Query 003554
Match_columns 811
No_of_seqs 26 out of 28
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 01:38:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003554.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003554hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1043 Ca2+-binding transmemb 100.0 1.3E-57 2.7E-62 488.5 3.3 496 105-687 2-499 (499)
2 KOG2077 JNK/SAPK-associated pr 60.1 14 0.00031 43.6 5.3 57 523-585 306-363 (832)
3 PF08580 KAR9: Yeast cortical 50.9 35 0.00075 40.5 6.6 53 562-614 54-119 (683)
4 cd09236 V_AnPalA_UmRIM20_like 49.2 91 0.002 33.7 8.9 34 592-625 190-223 (353)
5 PF09177 Syntaxin-6_N: Syntaxi 40.0 2E+02 0.0042 25.8 8.2 61 562-622 2-64 (97)
6 COG1510 Predicted transcriptio 38.4 63 0.0014 33.3 5.4 103 516-618 30-163 (177)
7 PF13949 ALIX_LYPXL_bnd: ALIX 37.8 43 0.00094 34.0 4.2 98 508-625 68-172 (296)
8 PF05205 COMPASS-Shg1: COMPASS 36.5 55 0.0012 30.3 4.3 94 103-219 11-104 (106)
9 PF12761 End3: Actin cytoskele 31.2 1.1E+02 0.0023 32.0 5.7 72 555-629 100-192 (195)
10 PRK00420 hypothetical protein; 30.4 1.1E+02 0.0024 29.3 5.4 92 518-610 10-111 (112)
11 PF10241 KxDL: Uncharacterized 28.8 1.6E+02 0.0034 26.5 5.7 35 573-612 41-79 (88)
12 PF11004 Kdo_hydroxy: 3-deoxy- 28.5 43 0.00094 36.4 2.6 35 420-462 8-42 (281)
13 PF05008 V-SNARE: Vesicle tran 28.0 3.3E+02 0.0071 23.0 7.3 54 561-620 21-77 (79)
14 PF04065 Not3: Not1 N-terminal 26.9 1.7E+02 0.0036 31.1 6.4 64 560-634 7-71 (233)
15 TIGR02609 doc_partner putative 25.0 1.2E+02 0.0027 26.3 4.3 53 532-584 17-72 (74)
16 TIGR02878 spore_ypjB sporulati 24.5 1.5E+02 0.0032 31.8 5.5 64 527-606 124-187 (233)
17 cd07307 BAR The Bin/Amphiphysi 24.4 5.2E+02 0.011 23.2 9.9 87 523-623 26-113 (194)
18 PLN00180 NDF6 (NDH-dependent f 23.1 70 0.0015 32.8 2.7 55 673-727 110-169 (180)
19 PRK09413 IS2 repressor TnpA; R 22.3 3.8E+02 0.0082 24.8 7.1 26 518-543 20-45 (121)
20 cd09235 V_Alix Middle V-domain 22.0 3.9E+02 0.0085 28.9 8.2 97 508-625 115-219 (339)
21 PF05008 V-SNARE: Vesicle tran 21.9 1.2E+02 0.0026 25.7 3.6 50 559-608 26-75 (79)
22 PF10239 DUF2465: Protein of u 21.5 4.3E+02 0.0094 29.0 8.4 89 486-590 128-221 (318)
23 PHA03298 envelope glycoprotein 21.1 44 0.00096 33.5 1.0 66 303-373 38-123 (167)
24 PF13767 DUF4168: Domain of un 20.4 1.9E+02 0.0041 25.1 4.5 42 557-614 3-44 (78)
25 PRK12472 hypothetical protein; 20.2 1.2E+02 0.0026 35.5 4.1 64 556-625 237-302 (508)
No 1
>KOG1043 consensus Ca2+-binding transmembrane protein LETM1/MRS7 [Function unknown]
Probab=100.00 E-value=1.3e-57 Score=488.54 Aligned_cols=496 Identities=30% Similarity=0.304 Sum_probs=465.2
Q ss_pred HHHHHHHhhccccCCCcccchHHHHHHHHHHHHHHHHhhcccCCccccccccccchhhhHHHHhhHHHHHHHHHHHHhhh
Q 003554 105 VEEMRVKLNQSLQGNDYNDGLVQSLHDAARVFELAIKEKGSVSKLSWLSTAWLGVDRNAWIKTLSYQASAYSLLQAACEI 184 (811)
Q Consensus 105 ~~emr~kl~~slq~e~~~~~LVqsLHdaARsfelav~e~~~~s~~swl~~aWlGvD~nAW~K~LSYQaAVysLLqaaiEI 184 (811)
...||.++-+++|++..+..+- +++|.+++|..+....+..+ +|.++|+++.+||+++|+++|++..+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~----~g~r~~~~~~~~~~t~~~~~--------~d~~~~~~~~s~~~s~~~~~~~~~~~ 69 (499)
T KOG1043|consen 2 SSVYRSKLLGSLQDENNEGILR----DGARFRELATKEKITSSRLP--------VDKLAWVKTESYKASLYSLLQAVNLI 69 (499)
T ss_pred hhHHHHHHhccccccccchhhh----hhHHHHHHHHHhhccccccc--------HHHHHHHhhhccchhhhhhhhhcccc
Confidence 4689999999999999888877 99999999999999999988 99999999999999999999999999
Q ss_pred hccCCCCCCCcchhHhHHhhhhhchhHHHHHhHhhccCCccchhhhcccchhhhhHhhhccccccccccceecccCCccc
Q 003554 185 SSCGDGRDRDVYVFVQRSLLRQSAPLESLIRDKLSAKLPEGYEWFWSEQVPAVVTSFINYFERDQRFTAATAVSGKGMSL 264 (811)
Q Consensus 185 sSrG~grDRdvnvFVqrsLs~~~apLE~~Ir~~Ls~r~P~a~eWfws~Q~P~vv~sFVn~lE~D~rF~aaTsv~~~~~~~ 264 (811)
+++|+.+|.+.|++|+|++.+.-+|+...|+..||+.||+.++|+|.+++|.....|+ ++++||..+|.++..+...
T Consensus 70 ~~r~~~~~~~~~~~~~~el~~~~~~~~~~~~~~lss~~a~~~~~~~a~~k~s~~~~~~---~~lqhy~~gtkll~~e~ki 146 (499)
T KOG1043|consen 70 SARGNASDLDSSVKVLRELVQQAAPLALKIKELLSSKHAKKTEAFWAKEKPSLKTKFV---KGLQHYVDGTKLLGKEIKI 146 (499)
T ss_pred ccccchhhhhhhHHHhHHHhhhccchhhhchhhccccchhhccccccccCccHHHHHH---HhhHHHhhhhhhhhhhhhh
Confidence 9999999999999999999999999999999999999999999999999999999999 8999999999998887665
Q ss_pred CCCCCCchhHHHHHHHHHHHHhhcCCcccccccchhhhhHHHHHHHhhhccceehhhHHHHHhhhhhhHHHHhhcCCCcc
Q 003554 265 GSGSSSDTSLLMLALTCIAAITKLGPAKVSCSQFSSMISDITGRLMDTLVDLVPISQAYYSIKDIGLHREFLAHFGPRAS 344 (811)
Q Consensus 265 ~~~~~SdVsLL~LalsC~aAi~KLGsakVSCp~F~S~i~D~~grLMdml~~fVpv~q~Y~~~kdiGL~rEFL~hFGpraa 344 (811)
++. .|++++..|..+..+.|+.+-+||.||.+||+.. .-+||..++|+-+.-.+|.++|.+|||+++.
T Consensus 147 sak-----lLlkll~g~~ltrrE~~qL~rt~~d~frLvPfs~-------flivPf~El~Lp~~lKlfp~~lpstfq~~kk 214 (499)
T KOG1043|consen 147 SAK-----LLLKLLKGYELTRRERGQLKRTCSDIFRLVPFSK-------FLIVPFMELLLPIFLKLFPNDLPSTFQESKK 214 (499)
T ss_pred hHH-----HHHHHHccCeeeHHHhhhHHhhccchheecccee-------eeeeehHHHHhHHHHhhccccchhhHHHHHH
Confidence 422 7999999999999999999999999999999988 7899999999999999999999999999999
Q ss_pred cccccCCCCccceehhHHHHHHHHHHHHhHhhhhhccccchhHHHHhhhhhHHHHHHHhccchhhhhccCCCcCcchhHH
Q 003554 345 ACRVKNDRDSEEVIFWVDLVQKQLQRAIDREKIWSRLTTSESIEVLERDLAIFGFFIALGRSTQSFLSRNGFDVVDDPIK 424 (811)
Q Consensus 345 ~~~~~~d~~~eEv~FWI~LvQkqL~~AidRE~IwSrLtTsesiEvLEkDLAiFGFFiaLGRsTr~fLS~~G~~dlDe~Ie 424 (811)
.|.++++ ..+|+.||.+++|++|+++++++++|+++.|+++| +++++++.||+ +++|.+|+-++.-+++-+.|-+++
T Consensus 215 ~~~k~~k-~~~~r~~~sk~Lq~tl~~~~~~~k~~~~~e~~qs~-~fd~f~~kvr~-~~~~~S~eeii~~aklf~de~~Ld 291 (499)
T KOG1043|consen 215 EEEKLSK-KYVERSEASKFLQKTLQQMIDRIKTWSNLETSQSI-EFDRFLGKVRF-IGLGVSTEEIIAFAKLFSDEITLD 291 (499)
T ss_pred HHHHhhh-hHHHHHHHHHHHHHHHHHHHhhhccchhhHHHHHH-HHHHHHHHhcc-cCCCccHHHHHHHHHHhccchhhh
Confidence 9999998 88999999999999999999999999999999999 99999999999 999999999999999999999999
Q ss_pred HHHHhhhcceEEEecccCccc--ceeeeeeeeeccccccccCCCCCCCCCCccCCCCCCCCCCCcccchhhhhhhhhhhh
Q 003554 425 SLIRYLIGGSVLYYPQLSSIS--SYQLYVEVVCEELDWLLFYPGSTGMPKQSHGHKSKREDPPNAEAIPQVLDVCSHWMQ 502 (811)
Q Consensus 425 dflRYLegGsvl~YPQLSSIS--sYQLfvEVVcEEl~WLpFYp~~~~~~~q~~~hk~~~~~~~~~E~i~~Vl~VCs~W~~ 502 (811)
++.|...+|...|||+.+-++ +|+.| +-
T Consensus 292 nLsR~qL~al~k~m~l~~~Gt~~~lr~~--------------------------------------------------lr 321 (499)
T KOG1043|consen 292 NLSRPQLVALCKYMDLNSFGTDKLLRYQ--------------------------------------------------LR 321 (499)
T ss_pred ccCHHHHHHHHHhhcccccCchHHHHHH--------------------------------------------------HH
Confidence 999999999999999987765 55443 34
Q ss_pred hhhhhcccccCCCchhHHHHHhhcchhHHHHHHHhcccccccccccccccccccccccchHHHHHHHHHHHHHHHHHHHH
Q 003554 503 SFIKHSKWLENPSNVKAAKFLSKGYDKLMDCMKEMGIARNGMIESAESVTYSRTEIDSDSFDKALESVEEALIRLEKLLQ 582 (811)
Q Consensus 503 sFikyS~WlenPsnvkaa~FLskgq~~L~eC~Eel~i~~~~~~~~~~~~~~~~~~~e~~sfdk~lesVe~Al~rlE~Llq 582 (811)
.||+|.+|-.+|.+++++.+++.++.+...|.++.+++-.-.++...++ .+.-...+||+++.+|..+|+|.+.+++
T Consensus 322 ~kik~ik~dD~~I~~eg~v~~ls~~el~~aC~~rgmra~gv~~e~l~~q---l~~wldlsl~~~vps~lL~Lsr~~~~~~ 398 (499)
T KOG1043|consen 322 KKIKEIKKDDKHIATEGAVESLSLLELQIACRERGMRALGVSEERLREQ---LRVWLDLSLDKKVPSVLLLLSRTFSLGQ 398 (499)
T ss_pred HHHHHhcccccchhhhhhhhHhhHHHHHHHHHhhhcchhccchhhhhHH---HHHHHhhhccccCchHHHHHhhhhhhhh
Confidence 6899999999999999999999999999999999988875555432222 4455678999999999999999999999
Q ss_pred HhhcccCcchHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCCCCCCcccccccccccCCCccccccccCCC
Q 003554 583 ALHVSSSNSGKEQLKAACSDLEKIRKLKKEAEFLEASVRAKAASLQQGGDDSDSGSSIGEKQWYLKGSKSRIADVVQDRP 662 (811)
Q Consensus 583 el~~ssS~SGke~lkaacsDLekIRkLKkeaEfleASfraKa~slq~g~d~~~~~~~~~~~~~y~k~k~~k~a~~~~d~~ 662 (811)
+.+.++|.+|+++. ++|+|+++++++|++++++++++|+++..+++++|+.+++++..++.+|..+|+.++++...+++
T Consensus 399 ~~~~~~s~~~~l~~-~~~~~~~~~~~~~~~~~~~~~~~~~~kl~~l~~~e~~~~~e~eee~~~~~~~k~~~~~~~~~~~~ 477 (499)
T KOG1043|consen 399 NSKAPSSSSGKLQI-AAPDDLEKLEKLKKEESELGAVDRKKKLELLREGEEIISEEEEEEEKQYGRAKDALKEKESAEKA 477 (499)
T ss_pred cccCCchhhhHhhh-hccccHHHhcccccccccccccchHHHHHhhhccccccchhhhccccccccccccccCCCccccc
Confidence 99999999999999 99999999999999999999999999999999999999999999999999999999999988888
Q ss_pred ccccccccCcccccccCCCCCCCCC
Q 003554 663 NEVVCKSRGLFGFFTRPSIRKPKPQ 687 (811)
Q Consensus 663 ~~~~~~~~~~w~~f~r~~~~k~~p~ 687 (811)
. ....++|++|++...++..|+
T Consensus 478 ~---~~~~s~~~~~~~~~~~~~~~~ 499 (499)
T KOG1043|consen 478 A---SQAKSPWGFFVRQERKKALPE 499 (499)
T ss_pred c---cccccccccccchhhhcccCC
Confidence 7 688999999999999988763
No 2
>KOG2077 consensus JNK/SAPK-associated protein-1 [Signal transduction mechanisms]
Probab=60.09 E-value=14 Score=43.61 Aligned_cols=57 Identities=25% Similarity=0.426 Sum_probs=38.7
Q ss_pred HhhcchhHHHHHHHhcccccccc-cccccccccccccccchHHHHHHHHHHHHHHHHHHHHHhh
Q 003554 523 LSKGYDKLMDCMKEMGIARNGMI-ESAESVTYSRTEIDSDSFDKALESVEEALIRLEKLLQALH 585 (811)
Q Consensus 523 Lskgq~~L~eC~Eel~i~~~~~~-~~~~~~~~~~~~~e~~sfdk~lesVe~Al~rlE~Llqel~ 585 (811)
|++-.+.|.+-..-|+|.||+.. ++.+-. .|-+-+.-.|+++..|-.|||.-..||+
T Consensus 306 LilENsqLLetKNALNiVKNDLIakVDeL~------~E~~vLrgElea~kqak~Klee~i~elE 363 (832)
T KOG2077|consen 306 LILENSQLLETKNALNIVKNDLIAKVDELT------CEKDVLRGELEAVKQAKLKLEEKIRELE 363 (832)
T ss_pred HHHhhHHHHhhhhHHHHHHHHHHHHHHhhc------cHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 45556777888889999998744 332222 1233456678888888889888777764
No 3
>PF08580 KAR9: Yeast cortical protein KAR9; InterPro: IPR013889 The KAR9 protein in Saccharomyces cerevisiae (Baker's yeast) is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules []. KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase [].
Probab=50.91 E-value=35 Score=40.55 Aligned_cols=53 Identities=21% Similarity=0.344 Sum_probs=39.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHh-----hcc---cCcchHHHHHHHhhhHHH-----HHHHHHHHH
Q 003554 562 SFDKALESVEEALIRLEKLLQAL-----HVS---SSNSGKEQLKAACSDLEK-----IRKLKKEAE 614 (811)
Q Consensus 562 sfdk~lesVe~Al~rlE~Llqel-----~~s---sS~SGke~lkaacsDLek-----IRkLKkeaE 614 (811)
-+.+-|+.||.|+.|||.|+... .+. .-+.+.++|..+|+|+|- |+.+|+-+|
T Consensus 54 ~L~~~l~~ID~ai~~~l~lIe~~v~~ie~~q~r~di~~~~~dl~e~vsqm~~~vK~~L~~vK~qve 119 (683)
T PF08580_consen 54 GLREGLEEIDSAISRFLDLIEVYVSAIEDLQLREDIANSLFDLIEEVSQMELDVKKTLISVKKQVE 119 (683)
T ss_pred HHHHhHHHHHHHHHHHHHHHHhhccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34677899999999999998763 111 011278999999999998 777787665
No 4
>cd09236 V_AnPalA_UmRIM20_like Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins. This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas PalA/RIM20 and Ustilago maydis RIM20, like Saccharomyces cerevisiae Rim20, participate in the response to the external pH via the Pal/Rim101 pathway; however, Saccharomyces cerevisiae Rim20 does not belong to this family. This pathway is a signaling cascade resulting in the activation of the transcription factor PacC/Rim101. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. Aspergillus nidulas Pa
Probab=49.21 E-value=91 Score=33.73 Aligned_cols=34 Identities=21% Similarity=0.236 Sum_probs=31.0
Q ss_pred hHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhhh
Q 003554 592 GKEQLKAACSDLEKIRKLKKEAEFLEASVRAKAA 625 (811)
Q Consensus 592 Gke~lkaacsDLekIRkLKkeaEfleASfraKa~ 625 (811)
.+.++...+.=|+++..||+|-+-++..+|.|+.
T Consensus 190 ~~~~i~~Lr~~l~~l~~l~~eR~~~~~~Lk~k~~ 223 (353)
T cd09236 190 LERHVRALRVSLEELDRLESRRRRKVERARTKAR 223 (353)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5778999999999999999999999999999876
No 5
>PF09177 Syntaxin-6_N: Syntaxin 6, N-terminal; InterPro: IPR015260 Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport []. ; GO: 0048193 Golgi vesicle transport, 0016020 membrane; PDB: 1LVF_B 2C5I_T 2C5J_A 2C5K_T 4DND_A.
Probab=39.98 E-value=2e+02 Score=25.79 Aligned_cols=61 Identities=30% Similarity=0.346 Sum_probs=46.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhc-ccCcchHHHHHHHhhhHH-HHHHHHHHHHHHHHHHHh
Q 003554 562 SFDKALESVEEALIRLEKLLQALHV-SSSNSGKEQLKAACSDLE-KIRKLKKEAEFLEASVRA 622 (811)
Q Consensus 562 sfdk~lesVe~Al~rlE~Llqel~~-ssS~SGke~lkaacsDLe-kIRkLKkeaEfleASfra 622 (811)
-|..+=+-|..++.++|.|++...- .+..+..+.++.+..||. .|+.|+.+.+-|+.+.+.
T Consensus 2 PF~~v~~ev~~sl~~l~~~~~~~~~~~~~~~~~~e~~~~~~eL~~~l~~ie~~L~DL~~aV~i 64 (97)
T PF09177_consen 2 PFFVVKDEVQSSLDRLESLYRRWQRLRSDTSSSEELKWLKRELRNALQSIEWDLEDLEEAVRI 64 (97)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTTHCC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHhcccCCCcHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3667778899999999999887543 333346677778888875 478888999999988876
No 6
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=38.44 E-value=63 Score=33.28 Aligned_cols=103 Identities=18% Similarity=0.166 Sum_probs=59.6
Q ss_pred chhHHHHHhhcchhHHHHHHHhccccccccc-------------ccccccc---cc-------------cccccchHHHH
Q 003554 516 NVKAAKFLSKGYDKLMDCMKEMGIARNGMIE-------------SAESVTY---SR-------------TEIDSDSFDKA 566 (811)
Q Consensus 516 nvkaa~FLskgq~~L~eC~Eel~i~~~~~~~-------------~~~~~~~---~~-------------~~~e~~sfdk~ 566 (811)
.+=|+=|||+.-=.|.|-+|.+|||+.++.+ ..+|+.- -. ..+-..-.|+-
T Consensus 30 ~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~G~Rk~~F~a~~df~~~f~t~f~ek~~ReId~t 109 (177)
T COG1510 30 QIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEKGDRKDYFEAEKDFSQIFRTLFEEKWKREIDPT 109 (177)
T ss_pred HHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhccCcchhhhcccchHHHHHHHHHHHHHHHHhhhH
Confidence 4567889999999999999999999977664 3334321 11 11111222455
Q ss_pred HHHHHHHHHHHHHHHHHhhcccCc-chHHHHHHHhhhHHHHHHH-HHHHHHHHH
Q 003554 567 LESVEEALIRLEKLLQALHVSSSN-SGKEQLKAACSDLEKIRKL-KKEAEFLEA 618 (811)
Q Consensus 567 lesVe~Al~rlE~Llqel~~ssS~-SGke~lkaacsDLekIRkL-KkeaEfleA 618 (811)
.+.+.+|+..++..++.-|+++-- .=+.+|+++-.-.+.+++| .+..||+++
T Consensus 110 ~e~l~k~~~e~~~~~~~~~~~~~~ke~~~~l~~~l~~~~~~~~ll~~l~e~~~~ 163 (177)
T COG1510 110 KEALKKLLEELNEDLDDRDLTERIKEIKSKLERLLKWSEDYYELLTRLLEFLES 163 (177)
T ss_pred HHHHHHHHHHccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 555555555555555554554433 2244555555555555553 455666654
No 7
>PF13949 ALIX_LYPXL_bnd: ALIX V-shaped domain binding to HIV ; PDB: 2XS1_A 2XS8_A 2R03_A 2R02_A 2OEX_B 2OEV_A 2OJQ_A 2R05_A.
Probab=37.81 E-value=43 Score=34.02 Aligned_cols=98 Identities=30% Similarity=0.313 Sum_probs=52.7
Q ss_pred cccccCCCchhHHHHHhhcchhHHHHHHHhcccccccccccccccccccccccchHHHHHHHHHHHHHH-------HHHH
Q 003554 508 SKWLENPSNVKAAKFLSKGYDKLMDCMKEMGIARNGMIESAESVTYSRTEIDSDSFDKALESVEEALIR-------LEKL 580 (811)
Q Consensus 508 S~WlenPsnvkaa~FLskgq~~L~eC~Eel~i~~~~~~~~~~~~~~~~~~~e~~sfdk~lesVe~Al~r-------lE~L 580 (811)
.+|.+.||..-++.|-. .|..+.+-+.-+. .++ ....+.++..+..+.. |+..
T Consensus 68 ~~W~r~~S~~~~~~l~~----~l~~~~~~L~~A~-------~sD---------~~~~~~~~~~~~~l~~L~~~~~~L~~~ 127 (296)
T PF13949_consen 68 ERWTRPPSSELNASLRK----ELQKYREYLEQAS-------ESD---------SQLRSKLESIEENLELLSGPIEELEAS 127 (296)
T ss_dssp TTCGSS-HHHHCHHHHH----HHHHHHHHHHHHH-------HHH---------HHHHHHHHHHHHHHHHHTSSHHHHHHH
T ss_pred CCCcCCCcHhhHHHHHH----HHHHHHHHHHHHH-------hhH---------HHHHHHHHHHHHHHHHHcCChhhHHhh
Confidence 48999999887776643 3444444443333 111 1122233333333322 3444
Q ss_pred HHHhhcccCcchHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhhh
Q 003554 581 LQALHVSSSNSGKEQLKAACSDLEKIRKLKKEAEFLEASVRAKAA 625 (811)
Q Consensus 581 lqel~~ssS~SGke~lkaacsDLekIRkLKkeaEfleASfraKa~ 625 (811)
+-......+....+.++.+..=|+++..|+++-+.+..-+|.|+.
T Consensus 128 lp~~~~~~~~~~~~~i~~L~~ll~~l~~l~~eR~~~~~~lk~~~~ 172 (296)
T PF13949_consen 128 LPSSSPSDSPQVSEVIRQLRELLNKLEELKKEREELLEQLKEKLQ 172 (296)
T ss_dssp S--B---SSGSS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH---
T ss_pred CCCCCcccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 444333344455788888888888889999999999998887543
No 8
>PF05205 COMPASS-Shg1: COMPASS (Complex proteins associated with Set1p) component shg1
Probab=36.55 E-value=55 Score=30.27 Aligned_cols=94 Identities=18% Similarity=0.281 Sum_probs=66.0
Q ss_pred chHHHHHHHhhccccCCCcccchHHHHHHHHHHHHHHHHhhcccCCccccccccccchhhhHHHHhhHHHHHHHHHHHHh
Q 003554 103 SDVEEMRVKLNQSLQGNDYNDGLVQSLHDAARVFELAIKEKGSVSKLSWLSTAWLGVDRNAWIKTLSYQASAYSLLQAAC 182 (811)
Q Consensus 103 s~~~emr~kl~~slq~e~~~~~LVqsLHdaARsfelav~e~~~~s~~swl~~aWlGvD~nAW~K~LSYQaAVysLLqaai 182 (811)
+-++.+|-.+-.-....+.-.-|.+.+.+.+..+ +.+.+|+++. -+..+.+||+.++
T Consensus 11 G~FD~lRk~~l~~~~~~~~~~~l~~~v~~~v~~~---------l~~~~~l~~~--------------nk~k~~alI~~~i 67 (106)
T PF05205_consen 11 GHFDKLRKECLADFDTSPAYQNLRQRVEEIVESE---------LERDPWLLSK--------------NKGKARALIEGAI 67 (106)
T ss_pred CChHHHHHHHHHhccccHHHHHHHHHHHHHHHHH---------HhcCcccCCc--------------chHHHHHHHHHHH
Confidence 4467777776555544445556666666665544 2344565432 2356778999999
Q ss_pred hhhccCCCCCCCcchhHhHHhhhhhchhHHHHHhHhh
Q 003554 183 EISSCGDGRDRDVYVFVQRSLLRQSAPLESLIRDKLS 219 (811)
Q Consensus 183 EIsSrG~grDRdvnvFVqrsLs~~~apLE~~Ir~~Ls 219 (811)
+=+.--.+.|+.|..+|...|..+...+|+.|++.|.
T Consensus 68 ~rs~~~~~~e~~i~~~vd~~l~~~~~~ie~~~~~~l~ 104 (106)
T PF05205_consen 68 DRSGVYKGVERIIDQVVDPKLNEIRPSIEEIIREELG 104 (106)
T ss_pred HHhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 9887766788999999999999888889999998875
No 9
>PF12761 End3: Actin cytoskeleton-regulatory complex protein END3
Probab=31.24 E-value=1.1e+02 Score=32.02 Aligned_cols=72 Identities=28% Similarity=0.437 Sum_probs=48.9
Q ss_pred ccccccchHHHHHHHHHHH-------------HH--HHHHHHH--HhhcccC----cchHHHHHHHhhhHHHHHHHHHHH
Q 003554 555 RTEIDSDSFDKALESVEEA-------------LI--RLEKLLQ--ALHVSSS----NSGKEQLKAACSDLEKIRKLKKEA 613 (811)
Q Consensus 555 ~~~~e~~sfdk~lesVe~A-------------l~--rlE~Llq--el~~ssS----~SGke~lkaacsDLekIRkLKkea 613 (811)
...+|++..|+-|..|+.+ |+ .+|.||. +-.++.. ..+...|+....||+.|+ ..+
T Consensus 100 rLkrELa~Le~~l~~~~~~~~~~~~~~~~~~~lvk~e~EqLL~YK~~ql~~~~~~~~~~~~~l~~v~~Dl~~ie---~QV 176 (195)
T PF12761_consen 100 RLKRELAELEEKLSKVEQAAESRRSDTDSKPALVKREFEQLLDYKERQLRELEEGRSKSGKNLKSVREDLDTIE---EQV 176 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCcchHHHHHHHHHHHHHHHHHHHHhhhccCCCCCCCHHHHHHHHHHHH---HHH
Confidence 3456677777777777654 33 2567763 3333322 234567888999998875 679
Q ss_pred HHHHHHHHhhhhhhhc
Q 003554 614 EFLEASVRAKAASLQQ 629 (811)
Q Consensus 614 EfleASfraKa~slq~ 629 (811)
+.||.-++.|-.-|++
T Consensus 177 ~~Le~~L~~k~~eL~~ 192 (195)
T PF12761_consen 177 DGLESHLSSKKQELQQ 192 (195)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 9999999998887775
No 10
>PRK00420 hypothetical protein; Validated
Probab=30.43 E-value=1.1e+02 Score=29.27 Aligned_cols=92 Identities=27% Similarity=0.273 Sum_probs=49.2
Q ss_pred hHHHHHhhcchhHHHHHHHhcccccc--cccccccc--c-ccccccc-cc-hH-HHHHHHHHHHHH-HHHHHHHHhhccc
Q 003554 518 KAAKFLSKGYDKLMDCMKEMGIARNG--MIESAESV--T-YSRTEID-SD-SF-DKALESVEEALI-RLEKLLQALHVSS 588 (811)
Q Consensus 518 kaa~FLskgq~~L~eC~Eel~i~~~~--~~~~~~~~--~-~~~~~~e-~~-sf-dk~lesVe~Al~-rlE~Llqel~~ss 588 (811)
++|.+|++|..||.+.--.-|.+.-. ..+..=|. . ......+ .. .. +..+..|++.|. +++.|...|.-.
T Consensus 10 ~~a~~Ll~Ga~ml~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~~ee~~~~~~~~~~~~~~~il~~ki~~L~~kL~~e- 88 (112)
T PRK00420 10 KAAELLLKGAKMLSKHCPVCGLPLFELKDGEVVCPVHGKVYIVKSDEEEKKVESKETLKEVEEVLIEKINYLAKKLKED- 88 (112)
T ss_pred HHHHHHHhHHHHccCCCCCCCCcceecCCCceECCCCCCeeeeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccc-
Confidence 57899999999988633222322210 00111110 0 0010101 11 11 223566667666 899999888765
Q ss_pred Ccch-HHHHHHHhhhHHHHHHHH
Q 003554 589 SNSG-KEQLKAACSDLEKIRKLK 610 (811)
Q Consensus 589 S~SG-ke~lkaacsDLekIRkLK 610 (811)
...+ -.+|-.+-.=|+|||+++
T Consensus 89 ~~~~ri~Ei~~~l~~l~ki~~~~ 111 (112)
T PRK00420 89 EDIERITEIIRYLEVLERIRKIK 111 (112)
T ss_pred cchhHHHHHHHHHHHHHHHHHHh
Confidence 3444 345666677788888875
No 11
>PF10241 KxDL: Uncharacterized conserved protein; InterPro: IPR019371 This entry represents a conserved region of 80 residues which defines a family of short proteins. There is a characteristic KxDL motif towards the C terminus. The function is unknown.
Probab=28.79 E-value=1.6e+02 Score=26.53 Aligned_cols=35 Identities=29% Similarity=0.334 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHhhcccCcchHHHHHHHhhhHHH----HHHHHHH
Q 003554 573 ALIRLEKLLQALHVSSSNSGKEQLKAACSDLEK----IRKLKKE 612 (811)
Q Consensus 573 Al~rlE~Llqel~~ssS~SGke~lkaacsDLek----IRkLKke 612 (811)
+-.||+.+-.++ ..|.+-|+..-+|||- ||.||..
T Consensus 41 s~~rl~~~~~~f-----~~~~~~l~~mK~DLd~i~krir~lk~k 79 (88)
T PF10241_consen 41 SQQRLAEARERF-----ARHTKLLKEMKKDLDYIFKRIRSLKAK 79 (88)
T ss_pred HHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444 3566667777777763 4445443
No 12
>PF11004 Kdo_hydroxy: 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase; InterPro: IPR021266 This bacterial family of proteins has no known function.
Probab=28.48 E-value=43 Score=36.43 Aligned_cols=35 Identities=37% Similarity=0.594 Sum_probs=27.6
Q ss_pred chhHHHHHHhhhcceEEEecccCcccceeeeeeeeeccccccc
Q 003554 420 DDPIKSLIRYLIGGSVLYYPQLSSISSYQLYVEVVCEELDWLL 462 (811)
Q Consensus 420 De~IedflRYLegGsvl~YPQLSSISsYQLfvEVVcEEl~WLp 462 (811)
.++=++.++-||+|.|||+|+|. .+.-|+|-.-|.
T Consensus 8 ~~~~~~~~~~LE~G~VL~fP~l~--------F~l~~~E~~fL~ 42 (281)
T PF11004_consen 8 EEPQRDAIEALEQGKVLYFPQLR--------FPLSPEERAFLD 42 (281)
T ss_pred cchHHHHHHHhhCCCEEEeCCCC--------CCCChhHHhhcC
Confidence 56678899999999999999875 455677776554
No 13
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=28.01 E-value=3.3e+02 Score=23.05 Aligned_cols=54 Identities=22% Similarity=0.369 Sum_probs=30.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhhcccCc---chHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Q 003554 561 DSFDKALESVEEALIRLEKLLQALHVSSSN---SGKEQLKAACSDLEKIRKLKKEAEFLEASV 620 (811)
Q Consensus 561 ~sfdk~lesVe~Al~rlE~Llqel~~ssS~---SGke~lkaacsDLekIRkLKkeaEfleASf 620 (811)
+.-.+.+..|+..|...+.+++++.+-..+ +.+.+++ .+||..|.+..-|+..|
T Consensus 21 ~~r~~~i~~~e~~l~ea~~~l~qMe~E~~~~p~s~r~~~~------~kl~~yr~~l~~lk~~l 77 (79)
T PF05008_consen 21 EQRKSLIREIERDLDEAEELLKQMELEVRSLPPSERNQYK------SKLRSYRSELKKLKKEL 77 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHCTS-HHHHHHHH------HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHH------HHHHHHHHHHHHHHHHh
Confidence 466677777777777777777765543333 3333332 25555555555554444
No 14
>PF04065 Not3: Not1 N-terminal domain, CCR4-Not complex component ; InterPro: IPR007207 The Ccr4-Not complex (Not1, Not2, Not3, Not4 and Not5) is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID []. This domain is the N-terminal region of the Not proteins.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=26.90 E-value=1.7e+02 Score=31.06 Aligned_cols=64 Identities=25% Similarity=0.493 Sum_probs=46.6
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHhhcccCcchHHHHHHHhhhHHH-HHHHHHHHHHHHHHHHhhhhhhhcCCCCC
Q 003554 560 SDSFDKALESVEEALIRLEKLLQALHVSSSNSGKEQLKAACSDLEK-IRKLKKEAEFLEASVRAKAASLQQGGDDS 634 (811)
Q Consensus 560 ~~sfdk~lesVe~Al~rlE~Llqel~~ssS~SGke~lkaacsDLek-IRkLKkeaEfleASfraKa~slq~g~d~~ 634 (811)
-.-+|+.|..|.|.+.-.+.+...++-+.+++-||.|.+ ||.| |+||.+ ||--....+++.|-.
T Consensus 7 Q~Eid~~lKkv~EG~~~F~~i~~K~~~~~n~~QKEK~E~---DLKkEIKKLQR--------~RdQIK~W~~~~diK 71 (233)
T PF04065_consen 7 QQEIDRTLKKVQEGVEEFDEIYEKVESATNQNQKEKLEA---DLKKEIKKLQR--------LRDQIKTWLSSNDIK 71 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcccCcchHHHHHH---HHHHHHHHHHH--------HHHHHHHHccCcccc
Confidence 345799999999999999999999998888899999987 5543 444443 444445555544444
No 15
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=24.97 E-value=1.2e+02 Score=26.26 Aligned_cols=53 Identities=15% Similarity=0.326 Sum_probs=34.8
Q ss_pred HHHHHhcccccccccccccc--cccccccccchHHHHHH-HHHHHHHHHHHHHHHh
Q 003554 532 DCMKEMGIARNGMIESAESV--TYSRTEIDSDSFDKALE-SVEEALIRLEKLLQAL 584 (811)
Q Consensus 532 eC~Eel~i~~~~~~~~~~~~--~~~~~~~e~~sfdk~le-sVe~Al~rlE~Llqel 584 (811)
+.++.+|+...+.-.+...+ ..+........|++.+. .+++++.+-.+.+++|
T Consensus 17 ~i~~~lgl~~Gd~v~v~~~~~~iii~~~~~~~~~~~~~~~~~~~~~~~y~~~l~~L 72 (74)
T TIGR02609 17 EVLESLGLKEGDTLYVDEEEGGLKLKRFDEGKELEKKMQMAVERAMSKYDEALKEL 72 (74)
T ss_pred HHHHHcCcCCCCEEEEEEECCEEEEEECCCCccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788888875544433222 11222222357888888 8999999999888887
No 16
>TIGR02878 spore_ypjB sporulation protein YpjB. Members of this protein, YpjB, family are restricted to a subset of endospore-forming bacteria, including Bacillus species but not CLostridium or some others. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon, where sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect. This protein family is not, however, a part of the endospore formation minimal gene set.
Probab=24.49 E-value=1.5e+02 Score=31.83 Aligned_cols=64 Identities=19% Similarity=0.273 Sum_probs=43.8
Q ss_pred chhHHHHHHHhcccccccccccccccccccccccchHHHHHHHHHHHHHHHHHHHHHhhcccCcchHHHHHHHhhhHHHH
Q 003554 527 YDKLMDCMKEMGIARNGMIESAESVTYSRTEIDSDSFDKALESVEEALIRLEKLLQALHVSSSNSGKEQLKAACSDLEKI 606 (811)
Q Consensus 527 q~~L~eC~Eel~i~~~~~~~~~~~~~~~~~~~e~~sfdk~lesVe~Al~rlE~Llqel~~ssS~SGke~lkaacsDLekI 606 (811)
|..|-+-+..|++.+.+...-..| ..++.|+..+.-||+. +.-.-+..++.|||.....||.+|
T Consensus 124 ~~~ln~Fl~~Y~~I~PSl~Idl~~--------------~~~q~v~~~i~~l~~~--r~~~~~~~~~~~~L~~~~~dl~~l 187 (233)
T TIGR02878 124 QEKLNEFLSLYDLIYPSLTIDVPE--------------DQVQRVDSHLSYLENF--RFQQRSEDEKEEQLSLMRGDLKAL 187 (233)
T ss_pred HHHHHHHHHHhhhcccceeeecCH--------------HHHHHHHHHHHHHHhh--hhhccChHHHHHHHHHHHHHHHHH
Confidence 566677777888887554443333 3567777777666643 334557778999999999998775
No 17
>cd07307 BAR The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-
Probab=24.37 E-value=5.2e+02 Score=23.21 Aligned_cols=87 Identities=24% Similarity=0.304 Sum_probs=54.9
Q ss_pred HhhcchhHHHHHHHhcccccccccccccccccccccccchHHHHHHHHHHHHHHHHHHHHHhhcccCcchHHHHHHHh-h
Q 003554 523 LSKGYDKLMDCMKEMGIARNGMIESAESVTYSRTEIDSDSFDKALESVEEALIRLEKLLQALHVSSSNSGKEQLKAAC-S 601 (811)
Q Consensus 523 Lskgq~~L~eC~Eel~i~~~~~~~~~~~~~~~~~~~e~~sfdk~lesVe~Al~rlE~Llqel~~ssS~SGke~lkaac-s 601 (811)
+.+....+.+++.+++-.-...+.. .+..++..+-+++..++.+.+++.-...+.--+.|+... .
T Consensus 26 ~~~~~~~~~~~l~~l~~~~~~~~~~--------------~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~v~~pL~~~~~~ 91 (194)
T cd07307 26 LPAAAEKLSEALQELGKELPDLSNT--------------DLGEALEKFGKIQKELEEFRDQLEQKLENKVIEPLKEYLKK 91 (194)
T ss_pred HHHHHHHHHHHHHHHhccCCCcccc--------------hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5566777888888887554111000 344667777777777777777776655555566677666 7
Q ss_pred hHHHHHHHHHHHHHHHHHHHhh
Q 003554 602 DLEKIRKLKKEAEFLEASVRAK 623 (811)
Q Consensus 602 DLekIRkLKkeaEfleASfraK 623 (811)
|+..++..+|..+-....+.+.
T Consensus 92 ~~~~~~~~~k~~~~~~~~yd~~ 113 (194)
T cd07307 92 DLKEIKKRRKKLDKARLDYDAA 113 (194)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 7777777777766554444433
No 18
>PLN00180 NDF6 (NDH-dependent flow 6); Provisional
Probab=23.06 E-value=70 Score=32.83 Aligned_cols=55 Identities=33% Similarity=0.450 Sum_probs=33.7
Q ss_pred ccccccCCCCCCCCCcccccccccccccccc---CC-ccchhhHHHHHHHHH-HHHHHHh
Q 003554 673 FGFFTRPSIRKPKPQESEYCEQTGSNIGIAN---SE-SNEIHRFELLRNELM-ELEKRVQ 727 (811)
Q Consensus 673 w~~f~r~~~~k~~p~~d~~~~~~~~~~~~~~---~e-snei~rFElLr~ELi-ELEkRvq 727 (811)
|+...=-++|-|-.+.++|-|+-..--+.=- .| -.+--|=||+|.||| |+|.||-
T Consensus 110 WG~~fFgSmKDPfYDSe~YRgdGGDGT~hW~Yd~QEd~E~sAReeL~REELiEEIEQkVG 169 (180)
T PLN00180 110 WGCLFFGSMKDPFYDSEEYRGDGGDGTGHWVYERQEDIEESARAELWREELIEEIEQKVG 169 (180)
T ss_pred HHHhheeccCCcccchHHhcccCCCCceeeEeehHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 7755556777777777777665433222110 01 112349999999998 4788874
No 19
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=22.33 E-value=3.8e+02 Score=24.79 Aligned_cols=26 Identities=8% Similarity=-0.051 Sum_probs=18.1
Q ss_pred hHHHHHhhcchhHHHHHHHhcccccc
Q 003554 518 KAAKFLSKGYDKLMDCMKEMGIARNG 543 (811)
Q Consensus 518 kaa~FLskgq~~L~eC~Eel~i~~~~ 543 (811)
.++.....+.....+..++|||+...
T Consensus 20 ~aV~~~~~~g~sv~evA~e~gIs~~t 45 (121)
T PRK09413 20 AIVQQSFEPGMTVSLVARQHGVAASQ 45 (121)
T ss_pred HHHHHHHcCCCCHHHHHHHHCcCHHH
Confidence 45666666666777777889997744
No 20
>cd09235 V_Alix Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules. This family contains the middle V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X) and related domains. It belongs to the V_Alix_like superfamily which includes the V-domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), is part of the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in membrane remodeling processes, including the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), the abscission reactions of mammalian cell division, and in apoptosis. The Alix V-domain is a dimerization domain, and contains a binding site, partially conserved in the
Probab=22.00 E-value=3.9e+02 Score=28.87 Aligned_cols=97 Identities=23% Similarity=0.347 Sum_probs=55.5
Q ss_pred cccccCCCchhHHHHHhhcchhHHHHHHHhcccccccccccccccccccccccch-HHHHHHHHHHHHHHH----HHHHH
Q 003554 508 SKWLENPSNVKAAKFLSKGYDKLMDCMKEMGIARNGMIESAESVTYSRTEIDSDS-FDKALESVEEALIRL----EKLLQ 582 (811)
Q Consensus 508 S~WlenPsnvkaa~FLskgq~~L~eC~Eel~i~~~~~~~~~~~~~~~~~~~e~~s-fdk~lesVe~Al~rl----E~Llq 582 (811)
.+|++.||..-++.|-.+. ....+-+.-+. ..+. ..+.++..+..+.-| +.|-.
T Consensus 115 ~~Wtr~pS~~~~~~l~~~~----~kyr~~L~~A~-----------------~sD~~v~~k~~~~~~~l~lLs~~~~~l~~ 173 (339)
T cd09235 115 ERWTRTPSNKLTKPLRAEG----SKYRTILDNAV-----------------QADKIVREKYESHREGIELLSKPEEELAN 173 (339)
T ss_pred CcCCCCChHHHhHHHHHHH----HHHHHHHHHHH-----------------hhHHHHHHHHHHHHHHHHHHcCCHHHHHH
Confidence 4799999999888765443 33333332222 1221 233344444433333 22322
Q ss_pred HhhcccC---cchHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhhh
Q 003554 583 ALHVSSS---NSGKEQLKAACSDLEKIRKLKKEAEFLEASVRAKAA 625 (811)
Q Consensus 583 el~~ssS---~SGke~lkaacsDLekIRkLKkeaEfleASfraKa~ 625 (811)
.+.-++. .++++.+.....=|+++-.||+|-+-++..+|.+.+
T Consensus 174 ~lPss~~~~~~~~~~~v~~Lr~~l~~l~~lk~eR~~~~~~Lk~~~d 219 (339)
T cd09235 174 AIPSASPAKTLQGSEAVQELRQLMEQVETIKAEREVIESELKSATF 219 (339)
T ss_pred hCCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 2321111 125677778888888888899999999999977633
No 21
>PF05008 V-SNARE: Vesicle transport v-SNARE protein N-terminus; InterPro: IPR007705 V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this []. This domain is the N-terminal half of the V-Snare proteins. ; GO: 0006886 intracellular protein transport, 0016020 membrane; PDB: 2V8S_V 1VCS_A 3ONL_C 3ONJ_A 2QYW_A.
Probab=21.91 E-value=1.2e+02 Score=25.65 Aligned_cols=50 Identities=28% Similarity=0.375 Sum_probs=42.9
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHhhcccCcchHHHHHHHhhhHHHHHH
Q 003554 559 DSDSFDKALESVEEALIRLEKLLQALHVSSSNSGKEQLKAACSDLEKIRK 608 (811)
Q Consensus 559 e~~sfdk~lesVe~Al~rlE~Llqel~~ssS~SGke~lkaacsDLekIRk 608 (811)
.+....+.|+..++.+..+|.-++.+..+..+.=+..|+...+||+++++
T Consensus 26 ~i~~~e~~l~ea~~~l~qMe~E~~~~p~s~r~~~~~kl~~yr~~l~~lk~ 75 (79)
T PF05008_consen 26 LIREIERDLDEAEELLKQMELEVRSLPPSERNQYKSKLRSYRSELKKLKK 75 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36677889999999999999999999888888999999999999988654
No 22
>PF10239 DUF2465: Protein of unknown function (DUF2465); InterPro: IPR018797 FAM98A, B and C are glycine-rich proteins found from worms to humans whose function is unknown.
Probab=21.48 E-value=4.3e+02 Score=29.02 Aligned_cols=89 Identities=21% Similarity=0.276 Sum_probs=56.3
Q ss_pred CcccchhhhhhhhhhhhhhhhhcccccCCCchhHHHHHhhcchhHHHHHHHhcccccccccccccccccccccccchHHH
Q 003554 486 NAEAIPQVLDVCSHWMQSFIKHSKWLENPSNVKAAKFLSKGYDKLMDCMKEMGIARNGMIESAESVTYSRTEIDSDSFDK 565 (811)
Q Consensus 486 ~~E~i~~Vl~VCs~W~~sFikyS~WlenPsnvkaa~FLskgq~~L~eC~Eel~i~~~~~~~~~~~~~~~~~~~e~~sfdk 565 (811)
+.++...+-..|..+= =.+.|.|+.+..++.+=|.++.+=+..+.=.-..-|-+ ...-.+.==.
T Consensus 128 ~s~~~~~l~~i~~~L~--------l~~p~~~i~~~~lf~~i~~ki~~~L~~lp~~~~~~PLl--------~~~L~~~Qw~ 191 (318)
T PF10239_consen 128 ESEVAQELKAICQALG--------LPKPPPNITASQLFSKIEAKIEELLSKLPPGHMGKPLL--------KKSLTDEQWE 191 (318)
T ss_pred ccHHHHHHHHHHHHhC--------CCCCCCCCCHHHHHHHHHHHHHHHHHhcCccccCCCCc--------CCCCCHHHHH
Confidence 3445555556665542 12348999999999999999988777653222111222 1111122235
Q ss_pred HHHHHHHHHH-----HHHHHHHHhhcccCc
Q 003554 566 ALESVEEALI-----RLEKLLQALHVSSSN 590 (811)
Q Consensus 566 ~lesVe~Al~-----rlE~Llqel~~ssS~ 590 (811)
.|+.+.++|. |.+-|+++|.|+=.+
T Consensus 192 ~Le~i~~~L~~EY~~RR~mLlkRLDVTvqS 221 (318)
T PF10239_consen 192 KLEKINQALSKEYECRRQMLLKRLDVTVQS 221 (318)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhheeee
Confidence 6777877776 899999999998655
No 23
>PHA03298 envelope glycoprotein L; Provisional
Probab=21.09 E-value=44 Score=33.50 Aligned_cols=66 Identities=30% Similarity=0.359 Sum_probs=50.3
Q ss_pred hHHHHHHHhhhccceehhhHHHHHhhhhhhHHHHhhcCCCccccc----------ccCCCCccceehh----------HH
Q 003554 303 SDITGRLMDTLVDLVPISQAYYSIKDIGLHREFLAHFGPRASACR----------VKNDRDSEEVIFW----------VD 362 (811)
Q Consensus 303 ~D~~grLMdml~~fVpv~q~Y~~~kdiGL~rEFL~hFGpraa~~~----------~~~d~~~eEv~FW----------I~ 362 (811)
.|.+|||.|-...+|+|.=.-.+-.|.|-+ -|||.-.+.. +++-|..-|++|| =+
T Consensus 38 ~dsigrlidgaeqlvsmrcmtsfehdaa~~-----ifgpey~pgg~mfe~lttII~kP~Cs~pEvI~wyksGtA~~VNPy 112 (167)
T PHA03298 38 CDSIGRLIDGAEQLVSMRCMTSFEHDAAAR-----IFGPEYLPGGDMFEDLLTIIFKPLCSNPEAIFWYKNGTAAKVNPY 112 (167)
T ss_pred ccccccccccHHHHhhhhhhccccccccee-----eeCCccCCCccHHHhhHhheeecccCCceeEEEecCCceEEeChH
Confidence 599999999999999998877777777764 5899766543 4666788899999 24
Q ss_pred HHHHHHHHHHh
Q 003554 363 LVQKQLQRAID 373 (811)
Q Consensus 363 LvQkqL~~Aid 373 (811)
+.-+-|+.||.
T Consensus 113 ~~ir~l~~ale 123 (167)
T PHA03298 113 LGCRILQDALE 123 (167)
T ss_pred HHHHHHHHHHh
Confidence 66666666553
No 24
>PF13767 DUF4168: Domain of unknown function (DUF4168)
Probab=20.35 E-value=1.9e+02 Score=25.06 Aligned_cols=42 Identities=31% Similarity=0.466 Sum_probs=26.6
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHHhhcccCcchHHHHHHHhhhHHHHHHHHHHHH
Q 003554 557 EIDSDSFDKALESVEEALIRLEKLLQALHVSSSNSGKEQLKAACSDLEKIRKLKKEAE 614 (811)
Q Consensus 557 ~~e~~sfdk~lesVe~Al~rlE~Llqel~~ssS~SGke~lkaacsDLekIRkLKkeaE 614 (811)
..+++.|-+|+..|+.-...--.-+++ |.|-+.++.|..++.
T Consensus 3 ~~el~~fA~A~~~ie~ir~~~~~~l~~----------------~~~~~~~~~l~~~a~ 44 (78)
T PF13767_consen 3 DAELDQFARAVLEIEPIRQEYQQELQA----------------AEDPEEIQELQEEAQ 44 (78)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH----------------ccCHHHHHHHHHHHH
Confidence 345667777766666555444333433 778888888877764
No 25
>PRK12472 hypothetical protein; Provisional
Probab=20.18 E-value=1.2e+02 Score=35.51 Aligned_cols=64 Identities=31% Similarity=0.279 Sum_probs=35.6
Q ss_pred cccccchHHHHHHHH--HHHHHHHHHHHHHhhcccCcchHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhhhh
Q 003554 556 TEIDSDSFDKALESV--EEALIRLEKLLQALHVSSSNSGKEQLKAACSDLEKIRKLKKEAEFLEASVRAKAA 625 (811)
Q Consensus 556 ~~~e~~sfdk~lesV--e~Al~rlE~Llqel~~ssS~SGke~lkaacsDLekIRkLKkeaEfleASfraKa~ 625 (811)
.+.|+...||+|+.+ |+|-.|.|..-|...-- -..-..+|.+|..|-+ .|++.+..+-=.+||+
T Consensus 237 a~~~l~~adk~l~~a~~d~~~~~a~~~~~~~~~~-~~~a~~~~~~a~~~~~-----~~~~~~~~~~~a~~~a 302 (508)
T PRK12472 237 ADAELKRADKALAAAKTDEAKARAEERQQKAAQQ-AAEAATQLDTAKADAE-----AKRAAAAATKEAAKAA 302 (508)
T ss_pred HHHHHHHHHHHHHhcccchhhhhHHHHHHHHHHH-HHHHHHHHHHHHHhHH-----HHHHHHHHHHHHHHHH
Confidence 345678888888876 67777777644443211 1122344555555544 3555566555555554
Done!