+...+|.+.+ ++|.+.++|+ .+=|-++|..+|||--
T Consensus 55 ~E~~~s~~~~~li~~L~-~~~~~~~~L~~~~~~~IvP~~NPDGv~ 98 (261)
T cd06908 55 GESPSSYVCQGLIDFLV-SNHPIAKVLREHLVFKIVPMLNPDGVF 98 (261)
T ss_pred CChHHHHHHHHHHHHHh-hCCHHHHHHHHhCcEEEEeeecCccee
Confidence 44443 44555888887 5688888877 3446689999999853
No 20
>PF01602 Adaptin_N: Adaptin N terminal region; InterPro: IPR002553 Proteins synthesized on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. Clathrin coats contain both clathrin and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors []. All AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). Each subunit has a specific function. Adaptin subunits recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal appendage domains. By contrast, GGAs are monomers composed of four domains, which have functions similar to AP subunits: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The GAE domain is similar to the AP gamma-adaptin ear domain, being responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. While clathrin mediates endocytic protein transport from ER to Golgi, coatomers (COPI, COPII) primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the N-terminal domain of various adaptins from different AP clathrin adaptor complexes (including AP1, AP2, AP3 and AP4), and from the beta and gamma subunits of various coatomer (COP) adaptors. This domain has a 2-layer alpha/alpha fold that forms a right-handed superhelix, and is a member of the ARM repeat superfamily []. The N-terminal region of the various AP adaptor proteins share strong sequence identity; by contrast, the C-terminal domains of different adaptins share similar structural folds, but have little sequence identity []. It has been proposed that the N-terminal domain interacts with another uniform component of the coated vesicles. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 1W63_C 2JKR_A 2JKT_A 2XA7_A 2VGL_B 3TJZ_E.
Probab=44.80 E-value=16 Score=28.19 Aligned_cols=52 Identities=12% Similarity=0.176 Sum_probs=37.1
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCChhhHHH
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKKL 56 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~~lKKL 56 (81)
+-++++|.+++...+.-||+-+-.. .+-+-.+.++..|.+.+. +++..++|=
T Consensus 82 n~l~kdl~~~n~~~~~lAL~~l~~i-~~~~~~~~l~~~v~~ll~-~~~~~VRk~ 133 (526)
T PF01602_consen 82 NSLQKDLNSPNPYIRGLALRTLSNI-RTPEMAEPLIPDVIKLLS-DPSPYVRKK 133 (526)
T ss_dssp HHHHHHHCSSSHHHHHHHHHHHHHH--SHHHHHHHHHHHHHHHH-SSSHHHHHH
T ss_pred HHHHHhhcCCCHHHHHHHHhhhhhh-cccchhhHHHHHHHHHhc-CCchHHHHH
Confidence 5688999999999999999876553 333334666777776444 888888883
No 21
>PF14805 THDPS_N_2: Tetrahydrodipicolinate N-succinyltransferase N-terminal; PDB: 3EG4_A 3TDT_A 2TDT_A 1KGT_A 1TDT_A 1KGQ_A 3BXY_A 3GOS_A 3TK8_A.
Probab=44.57 E-value=36 Score=21.02 Aligned_cols=48 Identities=19% Similarity=0.440 Sum_probs=31.7
Q ss_pred hhhh-cCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCC------ChhhHHHHHHHHHh
Q psy17939 7 HHIE-KGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQ------DHMIKKLLLIFWEI 63 (81)
Q Consensus 7 ~~Le-s~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~------n~~lKKLl~lY~e~ 63 (81)
..+. +..+.+=.+|+..+|.+.-+|+ +|-+-|.. |.=+||-+++|+.+
T Consensus 15 ~~l~~~~~~~~~~~av~~~i~~Ld~G~---------lRvAek~~~g~W~vneWvKkAILL~Frl 69 (70)
T PF14805_consen 15 DELTPSNADPELRDAVEEVIELLDSGE---------LRVAEKDADGEWVVNEWVKKAILLYFRL 69 (70)
T ss_dssp GG-BTTT--HHHHHHHHHHHHHHHTTS---------S-SEEEETTTEEEE-HHHHHHHHHHHHH
T ss_pred hhCCCccCCHHHHHHHHHHHHHhcCCC---------eEEEeecCCCCEEeeHHHHHHHHhcccc
Confidence 3344 3446777899999999999995 66555542 33499999999864
No 22
>COG5240 SEC21 Vesicle coat complex COPI, gamma subunit [Intracellular trafficking and secretion]
Probab=43.10 E-value=68 Score=28.20 Aligned_cols=68 Identities=15% Similarity=0.294 Sum_probs=51.9
Q ss_pred hHHHhhhhcCChH--HHHHHHHHHHHHHHcCCCCC-----cchHHHHHhhccCCChhhHHHHHHHHHhccCCCCCC
Q psy17939 3 PCVSHHIEKGDTK--IKIEALKKVIQMIANGERLP-----GILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPDG 71 (81)
Q Consensus 3 ~elk~~Les~~~~--~K~ealKkiI~~~~~G~~~~-----~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~~dG 71 (81)
+|-++.+.++... .=..++-++..+++.|+-+| +||..+-| ..+++|.-|+--+|+-.+-..+...||
T Consensus 25 qd~~~sfn~Spvs~r~~r~lls~l~yll~tge~f~e~~at~lff~i~K-lFQhkd~~Lrq~VY~aIkelS~~tedv 99 (898)
T COG5240 25 QDMNESFNKSPVSTRSARKLLSNLFYLLSTGELFPEATATNLFFAILK-LFQHKDLYLRQCVYSAIKELSKLTEDV 99 (898)
T ss_pred HHHHHHhccCCCChHHHHHHHHHHHHHHhccccchhhHHHHHHHHHHH-HHhcCChHHHHHHHHHHHHHhhcchhh
Confidence 4556677666543 33568899999999999885 58999998 666999999999998877666655543
No 23
>PF11761 CbiG_mid: Cobalamin biosynthesis central region; InterPro: IPR021745 Members of this family are involved in cobalamin synthesis. The gene encoded by P72862 from SWISSPROT has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [].
Probab=36.81 E-value=29 Score=20.75 Aligned_cols=17 Identities=41% Similarity=0.585 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHcCCCC
Q psy17939 18 IEALKKVIQMIANGERL 34 (81)
Q Consensus 18 ~ealKkiI~~~~~G~~~ 34 (81)
.+++|++-+++.||+++
T Consensus 18 ~~~~k~vsaalv~g~~V 34 (93)
T PF11761_consen 18 REAVKRVSAALVNGEPV 34 (93)
T ss_pred HHHHHHHHHHHHCCCEE
Confidence 57899999999999986
No 24
>cd06236 M14_AGBL5_like Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-5, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This eukaryotic subgroup includes the human AGBL5 and the mouse cytosolic carboxypeptidase (CCP)-5. ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however does not belong to this subgroup. AGTPBP-1/Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal
Probab=34.80 E-value=15 Score=28.50 Aligned_cols=39 Identities=21% Similarity=0.378 Sum_probs=30.0
Q ss_pred CcchHHHHHhhccCCChhhHHHHH-HHHHhccCCCCCCCc
Q psy17939 35 PGILMIIIRFVLPMQDHMIKKLLL-IFWEIVPKTTPDGKL 73 (81)
Q Consensus 35 ~~L~m~VIr~v~ps~n~~lKKLl~-lY~e~~~k~~~dGkL 73 (81)
+..++.++++++...+.+.+.|+= +=|-++|-.+|||-.
T Consensus 84 s~~~~~ll~~Ll~~~d~~a~~L~~~~~~~IvPmlNPDGv~ 123 (304)
T cd06236 84 SFVFNGFLKFLLNKDDPRAALLRRRFVFKLIPMLNPDGVY 123 (304)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCeEEEEEeEcccccc
Confidence 445678899998556788888875 556678999999964
No 25
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=33.60 E-value=31 Score=25.03 Aligned_cols=20 Identities=30% Similarity=0.441 Sum_probs=17.5
Q ss_pred hhHHHHHHHHHhccCCCCCC
Q psy17939 52 MIKKLLLIFWEIVPKTTPDG 71 (81)
Q Consensus 52 ~lKKLl~lY~e~~~k~~~dG 71 (81)
.+.+||-+||++.+.++.++
T Consensus 70 sy~~LL~~ff~ihDPT~~nr 89 (174)
T COG0225 70 SYEELLEVFFEIHDPTSLNR 89 (174)
T ss_pred cHHHHHHHHheecCCCCCCc
Confidence 47899999999999998764
No 26
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=31.48 E-value=52 Score=22.70 Aligned_cols=40 Identities=23% Similarity=0.358 Sum_probs=24.4
Q ss_pred HHHhhh----hcCChHHHHHHHHHHHHHHHcC--CCCCcchHHHHH
Q psy17939 4 CVSHHI----EKGDTKIKIEALKKVIQMIANG--ERLPGILMIIIR 43 (81)
Q Consensus 4 elk~~L----es~~~~~K~ealKkiI~~~~~G--~~~~~L~m~VIr 43 (81)
++...| .+.+=+.+.+|+.++-..+..| .+.++-|...+|
T Consensus 7 ~~~~~l~~~~~~~~W~~r~~al~~L~~l~~~~~~~~~~~~~~~~l~ 52 (228)
T PF12348_consen 7 EILAALEKKESESDWEERVEALQKLRSLIKGNAPEDFPPDFVECLR 52 (228)
T ss_dssp GS-TTHHHHHT-SSHHHHHHHHHHHHHHHHH-B-----HHHHHHHH
T ss_pred HHHHHHhccCCccCHHHHHHHHHHHHHHHHcCCccccHHHHHHHHH
Confidence 444555 4567788999999999988888 455555555555
No 27
>PF06918 DUF1280: Protein of unknown function (DUF1280); InterPro: IPR009689 This family represents a conserved region approximately 200 residues long within a number of proteins of unknown function that seem to be specific to Caenorhabditis elegans.
Probab=30.93 E-value=64 Score=23.87 Aligned_cols=36 Identities=25% Similarity=0.272 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCCh
Q psy17939 16 IKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDH 51 (81)
Q Consensus 16 ~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~ 51 (81)
.+++..-+.|..+.+|+++..++-.+++|+..+.+-
T Consensus 10 ~R~~~~l~~iq~ivg~~d~~~Fl~df~k~l~k~~~~ 45 (224)
T PF06918_consen 10 NRCERVLKAIQQIVGEEDVDQFLRDFIKFLDKSGEF 45 (224)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHHHHHhccCccc
Confidence 345555556666778889999999999999865543
No 28
>cd06235 M14_Nna1_like_2 Subgroup of the Peptidase M14-like domain of Nna-1 (Nervous system Nuclear protein induced by Axotomy), also known as ATP/GTP binding protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP), and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This eukaryotic subgroup includes the human Nna1/AGTPBP-1 and AGBL -2, -3, -4, and -5, and the mouse Nna1/CCP-1 and CCP -2 through -6. Nna1-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Nna1 is widely expressed in the developing and adult nervous systems, including cerebellar Purkinje and granule neurons, miral cells of the olfactory bulb and retinal photoreceptors. Nna1 is also induc
Probab=30.86 E-value=23 Score=26.29 Aligned_cols=38 Identities=24% Similarity=0.412 Sum_probs=27.2
Q ss_pred CcchHHHHHhhccCCChhhHHHHH-HHHHhccCCCCCCCc
Q psy17939 35 PGILMIIIRFVLPMQDHMIKKLLL-IFWEIVPKTTPDGKL 73 (81)
Q Consensus 35 ~~L~m~VIr~v~ps~n~~lKKLl~-lY~e~~~k~~~dGkL 73 (81)
+...+..+.+++ +++.+.++|+= +=|-++|..+|||-.
T Consensus 62 s~~~~~ll~~Ll-~~~~~~~~Ll~~~~~~iiPm~NPDG~~ 100 (258)
T cd06235 62 SFVMQGFIDFLL-SDSPEAQYLRENFIFKIIPMLNPDGVI 100 (258)
T ss_pred HHHHHHHHHHHh-cCCHHHHHHHhccEEEEEcccccccee
Confidence 345666777777 66777788765 445568999999964
No 29
>PF11640 TAN: Telomere-length maintenance and DNA damage repair; InterPro: IPR021668 ATM is a large protein kinase, in humans, critical for responding to DNA double-strand breaks (DSBs). Tel1, the orthologue from budding yeast, also regulates responses to DSBs. Tel1 is important for maintaining viability and for phosphorylation of the DNA damage signal transducer kinase Rad53 (an orthologue of mammalian CHK2). In addition to functioning in the response to DSBs, numerous findings indicate that Tel1/ATM regulates telomeres. The overall domain structure of Tel1/ATM is shared by proteins of the phosphatidylinositol 3-kinase (PI3K)-related kinase (PIKK) family, but this family carries a unique and functionally important TAN sequence motif, near its N-terminal, LxxxKxxE/DRxxxL. which is conserved specifically in the Tel1/ATM subclass of the PIKKs. The TAN motif is essential for both telomere length maintenance and Tel1 action in response to DNA damage []. It is classified as an 2.7.11.1 from EC. ; GO: 0004674 protein serine/threonine kinase activity
Probab=27.73 E-value=81 Score=21.31 Aligned_cols=44 Identities=11% Similarity=0.233 Sum_probs=32.1
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHcC--------CCCCcchHHHHHhhc
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIANG--------ERLPGILMIIIRFVL 46 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~G--------~~~~~L~m~VIr~v~ 46 (81)
.++-..|+|+...++-+|+..+.....+- +....+|-.+.+++.
T Consensus 7 ~~~~~~L~S~k~keR~~al~~L~~il~~~~~~~~l~~k~~~~ifeaL~~~i~ 58 (155)
T PF11640_consen 7 NSILRLLSSDKIKERNKALEDLRHILSSPPRVDSLNDKQWHSIFEALFRCIE 58 (155)
T ss_pred HHHHHHHhccccchHHHHHHHHHHHHcCccccccCCcchHHHHHHHHHHHHH
Confidence 46778999999999999999988776544 233456666666553
No 30
>PF03392 OS-D: Insect pheromone-binding family, A10/OS-D; InterPro: IPR005055 A class of small (14-20 Kd) water-soluble proteins, called odorant binding proteins (OBPs), first discovered in the insect sensillar lymph but also in the mucus of vertebrates, is postulated to mediate the solubilisation of hydrophobic odorant molecules, and thereby to facilitate their transport to the receptor neurons. The product of a gene expressed in the olfactory system of Drosophila melanogaster (Fruit fly), OS-D, shares features common to vertebrate odorant-binding proteins, but has a primary structure unlike odorant-binding proteins []. OS-D derivatives have subsequently been found in chemosensory organs of phylogenetically distinct insects, including cockroaches, phasmids and moths, suggesting that OS-D-like proteins seem to be conserved in the insect phylum.; PDB: 1KX9_A 1N8U_A 1KX8_A 1K19_A 1N8V_A 2GVS_A 2JNT_A.
Probab=26.75 E-value=1.7e+02 Score=18.76 Aligned_cols=60 Identities=27% Similarity=0.295 Sum_probs=30.8
Q ss_pred hhhcCChHHHHHHHHHHHHHHHcCC--CCCc----chHHHHHhhccCCChhhHHHHHHHHHhccCCCCCCCcc
Q psy17939 8 HIEKGDTKIKIEALKKVIQMIANGE--RLPG----ILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPDGKLL 74 (81)
Q Consensus 8 ~Les~~~~~K~ealKkiI~~~~~G~--~~~~----L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~~dGkL~ 74 (81)
.|+.|....--..+|++|--.+++. .++. .+-.|++++. ++.==.|=++..|+||+|+-+
T Consensus 27 lldkgpCt~~~~~lK~~ipeal~t~C~KCt~kQK~~~~kv~~~l~-------~~~P~~w~~l~~KyDp~~~y~ 92 (95)
T PF03392_consen 27 LLDKGPCTPEGKELKKVIPEALKTNCAKCTPKQKENARKVIKFLK-------KNYPDEWEELVKKYDPEGKYR 92 (95)
T ss_dssp HTSSSTSHHHHHHHHHHHHHHHHCTTTTS-HHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHTTT-TTH
T ss_pred HhcCCCCCHHHHHHHHHHHHHHHccccCCCHHHHHHHHHHHHHHH-------HcCHHHHHHHHHHHCCCcchh
Confidence 3456666555667777776555542 2322 3333333332 222223445578899999854
No 31
>PF00246 Peptidase_M14: Zinc carboxypeptidase This is family M14 in the peptidase classification. ; InterPro: IPR000834 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of sequences contain a diverse range of gene families, which include metallopeptidases belonging to MEROPS peptidase family M14 (carboxypeptidase A, clan MC), subfamilies M14A and M14B. The carboxypeptidase A family can be divided into two subfamilies: carboxypeptidase H (regulatory) and carboxypeptidase A (digestive) []. Members of the H family have longer C-termini than those of family A [], and carboxypeptidase M (a member of the H family) is bound to the membrane by a glycosylphosphatidylinositol anchor, unlike the majority of the M14 family, which are soluble []. The zinc ligands have been determined as two histidines and a glutamate, and the catalytic residue has been identified as a C-terminal glutamate, but these do not form the characteristic metalloprotease HEXXH motif [, ]. Members of the carboxypeptidase A family are synthesised as inactive molecules with propeptides that must be cleaved to activate the enzyme. Structural studies of carboxypeptidases A and B reveal the propeptide to exist as a globular domain, followed by an extended alpha-helix; this shields the catalytic site, without specifically binding to it, while the substrate-binding site is blocked by making specific contacts [, ]. Other examples of protein families in this entry include: Intron maturase Putative mitochondrial processing peptidase alpha subunit Superoxide dismutase [Mn] (1.15.1.1 from EC) Asparagine synthetase [glutamine-hydrolysing] 3 (6.3.5.4 from EC) Glucose-6-phosphate isomerase (5.3.1.9 from EC) ; GO: 0004181 metallocarboxypeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 3DGV_A 3OSL_C 3D4U_A 2NSM_A 1QMU_A 1H8L_A 2PJ2_A 2PJ9_A 1ZG8_A 1Z5R_A ....
Probab=26.61 E-value=10 Score=27.46 Aligned_cols=38 Identities=32% Similarity=0.425 Sum_probs=28.3
Q ss_pred CcchHHHHHhhccC-CChhhHHHHHHH-HHhccCCCCCCC
Q psy17939 35 PGILMIIIRFVLPM-QDHMIKKLLLIF-WEIVPKTTPDGK 72 (81)
Q Consensus 35 ~~L~m~VIr~v~ps-~n~~lKKLl~lY-~e~~~k~~~dGk 72 (81)
+...+..++.++-. +|..++.|+=-+ |-++|..+|||-
T Consensus 63 ~~~~l~~~~~L~~~~~~~~~~~ll~~~~i~iiP~~NPDG~ 102 (279)
T PF00246_consen 63 SEALLYLIEELLSGYDDPEVKELLDNVVIYIIPMVNPDGY 102 (279)
T ss_dssp HHHHHHHHHHHHHHTTSHHHHHHHHHEEEEEES-SSHHHH
T ss_pred hHHHHHHHHHhhccccchhhhhhcccceEEEEeeecccce
Confidence 34667777777722 788999998766 778999999984
No 32
>PF14711 Nitr_red_bet_C: Respiratory nitrate reductase beta C-terminal; PDB: 3IR7_B 1Y5N_B 1R27_D 3EGW_B 1Y5I_B 1Q16_B 1Y4Z_B 1Y5L_B 3IR6_B 3IR5_B ....
Probab=26.51 E-value=1e+02 Score=19.68 Aligned_cols=23 Identities=26% Similarity=0.433 Sum_probs=18.5
Q ss_pred HHhhhhcCChHHHHHHHHHHHHH
Q psy17939 5 VSHHIEKGDTKIKIEALKKVIQM 27 (81)
Q Consensus 5 lk~~Les~~~~~K~ealKkiI~~ 27 (81)
|-+.|.-||.+.-..+|+|+++|
T Consensus 35 LAnLftAGd~~~V~~~L~rL~Am 57 (83)
T PF14711_consen 35 LANLFTAGDEEPVRRALKRLLAM 57 (83)
T ss_dssp HHHHHSTT-HHHHHHHHHHHHHH
T ss_pred HHHHHccCChHHHHHHHHHHHHH
Confidence 55778889999999999999886
No 33
>PF04031 Las1: Las1-like ; InterPro: IPR007174 Las1 is an essential nuclear protein involved in cell morphogenesis and cell surface growth [].
Probab=25.21 E-value=1.6e+02 Score=20.35 Aligned_cols=32 Identities=25% Similarity=0.377 Sum_probs=27.0
Q ss_pred HHHhhhhcC--ChHHHHHHHHHHHHHHHcCCCCC
Q psy17939 4 CVSHHIEKG--DTKIKIEALKKVIQMIANGERLP 35 (81)
Q Consensus 4 elk~~Les~--~~~~K~ealKkiI~~~~~G~~~~ 35 (81)
++++.|=++ +.+.+.+|+.++-...++|..+|
T Consensus 12 ~V~~~l~s~~~~~~~~~~al~~v~~W~~R~~~lP 45 (154)
T PF04031_consen 12 QVYQWLYSSQDDPESRRRALERVSAWKSRGSKLP 45 (154)
T ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHHHHcCCCCc
Confidence 567777777 89999999999999999995454
No 34
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=24.63 E-value=65 Score=22.43 Aligned_cols=23 Identities=26% Similarity=0.345 Sum_probs=17.4
Q ss_pred CChhhHHHHHHHHHhccCCCCCC
Q psy17939 49 QDHMIKKLLLIFWEIVPKTTPDG 71 (81)
Q Consensus 49 ~n~~lKKLl~lY~e~~~k~~~dG 71 (81)
+-..+..|+-+||.+.+.++.+|
T Consensus 61 ~~is~~~Ll~~f~~~~dPt~~~~ 83 (155)
T PF01625_consen 61 SVISYEELLDVFFRIHDPTQVNG 83 (155)
T ss_dssp TTS-HHHHHHHHHHHS-TTSTSE
T ss_pred CcccHHHHHHHHHHhcCCccccc
Confidence 34567999999999999998665
No 35
>PF12719 Cnd3: Nuclear condensing complex subunits, C-term domain
Probab=24.32 E-value=3e+02 Score=20.32 Aligned_cols=65 Identities=11% Similarity=0.394 Sum_probs=50.0
Q ss_pred HHhhhhcCChHHHHHHHHHHHHHHHcCCCCC--cchHHH-HHhhccC--CChhhHHHHHHHHHhccCCCC
Q psy17939 5 VSHHIEKGDTKIKIEALKKVIQMIANGERLP--GILMII-IRFVLPM--QDHMIKKLLLIFWEIVPKTTP 69 (81)
Q Consensus 5 lk~~Les~~~~~K~ealKkiI~~~~~G~~~~--~L~m~V-Ir~v~ps--~n~~lKKLl~lY~e~~~k~~~ 69 (81)
+.+.|++.+++.+.-|..-+-.++++|.-.+ .+|-.. +.|.-|+ +|++++..+=+|+..|+...+
T Consensus 119 l~~~l~~~~~~~~~~a~EGl~KLlL~~~i~~~~~vL~~Lll~yF~p~t~~~~~LrQ~L~~Ffp~y~~s~~ 188 (298)
T PF12719_consen 119 LTKFLDSENPELQAIAVEGLCKLLLSGRISDPPKVLSRLLLLYFNPSTEDNQRLRQCLSVFFPVYASSSP 188 (298)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHHHcCcccCCcHHHHHHHHHHHHHHHcCCH
Confidence 4567788888888888888888999998665 555543 4566674 667999999999999987654
No 36
>PF08097 Toxin_26: Conotoxin T-superfamily; InterPro: IPR012631 This family consists of the T-superfamily of conotoxins. Eight different T-superfamily peptides from five Conus species were identified. These peptides share a consensus signal sequence, and a conserved arrangement of cysteine residues. T-superfamily peptides were found expressed in venom ducts of all major feeding types of Conus, suggesting that the T-superfamily is a large and diverse group of peptides, widely distributed in the 500 different Conus species [].; GO: 0005576 extracellular region
Probab=23.71 E-value=21 Score=14.90 Aligned_cols=6 Identities=33% Similarity=0.794 Sum_probs=4.2
Q ss_pred HHHHhh
Q psy17939 40 IIIRFV 45 (81)
Q Consensus 40 ~VIr~v 45 (81)
+|||||
T Consensus 4 pviryc 9 (11)
T PF08097_consen 4 PVIRYC 9 (11)
T ss_pred chhhee
Confidence 577776
No 37
>smart00755 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245.
Probab=23.53 E-value=1.5e+02 Score=16.71 Aligned_cols=40 Identities=25% Similarity=0.298 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHcCCCC-CcchHHHHHhhccCCChhhHHH
Q psy17939 17 KIEALKKVIQMIANGERL-PGILMIIIRFVLPMQDHMIKKL 56 (81)
Q Consensus 17 K~ealKkiI~~~~~G~~~-~~L~m~VIr~v~ps~n~~lKKL 56 (81)
..+.+|.++...+.+++. ..=+.+||--++.=+..+.+++
T Consensus 3 n~eYLKNVll~fl~~~e~~r~~ll~vi~tlL~fs~~e~~~~ 43 (46)
T smart00755 3 NFEYLKNVLLQFLTLRESERETLLKVISTVLQLSPEEMQKL 43 (46)
T ss_pred cHHHHHHHHHHHhccCcchHHHHHHHHHHHhCCCHHHHHHH
Confidence 467899999887777776 2334457766776566666655
No 38
>PF15658 Latrotoxin_C: Latrotoxin C-terminal domain
Probab=23.16 E-value=61 Score=22.48 Aligned_cols=41 Identities=20% Similarity=0.190 Sum_probs=30.4
Q ss_pred CCCcchHHHHHhhccCCChhhHHHHHHHHHhccCCCCCCCcccc
Q psy17939 33 RLPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTTPDGKLLQD 76 (81)
Q Consensus 33 ~~~~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~~dGkL~~E 76 (81)
|+..+.-.|++-++.-+..+|-++|.-|.|-.= |+|+|-|+
T Consensus 68 D~~evqs~I~~kI~sG~~neIs~~L~Sy~e~a~---p~~~Ls~k 108 (127)
T PF15658_consen 68 DFVEVQSKITKKIMSGKFNEISKILCSYAEKAC---PGSKLSPK 108 (127)
T ss_pred CHHHHHHHHHHHHHcCCchHHHHHHHHHHHHhC---cccCCCHH
Confidence 344567788888885566689999999999752 56888765
No 39
>KOG1062|consensus
Probab=23.01 E-value=1.8e+02 Score=26.08 Aligned_cols=65 Identities=20% Similarity=0.276 Sum_probs=52.3
Q ss_pred HHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCChhhHH-HHHHHHHhccCCCCC
Q psy17939 4 CVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKK-LLLIFWEIVPKTTPD 70 (81)
Q Consensus 4 elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~~lKK-Ll~lY~e~~~k~~~d 70 (81)
-|-+.|+..|..-|.+||+ +...+.|+.++-.+.-..+.|.-.+ +.+.|- +.+--.+..+++.||
T Consensus 354 tIleCL~DpD~SIkrralE-Ls~~lvn~~Nv~~mv~eLl~fL~~~-d~~~k~~~as~I~~laEkfaP~ 419 (866)
T KOG1062|consen 354 TILECLKDPDVSIKRRALE-LSYALVNESNVRVMVKELLEFLESS-DEDFKADIASKIAELAEKFAPD 419 (866)
T ss_pred HHHHHhcCCcHHHHHHHHH-HHHHHhccccHHHHHHHHHHHHHhc-cHHHHHHHHHHHHHHHHhcCCc
Confidence 3668899999999999997 5678899999999999999998866 555554 556666778888886
No 40
>cd03858 M14_CP_N-E_like Carboxypeptidase (CP) N/E-like subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes eight members, of which five (CPN, CPE, CPM, CPD, CPZ) are considered enzymatically active, while the other three are non-active (CPX1, PCX2, ACLP/AEBP1) and lack the critical active site and substrate-binding residues considered necessary for CP activity. These non-active members may function as binding proteins or display catalytic activity towards other substrates. Unlike the A/B CP subfamily, enzymes belonging to the N/E subfamily are not produced as inactive precursors that require proteolysis to produce the active form; rather, they rely on their substrate specificity and subcellular compartmentalization to prevent inappr
Probab=22.74 E-value=32 Score=26.44 Aligned_cols=39 Identities=23% Similarity=0.360 Sum_probs=29.7
Q ss_pred CcchHHHHHhhccC---CChhhHHHHHHH-HHhccCCCCCCCc
Q psy17939 35 PGILMIIIRFVLPM---QDHMIKKLLLIF-WEIVPKTTPDGKL 73 (81)
Q Consensus 35 ~~L~m~VIr~v~ps---~n~~lKKLl~lY-~e~~~k~~~dGkL 73 (81)
+.+.+..++.++.. .|..+++|+==+ |-++|-.||||--
T Consensus 69 ~~~~~~l~~~L~~~~~~~d~~~~~ll~~~~~~ivP~~NPDG~~ 111 (374)
T cd03858 69 RELLLRLAQYLCENYGAGDPRITRLVDNTRIHIMPSMNPDGYE 111 (374)
T ss_pred HHHHHHHHHHHHHHhccCCHHHHHHHhCCEEEEEcccCCchhh
Confidence 45677788877753 678889988655 7789999999954
No 41
>cd06905 Peptidase_M14-like_8 A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly differe
Probab=22.09 E-value=29 Score=27.24 Aligned_cols=39 Identities=26% Similarity=0.454 Sum_probs=28.8
Q ss_pred CcchHHHHHhhccC--CChhhHHHH-HHHHHhccCCCCCCCc
Q psy17939 35 PGILMIIIRFVLPM--QDHMIKKLL-LIFWEIVPKTTPDGKL 73 (81)
Q Consensus 35 ~~L~m~VIr~v~ps--~n~~lKKLl-~lY~e~~~k~~~dGkL 73 (81)
+.+.+.+++.++.+ +|.++++|| -+=|-++|-.||||--
T Consensus 72 ~~~~l~li~~Ll~~y~~d~~i~~lLd~~~~~IvP~vNPDG~e 113 (360)
T cd06905 72 SAVALYVIQTLLNGYGSDPEVTRLLDGYTFYILPRLNPDGAE 113 (360)
T ss_pred HHHHHHHHHHHHHhccCCHHHHHHHhcCeEEEEeeeCCChhe
Confidence 35567788888753 578899998 3445568999999964
No 42
>PF10508 Proteasom_PSMB: Proteasome non-ATPase 26S subunit; InterPro: IPR019538 The 26S proteasome is an enzymatic complex that degrades ubiquitinated proteins in eukaryotic cells. 26S proteasome non-ATPase regulatory subunit 5 is one of a number of chaperones that are involved in the assembly of the proteasome. The chaperones dissociate before 26S proteasome formation is complete [].; GO: 0044183 protein binding involved in protein folding
Probab=21.74 E-value=3.7e+02 Score=21.68 Aligned_cols=65 Identities=18% Similarity=0.206 Sum_probs=45.1
Q ss_pred hHHHhhhhcCChHHHHHHHHHHHHHHHcCCC------CCcchHHHHHhhccCCChhhHHHHHHHHHhccCCC
Q psy17939 3 PCVSHHIEKGDTKIKIEALKKVIQMIANGER------LPGILMIIIRFVLPMQDHMIKKLLLIFWEIVPKTT 68 (81)
Q Consensus 3 ~elk~~Les~~~~~K~ealKkiI~~~~~G~~------~~~L~m~VIr~v~ps~n~~lKKLl~lY~e~~~k~~ 68 (81)
..+...|.+++...|.-|++.+-....+.+. -++++..|+ +|+.++|.++.+-.---+....++.
T Consensus 80 ~~L~~gL~h~~~~Vr~l~l~~l~~~~~~~~~~~~~~~~~~l~~~i~-~~L~~~d~~Va~~A~~~L~~l~~~~ 150 (503)
T PF10508_consen 80 PFLQRGLTHPSPKVRRLALKQLGRIARHSEGAAQLLVDNELLPLII-QCLRDPDLSVAKAAIKALKKLASHP 150 (503)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhcCCHHHHHHhcCccHHHHHH-HHHcCCcHHHHHHHHHHHHHHhCCc
Confidence 4577888999999999998874333322221 267888888 4887999998877666666555543
No 43
>PF08713 DNA_alkylation: DNA alkylation repair enzyme; InterPro: IPR014825 These proteins are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein shows it to adopt a super coiled alpha helical structure. ; PDB: 3JY1_A 3JXY_A 3JX7_A 3JXZ_A 3BVS_A 2B6C_B 1T06_B 3L9T_A.
Probab=21.54 E-value=1.1e+02 Score=20.84 Aligned_cols=39 Identities=8% Similarity=0.118 Sum_probs=24.2
Q ss_pred HHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhc
Q psy17939 5 VSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVL 46 (81)
Q Consensus 5 lk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ 46 (81)
|++.|++-.++...+.|++.+. ++.++-++=++++|-++
T Consensus 1 i~~~L~~~~d~~~a~~~~~~~~---~~~~~~GV~~p~lr~la 39 (213)
T PF08713_consen 1 IRAELEALADPKYAKFMQRYMK---EKDPFLGVRTPDLRKLA 39 (213)
T ss_dssp HHHHHHHC--HHHHHHHHHHTT---TSSB-----HHHHHHHH
T ss_pred CHHHHHhcCCHHHHHHHHHhCC---CcccccCcCcHHHHHHH
Confidence 5788999999999998888777 56666666666666544
No 44
>PF12078 DUF3557: Domain of unknown function (DUF3557); InterPro: IPR021942 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 150 amino acids in length.
Probab=21.45 E-value=79 Score=20.59 Aligned_cols=16 Identities=31% Similarity=0.451 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHcCCCC
Q psy17939 19 EALKKVIQMIANGERL 34 (81)
Q Consensus 19 ealKkiI~~~~~G~~~ 34 (81)
||||+++..+..|+..
T Consensus 4 eA~k~L~~~lfggR~~ 19 (154)
T PF12078_consen 4 EAMKYLIKKLFGGRSH 19 (154)
T ss_pred HHHHHHHHHHcCCCCc
Confidence 7999999999999875
No 45
>PHA02650 hypothetical protein; Provisional
Probab=21.32 E-value=96 Score=20.00 Aligned_cols=11 Identities=0% Similarity=0.153 Sum_probs=7.1
Q ss_pred HHHHHHHhccC
Q psy17939 56 LLLIFWEIVPK 66 (81)
Q Consensus 56 Ll~lY~e~~~k 66 (81)
++++|+..++.
T Consensus 65 ~~flYLK~~~r 75 (81)
T PHA02650 65 FSFFVFKGYTR 75 (81)
T ss_pred HHHHHHHHhcc
Confidence 55677776653
No 46
>COG3067 NhaB Na+/H+ antiporter [Inorganic ion transport and metabolism]
Probab=20.90 E-value=67 Score=26.43 Aligned_cols=27 Identities=33% Similarity=0.493 Sum_probs=22.1
Q ss_pred CcchHHHHHhhccCCChhhHHHHHHHH
Q psy17939 35 PGILMIIIRFVLPMQDHMIKKLLLIFW 61 (81)
Q Consensus 35 ~~L~m~VIr~v~ps~n~~lKKLl~lY~ 61 (81)
.+||.+||++|+...+|.---|+|+|=
T Consensus 373 Q~LF~PiIqfVL~a~~~~Ql~lfyifN 399 (516)
T COG3067 373 QHLFSPIIQFVLQASEHAQLSLFYIFN 399 (516)
T ss_pred hhhhHHHHHHHHcCCcccchhHHHHHh
Confidence 479999999999888887766777663
No 47
>PF05997 Nop52: Nucleolar protein,Nop52; InterPro: IPR010301 Nop52 is believed to be involved in the generation of 28S rRNA [].; GO: 0006364 rRNA processing, 0030688 preribosome, small subunit precursor
Probab=20.90 E-value=3e+02 Score=19.82 Aligned_cols=46 Identities=20% Similarity=0.338 Sum_probs=32.6
Q ss_pred HHHhhhhcCChHHHHHHHHHHHHHHHcCCCCCcchHHHHHhhccCCChhhHH----HHHHHHH
Q psy17939 4 CVSHHIEKGDTKIKIEALKKVIQMIANGERLPGILMIIIRFVLPMQDHMIKK----LLLIFWE 62 (81)
Q Consensus 4 elk~~Les~~~~~K~ealKkiI~~~~~G~~~~~L~m~VIr~v~ps~n~~lKK----Ll~lY~e 62 (81)
.+-+.|-|++...+-.|++++-..+....... +..++.| |.|.+|-
T Consensus 4 ~~~k~LAs~d~~~R~~al~~l~~~l~~~~~~~-------------~~~~~~kLWKGLfy~mWm 53 (217)
T PF05997_consen 4 KFAKKLASNDKKTRDRALKSLRKWLSKRSQLL-------------TELDMLKLWKGLFYCMWM 53 (217)
T ss_pred HHHHHhhcCChhHHHHHHHHHHHHHHhccccC-------------CHHHHHHHHHHHHHHHHh
Confidence 35678999999999999998777666553332 4455555 6777776
No 48
>cd03863 M14_CPD_II The second carboxypeptidase (CP)-like domain of Carboxypeptidase D (CPD; EC 3.4.17.22), domain II. CPD differs from all other metallocarboxypeptidases in that it contains multiple CP-like domains. CPD belongs to the N/E-like subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPD is a single-chain protein containing a signal peptide, three tandem repeats of CP-like domains separated by short bridge regions, followed by a transmembrane domain, and a C-terminal cytosolic tail. The first two CP-like domains of CPD contain all of the essential active site and substrate-binding residues, while the third CP-like domain lacks critical residues necessary for enzymatic activity and is inactive towards standard CP substrates. Domain I is optimally ac
Probab=20.17 E-value=33 Score=27.06 Aligned_cols=39 Identities=23% Similarity=0.382 Sum_probs=29.8
Q ss_pred CcchHHHHHhhcc--CCChhhHHHH-HHHHHhccCCCCCCCc
Q psy17939 35 PGILMIIIRFVLP--MQDHMIKKLL-LIFWEIVPKTTPDGKL 73 (81)
Q Consensus 35 ~~L~m~VIr~v~p--s~n~~lKKLl-~lY~e~~~k~~~dGkL 73 (81)
+.+++..+++++- ..|.++++|+ -.-|-++|-.+|||--
T Consensus 74 ~~~~l~li~~L~~~y~~d~~v~~ll~~~~i~IvP~~NPDG~e 115 (375)
T cd03863 74 RELLLNLIEYLCKNFGTDPEVTDLVQSTRIHIMPSMNPDGYE 115 (375)
T ss_pred HHHHHHHHHHHHHhccCCHHHHHHHhCCEEEEEeccCCchHH
Confidence 4677788887764 3688999987 4556679999999953
Done!