Query psy4844
Match_columns 254
No_of_seqs 135 out of 342
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 19:10:12 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4844.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4844hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2102|consensus 100.0 1.1E-30 2.4E-35 267.7 3.4 236 3-253 7-248 (941)
2 PF13638 PIN_4: PIN domain; PD 99.6 4.1E-17 9E-22 131.3 2.4 119 71-195 1-133 (133)
3 COG1875 NYN ribonuclease and A 99.6 1.3E-15 2.8E-20 141.2 9.1 125 68-200 2-148 (436)
4 smart00670 PINc Large family o 99.3 1.7E-12 3.7E-17 100.4 4.5 104 71-181 1-110 (111)
5 PRK13764 ATPase; Provisional 98.4 8.7E-07 1.9E-11 88.3 7.8 115 70-197 2-130 (602)
6 COG1412 Uncharacterized protei 97.6 0.00016 3.6E-09 59.2 6.4 104 66-195 8-124 (136)
7 PRK12496 hypothetical protein; 96.4 0.01 2.2E-07 50.1 6.4 110 70-195 3-116 (164)
8 COG4956 Integral membrane prot 95.7 0.055 1.2E-06 50.1 8.2 111 69-202 161-288 (356)
9 COG1855 ATPase (PilT family) [ 95.6 0.046 1E-06 53.3 7.9 111 69-192 5-129 (604)
10 PF04900 Fcf1: Fcf1; InterPro 90.7 0.51 1.1E-05 36.2 4.7 85 90-195 7-92 (101)
11 PF14367 DUF4411: Domain of un 85.9 0.62 1.3E-05 39.0 2.6 36 72-107 2-51 (162)
12 COG1439 Predicted nucleic acid 83.4 2.3 5E-05 36.4 4.9 113 70-193 8-125 (177)
13 COG1569 Predicted nucleic acid 82.6 0.99 2.2E-05 37.2 2.3 121 71-201 3-137 (142)
14 TIGR00305 probable toxin-antit 79.0 9.5 0.00021 29.4 6.8 34 71-104 2-44 (114)
15 PF05991 NYN_YacP: YacP-like N 75.5 26 0.00057 29.3 8.9 53 148-203 77-129 (166)
16 PF01850 PIN: PIN domain; Int 67.3 3.7 7.9E-05 31.0 1.8 104 71-185 1-120 (121)
17 PF13470 PIN_3: PIN domain 62.8 1.6 3.5E-05 33.6 -1.0 35 71-105 2-46 (119)
18 PRK15431 ferrous iron transpor 57.1 8.7 0.00019 28.6 2.1 27 8-39 41-67 (78)
19 PRK04358 hypothetical protein; 36.3 69 0.0015 28.4 4.7 33 169-201 174-206 (217)
20 PF07788 DUF1626: Protein of u 35.6 1.1E+02 0.0023 22.3 4.9 39 152-190 29-70 (70)
21 PF04548 AIG1: AIG1 family; I 33.2 18 0.0004 31.1 0.7 55 77-131 103-163 (212)
22 TIGR03875 RNA_lig_partner RNA 29.5 1E+02 0.0022 27.1 4.7 33 169-201 170-202 (206)
23 PF11910 NdhO: Cyanobacterial 29.0 23 0.00051 25.4 0.5 14 9-22 2-15 (67)
24 cd05017 SIS_PGI_PMI_1 The memb 27.3 1.9E+02 0.0041 22.2 5.5 40 150-192 55-94 (119)
25 KOG4689|consensus 26.2 56 0.0012 31.5 2.6 120 69-191 131-278 (479)
26 PF02254 TrkA_N: TrkA-N domain 25.9 2.5E+02 0.0055 20.9 6.0 41 150-191 72-112 (116)
27 PF07454 SpoIIP: Stage II spor 25.6 1.2E+02 0.0026 27.6 4.6 84 120-203 70-159 (268)
28 PRK00702 ribose-5-phosphate is 25.4 1.1E+02 0.0023 27.1 4.1 40 158-197 32-75 (220)
29 KOG3670|consensus 25.1 1.1E+02 0.0024 29.6 4.4 93 92-186 151-250 (397)
30 PF08745 UPF0278: UPF0278 fami 24.4 59 0.0013 28.5 2.3 34 169-202 167-200 (205)
31 PF02254 TrkA_N: TrkA-N domain 24.3 1.8E+02 0.0038 21.7 4.8 25 168-192 21-45 (116)
32 KOG3046|consensus 24.2 56 0.0012 27.1 2.0 25 89-113 66-91 (147)
33 TIGR01170 rplA_mito ribosomal 23.6 1.2E+02 0.0026 24.9 3.9 37 167-203 51-87 (141)
34 cd03286 ABC_MSH6_euk MutS6 hom 23.2 3.7E+02 0.008 23.4 7.2 65 110-185 96-160 (218)
35 PF13344 Hydrolase_6: Haloacid 23.1 1.6E+02 0.0035 22.2 4.3 33 155-190 20-57 (101)
No 1
>KOG2102|consensus
Probab=99.96 E-value=1.1e-30 Score=267.71 Aligned_cols=236 Identities=37% Similarity=0.528 Sum_probs=204.4
Q ss_pred EEEEEcccCceeEeeeeeeccCCcCcCCCcCcccccchhccccCCCCCccccCCCCCCCCCCCCCCeEEEechHHHhhch
Q psy4844 3 YHVVQSSVWLVMKIVREHYLRDDLSCGSELCLACDTKEAILDKIPTSSKAILDKIPTSSSKKYMEPHYLLLDTNIILEQI 82 (254)
Q Consensus 3 ~~~~ktr~G~v~kvvrE~YLRdDI~Cg~~~C~~C~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~lVpDtnvll~~~ 82 (254)
.++.++++|++.|.|||+|+|+||.|+..+|..|... ...+.... +..+.+||.++|+|++++++
T Consensus 7 ~f~~~~~~~~~~~~vr~~~~r~~i~~~~~~~~~~~~~-----------~~~~~~~~----~~~~~~~~~~~~~~~~~~~~ 71 (941)
T KOG2102|consen 7 VFVRRTRRGRVTKRVREQYLRSDIECLQALCHSCNGS-----------SQPLGDER----SRAEARHYSLPATNPVLSQP 71 (941)
T ss_pred cccccccccCccccccchhhhhhhhhhhhhccccccc-----------ccCccchh----ccccccccccCCCCcccccc
Confidence 4577899999999999999999999999999999211 11111111 12344899999999999999
Q ss_pred hhccCC-CCCceeeeHHHHHHHhcCChhHHHHHHHHhcCCC-CcEEEEeCCccccccccCCCCCCcCCcccHHHHHHHHH
Q psy4844 83 DILEEP-TLCNVILVQTILQEVKHRSSSVYKRLKDLISNPS-RKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATW 160 (254)
Q Consensus 83 d~le~~-~~~~VII~qTVleev~~rs~~~y~RLr~li~~~~-~~~~vF~Ne~~~~T~v~r~~~es~~drndr~I~~aa~w 160 (254)
++++++ ...+++++++|+++++.++.+.|.|++.++.+.. ++|++|.||++..||.++.++|+.+++++++++.++.|
T Consensus 72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~ 151 (941)
T KOG2102|consen 72 DSLSNPGQRRDVIVPQSVLDEVRSRSSPVYPRIRPLISADSTKRFILFHNEFSRSTFAERAKDESANDRNDRAIRPAANW 151 (941)
T ss_pred ccccCCCccccccccccccccccccccccccccccccccccccceeecccCCCchhhcccccCCCcchhccccccccccc
Confidence 999988 8899999999999999999999999999998877 99999999999999999999999999999999999999
Q ss_pred HHHHhC-cCceEEEEeCC---hhhHHHHHhcCcceeeHHHHHHhCCCchhhhhhhcccchhhccCCCCCCCCCCCCHHHH
Q psy4844 161 YEEHLE-SAVRVILLSED---VRNRDLATQSGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDSLYPLHATPSEI 236 (254)
Q Consensus 161 Y~~Hl~-~~~~VvlvT~D---~~~~~ka~~~gi~~~s~~eYv~~~~~~~~L~D~l~~~~~~~~~~~~~~~y~ehL~~~~i 236 (254)
|..|++ ..++|+++|+| ...+.++...|+...++++|++.++..+.+.|.+.+.....+..+++.+|++|||++.+
T Consensus 152 ~~~h~~~~~~~~~~~~~d~~~~~~~~~~~~~~i~~~~~~~y~~~~~~~~~l~~~l~~~~~~~~~~~~k~~~~~~l~~~~~ 231 (941)
T KOG2102|consen 152 YDVHLPSLGPRVILVTTDVPSSVSRDNAVEHGIEPQTIKEYQKPLSPNHLLRDSLLQRVLESNFGSDKLLFSPYLPMAKI 231 (941)
T ss_pred chhcccccCcceEEEeccchhhhhhhcccccccchhhhhhhccccCcchhhhhhhhhhcccccccccceeeccccchhhH
Confidence 999998 46779999999 66677888899999999999999987678999997544322221347899999999999
Q ss_pred HhhhhcCceEEEEEEEE
Q psy4844 237 HAGIKNQSLLQGMNLYL 253 (254)
Q Consensus 237 ~~Gik~G~l~qG~l~v~ 253 (254)
.+|||+|+++||+|+++
T Consensus 232 ~~~~~~g~~~~g~l~i~ 248 (941)
T KOG2102|consen 232 KAGIKSGRLVQGTLRIS 248 (941)
T ss_pred hhhhcccceeeceEEec
Confidence 99999999999999985
No 2
>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J.
Probab=99.65 E-value=4.1e-17 Score=131.26 Aligned_cols=119 Identities=26% Similarity=0.351 Sum_probs=75.9
Q ss_pred EEechHHHhhchhhccCCCCCceeeeHHHHHHHhcCC-------------hhHHHH-HHHHhcCCCCcEEEEeCCccccc
Q psy4844 71 LLLDTNIILEQIDILEEPTLCNVILVQTILQEVKHRS-------------SSVYKR-LKDLISNPSRKFYVFVNEHHYET 136 (254)
Q Consensus 71 lVpDtnvll~~~d~le~~~~~~VII~qTVleev~~rs-------------~~~y~R-Lr~li~~~~~~~~vF~Ne~~~~T 136 (254)
+|||||++|+++++++......|+||++|++|+++.. ++...| |...++.....+.+ .....+.
T Consensus 1 ~V~DTnvll~~~~~l~~~~~~~ivIP~~Vl~ELd~lk~~~~~~~~~~~~~ar~~~~~l~~~~~~~~~~i~~--q~~~~~~ 78 (133)
T PF13638_consen 1 YVLDTNVLLHHPDLLEKLEQNKIVIPLTVLEELDRLKKSSRDRDRELRKRAREAIRWLEKLLKRGSRSIRV--QTSDEEI 78 (133)
T ss_dssp EEE-HHHHHHHHHHHHHHSSSEEEEEHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHCT-TTEEE--CTTTS-E
T ss_pred CEeehhHHhCChHHHhccccCEEEechHHHHHHHHHhccccchhHHHHHHHHHHHHHHHHHHhcCCCeEec--chhhhhc
Confidence 6899999999999998777788999999999997421 111222 33334443333332 1111100
Q ss_pred cccCCCCCCcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCcceeeHH
Q psy4844 137 YVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLTSSIE 195 (254)
Q Consensus 137 ~v~r~~~es~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~~s~~ 195 (254)
.. ........+|..|+.+|.||+++.+ ..+|||||+|.+++.+|.+.||+++|++
T Consensus 79 --~~-~~~~~~~~~D~~Il~~a~~~~~~~~-~~~vvLvT~D~~l~~~A~~~gi~~~~~~ 133 (133)
T PF13638_consen 79 --DE-DLNLDAQRNDDRILNCALYLQEENP-GRKVVLVTNDKNLRLKARAEGIPAVSYE 133 (133)
T ss_dssp --ES---S----HHHHHHHHHHHHHHHHCG-CEEEEEEE--HHHHHHHHHTT--EE---
T ss_pred --ch-hhhccccccHHHHHHHHHHHHHhcC-CCeEEEEeCCHHHHHHHhhcccccccCC
Confidence 00 0011246899999999999999986 7999999999999999999999998864
No 3
>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]
Probab=99.62 E-value=1.3e-15 Score=141.25 Aligned_cols=125 Identities=23% Similarity=0.289 Sum_probs=103.3
Q ss_pred CeEEEechHHHhhchhhccCCCCCceeeeHHHHHHHhc---------CChhHHHHHHHHhc-C------------CCCcE
Q psy4844 68 PHYLLLDTNIILEQIDILEEPTLCNVILVQTILQEVKH---------RSSSVYKRLKDLIS-N------------PSRKF 125 (254)
Q Consensus 68 ~~~lVpDtnvll~~~d~le~~~~~~VII~qTVleev~~---------rs~~~y~RLr~li~-~------------~~~~~ 125 (254)
++.+|+||||++|+|.+|.+|+.++||||.+|+||++. +++|...|+.+.++ + +++..
T Consensus 2 ~ktyVLDTnVLi~DP~Alf~F~eh~VvIP~~VlEELd~~Kr~~~evgrnAR~a~r~ld~L~~~~~~l~~giPl~~~G~~l 81 (436)
T COG1875 2 KKTYVLDTNVLIHDPTALFRFEEHDVVIPMVVIEELDATKRGHSEIGRNARQASRLLDELRNEHGRLKAGIPLGNKGGTL 81 (436)
T ss_pred ceEEEEecceeeeCcHHHhcccccceEeeehHHHHHHhhcccchhhHHHHHHHHHHHHHHHhhcCCccCCcccCCCCCeE
Confidence 36789999999999999999999999999999999994 78899999655554 2 25667
Q ss_pred EEEeCCccccccccCCCCCCcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCcceeeHHHHHHh
Q psy4844 126 YVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLTSSIEGYIST 200 (254)
Q Consensus 126 ~vF~Ne~~~~T~v~r~~~es~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~~s~~eYv~~ 200 (254)
.++.|.... ...+.-..+..||+.|++++..+++.-+ +.+|||||+|.++|.||++.||. .+||...
T Consensus 82 ~iel~~~~~----~~~~~~~~~~~~DnrIL~~~~~L~~~~~-~~~VvLVSKDi~~RvkA~a~Gl~---AeDY~~d 148 (436)
T COG1875 82 HVELNHQNS----TKLPNGFREGVNDNRILAVVLNLQEEEP-GRRVVLVSKDINLRVKASALGLA---AEDYEND 148 (436)
T ss_pred EEEEeccCc----cccccccccccchHHHHHHHHHHHhcCC-CCcEEEEECCccceeehhhcCcc---HHHhhhh
Confidence 777775422 2345556778899999999999998765 68999999999999999999999 6777664
No 4
>smart00670 PINc Large family of predicted nucleotide-binding domains. From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.
Probab=99.31 E-value=1.7e-12 Score=100.41 Aligned_cols=104 Identities=24% Similarity=0.251 Sum_probs=86.5
Q ss_pred EEechHHHhhchh--hccCCCC--CceeeeHHHHHHHhcCC-hhHHHHHHHHhcCCCCcEEEEeCCc-cccccccCCCCC
Q psy4844 71 LLLDTNIILEQID--ILEEPTL--CNVILVQTILQEVKHRS-SSVYKRLKDLISNPSRKFYVFVNEH-HYETYVEQEPGE 144 (254)
Q Consensus 71 lVpDtnvll~~~d--~le~~~~--~~VII~qTVleev~~rs-~~~y~RLr~li~~~~~~~~vF~Ne~-~~~T~v~r~~~e 144 (254)
+|+|||+++++++ +++.... .+++||++|++|++... .+.+.+++.+.......+.+|.|++ +..++++....+
T Consensus 1 ~vlDTnvli~~~~~~~~~~~~~~~~~~~i~~~v~~El~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (111)
T smart00670 1 VVLDTNVLIDGLIGKALEKLLEKKGEVYIPPTVLEELEYLAKLRSLKKLEELALEGKIKLKVLKEERKLEEEILERLSLK 80 (111)
T ss_pred CEeeHHHHHHHHHHHHHHHHHcCCCcEEECHHHHHHHHHHHHHHHHhhHHHHHHhcccccceeecCCCeEEEecccCChh
Confidence 4799999999998 7765433 67999999999999876 6789999999987778899999986 666777776666
Q ss_pred CcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhH
Q psy4844 145 SVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNR 181 (254)
Q Consensus 145 s~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~ 181 (254)
...+++|..|+++|.||. .++|+|+|.+++
T Consensus 81 ~~~~~~D~~il~~a~~~~-------~~~lvT~D~~l~ 110 (111)
T smart00670 81 LELLPNDALILATAKELG-------NVVLVTNDRDLR 110 (111)
T ss_pred hcCCCChHHHHHHHHHCC-------CCEEEeCCcccC
Confidence 667889999999999986 478999998754
No 5
>PRK13764 ATPase; Provisional
Probab=98.37 E-value=8.7e-07 Score=88.35 Aligned_cols=115 Identities=15% Similarity=0.224 Sum_probs=80.3
Q ss_pred EEEechHHHhhch--hhccCCC--CCceeeeHHHHHHHhcC----------ChhHHHHHHHHhcCCCCcEEEEeCCcccc
Q psy4844 70 YLLLDTNIILEQI--DILEEPT--LCNVILVQTILQEVKHR----------SSSVYKRLKDLISNPSRKFYVFVNEHHYE 135 (254)
Q Consensus 70 ~lVpDtnvll~~~--d~le~~~--~~~VII~qTVleev~~r----------s~~~y~RLr~li~~~~~~~~vF~Ne~~~~ 135 (254)
.+||||+|+++.. ++++... ...||||.+|++|+++. .....++|+++-. .+.+-+-.++.. .
T Consensus 2 ~yVlDTSVIIDGri~~~i~~g~~~~~~IiIP~~Vl~ELe~~A~~~r~~G~~gLeeL~~L~~l~~--~g~i~ie~~~~~-p 78 (602)
T PRK13764 2 KIVPDTSVVIDGRVSELIEKGEYIGGTIIIPEAVVAELEAQANQGREIGFSGLEELKKLRELAE--EGLIELEFVGER-P 78 (602)
T ss_pred eEEccceEEEechHHHHHHcCCccCCEEEeehHHHHHHHHHhhccchhhHHHHHHHHHHHHhhc--cCceEEEEeccc-c
Confidence 5789999999998 8887654 56799999999999951 1234555666532 344544444322 1
Q ss_pred ccccCCCCCCcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCcceeeHHHH
Q psy4844 136 TYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLTSSIEGY 197 (254)
Q Consensus 136 T~v~r~~~es~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~~s~~eY 197 (254)
++ ...........|..|+..|.- ..++|||+|.+.+.+|++.||+++.+...
T Consensus 79 ~~--~~~~~~~~gevD~~I~~~A~~--------~~~~lvT~D~~l~~~A~~~GI~V~~l~~~ 130 (602)
T PRK13764 79 TL--EQIKLAKGGEIDALIREVAKE--------LGATLVTSDRVQAEVARAKGIDVIYLKPE 130 (602)
T ss_pred ch--hhcccccCCCHHHHHHHHHHH--------cCCEEEeCCHHHHHHHHHcCCEEEEeCCC
Confidence 11 111222335677899998872 25899999999999999999999877654
No 6
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=97.61 E-value=0.00016 Score=59.23 Aligned_cols=104 Identities=18% Similarity=0.236 Sum_probs=65.8
Q ss_pred CCCeEEEechHHHhhc----hhhcc---CC-CC-CceeeeHHHHHHHhcCCh--hHHHH--HHHHhcCCCCcEEEEeCCc
Q psy4844 66 MEPHYLLLDTNIILEQ----IDILE---EP-TL-CNVILVQTILQEVKHRSS--SVYKR--LKDLISNPSRKFYVFVNEH 132 (254)
Q Consensus 66 ~~~~~lVpDtnvll~~----~d~le---~~-~~-~~VII~qTVleev~~rs~--~~y~R--Lr~li~~~~~~~~vF~Ne~ 132 (254)
..+.-+|+|||+++.- +|+++ .. .. ..+.||++|++|+..-.. +.-.| +....-. +-.+. |
T Consensus 8 ~~~~~VlvDTNfl~~~~q~~vdi~~~l~r~l~~~~~~~Ip~~Vi~EL~~l~~~~~~~~r~~ia~~~~e-r~~~~-----~ 81 (136)
T COG1412 8 RKPYQVLVDTNFLLYPYQFKVDIFEELERLLGAKYKPAIPSCVIRELEKLKRKHRGKARIAIALKYAE-RLECI-----H 81 (136)
T ss_pred CCceEEEecchHHHHHHHccCCHHHHHHHHhcccccccchHHHHHHHHHHHHhcCchHHHHHHHHHhh-ccCcc-----c
Confidence 3466789999999754 33333 22 23 479999999999985221 11111 2222110 11111 1
Q ss_pred cccccccCCCCCCcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCcceeeHH
Q psy4844 133 HYETYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLTSSIE 195 (254)
Q Consensus 133 ~~~T~v~r~~~es~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~~s~~ 195 (254)
+ ....|-+|+.+|.-+. .+++.|||.++++++++.||++++++
T Consensus 82 ------------~-~~~aDe~i~~~a~~~~-------~~iVaTnD~eLk~rlr~~GIPvi~lr 124 (136)
T COG1412 82 ------------K-GRYADECLLEAALKHG-------RYIVATNDKELKRRLRENGIPVITLR 124 (136)
T ss_pred ------------c-CCChHHHHHHHHHHcC-------CEEEEeCCHHHHHHHHHcCCCEEEEe
Confidence 1 1122778988886443 58999999999999999999999876
No 7
>PRK12496 hypothetical protein; Provisional
Probab=96.35 E-value=0.01 Score=50.11 Aligned_cols=110 Identities=17% Similarity=0.173 Sum_probs=64.7
Q ss_pred EEEechHHHhhchhhccCCCCCceeeeHHHHHHHhcCChhHHHHHHHHhcCCCCcEEEEeCCccccccccC---CCCCC-
Q psy4844 70 YLLLDTNIILEQIDILEEPTLCNVILVQTILQEVKHRSSSVYKRLKDLISNPSRKFYVFVNEHHYETYVEQ---EPGES- 145 (254)
Q Consensus 70 ~lVpDtnvll~~~d~le~~~~~~VII~qTVleev~~rs~~~y~RLr~li~~~~~~~~vF~Ne~~~~T~v~r---~~~es- 145 (254)
++|+||+.|++-..+ ....+++|..|++||+.... -.++..++.. +.+.|-.-+.-.-..+.+ ..|..
T Consensus 3 ~~VlDtS~~I~~~~~----~~~~i~tp~~V~~Ev~d~~~--~~~~~~l~~~--~~i~v~~p~~~~i~~v~~~a~~tgd~~ 74 (164)
T PRK12496 3 IKVLDASAFIHGYNP----EDGEHYTTPSVVEEVKDKES--RLILESAISA--GKLKILEPSPESIEKVEEAAIKTGDLM 74 (164)
T ss_pred EEEEEChHHHccchh----hCCCEEecHHHHHHHhCHHH--HHHHHHhccc--CCeEEECCCHHHHHHHHHHHHhcCCcc
Confidence 689999999977553 24679999999999997432 2233333321 223322111100000111 11110
Q ss_pred cCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCcceeeHH
Q psy4844 146 VNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLTSSIE 195 (254)
Q Consensus 146 ~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~~s~~ 195 (254)
.....|-.+++.|.-+ ..+|||+|...+.-|+..||.+.++.
T Consensus 75 ~Ls~~D~~~iaLA~el--------~~~lvtDD~~~~~vA~~lgi~v~~~~ 116 (164)
T PRK12496 75 RLSNTDIEVLALALEL--------NGTLYTDDYGIQNVAKKLNIKFENIK 116 (164)
T ss_pred ccchhhHHHHHHHHHh--------CCcEECcHHHHHHHHHHcCCeEeccc
Confidence 1233455555554433 25799999999999999999988876
No 8
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=95.66 E-value=0.055 Score=50.05 Aligned_cols=111 Identities=20% Similarity=0.312 Sum_probs=70.2
Q ss_pred eEEEechHHHhhc--hhhccCC-CCCceeeeHHHHHHHhc--------------CChhHHHHHHHHhcCCCCcEEEEeCC
Q psy4844 69 HYLLLDTNIILEQ--IDILEEP-TLCNVILVQTILQEVKH--------------RSSSVYKRLKDLISNPSRKFYVFVNE 131 (254)
Q Consensus 69 ~~lVpDtnvll~~--~d~le~~-~~~~VII~qTVleev~~--------------rs~~~y~RLr~li~~~~~~~~vF~Ne 131 (254)
..-|+||+++++- .|+++-- -.-++||||=||+|+|| |...+-+++++... -+..++.-+
T Consensus 161 ~~KILDTSvIIDGRI~di~~TGFleG~iiiP~FVL~ELQ~iADssD~lKR~RGRRGLdILn~iqk~~~---~~v~I~~~D 237 (356)
T COG4956 161 KPKILDTSVIIDGRIADILQTGFLEGTIIIPQFVLLELQHIADSSDDLKRNRGRRGLDILNEIQKEDP---IQVEIYEGD 237 (356)
T ss_pred CCeEeeeceEEcchHHHHHHhCCccceEeeeHHHHHHHHHHhhccchhhhhcccchhHHHHHHHhhCC---CcEEEccCC
Confidence 3668899999864 5666543 34569999999999996 23334555544331 122211111
Q ss_pred ccccccccCCCCCCcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCcceeeHHHHHHhCC
Q psy4844 132 HHYETYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLTSSIEGYISTLS 202 (254)
Q Consensus 132 ~~~~T~v~r~~~es~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~~s~~eYv~~~~ 202 (254)
| |...+ -|-.+++-|+-+ .=.+||||.|+-+-|.=.|++++++.|..+.++
T Consensus 238 f-----------~di~e-VD~KLvklAk~~--------~g~lvTND~NLnKVae~qgV~vLNINDLAnAVk 288 (356)
T COG4956 238 F-----------EDIPE-VDSKLVKLAKVT--------GGKLVTNDFNLNKVAELQGVQVLNINDLANAVK 288 (356)
T ss_pred c-----------cchhh-HHHHHHHHHHHh--------CCEEEeccCcHHHHHhhcCCceecHHHHHHHhC
Confidence 1 11111 133444444333 246899999999999999999999999999863
No 9
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=95.64 E-value=0.046 Score=53.25 Aligned_cols=111 Identities=23% Similarity=0.346 Sum_probs=77.2
Q ss_pred eEEEechHHHhhc--hhhccCCCCC--ceeeeHHHHHHHhcC----------ChhHHHHHHHHhcCCCCcEEEEeCCccc
Q psy4844 69 HYLLLDTNIILEQ--IDILEEPTLC--NVILVQTILQEVKHR----------SSSVYKRLKDLISNPSRKFYVFVNEHHY 134 (254)
Q Consensus 69 ~~lVpDtnvll~~--~d~le~~~~~--~VII~qTVleev~~r----------s~~~y~RLr~li~~~~~~~~vF~Ne~~~ 134 (254)
..+||||+|++.- -..+++-.+. +||||..|+.|+-++ .+...++|+++- +.+.--..|.++--.
T Consensus 5 ~~~v~DtSvivdGr~t~~v~~G~~~g~~viipeAvvsele~qAn~Gr~~G~~gLeEL~kL~~l~-~~g~i~~~~~gerp~ 83 (604)
T COG1855 5 MKYVPDTSVIVDGRITEYVESGEIEGATVIIPEAVVSELEAQANRGREIGFAGLEELKKLRDLA-DEGKIELEFVGERPT 83 (604)
T ss_pred cEEeccceEEEccchhhhhhhCcccccEEEeeHHHHHHHHHHhccchhhhhhHHHHHHHHHHHH-hcCcEEEEEEeccCc
Confidence 4789999999875 5566755444 599999999999853 134456677766 444456778887554
Q ss_pred cccccCCCCCCcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCccee
Q psy4844 135 ETYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLTS 192 (254)
Q Consensus 135 ~T~v~r~~~es~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~~ 192 (254)
.-.+.+.. ...-|..|+.+|.-|. -+|||.|.-.+.-|++.||.+.
T Consensus 84 ~~~Ik~ak----~GEid~miR~vA~e~~--------a~lVTsD~vQ~~va~a~Giev~ 129 (604)
T COG1855 84 LEEIKRAK----SGEIDAMIREVALEYG--------ATLVTSDRVQRDVARAKGIEVE 129 (604)
T ss_pred hhhhcccc----cccHHHHHHHHHHHhC--------cEEEechHHHHHHHHhcCceEE
Confidence 33333322 2233667888876553 5899999999999999999874
No 10
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=90.69 E-value=0.51 Score=36.22 Aligned_cols=85 Identities=14% Similarity=0.161 Sum_probs=51.5
Q ss_pred CCceeeeHHHHHHHhcCChhHHHHHHHHhcCCCCcEEEEeCCccccccccCCCCCCcCCcccHHHHHHHHHHHHHhCcCc
Q psy4844 90 LCNVILVQTILQEVKHRSSSVYKRLKDLISNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLESAV 169 (254)
Q Consensus 90 ~~~VII~qTVleev~~rs~~~y~RLr~li~~~~~~~~vF~Ne~~~~T~v~r~~~es~~drndr~I~~aa~wY~~Hl~~~~ 169 (254)
-..++||+-|++|++.-+.. +.+-..+.+. ..+-..-.+|.. + ....|.+|...|. + ..
T Consensus 7 ~~~~~vt~cVl~EL~~L~~~-~~~~~~~a~~--~~~~~~~c~h~~-~----------~~~addci~~~~~---~----~~ 65 (101)
T PF04900_consen 7 KVKPYVTQCVLEELESLGKK-FKGALRIAKR--KALERRKCNHKE-T----------PGSADDCILDLAG---K----NN 65 (101)
T ss_pred ccEEEecHHHHHHHHHhccc-ccchhhhhhc--hhhHhhcCCCCC-C----------CcCHHHHHHHHhc---c----CC
Confidence 35689999999999975522 2221122211 112222222221 1 2235678887774 2 12
Q ss_pred eEEEEeCChhhHHHHH-hcCcceeeHH
Q psy4844 170 RVILLSEDVRNRDLAT-QSGLLTSSIE 195 (254)
Q Consensus 170 ~VvlvT~D~~~~~ka~-~~gi~~~s~~ 195 (254)
..++.|+|.+++.+.+ ..|++++.+.
T Consensus 66 ~~~VaT~D~~Lr~~lr~~~GvPvi~l~ 92 (101)
T PF04900_consen 66 KYIVATQDKELRRRLRKIPGVPVIYLR 92 (101)
T ss_pred eEEEEecCHHHHHHHhcCCCCCEEEEE
Confidence 2888899999999999 7899998765
No 11
>PF14367 DUF4411: Domain of unknown function (DUF4411)
Probab=85.88 E-value=0.62 Score=38.99 Aligned_cols=36 Identities=31% Similarity=0.462 Sum_probs=25.2
Q ss_pred EechHHHhh-----ch-hh-------ccCC-CCCceeeeHHHHHHHhcCC
Q psy4844 72 LLDTNIILE-----QI-DI-------LEEP-TLCNVILVQTILQEVKHRS 107 (254)
Q Consensus 72 VpDtnvll~-----~~-d~-------le~~-~~~~VII~qTVleev~~rs 107 (254)
++|||+++. |+ |+ |+.. ....++++..|.+|+...+
T Consensus 2 llDtN~~I~a~~~yY~~d~~p~fW~~L~~~~~~g~i~~~~~V~~El~~~~ 51 (162)
T PF14367_consen 2 LLDTNVFIQAWNRYYPFDIFPSFWDWLEQLIESGRIISPDEVYDELERGD 51 (162)
T ss_pred ccchHHHHHHHHhcCCchHHHHHHHHHHHHHhCCeEeehHHHHHHHhhCC
Confidence 579999983 22 33 2221 4567999999999999764
No 12
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=83.39 E-value=2.3 Score=36.44 Aligned_cols=113 Identities=24% Similarity=0.285 Sum_probs=64.3
Q ss_pred EEEechHHHhhc-hhhccCCCCCceeeeHHHHHHHhcCChhHHHHHHHHhcCCCCcEEEE-eCCcccccc--ccCCCCCC
Q psy4844 70 YLLLDTNIILEQ-IDILEEPTLCNVILVQTILQEVKHRSSSVYKRLKDLISNPSRKFYVF-VNEHHYETY--VEQEPGES 145 (254)
Q Consensus 70 ~lVpDtnvll~~-~d~le~~~~~~VII~qTVleev~~rs~~~y~RLr~li~~~~~~~~vF-~Ne~~~~T~--v~r~~~es 145 (254)
..|+||.++++- ++++.+-. .+-...|++|++.+..+ ..+..++. .+++-+- .|....+-- ..+..++.
T Consensus 8 ~~vlDtsa~I~g~~~~~~~g~---~yttp~Vv~Eikd~~s~--~~~e~~~~--~~~~kv~~P~~e~vk~V~e~a~~tgd~ 80 (177)
T COG1439 8 LYVLDTSAFINGKIPLLLDGR---LYTTPSVVEEIKDRESR--SLLELLLE--SGKVKVAEPSTEYVKEVREAAKKTGDL 80 (177)
T ss_pred eEEecchhhccCCCCcccCCc---ccccHHHHHHHhchhhh--HHHHHHhh--hcCeeEecCCHHHHHHHHHHHHhhCcc
Confidence 678899999986 66663322 33344999999987654 22333332 1222222 122111000 00111221
Q ss_pred -cCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCcceee
Q psy4844 146 -VNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLTSS 193 (254)
Q Consensus 146 -~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~~s 193 (254)
...-.|-.+++.|.-+... ..|+++|+|....--|...||..++
T Consensus 81 ~~LS~tDi~VlalAlel~~~----~~v~l~TdDysvQNVa~~Lgi~~~~ 125 (177)
T COG1439 81 GNLSPTDIEVLALALELGEE----VQVALATDDYSVQNVALQLGLNVRS 125 (177)
T ss_pred cccChhhHHHHHHHHhhccc----cceeEEecchHHHHHHHHhCceEEe
Confidence 1122355566666555442 5599999999999999999999876
No 13
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=82.60 E-value=0.99 Score=37.21 Aligned_cols=121 Identities=17% Similarity=0.215 Sum_probs=61.6
Q ss_pred EEechHHHhhchh-----------hccCCCCCceeeeHHHHHHHhcCChhHHHHHHHHhcCCCC-cEEEEeCCccccccc
Q psy4844 71 LLLDTNIILEQID-----------ILEEPTLCNVILVQTILQEVKHRSSSVYKRLKDLISNPSR-KFYVFVNEHHYETYV 138 (254)
Q Consensus 71 lVpDtnvll~~~d-----------~le~~~~~~VII~qTVleev~~rs~~~y~RLr~li~~~~~-~~~vF~Ne~~~~T~v 138 (254)
+|.||||++..+= ++....+ ..+...+.++|+..... |-++++-+..... ..+.-..+......+
T Consensus 3 VViDTNV~isaLi~p~Gl~~~l~~ll~~~~i-~n~tS~eil~El~~v~~--~pKl~k~l~~e~~~~~v~~l~~~~~~i~I 79 (142)
T COG1569 3 VVIDTNVWISALISPGGLPGELISLLIKEKI-ENYTSEEILDELEEVLS--YPKLKKYLPLEVLGELVLVLFESVSLIAI 79 (142)
T ss_pred EEEEhhHHHHHHhCCCCCcHHHHHHHhhCce-EEEecHHHHHHHHHHHh--hHHHHhhcchHHHHHHHHHHHHhheeEee
Confidence 5789999986541 2222223 45677889999864321 1122222211100 000000111111111
Q ss_pred cCCC-CCCcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcC-cceeeHHHHHHhC
Q psy4844 139 EQEP-GESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSG-LLTSSIEGYISTL 201 (254)
Q Consensus 139 ~r~~-~es~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~g-i~~~s~~eYv~~~ 201 (254)
.+.. -+.-.|.+|+..++.| |.. ..=+|||.|.++...=-..+ +.++|..||++.+
T Consensus 80 ~p~~~f~~~RDp~Dn~~L~~A--~~~-----kA~~lvTgD~dLL~lr~~n~~~~Iltp~eF~~~~ 137 (142)
T COG1569 80 NPLEKFNICRDPKDNKLLALA--YES-----KADYLVTGDQDLLVLRDENKRVEILTPQEFLEEV 137 (142)
T ss_pred cccccccccCCchHHHHHHHH--Hhc-----cCCEEEEcchhhheecccCCcEEEcCHHHHHHHH
Confidence 1111 2345677788877665 222 22377899987655444444 8899999999864
No 14
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=79.03 E-value=9.5 Score=29.41 Aligned_cols=34 Identities=24% Similarity=0.302 Sum_probs=22.6
Q ss_pred EEechHHHhhchh-------hccC--CCCCceeeeHHHHHHHh
Q psy4844 71 LLLDTNIILEQID-------ILEE--PTLCNVILVQTILQEVK 104 (254)
Q Consensus 71 lVpDtnvll~~~d-------~le~--~~~~~VII~qTVleev~ 104 (254)
+|+||||++..+- +++. ...-.+++....++|+.
T Consensus 2 vvlDTNVli~all~~~~~~~l~~~~~~~~~~~~~s~~~l~E~~ 44 (114)
T TIGR00305 2 VVIDTNVWISALIWKGLPGKLIKLIIDNKIVNCTSVEILQEVE 44 (114)
T ss_pred EEEEhHHHHHHHhCCCCHHHHHHHHHhCCEEEEECHHHHHHHH
Confidence 6889999987553 2211 12345788888888884
No 15
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=75.51 E-value=26 Score=29.31 Aligned_cols=53 Identities=17% Similarity=0.233 Sum_probs=41.0
Q ss_pred CcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCcceeeHHHHHHhCCC
Q psy4844 148 DRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLTSSIEGYISTLSN 203 (254)
Q Consensus 148 drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~~s~~eYv~~~~~ 203 (254)
...|-.|..-+.-..+ ....|++||.|...+..|.+.|..++|.++|...+..
T Consensus 77 ~tAD~~Ie~~v~~~~~---~~~~v~VVTSD~~iq~~~~~~GA~~iss~ef~~~l~~ 129 (166)
T PF05991_consen 77 ETADDYIERLVRELKN---RPRQVTVVTSDREIQRAARGRGAKRISSEEFLRELKA 129 (166)
T ss_pred CCHHHHHHHHHHHhcc---CCCeEEEEeCCHHHHHHHhhCCCEEEcHHHHHHHHHH
Confidence 3456667665543222 2478999999999999999999999999999998743
No 16
>PF01850 PIN: PIN domain; InterPro: IPR002716 The PilT protein, N-terminal domain (PIN) is a compact domain of about 100 amino acids. The domain has two nearly invariant aspartates and forms a coiled-coil with other monomer units to polymerise a pilus fibre []. The function of the PIN domain is unknown but a role in signalling appears likely given the presence of this domain in some bacterial plasmid stability proteins and Dis3 from yeast that is implicated in mitotic control [].; PDB: 3TND_G 2H1O_B 2BSQ_B 2H1C_A 2FE1_A 3ZVK_C 1V8P_F 1V8O_C 3H87_A 1O4W_A ....
Probab=67.26 E-value=3.7 Score=30.99 Aligned_cols=104 Identities=18% Similarity=0.172 Sum_probs=51.2
Q ss_pred EEechHHHhhchhhccCC----------CCCceeeeHHHHHHHhcCChh------HHHHHHHHhcCCCCcEEEEeCCccc
Q psy4844 71 LLLDTNIILEQIDILEEP----------TLCNVILVQTILQEVKHRSSS------VYKRLKDLISNPSRKFYVFVNEHHY 134 (254)
Q Consensus 71 lVpDtnvll~~~d~le~~----------~~~~VII~qTVleev~~rs~~------~y~RLr~li~~~~~~~~vF~Ne~~~ 134 (254)
+++|||+++..+ ..++ ....++++..++-|+-..-.+ .-......+..+.-++.- .+....
T Consensus 1 i~lDTsili~~~--~~~~~~~~~~~~~~~~~~~~is~~~~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~-~~~~~~ 77 (121)
T PF01850_consen 1 ILLDTSILIALL--RDEENHEKARELLERAIEIVISSLVLAELLYVLRRRSKQQKAIALLELLILLSNFNILP-ITSEVF 77 (121)
T ss_dssp EEE-HHHHHHHH--SHSCHHHHHHHHHHTHSEEEEEHHHHHHHHHHHHHSHCHHHHHHHHHHHHHHCTSEEEE-BCHHHH
T ss_pred EEEcChhhcccc--CCChhHHHHHHHHhcCCCEEEcHHHHHHHHHHhhhccccchhhhHHHHHHHHhhhcccc-chhHHH
Confidence 478999999777 2221 127799999999998742211 111222222222222222 122221
Q ss_pred cccccCCCCCCcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHH
Q psy4844 135 ETYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLAT 185 (254)
Q Consensus 135 ~T~v~r~~~es~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~ 185 (254)
.++.. .......+..|-.|.++|..+.- .+++|.|.+...-|+
T Consensus 78 ~~~~~-~~~~~~~~~~Da~~~a~A~~~~~-------~~v~T~D~~f~~~a~ 120 (121)
T PF01850_consen 78 ERAAE-LMRKYGLDFADALIAATAKENGA-------PLVVTFDKDFRKVAK 120 (121)
T ss_dssp HHHHH-HHHHHHSSHHHHHHHHHHHHHT--------EEE-ESSHHHHHHHC
T ss_pred HHHHH-HHHhccCChhHHHHHHHHHHcCC-------EEEEECCcCHHhccC
Confidence 11111 01111155667777777755422 245599998666553
No 17
>PF13470 PIN_3: PIN domain
Probab=62.82 E-value=1.6 Score=33.62 Aligned_cols=35 Identities=26% Similarity=0.418 Sum_probs=23.8
Q ss_pred EEechHHHhhchhhcc----------CCCCCceeeeHHHHHHHhc
Q psy4844 71 LLLDTNIILEQIDILE----------EPTLCNVILVQTILQEVKH 105 (254)
Q Consensus 71 lVpDtnvll~~~d~le----------~~~~~~VII~qTVleev~~ 105 (254)
+|+||||++..+-.=+ ....-.+++...++.|+..
T Consensus 2 VvlDTNVli~~ll~~~~~~~~l~~~~~~~~~~~~~s~~~l~E~~~ 46 (119)
T PF13470_consen 2 VVLDTNVLISALLSREPAARKLLDLAEDGRIELYISPEILDELER 46 (119)
T ss_pred EEEEechhHHHHhCCCchHHHHHHHHHcCCCeEEecHHHHHHHHH
Confidence 5889999997654111 1123457889999999884
No 18
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=57.13 E-value=8.7 Score=28.61 Aligned_cols=27 Identities=22% Similarity=0.373 Sum_probs=20.5
Q ss_pred cccCceeEeeeeeeccCCcCcCCCcCcccccc
Q psy4844 8 SSVWLVMKIVREHYLRDDLSCGSELCLACDTK 39 (254)
Q Consensus 8 tr~G~v~kvvrE~YLRdDI~Cg~~~C~~C~~~ 39 (254)
.++|+|.|+. =++=+|++.+|..|...
T Consensus 41 ~~kGkverv~-----~~~~gC~sGsCk~C~e~ 67 (78)
T PRK15431 41 ESMGKAVRIQ-----EEPDGCLSGSCKSCPEG 67 (78)
T ss_pred HHCCCeEeec-----cCCCCCCCCCCCCCCCC
Confidence 4689999876 23448999999999754
No 19
>PRK04358 hypothetical protein; Provisional
Probab=36.29 E-value=69 Score=28.37 Aligned_cols=33 Identities=21% Similarity=0.221 Sum_probs=27.9
Q ss_pred ceEEEEeCChhhHHHHHhcCcceeeHHHHHHhC
Q psy4844 169 VRVILLSEDVRNRDLATQSGLLTSSIEGYISTL 201 (254)
Q Consensus 169 ~~VvlvT~D~~~~~ka~~~gi~~~s~~eYv~~~ 201 (254)
...+|||+|.....-|+..||...+...|...+
T Consensus 174 Lda~lvTdD~giqn~A~~LGI~~~~~~~F~~~L 206 (217)
T PRK04358 174 LDAAVVSADEGIRKWAERLGLRFVDARKFPRML 206 (217)
T ss_pred hCCEEEeCCHHHHHHHHHcCCeeecHHHHHHHH
Confidence 468899999999999999999999876665543
No 20
>PF07788 DUF1626: Protein of unknown function (DUF1626); InterPro: IPR012431 This is a family consisting of sequences from hypothetical proteins of unknown function expressed by certain species of archaea. One member (Q9YCN7 from SWISSPROT) is thought to be similar to tropomyosin [].
Probab=35.61 E-value=1.1e+02 Score=22.29 Aligned_cols=39 Identities=26% Similarity=0.421 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHhCcC-ceEEEEeC--ChhhHHHHHhcCcc
Q psy4844 152 RALRRVATWYEEHLESA-VRVILLSE--DVRNRDLATQSGLL 190 (254)
Q Consensus 152 r~I~~aa~wY~~Hl~~~-~~VvlvT~--D~~~~~ka~~~gi~ 190 (254)
..+..-+.||.+..+-+ .++++||- |...++.|++.||.
T Consensus 29 ~~f~rk~~lYek~~grk~~r~ivVtp~id~~a~~~A~~LGIe 70 (70)
T PF07788_consen 29 YIFKRKAELYEKVHGRKVDRLIVVTPYIDDRAKEMAEELGIE 70 (70)
T ss_pred HHHHHHHHHHHHHHCCCcceEEEEEeecCHHHHHHHHHhCCC
Confidence 34567789999988744 67888885 44556677888873
No 21
>PF04548 AIG1: AIG1 family; InterPro: IPR006703 This entry represents a domain found in Arabidopsis protein AIG1 which appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 (avrRpt2-induced gene) exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2 []. The domain is also apparently found in a number of mammalian proteins, for example the rat immune-associated nucleotide 4 protein. ; GO: 0005525 GTP binding; PDB: 3LXX_A 3BB4_A 3DEF_A 3BB3_A 2J3E_A 3V70_B 3BB1_A 1H65_B 2XTP_A 3P1J_C ....
Probab=33.22 E-value=18 Score=31.07 Aligned_cols=55 Identities=25% Similarity=0.343 Sum_probs=38.8
Q ss_pred HHhhchhhccCCCCCceeeeHHHHHHHhcCChhHHHH------HHHHhcCCCCcEEEEeCC
Q psy4844 77 IILEQIDILEEPTLCNVILVQTILQEVKHRSSSVYKR------LKDLISNPSRKFYVFVNE 131 (254)
Q Consensus 77 vll~~~d~le~~~~~~VII~qTVleev~~rs~~~y~R------Lr~li~~~~~~~~vF~Ne 131 (254)
++-.-.++|-...++++||+-|-.+++...+...|-+ |+++++.-++++.+|.|.
T Consensus 103 ~l~~l~~~FG~~~~k~~ivvfT~~d~~~~~~~~~~l~~~~~~~l~~li~~c~~R~~~f~n~ 163 (212)
T PF04548_consen 103 VLELLQEIFGEEIWKHTIVVFTHADELEDDSLEDYLKKESNEALQELIEKCGGRYHVFNNK 163 (212)
T ss_dssp HHHHHHHHHCGGGGGGEEEEEEEGGGGTTTTHHHHHHHHHHHHHHHHHHHTTTCEEECCTT
T ss_pred HHHHHHHHccHHHHhHhhHHhhhccccccccHHHHHhccCchhHhHHhhhcCCEEEEEecc
Confidence 3333344554457889999999999888776433322 777887778899999987
No 22
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=29.50 E-value=1e+02 Score=27.09 Aligned_cols=33 Identities=21% Similarity=0.240 Sum_probs=27.7
Q ss_pred ceEEEEeCChhhHHHHHhcCcceeeHHHHHHhC
Q psy4844 169 VRVILLSEDVRNRDLATQSGLLTSSIEGYISTL 201 (254)
Q Consensus 169 ~~VvlvT~D~~~~~ka~~~gi~~~s~~eYv~~~ 201 (254)
...++||+|.....-|+..||...+...|...+
T Consensus 170 Lda~lvTdD~giqn~A~~Lgi~~~~~~~f~~~L 202 (206)
T TIGR03875 170 LDAAVVSADEGIRKWAERLGLRFVDARNFPEML 202 (206)
T ss_pred cCcEEEeCcHHHHHHHHHcCCeeecHHHHHHHH
Confidence 568999999999999999999998866665543
No 23
>PF11910 NdhO: Cyanobacterial and plant NDH-1 subunit O; InterPro: IPR020905 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit O. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0005886 plasma membrane
Probab=29.02 E-value=23 Score=25.42 Aligned_cols=14 Identities=21% Similarity=0.316 Sum_probs=12.8
Q ss_pred ccCceeEeeeeeec
Q psy4844 9 SVWLVMKIVREHYL 22 (254)
Q Consensus 9 r~G~v~kvvrE~YL 22 (254)
|+|.++|++||.|.
T Consensus 2 KKG~lVrv~re~~~ 15 (67)
T PF11910_consen 2 KKGSLVRVNREKYE 15 (67)
T ss_pred CcceEEEeehHhhc
Confidence 68999999999995
No 24
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=27.30 E-value=1.9e+02 Score=22.17 Aligned_cols=40 Identities=10% Similarity=0.183 Sum_probs=28.5
Q ss_pred ccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCccee
Q psy4844 150 NDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLTS 192 (254)
Q Consensus 150 ndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~~ 192 (254)
+.+.++.+++...++ +.++|.+|.+......|...|..++
T Consensus 55 ~t~e~i~~~~~a~~~---g~~iI~IT~~~~l~~~~~~~~~~~~ 94 (119)
T cd05017 55 NTEETLSAVEQAKER---GAKIVAITSGGKLLEMAREHGVPVI 94 (119)
T ss_pred CCHHHHHHHHHHHHC---CCEEEEEeCCchHHHHHHHcCCcEE
Confidence 456788888877664 6899999987766666665665544
No 25
>KOG4689|consensus
Probab=26.19 E-value=56 Score=31.52 Aligned_cols=120 Identities=15% Similarity=0.173 Sum_probs=68.3
Q ss_pred eEEEechHHHhhchhhccCC-----CCCc-eeeeHHHHHHHhcCC-------------hhHHHHHHHHhcCCCCcEEEEe
Q psy4844 69 HYLLLDTNIILEQIDILEEP-----TLCN-VILVQTILQEVKHRS-------------SSVYKRLKDLISNPSRKFYVFV 129 (254)
Q Consensus 69 ~~lVpDtnvll~~~d~le~~-----~~~~-VII~qTVleev~~rs-------------~~~y~RLr~li~~~~~~~~vF~ 129 (254)
.-+++|++|...+.-.|+.+ ..++ ++.+++|.++++.-. .....|.-.++++. +.-++.+
T Consensus 131 t~~~l~~~~~~sh~n~l~~~Rslis~~~~~~~~~~kvv~~l~~tek~dd~vld~~~~~~qE~dr~~~lL~r~-~n~~I~a 209 (479)
T KOG4689|consen 131 TEIDLEDDVHSSHANNLSDRRSLISIDTNILMNHLKVVRILKTTEKPDDLVLDIPWVVMQEVDRMGKLLKRA-QNKAIPA 209 (479)
T ss_pred eeeehhhhhHHhhhhHHHHHHHHHHHhhhhhhcchhHHHhhhccCCCcceeeecchHHHHHHHHHHHHHhhh-ccchHHH
Confidence 34566777777766666643 2344 455777777777411 11223333344322 2233333
Q ss_pred CCcccccccc------C--CCCCCcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHH-HhcCcce
Q psy4844 130 NEHHYETYVE------Q--EPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLA-TQSGLLT 191 (254)
Q Consensus 130 Ne~~~~T~v~------r--~~~es~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka-~~~gi~~ 191 (254)
|-|+.+..-. . ...-.+..-+|..|++++...++-++ --|+++|+|.+.|-|+ .-.|++.
T Consensus 210 ~~~~~dSl~~~~Gl~~q~~~Q~~~p~~~~ddsvl~ccl~~~eI~~--cfvillt~d~Nlrnkga~i~~V~~ 278 (479)
T KOG4689|consen 210 VHFINDSLKNQDGLSIQLASQKHYPDENNDDSVLKCCLQHQEIFP--CFVILLTDDRNLRNKGALISGVKS 278 (479)
T ss_pred HHHhhhhhccccchHHHHHHhhcCCcccccchHHHHHHHHHHhhh--heeeeecccchhhhcccceecccc
Confidence 3333322000 0 00111344567789999999999886 5899999999999997 4456654
No 26
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....
Probab=25.87 E-value=2.5e+02 Score=20.86 Aligned_cols=41 Identities=24% Similarity=0.226 Sum_probs=31.3
Q ss_pred ccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHHhcCcce
Q psy4844 150 NDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQSGLLT 191 (254)
Q Consensus 150 ndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~~~gi~~ 191 (254)
+|-.-..++.+..+..+ ..+++...+|.+.....+..|+..
T Consensus 72 ~d~~n~~~~~~~r~~~~-~~~ii~~~~~~~~~~~l~~~g~d~ 112 (116)
T PF02254_consen 72 DDEENLLIALLARELNP-DIRIIARVNDPENAELLRQAGADH 112 (116)
T ss_dssp SHHHHHHHHHHHHHHTT-TSEEEEEESSHHHHHHHHHTT-SE
T ss_pred CHHHHHHHHHHHHHHCC-CCeEEEEECCHHHHHHHHHCCcCE
Confidence 45556777777777665 788999999999998888888864
No 27
>PF07454 SpoIIP: Stage II sporulation protein P (SpoIIP); InterPro: IPR010897 This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation []. SpoIIP is one of the three genes (spoIID, spoIIM and spoIIP, [, , ]), under the control of sigma E, that have been shown to be essential for the engulfment of the forespore by the mother cell. Their products are involved in degradation of the septal peptidoglycan and mutations in spoIID, spoIIM or spoIIP block sporulation at morphological stage II, prior to the stage of engulfment. These three genes are absolutely conserved (sometimes even duplicated) in all endospore formers [].
Probab=25.56 E-value=1.2e+02 Score=27.63 Aligned_cols=84 Identities=12% Similarity=0.122 Sum_probs=51.1
Q ss_pred CCCCcEEEEeCCccccccccCCCCCCcCCc-----ccHHHHHHHHHHHHHhC-cCceEEEEeCChhhHHHHHhcCcceee
Q psy4844 120 NPSRKFYVFVNEHHYETYVEQEPGESVNDR-----NDRALRRVATWYEEHLE-SAVRVILLSEDVRNRDLATQSGLLTSS 193 (254)
Q Consensus 120 ~~~~~~~vF~Ne~~~~T~v~r~~~es~~dr-----ndr~I~~aa~wY~~Hl~-~~~~VvlvT~D~~~~~ka~~~gi~~~s 193 (254)
+..+.-++..+.|..|.|.+-.......+. ...-|..++.++.+.|. .++.|+.-+...+...-+.+-...-.+
T Consensus 70 ~~~~~~V~IYhTH~~EsY~p~~~~~~~~~~~~~~~~~~nV~~VG~~L~~~Le~~Gi~v~h~~t~~d~~~y~~sY~~Sr~t 149 (268)
T PF07454_consen 70 TSGKPQVLIYHTHSTESYLPSDGLKSVPGPGGATDEEVNVVKVGDRLAQELEKYGIGVIHDKTIHDYPSYNQSYKRSRET 149 (268)
T ss_pred CCCCCEEEEEeCCCccccccccccccCCCCCccccccchHHHHHHHHHHHHHHCCCcEEEeCCCCCcchhHHHHHHHHHH
Confidence 445666777889999999866322222222 34569999999999996 357777765432221222222222345
Q ss_pred HHHHHHhCCC
Q psy4844 194 IEGYISTLSN 203 (254)
Q Consensus 194 ~~eYv~~~~~ 203 (254)
++++++..++
T Consensus 150 v~~~l~~~p~ 159 (268)
T PF07454_consen 150 VKKALKENPD 159 (268)
T ss_pred HHHHHHHCCC
Confidence 6777776554
No 28
>PRK00702 ribose-5-phosphate isomerase A; Provisional
Probab=25.44 E-value=1.1e+02 Score=27.06 Aligned_cols=40 Identities=15% Similarity=0.204 Sum_probs=30.4
Q ss_pred HHHHHHHhCcCc----eEEEEeCChhhHHHHHhcCcceeeHHHH
Q psy4844 158 ATWYEEHLESAV----RVILLSEDVRNRDLATQSGLLTSSIEGY 197 (254)
Q Consensus 158 a~wY~~Hl~~~~----~VvlvT~D~~~~~ka~~~gi~~~s~~eY 197 (254)
+.|+.++|+... ++..+|++......+...|+++.++.++
T Consensus 32 ~~~l~~~L~~~~~~~~~itvVt~S~~~a~~l~~~gi~v~~l~~~ 75 (220)
T PRK00702 32 AAYFIDALGERVKEGLIIGGVPTSEASTELAKELGIPLFDLNEV 75 (220)
T ss_pred HHHHHHHHHhhhccCCCEEEECCcHHHHHHHHhCCCeEEcHHHC
Confidence 345555554222 5899999999988888889999998887
No 29
>KOG3670|consensus
Probab=25.09 E-value=1.1e+02 Score=29.56 Aligned_cols=93 Identities=16% Similarity=0.154 Sum_probs=56.5
Q ss_pred ceeeeHHHHHHHhcCChhHHHHHHHHhcCC---C-CcEEEEe--CCccccccccCCCCCCcCCcccHHHHHHHHHHHHHh
Q psy4844 92 NVILVQTILQEVKHRSSSVYKRLKDLISNP---S-RKFYVFV--NEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHL 165 (254)
Q Consensus 92 ~VII~qTVleev~~rs~~~y~RLr~li~~~---~-~~~~vF~--Ne~~~~T~v~r~~~es~~drndr~I~~aa~wY~~Hl 165 (254)
||.+|-.--+.+=++...+.+||++..+=. + +=+.+|. |+.|..+.- +....+..+.-.+-|++|.+.++.++
T Consensus 151 NvA~~Ga~s~Dlp~QAr~Lv~rik~~~~i~~~~dWKLi~IfIG~ND~c~~c~~-~~~~~~~~~~~~~~i~~Al~~L~~nv 229 (397)
T KOG3670|consen 151 NVAEPGAESEDLPDQARDLVSRIKKDKEINMKNDWKLITIFIGTNDLCAYCEG-PETPPSPVDQHKRNIRKALEILRDNV 229 (397)
T ss_pred ccccccccchhhHHHHHHHHHHHHhccCcccccceEEEEEEeccchhhhhccC-CCCCCCchhHHHHHHHHHHHHHHhcC
Confidence 455555555555555556667776655321 1 3345664 888875542 13344666666788999999999999
Q ss_pred CcCceEEEEe-CChhhHHHHHh
Q psy4844 166 ESAVRVILLS-EDVRNRDLATQ 186 (254)
Q Consensus 166 ~~~~~VvlvT-~D~~~~~ka~~ 186 (254)
| +.-|+||. -+.....+|..
T Consensus 230 P-R~iV~lvg~~~~~~l~q~~~ 250 (397)
T KOG3670|consen 230 P-RTIVSLVGMFNVSLLRQASK 250 (397)
T ss_pred C-ceEEEEecCCCHHHHHHhhc
Confidence 8 55555553 34455555544
No 30
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=24.45 E-value=59 Score=28.55 Aligned_cols=34 Identities=15% Similarity=0.281 Sum_probs=15.2
Q ss_pred ceEEEEeCChhhHHHHHhcCcceeeHHHHHHhCC
Q psy4844 169 VRVILLSEDVRNRDLATQSGLLTSSIEGYISTLS 202 (254)
Q Consensus 169 ~~VvlvT~D~~~~~ka~~~gi~~~s~~eYv~~~~ 202 (254)
..-++||+|...+.-|+..||..+....|...++
T Consensus 167 l~a~lvt~D~gi~~~A~~lGi~~i~~~~F~~~Le 200 (205)
T PF08745_consen 167 LDAVLVTDDYGIQNWAEKLGIRFIDARDFPRMLE 200 (205)
T ss_dssp HT--EE---HHHHHHHHHTT--EE----------
T ss_pred cCCEEEeCCHhHHHHHHHCCCEEEeccccccccc
Confidence 3467999999999999999999988887776654
No 31
>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus. The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....
Probab=24.25 E-value=1.8e+02 Score=21.73 Aligned_cols=25 Identities=12% Similarity=0.283 Sum_probs=21.7
Q ss_pred CceEEEEeCChhhHHHHHhcCccee
Q psy4844 168 AVRVILLSEDVRNRDLATQSGLLTS 192 (254)
Q Consensus 168 ~~~VvlvT~D~~~~~ka~~~gi~~~ 192 (254)
..+|+++..|.+...++.+.|+.++
T Consensus 21 ~~~vvvid~d~~~~~~~~~~~~~~i 45 (116)
T PF02254_consen 21 GIDVVVIDRDPERVEELREEGVEVI 45 (116)
T ss_dssp TSEEEEEESSHHHHHHHHHTTSEEE
T ss_pred CCEEEEEECCcHHHHHHHhcccccc
Confidence 4689999999999999999997753
No 32
>KOG3046|consensus
Probab=24.24 E-value=56 Score=27.09 Aligned_cols=25 Identities=16% Similarity=0.430 Sum_probs=22.8
Q ss_pred CCCceeeeHHHHHHHh-cCChhHHHH
Q psy4844 89 TLCNVILVQTILQEVK-HRSSSVYKR 113 (254)
Q Consensus 89 ~~~~VII~qTVleev~-~rs~~~y~R 113 (254)
.++++-||+-|+++++ +||+-.|.|
T Consensus 66 k~n~i~IPleVl~yIddGrNPd~ytk 91 (147)
T KOG3046|consen 66 KLNDIQIPLEVLEYIDDGRNPDLYTK 91 (147)
T ss_pred hhccccCcHHHHHHHhcCCCccHHHH
Confidence 6788999999999998 689999998
No 33
>TIGR01170 rplA_mito ribosomal protein L1, mitochondrial. This model represents the mitochondrial homolog of bacterial ribosomal protein L1. Unlike chloroplast L1, this form was not sufficiently similar to bacterial forms to include in a single bacterial/organellar L1.
Probab=23.56 E-value=1.2e+02 Score=24.90 Aligned_cols=37 Identities=8% Similarity=0.184 Sum_probs=31.5
Q ss_pred cCceEEEEeCChhhHHHHHhcCcceeeHHHHHHhCCC
Q psy4844 167 SAVRVILLSEDVRNRDLATQSGLLTSSIEGYISTLSN 203 (254)
Q Consensus 167 ~~~~VvlvT~D~~~~~ka~~~gi~~~s~~eYv~~~~~ 203 (254)
...+|.+++++....+.|++.|..++..+|+++.+.+
T Consensus 51 k~~kV~Vf~~~~~~~~~Ak~aGa~~vg~edLi~~i~~ 87 (141)
T TIGR01170 51 KEPKIAVFTKGASEVEEAREAGADYVGGDDLIKKIED 87 (141)
T ss_pred CCCEEEEECCChHHHHHHHHcCCCEeCHHHHHHHHhc
Confidence 3578999998887778899999999999999998753
No 34
>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=23.18 E-value=3.7e+02 Score=23.38 Aligned_cols=65 Identities=9% Similarity=0.021 Sum_probs=42.7
Q ss_pred HHHHHHHHhcCCCCcEEEEeCCccccccccCCCCCCcCCcccHHHHHHHHHHHHHhCcCceEEEEeCChhhHHHHH
Q psy4844 110 VYKRLKDLISNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLAT 185 (254)
Q Consensus 110 ~y~RLr~li~~~~~~~~vF~Ne~~~~T~v~r~~~es~~drndr~I~~aa~wY~~Hl~~~~~VvlvT~D~~~~~ka~ 185 (254)
...+++.+++...++-.|+.+|....|- + ....+|..+..+|-... .+..++++|-+.+......
T Consensus 96 e~~~~~~il~~~~~~sLvLlDE~~~Gt~--------~--~dg~~la~ail~~L~~~-~~~~~i~~TH~~el~~~~~ 160 (218)
T cd03286 96 ELSETANILRHATPDSLVILDELGRGTS--------T--HDGYAIAHAVLEYLVKK-VKCLTLFSTHYHSLCDEFH 160 (218)
T ss_pred HHHHHHHHHHhCCCCeEEEEecccCCCC--------c--hHHHHHHHHHHHHHHHh-cCCcEEEEeccHHHHHHhh
Confidence 4566778888777777888899887662 1 12345666634444433 2688999999988765543
No 35
>PF13344 Hydrolase_6: Haloacid dehalogenase-like hydrolase; PDB: 2HO4_B 1YV9_A 1WVI_B 3EPR_A 2P27_A 2OYC_A 2CFT_A 2P69_A 2CFS_A 2CFR_A ....
Probab=23.07 E-value=1.6e+02 Score=22.23 Aligned_cols=33 Identities=12% Similarity=0.140 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhCcCceEEEEeCCh-----hhHHHHHhcCcc
Q psy4844 155 RRVATWYEEHLESAVRVILLSEDV-----RNRDLATQSGLL 190 (254)
Q Consensus 155 ~~aa~wY~~Hl~~~~~VvlvT~D~-----~~~~ka~~~gi~ 190 (254)
..+..++++ .+.+++||||+. ....+.+..|+.
T Consensus 20 ~e~l~~L~~---~g~~~~~lTNns~~s~~~~~~~L~~~Gi~ 57 (101)
T PF13344_consen 20 VEALDALRE---RGKPVVFLTNNSSRSREEYAKKLKKLGIP 57 (101)
T ss_dssp HHHHHHHHH---TTSEEEEEES-SSS-HHHHHHHHHHTTTT
T ss_pred HHHHHHHHH---cCCCEEEEeCCCCCCHHHHHHHHHhcCcC
Confidence 334444444 368999999985 445566777877
Done!