Query psy1263
Match_columns 115
No_of_seqs 105 out of 374
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 15:31:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1263.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1263hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1062|consensus 100.0 1.3E-38 2.8E-43 268.3 11.0 115 1-115 206-320 (866)
2 KOG1077|consensus 99.9 9.5E-26 2E-30 189.4 10.5 111 5-115 215-336 (938)
3 PF01602 Adaptin_N: Adaptin N 99.1 1.1E-09 2.4E-14 88.9 10.9 90 8-114 182-273 (526)
4 KOG1059|consensus 98.7 3.1E-08 6.7E-13 84.8 5.6 94 1-113 205-304 (877)
5 PTZ00429 beta-adaptin; Provisi 97.8 0.00017 3.7E-09 62.9 9.3 64 42-111 232-297 (746)
6 PF09324 DUF1981: Domain of un 93.7 0.74 1.6E-05 29.6 7.6 71 42-113 11-83 (86)
7 KOG1992|consensus 83.9 14 0.0003 33.4 9.8 100 2-107 529-634 (960)
8 PF03378 CAS_CSE1: CAS/CSE pro 77.3 21 0.00046 29.5 8.5 84 11-101 19-104 (435)
9 TIGR03092 SASP_sspI small, aci 76.9 4.4 9.6E-05 25.1 3.3 31 64-94 15-45 (65)
10 PF14098 SSPI: Small, acid-sol 76.7 4.6 0.0001 25.0 3.4 30 64-93 16-45 (65)
11 PRK02955 small acid-soluble sp 74.8 4.8 0.0001 25.2 3.1 31 64-94 18-48 (68)
12 PF10274 ParcG: Parkin co-regu 65.3 43 0.00093 24.7 7.0 72 8-90 70-145 (183)
13 KOG1058|consensus 57.2 24 0.00051 31.8 5.0 66 42-113 219-284 (948)
14 PF12142 PPO1_DWL: Polyphenol 54.2 3.9 8.3E-05 24.4 -0.2 17 32-48 34-50 (54)
15 TIGR02568 LcrE type III secret 52.7 99 0.0021 23.4 8.1 44 35-78 84-127 (240)
16 PF09409 PUB: PUB domain; Int 52.6 30 0.00065 21.8 3.8 43 8-50 2-44 (87)
17 PF05918 API5: Apoptosis inhib 48.5 87 0.0019 27.1 6.9 85 14-112 55-139 (556)
18 PF01465 GRIP: GRIP domain; I 48.5 18 0.00039 20.5 2.1 27 52-78 12-38 (46)
19 KOG2305|consensus 46.7 44 0.00095 26.2 4.5 71 15-99 128-210 (313)
20 COG3283 TyrR Transcriptional r 42.6 16 0.00034 30.5 1.6 14 41-54 305-318 (511)
21 PF02526 GBP_repeat: Glycophor 38.5 55 0.0012 17.8 2.8 21 60-81 16-36 (38)
22 PF03224 V-ATPase_H_N: V-ATPas 34.2 1E+02 0.0022 23.8 5.0 32 40-71 275-309 (312)
23 PF01603 B56: Protein phosphat 33.5 2.3E+02 0.0049 23.1 7.0 55 18-77 109-163 (409)
24 COG5096 Vesicle coat complex, 31.0 67 0.0014 28.8 3.7 47 40-88 103-151 (757)
25 PF08506 Cse1: Cse1; InterPro 30.4 2.4E+02 0.0052 22.8 6.7 46 7-58 126-171 (370)
26 PRK10628 LigB family dioxygena 29.6 40 0.00088 25.9 2.0 36 32-73 47-82 (246)
27 smart00755 Grip golgin-97, Ran 29.3 78 0.0017 18.0 2.7 26 52-78 11-36 (46)
28 PF13929 mRNA_stabil: mRNA sta 29.2 2.5E+02 0.0054 22.3 6.3 90 18-114 114-213 (292)
29 KOG0412|consensus 29.0 68 0.0015 28.7 3.4 28 31-58 631-658 (773)
30 cd00068 GGL G protein gamma su 27.2 1E+02 0.0022 18.1 3.0 30 16-45 22-54 (57)
31 KOG2085|consensus 26.8 2.7E+02 0.0058 23.5 6.3 54 46-99 176-249 (457)
32 PF10083 DUF2321: Uncharacteri 26.6 2.5E+02 0.0055 20.3 6.1 42 38-79 74-118 (158)
33 KOG4113|consensus 25.6 15 0.00032 24.5 -0.9 44 2-45 8-52 (99)
34 PF13646 HEAT_2: HEAT repeats; 25.1 1.6E+02 0.0034 17.4 7.2 30 40-75 11-40 (88)
35 PLN03076 ARF guanine nucleotid 25.1 2.7E+02 0.0058 27.7 6.8 91 18-113 1156-1248(1780)
36 PF14225 MOR2-PAG1_C: Cell mor 24.9 88 0.0019 24.2 3.1 18 41-58 200-217 (262)
37 PF06570 DUF1129: Protein of u 24.5 1.3E+02 0.0029 21.9 3.9 31 52-82 16-46 (206)
38 PF05232 BTP: Bacterial Transm 23.9 70 0.0015 19.5 1.9 16 84-99 7-22 (67)
39 PF13797 Post_transc_reg: Post 23.8 2E+02 0.0044 18.4 4.2 54 43-104 11-65 (87)
40 COG4025 Predicted membrane pro 23.3 1E+02 0.0023 24.1 3.1 16 36-51 18-33 (284)
41 PF01206 TusA: Sulfurtransfera 22.9 1.5E+02 0.0033 17.3 3.4 37 35-71 3-47 (70)
42 PHA03325 nuclear-egress-membra 22.9 2.1E+02 0.0046 23.7 5.0 35 44-78 219-258 (418)
43 KOG1916|consensus 22.4 1E+02 0.0023 28.7 3.4 22 37-58 1191-1212(1283)
44 PF10350 DUF2428: Putative dea 22.0 3.4E+02 0.0073 20.5 5.8 57 14-74 185-241 (255)
45 COG4344 Uncharacterized protei 21.4 70 0.0015 23.2 1.8 26 34-59 109-134 (175)
46 PF12811 BaxI_1: Bax inhibitor 20.3 85 0.0018 24.6 2.2 35 24-58 234-273 (274)
47 COG4760 Predicted membrane pro 20.0 82 0.0018 24.2 2.0 19 40-58 257-275 (276)
No 1
>KOG1062|consensus
Probab=100.00 E-value=1.3e-38 Score=268.31 Aligned_cols=115 Identities=61% Similarity=0.938 Sum_probs=113.8
Q ss_pred CcccChhcHHHHHhhHHHHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhhCCC
Q psy1263 1 MCENSIDTLHHFKKIVPNLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGKNDVEASEAMNDILAQVATNTET 80 (115)
Q Consensus 1 ~~~~~~~~~~~~~~~vp~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~~~~ 80 (115)
+|+++|+..+.|++++|.||.||++++++++++||+|+|||||||||+|||+|+.||.+|++.+|.|+|+|.++++++|+
T Consensus 206 ~c~~~~~~l~~fr~l~~~lV~iLk~l~~~~yspeydv~gi~dPFLQi~iLrlLriLGq~d~daSd~M~DiLaqvatntds 285 (866)
T KOG1062|consen 206 LCKISPDALSYFRDLVPSLVKILKQLTNSGYSPEYDVHGISDPFLQIRILRLLRILGQNDADASDLMNDILAQVATNTDS 285 (866)
T ss_pred HHhcCHHHHHHHHHHHHHHHHHHHHHhcCCCCCccCccCCCchHHHHHHHHHHHHhcCCCccHHHHHHHHHHHHHhcccc
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcchhHHHHHHHHHHHHhcCCChhHHHHHHHHhcC
Q psy1263 81 SKNVGNTILYETVLSIMDIKSESGLRSFFTTFTAK 115 (115)
Q Consensus 81 ~~na~~AILyEav~ti~~~~~~~~L~~~av~~lgk 115 (115)
++|+|||||||||+||++++++++||++|+|+|||
T Consensus 286 skN~GnAILYE~V~TI~~I~~~~~LrvlainiLgk 320 (866)
T KOG1062|consen 286 SKNAGNAILYECVRTIMDIRSNSGLRVLAINILGK 320 (866)
T ss_pred cccchhHHHHHHHHHHHhccCCchHHHHHHHHHHH
Confidence 99999999999999999999999999999999997
No 2
>KOG1077|consensus
Probab=99.93 E-value=9.5e-26 Score=189.44 Aligned_cols=111 Identities=23% Similarity=0.362 Sum_probs=101.5
Q ss_pred ChhcHHHHHhhHHHHHHHHHHHHhcC-CC-CCccccCCCchHHHHHHHHHHHhhCC-CCHHHHHHHHHHHHHHHhhCC--
Q psy1263 5 SIDTLHHFKKIVPNLVRNLKNLILAG-YS-PEHDVSGVSDPFLQVKILKLLRILGK-NDVEASEAMNDILAQVATNTE-- 79 (115)
Q Consensus 5 ~~~~~~~~~~~vp~lv~iL~~lv~~~-~~-~eY~y~gvp~PwLQvklLrlL~~l~~-~d~~~~~~l~~vL~~i~~~~~-- 79 (115)
...+|+.|+.++|..+.+|.+++... .+ .||.||+||+||||||++|+|+.++. .|+....++.++|.+|+.+++
T Consensus 215 vk~~p~~yk~~~~~avs~L~riv~~~~t~~qdYTyy~vP~PWL~vKl~rlLq~~p~~~D~~~r~~l~evl~~iLnk~~~~ 294 (938)
T KOG1077|consen 215 VKKNPESYKTCLPLAVSRLSRIVVVVGTSLQDYTYYFVPAPWLQVKLLRLLQIYPTPEDPSTRARLNEVLERILNKAQEP 294 (938)
T ss_pred HHcCCHHHhhhHHHHHHHHHHHHhhcccchhhceeecCCChHHHHHHHHHHHhCCCCCCchHHHHHHHHHHHHHhccccC
Confidence 34567999999999999999999777 56 79999999999999999999999997 599999999999999999865
Q ss_pred -C-----CcchhHHHHHHHHHHHHhcCCChhHHHHHHHHhcC
Q psy1263 80 -T-----SKNVGNTILYETVLSIMDIKSESGLRSFFTTFTAK 115 (115)
Q Consensus 80 -~-----~~na~~AILyEav~ti~~~~~~~~L~~~av~~lgk 115 (115)
. .+||.||||||||++|+++|++++|++.|+|+||+
T Consensus 295 ~~~k~vq~~na~naVLFeaI~l~~h~D~e~~ll~~~~~~Lg~ 336 (938)
T KOG1077|consen 295 PKSKKVQHSNAKNAVLFEAISLAIHLDSEPELLSRAVNQLGQ 336 (938)
T ss_pred ccccchHhhhhHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 2 24899999999999999999999999999999984
No 3
>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=99.09 E-value=1.1e-09 Score=88.94 Aligned_cols=90 Identities=24% Similarity=0.406 Sum_probs=77.3
Q ss_pred cHHHHHhhHHHHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCCCCHHHH--HHHHHHHHHHHhhCCCCcchh
Q psy1263 8 TLHHFKKIVPNLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGKNDVEAS--EAMNDILAQVATNTETSKNVG 85 (115)
Q Consensus 8 ~~~~~~~~vp~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~~d~~~~--~~l~~vL~~i~~~~~~~~na~ 85 (115)
+++.+..++|.++++|.+++ +.++||+|++++++|+.+.+.++... +.+.+.+...++ +++
T Consensus 182 ~~~~~~~~~~~~~~~L~~~l-----------~~~~~~~q~~il~~l~~~~~~~~~~~~~~~~i~~l~~~l~------s~~ 244 (526)
T PF01602_consen 182 NDDSYKSLIPKLIRILCQLL-----------SDPDPWLQIKILRLLRRYAPMEPEDADKNRIIEPLLNLLQ------SSS 244 (526)
T ss_dssp THHHHTTHHHHHHHHHHHHH-----------TCCSHHHHHHHHHHHTTSTSSSHHHHHHHHHHHHHHHHHH------HHH
T ss_pred CcchhhhhHHHHHHHhhhcc-----------cccchHHHHHHHHHHHhcccCChhhhhHHHHHHHHHHHhh------ccc
Confidence 45555689999999999988 89999999999999999999777666 556666666665 789
Q ss_pred HHHHHHHHHHHHhcCCChhHHHHHHHHhc
Q psy1263 86 NTILYETVLSIMDIKSESGLRSFFTTFTA 114 (115)
Q Consensus 86 ~AILyEav~ti~~~~~~~~L~~~av~~lg 114 (115)
.||+|||++++.++.+++.+...+++.|+
T Consensus 245 ~~V~~e~~~~i~~l~~~~~~~~~~~~~L~ 273 (526)
T PF01602_consen 245 PSVVYEAIRLIIKLSPSPELLQKAINPLI 273 (526)
T ss_dssp HHHHHHHHHHHHHHSSSHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHhhcchHHHHhhHHHHH
Confidence 99999999999999999998899988875
No 4
>KOG1059|consensus
Probab=98.67 E-value=3.1e-08 Score=84.81 Aligned_cols=94 Identities=19% Similarity=0.342 Sum_probs=80.7
Q ss_pred CcccChhcHHHHHhhHHHHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhhCCC
Q psy1263 1 MCENSIDTLHHFKKIVPNLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGKNDVEASEAMNDILAQVATNTET 80 (115)
Q Consensus 1 ~~~~~~~~~~~~~~~vp~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~~~~ 80 (115)
+|+.+.++|+.|-.+.|.|.++|-. ..+-|..+|+++++..|.+-.|....++.+=|+..+.+|
T Consensus 205 ICELArKnPknyL~LAP~ffklltt--------------SsNNWmLIKiiKLF~aLtplEPRLgKKLieplt~li~sT-- 268 (877)
T KOG1059|consen 205 ICELARKNPQNYLQLAPLFYKLLVT--------------SSNNWVLIKLLKLFAALTPLEPRLGKKLIEPITELMEST-- 268 (877)
T ss_pred HHHHHhhCCcccccccHHHHHHHhc--------------cCCCeehHHHHHHHhhccccCchhhhhhhhHHHHHHHhh--
Confidence 5889999999999999999998877 567899999999999999989999999999999999988
Q ss_pred CcchhHHHHHHHHHHHHhc-----CCC-hhHHHHHHHHh
Q psy1263 81 SKNVGNTILYETVLSIMDI-----KSE-SGLRSFFTTFT 113 (115)
Q Consensus 81 ~~na~~AILyEav~ti~~~-----~~~-~~L~~~av~~l 113 (115)
...++||||||||++. .++ .....+|+.-|
T Consensus 269 ---~AmSLlYECvNTVVa~s~s~g~~d~~asiqLCvqKL 304 (877)
T KOG1059|consen 269 ---VAMSLLYECVNTVVAVSMSSGMSDHSASIQLCVQKL 304 (877)
T ss_pred ---HHHHHHHHHHHHheeehhccCCCCcHHHHHHHHHHH
Confidence 8899999999999998 222 33556666544
No 5
>PTZ00429 beta-adaptin; Provisional
Probab=97.78 E-value=0.00017 Score=62.86 Aligned_cols=64 Identities=20% Similarity=0.284 Sum_probs=45.4
Q ss_pred chHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhhCCCCcchhHHHHHHHHHHHHhcCCC--hhHHHHHHH
Q psy1263 42 DPFLQVKILKLLRILGKNDVEASEAMNDILAQVATNTETSKNVGNTILYETVLSIMDIKSE--SGLRSFFTT 111 (115)
Q Consensus 42 ~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~~~~~~na~~AILyEav~ti~~~~~~--~~L~~~av~ 111 (115)
+||.|+.+|++|..+.+.+.. +..+++..+...... +| .||+|||+++++++.+. ++++..++.
T Consensus 232 ~EW~Qi~IL~lL~~y~P~~~~---e~~~il~~l~~~Lq~-~N--~AVVl~Aik~il~l~~~~~~~~~~~~~~ 297 (746)
T PTZ00429 232 NEWGQLYILELLAAQRPSDKE---SAETLLTRVLPRMSH-QN--PAVVMGAIKVVANLASRCSQELIERCTV 297 (746)
T ss_pred ChHHHHHHHHHHHhcCCCCcH---HHHHHHHHHHHHhcC-CC--HHHHHHHHHHHHHhcCcCCHHHHHHHHH
Confidence 599999999999998775433 345566666554322 23 69999999999999764 556555543
No 6
>PF09324 DUF1981: Domain of unknown function (DUF1981); InterPro: IPR015403 This domain is functionally uncharacterised and found in various plant and yeast protein transport proteins. It is noramlly associated with and C-termianl to the SEC7 domain. The SEC7 domain was named after the first protein found to contain such a region []. It has been shown to be linked with guanine nucleotide exchange function [, ].
Probab=93.69 E-value=0.74 Score=29.59 Aligned_cols=71 Identities=10% Similarity=0.182 Sum_probs=57.2
Q ss_pred chHHHHHHHHHHHhhC--CCCHHHHHHHHHHHHHHHhhCCCCcchhHHHHHHHHHHHHhcCCChhHHHHHHHHh
Q psy1263 42 DPFLQVKILKLLRILG--KNDVEASEAMNDILAQVATNTETSKNVGNTILYETVLSIMDIKSESGLRSFFTTFT 113 (115)
Q Consensus 42 ~PwLQvklLrlL~~l~--~~d~~~~~~l~~vL~~i~~~~~~~~na~~AILyEav~ti~~~~~~~~L~~~av~~l 113 (115)
+--.|-.+|+=+..+- ..+.++++.+.+++.+++.+--..--+|.-++|++++.+.. +.++++...|...+
T Consensus 11 ~~~fQ~~fL~Pf~~i~~~~~~~~vre~il~ci~qil~~~~~~i~SGW~~if~il~~aa~-~~~e~lv~~af~~~ 83 (86)
T PF09324_consen 11 NFNFQKDFLKPFEYIMSNNPSIDVRELILECILQILQSRGENIKSGWKVIFSILRAAAK-DNDESLVRLAFQIV 83 (86)
T ss_pred ccHHHHHHHHHHHHHHhccCcHHHHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHh-CCCccHHHHHHHHH
Confidence 3447888888888873 35889999999999999987444445899999999999876 66789999988765
No 7
>KOG1992|consensus
Probab=83.89 E-value=14 Score=33.42 Aligned_cols=100 Identities=24% Similarity=0.287 Sum_probs=63.8
Q ss_pred cccChhcHHHHHhhHHHHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCCC----CHHHHHHHHHHHHHHHhh
Q psy1263 2 CENSIDTLHHFKKIVPNLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGKN----DVEASEAMNDILAQVATN 77 (115)
Q Consensus 2 ~~~~~~~~~~~~~~vp~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~~----d~~~~~~l~~vL~~i~~~ 77 (115)
|+.++.+.-.=..+.|.....|..+....-.|+ +-.++|+.--|||.++.+... -+....++.+++.++..|
T Consensus 529 re~~~~~if~~~~iap~~~~ll~nLf~a~s~p~----~~EneylmKaImRii~i~~~~i~p~~~~~l~~Lteiv~~v~KN 604 (960)
T KOG1992|consen 529 RENSNAKIFGAEDIAPFVEILLTNLFKALSLPG----KAENEYLMKAIMRIISILQSAIIPHAPELLRQLTEIVEEVSKN 604 (960)
T ss_pred ccCccccccchhhcchHHHHHHHHHHHhccCCc----ccccHHHHHHHHHHHHhCHHhhhhhhhHHHHHHHHHHHHHhcC
Confidence 333333333344678888888898885553333 367899999999999988753 234445555555555443
Q ss_pred CCCCcchhHHHHHHHHHHHHhc--CCChhHHH
Q psy1263 78 TETSKNVGNTILYETVLSIMDI--KSESGLRS 107 (115)
Q Consensus 78 ~~~~~na~~AILyEav~ti~~~--~~~~~L~~ 107 (115)
. ++-.-|.-|||+|-+++.. +.++++.+
T Consensus 605 P--s~P~fnHYLFEsi~~li~~t~~~~~~~vs 634 (960)
T KOG1992|consen 605 P--SNPQFNHYLFESIGLLIRKTCKANPSAVS 634 (960)
T ss_pred C--CCchhHHHHHHHHHHHHHHHhccCchHHH
Confidence 2 2235678999999998876 44444433
No 8
>PF03378 CAS_CSE1: CAS/CSE protein, C-terminus; InterPro: IPR005043 Mammalian cellular apoptosis susceptibility (CAS) proteins and the yeast chromosome-segregation protein, CSE1 are homologous []. CAS is involved in both cellular apoptosis and proliferation [, ]. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle [], as is the protein MEK, which is thought to regulate the intracellular localization (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway []. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins []. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins []. This entry represents the C-terminal portion of these proteins. Structural studies of the yeast CSE1 protein indicate that this domain binds to both the transport-orchestrating protein RanGTP and the cargo molecule that is being exported [].; GO: 0005515 protein binding; PDB: 1Z3H_B 1WA5_C.
Probab=77.34 E-value=21 Score=29.54 Aligned_cols=84 Identities=18% Similarity=0.280 Sum_probs=52.5
Q ss_pred HHHhhHHHHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhh-CCCCcch-hHHH
Q psy1263 11 HFKKIVPNLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGKNDVEASEAMNDILAQVATN-TETSKNV-GNTI 88 (115)
Q Consensus 11 ~~~~~vp~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~-~~~~~na-~~AI 88 (115)
...+....+...|=+++....+ -.+.|+.--+||++..+..+-......+.+-|..++.. .+..+|. -+=-
T Consensus 19 di~p~~~~ll~~Lf~~i~~~~s-------~ENeylMk~iMRvl~~~~e~~~p~~~~il~~L~~il~~v~kNPsnP~FnHy 91 (435)
T PF03378_consen 19 DIQPFAQQLLQNLFALIEKPGS-------AENEYLMKCIMRVLSVLQEDILPIAVEILQHLTAILKEVSKNPSNPRFNHY 91 (435)
T ss_dssp GTTCCHHHHHHHHHHHHHTT-S-------TC-HHHHHHHHHHHHHSTTTTGGGHHHHHHHHHHHHHHHHTS---HHHHHH
T ss_pred HhhhhHHHHHHHHHHHHhcCCC-------ccchHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCCcchhhh
Confidence 3345566666666666655443 67899999999999998876444444454545555443 2334454 3457
Q ss_pred HHHHHHHHHhcCC
Q psy1263 89 LYETVLSIMDIKS 101 (115)
Q Consensus 89 LyEav~ti~~~~~ 101 (115)
+||++.+++..-.
T Consensus 92 lFEsi~~lir~~~ 104 (435)
T PF03378_consen 92 LFESIGALIRFVC 104 (435)
T ss_dssp HHHHHHHHHHHS-
T ss_pred HHHHHHHHHHhcc
Confidence 9999999998844
No 9
>TIGR03092 SASP_sspI small, acid-soluble spore protein I. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspI. The gene in Bacillus subtilis previously was designated ysfA.
Probab=76.87 E-value=4.4 Score=25.10 Aligned_cols=31 Identities=16% Similarity=0.302 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHhhCCCCcchhHHHHHHHHH
Q psy1263 64 SEAMNDILAQVATNTETSKNVGNTILYETVL 94 (115)
Q Consensus 64 ~~~l~~vL~~i~~~~~~~~na~~AILyEav~ 94 (115)
.+++.+++...+++.+-.--.|-.||||++=
T Consensus 15 ~~elk~~I~daI~sgEEk~LPGLGVlFE~~W 45 (65)
T TIGR03092 15 KEQLEATIVDAIQSGEEKMLPGLGVLFEAIW 45 (65)
T ss_pred HHHHHHHHHHHHhccchhcCCccHHHHHHHH
Confidence 5788899999999888778899999999863
No 10
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=76.68 E-value=4.6 Score=25.03 Aligned_cols=30 Identities=20% Similarity=0.379 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHhhCCCCcchhHHHHHHHH
Q psy1263 64 SEAMNDILAQVATNTETSKNVGNTILYETV 93 (115)
Q Consensus 64 ~~~l~~vL~~i~~~~~~~~na~~AILyEav 93 (115)
.+++.+++...+++.+-.--.|-.||||.+
T Consensus 16 ~~el~~~I~daI~sgEE~~LPGLGVlFE~~ 45 (65)
T PF14098_consen 16 KEELKDTIEDAIQSGEEKALPGLGVLFEVI 45 (65)
T ss_pred HHHHHHHHHHHHhccchhcCCchHHHHHHH
Confidence 678889999999988888889999999986
No 11
>PRK02955 small acid-soluble spore protein SspI; Provisional
Probab=74.78 E-value=4.8 Score=25.16 Aligned_cols=31 Identities=16% Similarity=0.302 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHhhCCCCcchhHHHHHHHHH
Q psy1263 64 SEAMNDILAQVATNTETSKNVGNTILYETVL 94 (115)
Q Consensus 64 ~~~l~~vL~~i~~~~~~~~na~~AILyEav~ 94 (115)
.+++.+.+...+++.+-.--.|-.||||.+=
T Consensus 18 ~eel~~~I~daIqsgEEk~LPGLGVlFE~~W 48 (68)
T PRK02955 18 KEELEGTIVDAIQSGEEKMLPGLGVLFEVIW 48 (68)
T ss_pred HHHHHHHHHHHHhccchhcCCcchhHHHHHH
Confidence 6788899999999888777899999999863
No 12
>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=65.27 E-value=43 Score=24.71 Aligned_cols=72 Identities=24% Similarity=0.263 Sum_probs=53.4
Q ss_pred cHHHHHhhHHHHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhhCC----CCcc
Q psy1263 8 TLHHFKKIVPNLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGKNDVEASEAMNDILAQVATNTE----TSKN 83 (115)
Q Consensus 8 ~~~~~~~~vp~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~~~----~~~n 83 (115)
..+...+++|++|--|++-+. ..+|=.-...|++||.+....+.+-+.|..-+.+++.--. ...|
T Consensus 70 ~~~kilPvlPqLI~plk~AL~-----------tr~~~V~~~~L~~Lq~Lv~~~~~vG~aLvPyyrqLLp~ln~f~~k~~n 138 (183)
T PF10274_consen 70 GGEKILPVLPQLIIPLKRALN-----------TRDPEVFCATLKALQQLVTSSDMVGEALVPYYRQLLPVLNLFKNKNVN 138 (183)
T ss_pred chhHHHHHHHHHHHHHHHHHh-----------CCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHhcccC
Confidence 456677889999999998765 6788899999999999966666666777777777765422 4456
Q ss_pred hhHHHHH
Q psy1263 84 VGNTILY 90 (115)
Q Consensus 84 a~~AILy 90 (115)
.|.+|=|
T Consensus 139 ~gd~i~y 145 (183)
T PF10274_consen 139 LGDGIDY 145 (183)
T ss_pred CCccccc
Confidence 6666655
No 13
>KOG1058|consensus
Probab=57.16 E-value=24 Score=31.84 Aligned_cols=66 Identities=11% Similarity=0.185 Sum_probs=47.5
Q ss_pred chHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhhCCCCcchhHHHHHHHHHHHHhcCCChhHHHHHHHHh
Q psy1263 42 DPFLQVKILKLLRILGKNDVEASEAMNDILAQVATNTETSKNVGNTILYETVLSIMDIKSESGLRSFFTTFT 113 (115)
Q Consensus 42 ~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~~~~~~na~~AILyEav~ti~~~~~~~~L~~~av~~l 113 (115)
++-||.-++.+.+.-...++....+...++-..++.+ ..||.|||--+++.+.++|.++..|++.+
T Consensus 219 ~~~LqlViVE~Irkv~~~~p~~~~~~i~~i~~lL~st------ssaV~fEaa~tlv~lS~~p~alk~Aa~~~ 284 (948)
T KOG1058|consen 219 NDSLQLVIVELIRKVCLANPAEKARYIRCIYNLLSST------SSAVIFEAAGTLVTLSNDPTALKAAASTY 284 (948)
T ss_pred cHHHHHHHHHHHHHHHhcCHHHhhHHHHHHHHHHhcC------CchhhhhhcceEEEccCCHHHHHHHHHHH
Confidence 3566666666666555555555556666666666544 56899999999999999999988888754
No 14
>PF12142 PPO1_DWL: Polyphenol oxidase middle domain; InterPro: IPR022739 This domain is found in bacteria and eukaryotes and is approximately 50 amino acids in length. It is found in association with PF00264 from PFAM and PF12143 from PFAM. Most members are annotated as being polyphenol oxidases, and many are from plants or plastids. There is a conserved DWL sequence motif. ; GO: 0004097 catechol oxidase activity, 0055114 oxidation-reduction process; PDB: 1BT3_A 1BUG_B 1BT1_B 1BT2_B 2P3X_A.
Probab=54.16 E-value=3.9 Score=24.45 Aligned_cols=17 Identities=24% Similarity=0.239 Sum_probs=6.4
Q ss_pred CCCccccCCCchHHHHH
Q psy1263 32 SPEHDVSGVSDPFLQVK 48 (115)
Q Consensus 32 ~~eY~y~gvp~PwLQvk 48 (115)
.-.|.|..++.||+-.|
T Consensus 34 ~LgY~Y~~v~~PW~~~k 50 (54)
T PF12142_consen 34 KLGYTYQDVPIPWLNSK 50 (54)
T ss_dssp CCTEEE-----TT----
T ss_pred HcCccccCCCCccccCc
Confidence 35699999999998654
No 15
>TIGR02568 LcrE type III secretion regulator YopN/LcrE/InvE/MxiC. This protein is found in type III secretion operons and, in Yersinia is localized to the cell surface and is involved in the Low-Calicium Response (LCR), possibly by sensing the calcium concentration. In Salmonella, the gene is known as InvE and is believed to perform an essential role in the secretion process and interacts with the proteins SipBCD and SicA.//Altered name to reflect regulatory role. Added GO and role IDs. Negative regulation of type III secretion in Y pestis is mediated in part by a multiprotein complex that has been proposed to act as a physical impediment to type III secretion by blocking the entrance to the secretion apparatus prior to contact with mammalian cells. This complex is composed of YopN, its heterodimeric secretion chaperone SycN-YscB, and TyeA. PubMed: 15701523
Probab=52.71 E-value=99 Score=23.35 Aligned_cols=44 Identities=14% Similarity=0.018 Sum_probs=36.8
Q ss_pred ccccCCCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhhC
Q psy1263 35 HDVSGVSDPFLQVKILKLLRILGKNDVEASEAMNDILAQVATNT 78 (115)
Q Consensus 35 Y~y~gvp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~~ 78 (115)
|.=...|||+-|+-.|+-+..-...++...+.+...+.+.+...
T Consensus 84 ~l~~~f~D~s~~~laL~~ll~~~~~~~~~~~~l~~~~~~ll~~~ 127 (240)
T TIGR02568 84 LARGAFPDPSDQALALRAALQRLELDPAERKALEEAAQALLELE 127 (240)
T ss_pred HHHhhCCChHHHHHHHHHHHHhccCChhHHHHHHHHHHHHHHHh
Confidence 55578999999999999998888878888888888887777653
No 16
>PF09409 PUB: PUB domain; InterPro: IPR018997 The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain []. This domain is also found on other proteins linked to the ubiquitin-proteasome system. ; PDB: 2CM0_A 2CCQ_A 2D5U_A 2HPL_A 2HPJ_A.
Probab=52.65 E-value=30 Score=21.75 Aligned_cols=43 Identities=23% Similarity=0.243 Sum_probs=36.8
Q ss_pred cHHHHHhhHHHHHHHHHHHHhcCCCCCccccCCCchHHHHHHH
Q psy1263 8 TLHHFKKIVPNLVRNLKNLILAGYSPEHDVSGVSDPFLQVKIL 50 (115)
Q Consensus 8 ~~~~~~~~vp~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklL 50 (115)
+++.+..++..+.+++..|+.+.-.+.|.-=...+|-.|-+++
T Consensus 2 ~~~~~~~al~~L~~il~NI~~~P~~~kyR~Ir~~N~~f~~~i~ 44 (87)
T PF09409_consen 2 DPEAFQKALETLEKILSNILSNPNEEKYRRIRLSNKTFQEKIL 44 (87)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHSTT-CGGGEEETTSHHHHHHTT
T ss_pred CHHHHHHHHHHHHHHHHHHccCCCcccceEeecCcchHHHHhc
Confidence 5678889999999999999998888889889999999998776
No 17
>PF05918 API5: Apoptosis inhibitory protein 5 (API5); InterPro: IPR008383 This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organisms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterised by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in Homo sapiens chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors [,].; PDB: 3U0R_A 3V6A_A.
Probab=48.45 E-value=87 Score=27.07 Aligned_cols=85 Identities=16% Similarity=0.251 Sum_probs=49.1
Q ss_pred hhHHHHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhhCCCCcchhHHHHHHHH
Q psy1263 14 KIVPNLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGKNDVEASEAMNDILAQVATNTETSKNVGNTILYETV 93 (115)
Q Consensus 14 ~~vp~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~~~~~~na~~AILyEav 93 (115)
++-..+++.+-.|++ =.|+=..+.-+|=|-.|.+++++...++.|||.|.++.-| ..-..++-.++
T Consensus 55 ~l~~~Ai~a~~DLcE-----------Ded~~iR~~aik~lp~~ck~~~~~v~kvaDvL~QlL~tdd---~~E~~~v~~sL 120 (556)
T PF05918_consen 55 DLQEEAINAQLDLCE-----------DEDVQIRKQAIKGLPQLCKDNPEHVSKVADVLVQLLQTDD---PVELDAVKNSL 120 (556)
T ss_dssp GGHHHHHHHHHHHHT------------SSHHHHHHHHHHGGGG--T--T-HHHHHHHHHHHTT------HHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHh-----------cccHHHHHHHHHhHHHHHHhHHHHHhHHHHHHHHHHhccc---HHHHHHHHHHH
Confidence 444556666666664 3446677778888888888888888999999999998543 23344444555
Q ss_pred HHHHhcCCChhHHHHHHHH
Q psy1263 94 LSIMDIKSESGLRSFFTTF 112 (115)
Q Consensus 94 ~ti~~~~~~~~L~~~av~~ 112 (115)
..++..|+...|.+...++
T Consensus 121 ~~ll~~d~k~tL~~lf~~i 139 (556)
T PF05918_consen 121 MSLLKQDPKGTLTGLFSQI 139 (556)
T ss_dssp HHHHHH-HHHHHHHHHHHH
T ss_pred HHHHhcCcHHHHHHHHHHH
Confidence 5555555555555444443
No 18
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=48.45 E-value=18 Score=20.53 Aligned_cols=27 Identities=19% Similarity=0.309 Sum_probs=15.7
Q ss_pred HHHhhCCCCHHHHHHHHHHHHHHHhhC
Q psy1263 52 LLRILGKNDVEASEAMNDILAQVATNT 78 (115)
Q Consensus 52 lL~~l~~~d~~~~~~l~~vL~~i~~~~ 78 (115)
++++|..+++..++++..+|+.++.-+
T Consensus 12 l~~fl~~~~~~~~~~llpvi~tlL~fs 38 (46)
T PF01465_consen 12 LLQFLESREPSEREQLLPVIATLLKFS 38 (46)
T ss_dssp HHHHHTTSS---HHHHHHHHHHHTT--
T ss_pred HHHHhcCCchhhHHHHHHHHHHHHCCC
Confidence 456666666677777888888777554
No 19
>KOG2305|consensus
Probab=46.67 E-value=44 Score=26.23 Aligned_cols=71 Identities=13% Similarity=0.168 Sum_probs=49.2
Q ss_pred hHHHHHHHHHHHHhcCCCCCccc---cCCCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhhCC-C--------Cc
Q psy1263 15 IVPNLVRNLKNLILAGYSPEHDV---SGVSDPFLQVKILKLLRILGKNDVEASEAMNDILAQVATNTE-T--------SK 82 (115)
Q Consensus 15 ~vp~lv~iL~~lv~~~~~~eY~y---~gvp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~~~-~--------~~ 82 (115)
+...+++.-+-|+.+...|.|.. -=||+||- .++..++-.++..++=+..= . .+
T Consensus 128 ~s~gL~~k~q~lvaHPvNPPyfiPLvElVPaPwT--------------sp~tVdrt~~lM~sigq~pV~l~rei~Gf~ln 193 (313)
T KOG2305|consen 128 FSAGLINKEQCLVAHPVNPPYFIPLVELVPAPWT--------------SPDTVDRTRALMRSIGQEPVTLKREILGFALN 193 (313)
T ss_pred HhhhhhhhhheeEecCCCCCcccchheeccCCCC--------------ChhHHHHHHHHHHHhCCCCcccccccccceec
Confidence 34456666666777777777765 56889995 56667777777777655421 1 23
Q ss_pred chhHHHHHHHHHHHHhc
Q psy1263 83 NVGNTILYETVLSIMDI 99 (115)
Q Consensus 83 na~~AILyEav~ti~~~ 99 (115)
-.++|||-|.-+++.+-
T Consensus 194 riq~Ailne~wrLvasG 210 (313)
T KOG2305|consen 194 RIQYAILNETWRLVASG 210 (313)
T ss_pred cccHHHHHHHHHHHHcc
Confidence 48999999999988654
No 20
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=42.56 E-value=16 Score=30.54 Aligned_cols=14 Identities=43% Similarity=0.698 Sum_probs=12.8
Q ss_pred CchHHHHHHHHHHH
Q psy1263 41 SDPFLQVKILKLLR 54 (115)
Q Consensus 41 p~PwLQvklLrlL~ 54 (115)
-+|-||.|+||+|+
T Consensus 305 mSp~lQaKLLRFL~ 318 (511)
T COG3283 305 MSPRLQAKLLRFLN 318 (511)
T ss_pred cCHHHHHHHHHHhc
Confidence 47999999999997
No 21
>PF02526 GBP_repeat: Glycophorin-binding protein; InterPro: IPR003681 The glycophorin-binding protein contains a tandem repeat. The repeated sequence determines the binding domain for an erythrocyte receptor binding protein of Plasmodium falciparum, the malarial parasite []. Erythrocyte invasion by the malarial merozoite is a receptor-mediated process, an obligatory step in the development of the parasite. The P. falciparum protein binds to the erythrocyte receptor glycophorin.
Probab=38.53 E-value=55 Score=17.77 Aligned_cols=21 Identities=33% Similarity=0.501 Sum_probs=16.0
Q ss_pred CHHHHHHHHHHHHHHHhhCCCC
Q psy1263 60 DVEASEAMNDILAQVATNTETS 81 (115)
Q Consensus 60 d~~~~~~l~~vL~~i~~~~~~~ 81 (115)
|+.++..+ +|+-+|++++|..
T Consensus 16 dpeyrkh~-~v~yqil~~tdpn 36 (38)
T PF02526_consen 16 DPEYRKHL-NVLYQILTNTDPN 36 (38)
T ss_pred CHHHHHHH-HHHHHHHccCCCC
Confidence 67766655 7999999998764
No 22
>PF03224 V-ATPase_H_N: V-ATPase subunit H; InterPro: IPR004908 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) (3.6.3.14 from EC) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release []. V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins []. This entry represents subunit H (also known as Vma13p) found in the V1 complex of V-ATPases. This subunit has a regulatory function, being responsible for activating ATPase activity and coupling ATPase activity to proton flow []. The yeast enzyme contains five motifs similar to the HEAT or Armadillo repeats seen in the importins, and can be divided into two distinct domains: a large N-terminal domain consisting of stacked alpha helices, and a smaller C-terminal alpha-helical domain with a similar superhelical topology to an armadillo repeat []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0000221 vacuolar proton-transporting V-type ATPase, V1 domain; PDB: 1HO8_A.
Probab=34.20 E-value=1e+02 Score=23.81 Aligned_cols=32 Identities=19% Similarity=0.252 Sum_probs=24.4
Q ss_pred CCchHHHHHHHHHHHhhCC---CCHHHHHHHHHHH
Q psy1263 40 VSDPFLQVKILKLLRILGK---NDVEASEAMNDIL 71 (115)
Q Consensus 40 vp~PwLQvklLrlL~~l~~---~d~~~~~~l~~vL 71 (115)
.-..-++.+++++++.|.. .|++..+.+..+-
T Consensus 275 ~~~~mv~~~~l~~l~~L~~rk~~Dedl~edl~~L~ 309 (312)
T PF03224_consen 275 NIELMVLCGLLKTLQNLSERKWSDEDLTEDLEFLK 309 (312)
T ss_dssp HHHHHHHH-HHHHHHHHHSS--SSHHHHHHHHHHH
T ss_pred HHHHHHHccHHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence 5557789999999999986 5888888876543
No 23
>PF01603 B56: Protein phosphatase 2A regulatory B subunit (B56 family); InterPro: IPR002554 Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family [].; GO: 0008601 protein phosphatase type 2A regulator activity, 0007165 signal transduction, 0000159 protein phosphatase type 2A complex; PDB: 2NYM_B 2NYL_B 2IAE_E 2NPP_B 3FGA_B 2JAK_A.
Probab=33.55 E-value=2.3e+02 Score=23.13 Aligned_cols=55 Identities=18% Similarity=0.120 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhh
Q psy1263 18 NLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGKNDVEASEAMNDILAQVATN 77 (115)
Q Consensus 18 ~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~ 77 (115)
-+-++|.+.+.+..-.. ...=+-+-=+.+++..|...|+..++.+.++|.++..+
T Consensus 109 ~vY~il~~~i~~~~~~~-----~~~~i~~~fi~~Ll~l~~S~D~rER~~lk~~l~~iy~k 163 (409)
T PF01603_consen 109 LVYEILLRFIESPPFDP-----AKKYIDQKFIKKLLELFDSPDPRERDYLKTILHRIYGK 163 (409)
T ss_dssp HHHHHHHHHHTSTT--C-----CTTTS-HHHHHHHHHTTTSSTHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCccccH-----HHHHcCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence 45566666665431111 22234556678899999999999999999999999987
No 24
>COG5096 Vesicle coat complex, various subunits [Intracellular trafficking and secretion]
Probab=30.99 E-value=67 Score=28.81 Aligned_cols=47 Identities=15% Similarity=0.109 Sum_probs=37.3
Q ss_pred CCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhhC--CCCcchhHHH
Q psy1263 40 VSDPFLQVKILKLLRILGKNDVEASEAMNDILAQVATNT--ETSKNVGNTI 88 (115)
Q Consensus 40 vp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~~--~~~~na~~AI 88 (115)
=|+|.++.--||+|..++ +++..+.+.+.+.+.++.. ...|+|..||
T Consensus 103 d~N~~iR~~AlR~ls~l~--~~el~~~~~~~ik~~l~d~~ayVRk~Aalav 151 (757)
T COG5096 103 DPNEEIRGFALRTLSLLR--VKELLGNIIDPIKKLLTDPHAYVRKTAALAV 151 (757)
T ss_pred CCCHHHHHHHHHHHHhcC--hHHHHHHHHHHHHHHccCCcHHHHHHHHHHH
Confidence 378999999999999887 4578888889888888764 3566777665
No 25
>PF08506 Cse1: Cse1; InterPro: IPR013713 The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments. This domain is found in exportin Cse1 (also known as importin-alpha re-exporter). Exportin Cse1 mediates nuclear transport of importin-alpha back into the cytosol, where importin-alpha functions as a transporter of proteins carrying nuclear localisation signals (NLS) from the cytoplasm into the nucleus [, , ]. This domain contains HEAT repeats. More information about these proteins can be found at Protein of the Month: Importins [].; GO: 0006886 intracellular protein transport; PDB: 1Z3H_B 1WA5_C.
Probab=30.44 E-value=2.4e+02 Score=22.80 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=33.9
Q ss_pred hcHHHHHhhHHHHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCC
Q psy1263 7 DTLHHFKKIVPNLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGK 58 (115)
Q Consensus 7 ~~~~~~~~~vp~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~ 58 (115)
+.-+.+..++|.++...-+++.+ ...++.|. ++..+.|++|.....
T Consensus 126 kY~e~f~~~l~~fv~~vw~lL~~-~~~~~~~D-----~lv~~al~FL~~v~~ 171 (370)
T PF08506_consen 126 KYEEEFEPFLPTFVQAVWNLLTK-ISQQPKYD-----ILVSKALQFLSSVAE 171 (370)
T ss_dssp H-HHHHHHHHHHHHHHHHHHHTC---SSGGGH-----HHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-hhhccccc-----HHHHHHHHHHHHHHc
Confidence 34567888999999998888766 66666663 688899999987654
No 26
>PRK10628 LigB family dioxygenase; Provisional
Probab=29.59 E-value=40 Score=25.91 Aligned_cols=36 Identities=14% Similarity=0.263 Sum_probs=26.1
Q ss_pred CCCccccCCCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHH
Q psy1263 32 SPEHDVSGVSDPFLQVKILKLLRILGKNDVEASEAMNDILAQ 73 (115)
Q Consensus 32 ~~eY~y~gvp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~ 73 (115)
..-|||||+|...-+ +++=.+++++..+++.+.|.+
T Consensus 47 ~~i~DF~GFP~elY~------~~Ypa~G~p~LA~~i~~ll~~ 82 (246)
T PRK10628 47 RTIHDFGGFPQALYD------THYPAPGSPALAQRLVELLAP 82 (246)
T ss_pred CcccCCCCCCHHHee------ecCCCCCCHHHHHHHHHHhhh
Confidence 345999999986544 445555788888888888776
No 27
>smart00755 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245.
Probab=29.26 E-value=78 Score=18.00 Aligned_cols=26 Identities=23% Similarity=0.372 Sum_probs=15.4
Q ss_pred HHHhhCCCCHHHHHHHHHHHHHHHhhC
Q psy1263 52 LLRILGKNDVEASEAMNDILAQVATNT 78 (115)
Q Consensus 52 lL~~l~~~d~~~~~~l~~vL~~i~~~~ 78 (115)
+|++|...|.. +++|..++..+++-+
T Consensus 11 ll~fl~~~e~~-r~~ll~vi~tlL~fs 36 (46)
T smart00755 11 LLQFLTLRESE-RETLLKVISTVLQLS 36 (46)
T ss_pred HHHHhccCcch-HHHHHHHHHHHhCCC
Confidence 34555555544 677777777766543
No 28
>PF13929 mRNA_stabil: mRNA stabilisation
Probab=29.17 E-value=2.5e+02 Score=22.32 Aligned_cols=90 Identities=20% Similarity=0.188 Sum_probs=49.8
Q ss_pred HHHHHHHHHHhcC-CCCCccccCCC-chHHHHHHHHHHHhhCCC-----CHHHHHHHHHHHHHHHhhCCCCcchhHHHHH
Q psy1263 18 NLVRNLKNLILAG-YSPEHDVSGVS-DPFLQVKILKLLRILGKN-----DVEASEAMNDILAQVATNTETSKNVGNTILY 90 (115)
Q Consensus 18 ~lv~iL~~lv~~~-~~~eY~y~gvp-~PwLQvklLrlL~~l~~~-----d~~~~~~l~~vL~~i~~~~~~~~na~~AILy 90 (115)
.++.-|+-++.+- ...+.+|.+.- .-=..++.|++.+.+.++ |+ +-+.-+|...+.+. |+.--.+|
T Consensus 114 Dli~FL~~~i~~~~~~k~~~Y~~LVk~N~~Vv~aL~L~~~~~~~~~Ii~d~---evislLL~sMv~~~----~~~l~alY 186 (292)
T PF13929_consen 114 DLISFLKLVIINLSSNKSFNYWDLVKRNKIVVEALKLYDGLNPDESIIFDE---EVISLLLKSMVIDE----NTKLNALY 186 (292)
T ss_pred HHHHHHHHHHhccccccchHHHHHHHhhHHHHHHHHHhhccCcccceeeCh---HHHHHHHHHHHhcc----ccchhhHH
Confidence 4666677655444 45555564432 334556777777755442 22 22333344333323 22556799
Q ss_pred HHHHHHHhc---CCChhHHHHHHHHhc
Q psy1263 91 ETVLSIMDI---KSESGLRSFFTTFTA 114 (115)
Q Consensus 91 Eav~ti~~~---~~~~~L~~~av~~lg 114 (115)
|.|+.+..- ..+.......+++|+
T Consensus 187 EvV~~l~~t~~~~l~~~vi~~Il~~L~ 213 (292)
T PF13929_consen 187 EVVDFLVSTFSKSLTRNVIISILEILA 213 (292)
T ss_pred HHHHHHHhccccCCChhHHHHHHHHHH
Confidence 999999854 334566666666665
No 29
>KOG0412|consensus
Probab=29.04 E-value=68 Score=28.65 Aligned_cols=28 Identities=14% Similarity=0.261 Sum_probs=22.8
Q ss_pred CCCCccccCCCchHHHHHHHHHHHhhCC
Q psy1263 31 YSPEHDVSGVSDPFLQVKILKLLRILGK 58 (115)
Q Consensus 31 ~~~eY~y~gvp~PwLQvklLrlL~~l~~ 58 (115)
...||.+|-..+||.|--+.++=+.+..
T Consensus 631 s~edy~~~ea~d~~Vq~fl~~v~~l~~~ 658 (773)
T KOG0412|consen 631 SEEDYAAYEANDPWVQQFLSSVEQLLAE 658 (773)
T ss_pred cHHHHhhhccCChHHHHHHHHHHHHHHh
Confidence 3568999999999999888877776654
No 30
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=27.20 E-value=1e+02 Score=18.13 Aligned_cols=30 Identities=13% Similarity=0.248 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHhcCCCCCccccCCC---chHH
Q psy1263 16 VPNLVRNLKNLILAGYSPEHDVSGVS---DPFL 45 (115)
Q Consensus 16 vp~lv~iL~~lv~~~~~~eY~y~gvp---~PwL 45 (115)
+.....-|..-+++....|+...|++ +||.
T Consensus 22 vS~a~~~l~~y~e~~~~~Dpll~g~~~~~NP~~ 54 (57)
T cd00068 22 VSKAAAELLKYCEQNAENDPLLTGPPSPSNPWI 54 (57)
T ss_pred HHHHHHHHHHHHHhcCCCCCCCCCCCCCCCCCC
Confidence 44555566666677778888888876 7773
No 31
>KOG2085|consensus
Probab=26.75 E-value=2.7e+02 Score=23.54 Aligned_cols=54 Identities=30% Similarity=0.360 Sum_probs=40.7
Q ss_pred HHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhh-C-------------------CCCcchhHHHHHHHHHHHHhc
Q psy1263 46 QVKILKLLRILGKNDVEASEAMNDILAQVATN-T-------------------ETSKNVGNTILYETVLSIMDI 99 (115)
Q Consensus 46 QvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~-~-------------------~~~~na~~AILyEav~ti~~~ 99 (115)
|-=+||+|.+|..+|+...|-+-.+|.+|..+ . ++.+-.|-|=|-|.+--|+.-
T Consensus 176 ~~FvlkLLdLFdSEDpRERe~LKT~LhrIygKfl~~r~firk~iNNif~~FIyEte~hnGIaELLEIlgSiIng 249 (457)
T KOG2085|consen 176 QKFVLKLLDLFDSEDPREREFLKTILHRIYGKFLVHRPFIRKSINNIFLRFIYETERHNGIAELLEILGSIING 249 (457)
T ss_pred HHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHhhhHHHHHHhhcchhhhhcccccccCCHHHHHHHHHHhcCc
Confidence 34478899999999999999999999999763 1 234457777777777766654
No 32
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.58 E-value=2.5e+02 Score=20.31 Aligned_cols=42 Identities=12% Similarity=0.244 Sum_probs=30.5
Q ss_pred cCCCchHHHHHHHHHHHhhCC---CCHHHHHHHHHHHHHHHhhCC
Q psy1263 38 SGVSDPFLQVKILKLLRILGK---NDVEASEAMNDILAQVATNTE 79 (115)
Q Consensus 38 ~gvp~PwLQvklLrlL~~l~~---~d~~~~~~l~~vL~~i~~~~~ 79 (115)
=|.|=||-+.+|=-.-++... -+++.+|++...+..++..+.
T Consensus 74 CGkpyPWt~~~L~aa~el~ee~eeLs~deke~~~~sl~dL~~d~P 118 (158)
T PF10083_consen 74 CGKPYPWTENALEAANELIEEDEELSPDEKEQFKESLPDLTKDTP 118 (158)
T ss_pred CCCCCchHHHHHHHHHHHHHHhhcCCHHHHHHHHhhhHHHhhcCC
Confidence 477889999887655555543 267788888888888886654
No 33
>KOG4113|consensus
Probab=25.64 E-value=15 Score=24.53 Aligned_cols=44 Identities=20% Similarity=0.181 Sum_probs=30.4
Q ss_pred cccChhcHHHHHhhHHHHHHHHHHHHhcC-CCCCccccCCCchHH
Q psy1263 2 CENSIDTLHHFKKIVPNLVRNLKNLILAG-YSPEHDVSGVSDPFL 45 (115)
Q Consensus 2 ~~~~~~~~~~~~~~vp~lv~iL~~lv~~~-~~~eY~y~gvp~PwL 45 (115)
|.+++++...-..-+|...+.+.+...+. .++.=++-+|+|||-
T Consensus 8 lq~~~~~~~n~~~~~p~~rkk~~~~~d~~~te~~~dF~lVkDmf~ 52 (99)
T KOG4113|consen 8 LQINEDNYINEERDVPSMRKKLEARTDSDNTEPLSDFFLVKDMFA 52 (99)
T ss_pred EEcCcccccccccccccchhhhhhhccccCCCcccceEeecccee
Confidence 55666655555666777777775555444 667788899999994
No 34
>PF13646 HEAT_2: HEAT repeats; PDB: 1OYZ_A 3FGA_A 2PF4_C 2IAE_A 3B2A_A.
Probab=25.15 E-value=1.6e+02 Score=17.45 Aligned_cols=30 Identities=20% Similarity=0.254 Sum_probs=19.3
Q ss_pred CCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHH
Q psy1263 40 VSDPFLQVKILKLLRILGKNDVEASEAMNDILAQVA 75 (115)
Q Consensus 40 vp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~ 75 (115)
=++|..+....+.|+.++. ++..+.|.+.+
T Consensus 11 ~~~~~vr~~a~~~L~~~~~------~~~~~~L~~~l 40 (88)
T PF13646_consen 11 DPDPQVRAEAARALGELGD------PEAIPALIELL 40 (88)
T ss_dssp SSSHHHHHHHHHHHHCCTH------HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHcCC------HhHHHHHHHHH
Confidence 4678888888888885542 23445555555
No 35
>PLN03076 ARF guanine nucleotide exchange factor (ARF-GEF); Provisional
Probab=25.10 E-value=2.7e+02 Score=27.68 Aligned_cols=91 Identities=13% Similarity=0.131 Sum_probs=61.6
Q ss_pred HHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCC--CCHHHHHHHHHHHHHHHhhCCCCcchhHHHHHHHHHH
Q psy1263 18 NLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGK--NDVEASEAMNDILAQVATNTETSKNVGNTILYETVLS 95 (115)
Q Consensus 18 ~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~--~d~~~~~~l~~vL~~i~~~~~~~~na~~AILyEav~t 95 (115)
..+.-|+|+...-...+ -.++--.|-.+||=|..+-. .+.++.|.+.+++.+++..--..=-+|.-.+|+.+.+
T Consensus 1156 fAidsLrQLs~kfle~e----EL~~f~FQkefLkPfe~im~~s~~~eVrE~ILeCv~qmI~s~~~nIkSGWktIF~VLs~ 1231 (1780)
T PLN03076 1156 FAMDSLRQLSMKFLERE----ELANYNFQNEFMKPFVIVMRKSNAVEIRELIIRCVSQMVLSRVNNVKSGWKSMFMVFTT 1231 (1780)
T ss_pred HHHHHHHHHHHHhcchh----hhhchhHHHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHhhhhcCcHHHHHHHHH
Confidence 34555777665443322 13444568888888887554 4778999999999999876322222588888888888
Q ss_pred HHhcCCChhHHHHHHHHh
Q psy1263 96 IMDIKSESGLRSFFTTFT 113 (115)
Q Consensus 96 i~~~~~~~~L~~~av~~l 113 (115)
++. +.++++...|+..+
T Consensus 1232 aa~-d~~e~iV~lAFetl 1248 (1780)
T PLN03076 1232 AAY-DDHKNIVLLAFEII 1248 (1780)
T ss_pred HHh-CccHHHHHHHHHHH
Confidence 864 66778888887765
No 36
>PF14225 MOR2-PAG1_C: Cell morphogenesis C-terminal
Probab=24.94 E-value=88 Score=24.16 Aligned_cols=18 Identities=33% Similarity=0.632 Sum_probs=14.9
Q ss_pred CchHHHHHHHHHHHhhCC
Q psy1263 41 SDPFLQVKILKLLRILGK 58 (115)
Q Consensus 41 p~PwLQvklLrlL~~l~~ 58 (115)
.-||+|.++|++|..+-+
T Consensus 200 ~~~w~~~~~L~iL~~ll~ 217 (262)
T PF14225_consen 200 GPPWLRRKTLQILKVLLP 217 (262)
T ss_pred CcHHHHHHHHHHHHHHhc
Confidence 347999999999998875
No 37
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=24.52 E-value=1.3e+02 Score=21.89 Aligned_cols=31 Identities=26% Similarity=0.408 Sum_probs=20.8
Q ss_pred HHHhhCCCCHHHHHHHHHHHHHHHhhCCCCc
Q psy1263 52 LLRILGKNDVEASEAMNDILAQVATNTETSK 82 (115)
Q Consensus 52 lL~~l~~~d~~~~~~l~~vL~~i~~~~~~~~ 82 (115)
-|+.-+.+|++.-+.+.|+|.+++.....++
T Consensus 16 ~L~~~~~~e~~~e~~L~eil~~LleaQk~G~ 46 (206)
T PF06570_consen 16 YLRSSGVSEEEIEELLEEILPHLLEAQKKGK 46 (206)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHHHHHhCCC
Confidence 3334455677888888888888887644433
No 38
>PF05232 BTP: Bacterial Transmembrane Pair family; InterPro: IPR007896 This domain represents a conserved pair of transmembrane helices. It appears to be found as two tandem repeats in a family of hypothetical proteins.
Probab=23.86 E-value=70 Score=19.53 Aligned_cols=16 Identities=19% Similarity=0.407 Sum_probs=13.4
Q ss_pred hhHHHHHHHHHHHHhc
Q psy1263 84 VGNTILYETVLSIMDI 99 (115)
Q Consensus 84 a~~AILyEav~ti~~~ 99 (115)
.-||++||..-+++..
T Consensus 7 i~hai~FE~~~l~~~~ 22 (67)
T PF05232_consen 7 ILHAILFEVGALLISV 22 (67)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5799999999887765
No 39
>PF13797 Post_transc_reg: Post-transcriptional regulator
Probab=23.84 E-value=2e+02 Score=18.41 Aligned_cols=54 Identities=24% Similarity=0.270 Sum_probs=35.0
Q ss_pred hHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHHHhh-CCCCcchhHHHHHHHHHHHHhcCCChh
Q psy1263 43 PFLQVKILKLLRILGKNDVEASEAMNDILAQVATN-TETSKNVGNTILYETVLSIMDIKSESG 104 (115)
Q Consensus 43 PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i~~~-~~~~~na~~AILyEav~ti~~~~~~~~ 104 (115)
||++.|+=. ++.+|-+ .-..+.+.++|..-.=+ .+. .=|+|+|+-|.++.+++=
T Consensus 11 p~l~sK~eE-f~~lGY~-~vt~~dlw~yl~~~~WK~~~~------~~l~e~V~DIlsl~~~~~ 65 (87)
T PF13797_consen 11 PALQSKAEE-FHLLGYE-SVTEEDLWSYLTEKKWKKKKP------PRLHELVNDILSLKPNDY 65 (87)
T ss_pred HHHHHHHHH-HHHhCcC-cCCHHHHHHHHHHHHhccCCC------cCHHHHHHHHHcCCHHHH
Confidence 777777643 3455542 22267888888765433 322 448999999999987754
No 40
>COG4025 Predicted membrane protein [Function unknown]
Probab=23.33 E-value=1e+02 Score=24.06 Aligned_cols=16 Identities=38% Similarity=0.549 Sum_probs=13.0
Q ss_pred cccCCCchHHHHHHHH
Q psy1263 36 DVSGVSDPFLQVKILK 51 (115)
Q Consensus 36 ~y~gvp~PwLQvklLr 51 (115)
-|-.+..||+.+|++|
T Consensus 18 g~v~~~~~~i~~~l~k 33 (284)
T COG4025 18 GYVTVNLPWIVVKLLK 33 (284)
T ss_pred cEEEEcccHHHHHHhh
Confidence 3456889999999987
No 41
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=22.95 E-value=1.5e+02 Score=17.34 Aligned_cols=37 Identities=30% Similarity=0.299 Sum_probs=26.8
Q ss_pred ccccCCCchHHHHHHHHHHHhhCCC--------CHHHHHHHHHHH
Q psy1263 35 HDVSGVSDPFLQVKILKLLRILGKN--------DVEASEAMNDIL 71 (115)
Q Consensus 35 Y~y~gvp~PwLQvklLrlL~~l~~~--------d~~~~~~l~~vL 71 (115)
.|.-|.++|.=.+++.+.|..+..+ |+...+.+...+
T Consensus 3 lD~rg~~CP~Pll~~~~~l~~l~~G~~l~v~~d~~~~~~di~~~~ 47 (70)
T PF01206_consen 3 LDLRGLSCPMPLLKAKKALKELPPGEVLEVLVDDPAAVEDIPRWC 47 (70)
T ss_dssp EECSS-STTHHHHHHHHHHHTSGTT-EEEEEESSTTHHHHHHHHH
T ss_pred EeCCCCCCCHHHHHHHHHHHhcCCCCEEEEEECCccHHHHHHHHH
Confidence 4667899999999999999999763 555555554443
No 42
>PHA03325 nuclear-egress-membrane-like protein; Provisional
Probab=22.88 E-value=2.1e+02 Score=23.72 Aligned_cols=35 Identities=29% Similarity=0.264 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhhCCC-----CHHHHHHHHHHHHHHHhhC
Q psy1263 44 FLQVKILKLLRILGKN-----DVEASEAMNDILAQVATNT 78 (115)
Q Consensus 44 wLQvklLrlL~~l~~~-----d~~~~~~l~~vL~~i~~~~ 78 (115)
|+|..+|++|.-.+.+ ++.+....+.++.+|-+.+
T Consensus 219 f~Qn~fl~ll~d~~ldi~~vFe~~yhS~a~rll~qI~~~~ 258 (418)
T PHA03325 219 FYQNSFLKLLADSGLDIPDVFEPCYHSEAYRLLFQIGQLT 258 (418)
T ss_pred HHHHHHHHHHHHcCCCHHHhcccccccHHHHHHHHHHccC
Confidence 5788888888887764 5566677788888887653
No 43
>KOG1916|consensus
Probab=22.44 E-value=1e+02 Score=28.68 Aligned_cols=22 Identities=23% Similarity=0.197 Sum_probs=18.2
Q ss_pred ccCCCchHHHHHHHHHHHhhCC
Q psy1263 37 VSGVSDPFLQVKILKLLRILGK 58 (115)
Q Consensus 37 y~gvp~PwLQvklLrlL~~l~~ 58 (115)
+.--|+|.-|--+|.++|-+..
T Consensus 1191 ~a~~~~~l~q~vllsliqqla~ 1212 (1283)
T KOG1916|consen 1191 FAMNPCPLSQGVLLSLIQQLAC 1212 (1283)
T ss_pred cCCCCCcchHHHHHHHHHHHHh
Confidence 3445889999999999998875
No 44
>PF10350 DUF2428: Putative death-receptor fusion protein (DUF2428); InterPro: IPR019442 This domain is found in a family of proteins of unknown function that are conserved from plants to humans. Several of these proteins have been annotated as being HEAT repeat-containing proteins while others are designated as death-receptor interacting proteins, but neither of these has yet been confirmed. Aberrations in the genes encoding these proteins have been observed in benign thyroid adenomas [].
Probab=21.95 E-value=3.4e+02 Score=20.52 Aligned_cols=57 Identities=16% Similarity=0.265 Sum_probs=36.9
Q ss_pred hhHHHHHHHHHHHHhcCCCCCccccCCCchHHHHHHHHHHHhhCCCCHHHHHHHHHHHHHH
Q psy1263 14 KIVPNLVRNLKNLILAGYSPEHDVSGVSDPFLQVKILKLLRILGKNDVEASEAMNDILAQV 74 (115)
Q Consensus 14 ~~vp~lv~iL~~lv~~~~~~eY~y~gvp~PwLQvklLrlL~~l~~~d~~~~~~l~~vL~~i 74 (115)
.+.+..++.|-++.......+.+-.. ..-||.-|-+|+.+..+ ...++.+..-+.+.
T Consensus 185 ~ll~~~~~~Ll~ia~~~~~~~~~~~~---d~~qVHAlNiLr~if~d-s~L~~~~~~yi~~~ 241 (255)
T PF10350_consen 185 PLLHRTMKSLLEIAKSPSTQHEDEKS---DLPQVHALNILRAIFRD-SKLSEDVSPYIEDA 241 (255)
T ss_pred hHHHHHHHHHHHHhcCCccccccccc---chHHHHHHHHHHHHHhc-chhHHHHHHHHHHH
Confidence 67788888888877665543332211 48899999999999884 44444444444443
No 45
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.41 E-value=70 Score=23.23 Aligned_cols=26 Identities=19% Similarity=0.249 Sum_probs=22.4
Q ss_pred CccccCCCchHHHHHHHHHHHhhCCC
Q psy1263 34 EHDVSGVSDPFLQVKILKLLRILGKN 59 (115)
Q Consensus 34 eY~y~gvp~PwLQvklLrlL~~l~~~ 59 (115)
+|...-+++-||+..|+|.-+.+.++
T Consensus 109 ~~y~~~l~n~~l~l~ilr~~~~~spe 134 (175)
T COG4344 109 KLYVRLLKNGWLVLLILRKVRKFSPE 134 (175)
T ss_pred HHHHHHcCcchHHHHHHHHHHhcCHH
Confidence 56667789999999999999999864
No 46
>PF12811 BaxI_1: Bax inhibitor 1 like ; InterPro: IPR010539 Bax inhibitor-1 (BI1) family contains six known genes in human. Some members of BI1 family have been proved to play important roles in cell death [, ].
Probab=20.33 E-value=85 Score=24.64 Aligned_cols=35 Identities=23% Similarity=0.280 Sum_probs=25.9
Q ss_pred HHHHhcCCCCCccccC-----CCchHHHHHHHHHHHhhCC
Q psy1263 24 KNLILAGYSPEHDVSG-----VSDPFLQVKILKLLRILGK 58 (115)
Q Consensus 24 ~~lv~~~~~~eY~y~g-----vp~PwLQvklLrlL~~l~~ 58 (115)
++-+.++.|.+|..+. |.==||=+++||+|++|..
T Consensus 234 e~~v~~gaPk~~eW~~AfGL~vTLVWLYlEILRLL~~l~~ 273 (274)
T PF12811_consen 234 EQGVRQGAPKKMEWYAAFGLLVTLVWLYLEILRLLSKLQN 273 (274)
T ss_pred HHHHHcCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4456667777777654 3446999999999999864
No 47
>COG4760 Predicted membrane protein [Function unknown]
Probab=20.03 E-value=82 Score=24.23 Aligned_cols=19 Identities=37% Similarity=0.520 Sum_probs=15.3
Q ss_pred CCchHHHHHHHHHHHhhCC
Q psy1263 40 VSDPFLQVKILKLLRILGK 58 (115)
Q Consensus 40 vp~PwLQvklLrlL~~l~~ 58 (115)
|.==||=++|||+|.++..
T Consensus 257 VTLVWLY~EiLRLLSy~Qn 275 (276)
T COG4760 257 VTLVWLYLEILRLLSYLQN 275 (276)
T ss_pred HHHHHHHHHHHHHHHHhhc
Confidence 3446999999999998853
Done!